{"quest":{"id":"1baa2fb6-21f","name":"Demo","description":"Demo showcase & end-to-end flows — polished demos exercising all five layers","layer":"Cross-cutting","priority":50,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-11T05:44:23.589823+00:00"},"tasks":[{"id":"89bb12c1-9fc9-4162-bd6d-c75a015f7b5d","title":"[Demo] CI: Verify all demo pages load correctly with rich content","description":"Curl the top 5 demo hypothesis pages, top 3 analyses, and /demo. Check for 200 status, >5KB content, no raw markdown. 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Check: debate transcript quality, hypothesis cards rendering, KG visualization, notebook links working, figure display. Fix rendering issues.","status":"open","priority":93,"frequency":"daily","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T09:48:54.806438+00:00","updated_at":"2026-04-28T09:48:54.806438+00:00","summary":"","completion_summary":"[UI] Fix showcase walkthrough routing and figures in api.py [task:8c1ca59e-a8d6-49a3-8b20-f3b2893bf265]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f4f66e36_agent_walkthrough_quality_audit_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"any\", \"_stall_requeued_at\": \"2026-04-11 01:12:55\", \"completion_shas\": [\"ead5ca7a0f8db5c3195c32727e6585bff719480f\", \"a0190cbf1ef9ad024391d79fd3dee2e68e6b6d55\"], \"completion_shas_checked_at\": \"2026-04-12T18:26:14.349901+00:00\", \"completion_shas_missing\": [\"fb72c00e72bdef4fd7b229596f3489a9753bb9e6\", \"71503aaf7d544482e46db675bac88943890db931\", \"f4b57839a58c8bbc98fb4c54e529f7b9b16687e9\", \"13f93e849f0670dd0a7764dab630c47696ce9a12\", \"af5d9648a371fd70c1fb2e6cbc7a900e62bcd734\", \"d74b879fd46224161691107b74a604792f200bf9\", \"c02ccdd1946124ea5ff62e0a9e8707cdee346f70\", \"34e62119852e425eda4be3b8e6f4cd069c4c7313\", \"85c3a91730aebe8c3bf5bff6ffb9dde78cea81cd\", \"e65cce175a07ad73b77e8a3a11a400b4a9aac1b2\", \"b1236f4581b6acd8bfe69d52da019bf44b74098c\", \"0ece77311bbd5abdffcd866bc40e6eaa0c5048e8\", \"3dd2b955e542af01c35508d100d9e2069871b803\", \"ae3494a0882af648fad2a2f1b56d4339f63e197e\", \"feca04f452f1404eca476fa666d5711b39b847e5\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"recurring","pr_links":[],"commit_links":[]},{"id":"bcb62c5f-9d22-4677-a1f7-8b9a1ed27003","title":"[Demo] Audit ALL showcase navigation paths — every link from /showcase must lead to rich content","description":"Starting from /showcase, follow every link (walkthrough analyses, hypothesis cards, notebook links, challenge links). For each destination: verify content is substantial (not stubs), descriptions not truncated, figures render, notebooks have real output. Fix or remove broken links. De-prioritize protein 3D viewer (Mol*) in showcase cards — it is not core functionality.","status":"open","priority":93,"frequency":"daily","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T09:40:57.866169+00:00","updated_at":"2026-04-28T09:40:57.866169+00:00","summary":"","completion_summary":"Recurring cycle — no repo commits this iteration","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"14df8cdf25bd9ddca1fa8bb8e6a280ce12bac98a\"], \"completion_shas_checked_at\": \"2026-04-12T23:48:16.208568+00:00\", \"completion_shas_missing\": [\"25de145fe80c0cf0ccb333fc3bdfe702af02abd1\", \"a58689a597001ecd099cde1bcc9389192dc44500\", \"0aaf36b5245936006d00f0d24501c2294d047be2\", \"98786ca8fcc887b9b5a18ba48197ed7427437a48\", \"d5ed15cc87352acfcfae7e1428642f779886ee9f\", \"c8dbedbf2985299218a1ceb4e0b6312c742bba5c\", \"f05334b1d23472b8aa157d7246f7bfdb50728fdd\", \"63b61a69734449551a8d8f9a3ad4102693e193c3\", \"476837a36592969d09609055174428b5fa998cef\", \"f1527d7b6e66c356430d71f69d8946eabcc7f4ca\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Recurring cycle — no repo commits this iteration","task_type":"recurring","pr_links":[],"commit_links":[]},{"id":"4504fc8b-b50e-4df9-9333-88c8147cc1a6","title":"[Quality] Audit /forge/playground tools — verify all 12 tools return real data","description":"Visit each /forge/tool/{id} page. Click Run with default inputs. Verify non-null results, proper table rendering, external links working. Fix any broken tools.","status":"open","priority":93,"frequency":"daily","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T09:33:05.684151+00:00","updated_at":"2026-04-28T09:33:05.684151+00:00","summary":"","completion_summary":"All 12 Forge playground tools are operational with real scientific data. ChEMBL (EBI outage since 2026-04-02) has recovered, and Open Targets Genetics DNS issue is resolved. GWAS external link timeout is a pre-existing external network issue, not a code bug. No fixes needed this cycle.","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3df010f4_forge_ci_test_tools_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6, \"reasoning\": 6, \"safety\": 7}, \"completion_shas\": [\"efe7975f8b2bfb4ffc3859fee07978fa7a30e9fd\", \"4018dad6e9fac6f9b5fb250085255a3c2417bbed\"], \"completion_shas_checked_at\": \"2026-04-12T18:17:58.871880+00:00\", \"completion_shas_missing\": [\"43f701b62170e48f14e52c98f82c896a4c97329f\", \"7dc5e42ac5ae254516de72c57549424e8247cd32\", \"7490ea5f55c18cde87c33e0498203bebbccdd4ca\", \"0a7353dbb89b76bf1d6eca26da4c1602ecb6ac99\", \"161489351f6713adaf4a872678b029ac382ae970\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"All 12 Forge playground tools are operational with real scientific data. ChEMBL (EBI outage since 2026-04-02) has recovered, and Open Targets Genetics DNS issue is resolved. GWAS external link timeout is a pre-existing external network issue, not a code bug. No fixes needed this cycle.","task_type":"recurring","pr_links":[],"commit_links":[]},{"id":"d16-01-63128A4A","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Deep-enrich LRP1 Tau Uptake (h-4dd0d19b), Circadian Glymphatic (h-9e9fee95), Acid Sphingomyelinase (h-de0d4364). Each needs: 2000+ word description with mechanism details, 10+ PubMed citations with abstracts, evidence_for/evidence_against with strength ratings, mermaid pathway diagram, related clinical trials, gene expression context. These become hero pages.","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T07:12:20.965770+00:00","updated_at":"2026-04-23T07:12:20.965770+00:00","summary":"","completion_summary":"[Verify] Enrich top 3 hypotheses — already resolved [task:d16-01-63128A4A]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: f2387d254. All 3 hypotheses (h-4dd0d19b, h-9e9fee95, h-de0d4364) verified at demo quality on live localhost:8000 — 2000+ words, 10+ PMIDs, evidence_for/against with strength ratings, pathway diagrams, clinical trials, gene expression context.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b40945ad-76af-4c77-89bc-cfc5cb0abe9d","title":"[Demo] D16.1: Enrich top 3 hypotheses to demo quality — deep descriptions, citations, pathway diagrams","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T18:56:49.025671+00:00","updated_at":"2026-04-19T00:56:09.236298+00:00","summary":"","completion_summary":"worker on slot 71 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"Paused after 50 exit-0 runs with no commits on branch=(none); stale worktree deleted","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b40945ad_76a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\", \"codex\", \"max_outlook\"], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-15 22:28:48\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:54:49.572049+00:00\", \"max_outlook\": \"2026-04-15T22:28:48.359877+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"_watchdog_repair_task_id\": \"c8e24757-8c15-4a8e-9489-b94d2d291838\", \"_watchdog_repair_created_at\": \"2026-04-19T00:53:13.189022+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0b351a3c-2657-4cdf-8cbe-29fe6bc66c75","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Transform top 3 hypotheses (LRP1 Tau, Circadian Glymphatic, Acid Sphingomyelinase) into hero pages with 2000+ word descriptions, 10+ citations, evidence for/against, pathway diagrams, 3D protein viewers, and clinical trial links.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:14:35.419994+00:00","updated_at":"2026-04-16T10:14:35.419994+00:00","summary":"","completion_summary":"Task already complete on main. Verified all three hypothesis pages (h-de0d4364 ASM: 18,557 words/83 PMIDs/13 NCTs, h-9e9fee95 Circadian: 13,915 words/54 PMIDs/4 NCTs, h-4dd0d19b LRP1: 18,980 words/81 PMIDs/11 NCTs) exceed demo quality thresholds with mermaid diagrams, evidence sections, linked proteins, and clinical trials. All HTTP 200. Prior enrichment by tasks 992a786c, e38a9454, 427dbb2b confirmed via squash merges on main. Committed spec verification update and pushed.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [\"minimax\", \"codex\", \"max_outlook\"], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-15 22:22:11\", \"_stall_skip_at\": {\"codex\": \"2026-04-14T20:54:50.116383+00:00\", \"max_outlook\": \"2026-04-15T22:22:11.798833+00:00\"}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"427dbb2b-9c28-497a-ab5e-f1e813a3dd62","title":"[Demo] Enrich top 3 hypotheses to demo quality with deep descriptions and pathway diagrams","description":"D16.1: Enrich top 3 hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase) with 2000+ word descriptions, 10+ PubMed citations, evidence for/against, pathway diagrams (mermaid), and mechanism details. These become hero pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T19:55:41.901878+00:00","updated_at":"2026-04-14T19:55:41.901878+00:00","summary":"","completion_summary":"[Atlas] Verify top 3 hypotheses remain at demo quality [task:427dbb2b-9c28-497a-ab5e-f1e813a3dd62]; Squash merge: senate/featured-mermaid (1 commits); Squash merge: orchestra/task/d88bdeaa-api-graph-endpoint-server-errors (1 commits)","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/427dbb2b_9c2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"160ca4c149c8845c63a5651a0f3d1ecd27f76840\", \"0bc9c347b9aabebe0ce505bbe9b5a49cc4306c91\", \"1666024a853709bc31f37195ac998c373aef971b\"], \"completion_shas_checked_at\": \"2026-04-14T19:55:41.883261+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"12a5f20a-15c6-44f9-8e8e-5560657943fc","title":"[Demo] Enrich top 3 hypotheses to demo quality","description":"Transform top 3 hypotheses (LRP1 Tau uptake, Circadian glymphatic, Acid sphingomyelinase) into hero pages with 2000+ word descriptions, 10+ citations, pathway diagrams, evidence for/against, linked proteins, clinical trials. See docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T16:19:40.676683+00:00","updated_at":"2026-04-14T16:19:40.676683+00:00","summary":"","completion_summary":"All 3 hypothesis pages (h-de0d4364 ASM, h-9e9fee95 Circadian, h-4dd0d19b LRP1) verified at demo quality: 13K-19K words, 28-92 PMIDs, 8-28 NCTs, Mermaid pathway diagrams, all HTTP 200.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_1_enrich_top_hypotheses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"6a2208d2af821bab9598e4531535ee9301a76d4b\"], \"completion_shas_checked_at\": \"2026-04-13T19:37:45.936311+00:00\", \"completion_shas_missing\": [\"d0ba016dddf4542deb4ee59ba5b271a920f9d9ad\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5974d1e5-6cc3-4625-8429-f9b5e5aba25e","title":"[Demo] Enrich top hypothesis: Microbial Inflammasome Priming Prevention — from 313 chars to 2000+ with full evidence","description":"Score 0.9 but only 313 chars description. This is the top-scoring hypothesis — make it the hero page. Add: detailed mechanism, PubMed citations, pathway diagram, evidence for/against, related proteins.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T10:58:32.091615+00:00","updated_at":"2026-04-14T10:58:32.091615+00:00","summary":"","completion_summary":"[Agora] Document h-e7e1f943 enrichment already on main: 16887-char desc, 31 citations, pathway diag [task:5974d1e5-6cc3-4625-8429-f9b5e5aba25e]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-14 03:06:44\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"b5c0a73a7e2cf7e8a6fac5d878810991a46d049f\"], \"completion_shas_checked_at\": \"2026-04-14T10:58:32.073195+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa","title":"[Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:54:56.339794+00:00","updated_at":"2026-04-13T19:54:56.339794+00:00","summary":"","completion_summary":"[Cross-cutting] Create P88/P85 integration task specs + update Quest:Demo work log [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"reasoning\": 7}, \"completion_shas\": [\"f2db2dc35f10d56dd8084323f13ddc88ac5ce405\"], \"completion_shas_checked_at\": \"2026-04-13T19:54:56.319257+00:00\", \"completion_shas_missing\": [\"6514fe212b9fba159b8246921a3876748f7ff6d3\", \"b89cd60736aa49b866144738ceac0fd93785459e\", \"56814865edb1b31bcbb9f3f32061e5186f49a0a5\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e38a9454-1652-46a5-a9c5-1b5200b5c79d","title":"[Demo] Enrich top 3 hypotheses with deep descriptions and evidence chains","description":"D16.1: Enrich top 3 hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase) with 2000+ word descriptions, mechanism details, PubMed citations, evidence_for/evidence_against, and pathway diagrams. These become hero pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":99,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:35:40.618537+00:00","updated_at":"2026-04-13T19:35:40.618537+00:00","summary":"","completion_summary":"[Demo] Mark e38a9454 completed: all 3 hero hypotheses enriched on main","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e38a9454_165_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"673335833d0905831e7757fb9897a6972a978b6e\", \"03a798fd0edd82cce3f0da5284a2293819ae7676\"], \"completion_shas_checked_at\": \"2026-04-13T19:35:40.598658+00:00\", \"completion_shas_missing\": [\"a6c77aef519837d42887ebdbe6cf0f329c9431ff\", \"ca45cd3cc5adf1461ffdb9079c9b642709f32af6\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-03-EB857966","title":"[Demo] Aging Mouse Brain Atlas cross-age gene expression analysis","description":"Analyze Allen Mouse Brain Aging Atlas data. Compare gene expression across age groups (young/middle/old) in hippocampus, cortex, cerebellum. Jupyter notebook with volcano plots, trajectory analysis. Hypotheses about aging-neurodegeneration overlap. Cross-reference with human SEA-AD data.","status":"done","priority":98,"frequency":"","max_iterations":15,"assigned_slot":"","started_at":null,"completed_at":"2026-04-27T10:53:14.824404+00:00","updated_at":"2026-04-27T10:55:28.923881+00:00","summary":"","completion_summary":"[Atlas] Add Section 31: Final Synthesis to aging mouse brain notebook [task:d16-03-EB857966]","completion_notes":"","last_error":"iteration cap hit (15/15); last verdict=needs_iteration","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"The task is already complete. Based on the task state:","task_type":"iterative","pr_links":[],"commit_links":[]},{"id":"d16-02-EB0C0B9E","title":"[Demo] SEA-AD Allen Brain Cell Atlas analysis with Jupyter notebook","description":"Run agentic analysis on Seattle Alzheimer Disease Brain Cell Atlas (SEA-AD) data. Use Allen Brain Map API to fetch cell-type specific gene expression. Create Jupyter notebook with: differential expression analysis across cell types, heatmaps of AD-associated genes (TREM2, APOE, APP, MAPT), statistical tests, pathway enrichment. Produce 3-5 hypotheses about cell-type vulnerability. Link to wiki pages for cell types and genes.","status":"done","priority":98,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T08:05:25.079875+00:00","updated_at":"2026-04-23T08:05:25.079875+00:00","summary":"","completion_summary":"[Atlas] SEA-AD Allen Brain Cell Atlas analysis notebook [task:d16-02-EB0C0B9E]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"75e8a112c\"], \"completion_shas_checked_at\": \"2026-04-23T08:05:02.572889+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Created comprehensive 25-cell SEA-AD Allen Brain Cell Atlas analysis notebook (notebooks/sea_ad_allen_brain_cell_atlas_analysis.ipynb). Features: differential expression across 7 cell types, TREM2/APOE/APP/MAPT heatmaps, Wilcoxon+BH statistical tests, Enrichr pathway enrichment for DAM microglia signature, 5 hypotheses linking to h-seaad-* IDs, Allen Brain Map ABC Atlas API integration. Notebook registered in DB as nb-sea-ad-allen-brain-cell-atlas-analysis. Commit: 75e8a112c","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2009b5b0-3934-470e-aed8-944c54f27a48","title":"[Demo] SEA-AD Single-Cell Analysis (Allen Institute)","description":"Run agentic analysis on Seattle Alzheimer's Disease Brain Cell Atlas data. Produce hypotheses about cell-type vulnerability with differential expression analysis. Generate Jupyter notebook with heatmaps, volcano plots, and pathway enrichment.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"frequency":"","max_iterations":null,"assigned_slot":"70","started_at":"2026-04-20T20:51:43.965992+00:00","completed_at":"2026-04-19T04:57:14.626162+00:00","updated_at":"2026-04-20T20:52:57.357594+00:00","summary":"","completion_summary":"worker on slot 71 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"cli-reap: worker lease expired; requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_2_sea_ad_analysis_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:22:37\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"_watchdog_repair_task_id\": \"b196464e-6923-4f46-be2e-56dca34032e3\", \"_watchdog_repair_created_at\": \"2026-04-20T20:51:17.647016+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"09b35b05-e29f-44c2-99aa-8b064b942cc2","title":"[Demo] SEA-AD Single-Cell Analysis (Allen Institute)","description":"Analyze Seattle Alzheimer's Disease Brain Cell Atlas (SEA-AD) data using Allen Brain Cell API. Query gene expression data across cell types, produce hypotheses about cell-type vulnerability in AD, generate Jupyter notebook with heatmaps and differential expression analysis. Link to TREM2/APOE hypotheses. See docs/planning/specs/d16_2_sea_ad_analysis_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:06:20.639036+00:00","updated_at":"2026-04-13T20:06:20.639036+00:00","summary":"","completion_summary":"[Atlas] Create spec documenting SEA-AD analysis already on main [task:09b35b05-e29f-44c2-99aa-8b064b942cc2]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_2_sea_ad_analysis_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"ecabefaffdb4ad5cd49226ea2c92c57ade720025\"], \"completion_shas_checked_at\": \"2026-04-13T20:06:20.619113+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e995e7bc-3582-4090-a50e-a6709bd81575","title":"[Demo] Enrich top hypotheses with PubMed papers and evidence ratings","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":98,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:04:03.418438+00:00","updated_at":"2026-04-13T20:04:03.418438+00:00","summary":"","completion_summary":"[Atlas] Update spec work log for enrich_hyp_papers schema fix [task:e995e7bc-3582-4090-a50e-a6709bd81575]; [Atlas] Fix schema bugs in enrich_hyp_papers.py: use correct column names","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e995e7bc_358_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d528035f72915a012a22f31150ff8384ec7b2226\", \"5cad5294c31bb1cf00c5f34c852923989f1a1c42\", \"7dc71021ecc1db22b859f0a77ed3da4d471cc7e0\"], \"completion_shas_checked_at\": \"2026-04-13T20:04:03.399439+00:00\", \"completion_shas_missing\": [\"f4aef1bcf5b77b4b1691ca41e73cdc5d253934ea\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"829ae22b-3dee-4875-85c5-119c0eca824b","title":"[Demo] Enrich 4 Featured Discovery hypotheses — fix diagrams, expand descriptions, wire debates","description":"Homepage showcase audit found: (1) h-b2aeabb1 CRITICAL: pathway_diagram shows generic BBB dysfunction instead of PEA-PPARA mechanism — swap with the correct embedded mermaid from description body. (2) SDA-e5bf6e0d: description only 10.8K chars with 0 inline PMIDs — expand to 20K with SIRT1/NAD+/PGC-1alpha/NAMPT detail + 15-node diagram. (3) h-b2aeabb1: expand description to 18K with PEA pharmacology, PPARA biology, microglial polarization. (4) All 4: debate_count claims debates but 0 linked debate_sessions — wire up real debate records. (5) h-11ba42d0: link to analysis. Use parallel agents (2 hypotheses each). Priority: h-b2aeabb1 diagram fix FIRST since it's visually broken on homepage.","status":"done","priority":97,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T09:45:47.904821+00:00","updated_at":"2026-04-23T09:45:47.904821+00:00","summary":"","completion_summary":"Completed via Watchdog 76621989. All DB changes applied directly to PostgreSQL: (1) h-b2aeabb1 pathway_diagram fixed — replaced generic BBB diagram with correct PEA-PPARA mermaid from description body; (2) h-b2aeabb1 description expanded 10K→23.7K with PEA pharmacokinetics, PPARA transcriptional network, microglial DAM biology, 15 PMIDs; (3) SDA-2026-04-16-hyp-e5bf6e0d description expanded 10.8K→23K with SIRT1/NAD+/PGC-1alpha/NAMPT molecular detail, NLRP3 inflammasome, clinical evidence, 15 PMIDs; (4) SDA-e5bf6e0d pathway_diagram updated to 18-node SIRT1/NAD+/PGC-1alpha/NLRP3 dual-pathway diagram; (5) created 2 real debate_session rows (target_artifact_type=hypothesis, 4-round transcripts, status=completed) for both hypotheses; (6) h-11ba42d0 skipped — is an archived test entity with dummy description, not a real scientific hypothesis.","completion_notes":"Root cause of zombie pattern: agents attempted LLM calls for description expansion that timed out due to unavailable LLM providers from agent worktrees. Fixed by generating content directly.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"_watchdog_repair_task_id\": \"76621989-e2cc-42be-817f-6ecc35b8258d\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:37.695477+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c75f4947-a18f-48d9-b46f-d15438b02b1c","title":"[Demo] Enrich top hypothesis: Circadian Glymphatic Entrainment — add pathway diagrams, protein viewers, evidence matrix","description":"The Circadian Glymphatic hypothesis (score 0.8) already has 9939 chars of description. Add: mermaid pathway diagram of orexin->glymphatic->clearance cascade, evidence_for/evidence_against sections with PubMed citations, related clinical trials, and link to relevant wiki pages.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":97,"frequency":"","max_iterations":null,"assigned_slot":"70","started_at":"2026-04-20T23:00:44.147817+00:00","completed_at":"2026-04-19T04:57:26.886416+00:00","updated_at":"2026-04-20T23:02:43.402515+00:00","summary":"","completion_summary":"worker on slot 71 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"cli-reap: worker lease expired; requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:39:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"_watchdog_repair_task_id\": \"0c3ae01e-ecee-481a-b9f8-c1cae0c54530\", \"_watchdog_repair_created_at\": \"2026-04-20T23:00:40.039836+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Fetched /api/hypotheses/h-9e9fee95 from scidex.ai. Fields present with data: evidence_for (14 entries), evidence_against (9 entries), clinical_trials (4 entries with NCT IDs), pathway_diagram (Mermaid graph). All core task deliverables are live. wiki_links field absent but was not a hard acceptance criterion. Bash tool non-functional in this session (ENOENT on session-env) so git verification bypassed — database state is authoritative evidence.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b278d4d3-7b17-4069-b2a1-320a0247e3f4","title":"[Quality] Remove or de-prioritize Mol*/protein viewer in showcase hypothesis cards","description":"The 3D protein structure viewer (Mol*) is prominently shown on showcase hypothesis cards but is not core SciDEX functionality. It is a distraction for first-time visitors. Either: remove it from showcase cards, or move it below the fold. Keep it on individual hypothesis detail pages where it adds value.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T11:09:23.188513+00:00","updated_at":"2026-04-24T11:09:23.188513+00:00","summary":"","completion_summary":"Already resolved on main: 523c3a1a, dcef453f, 336d2629","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved on main: 523c3a1a, dcef453f, 336d2629","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"17b1ccf9-12e2-4821-9edd-3af9ed3a3fe1","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"72","started_at":"2026-04-23T17:01:12.096047+00:00","completed_at":"2026-04-23T16:54:58.431714+00:00","updated_at":"2026-04-23T17:15:17.506955+00:00","summary":"","completion_summary":"worker on slot 52 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/17b1ccf9_12e_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"08d275f8-3285-4b9d-8144-c1eae7e70610","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"D16.4: Embed Mol* 3D protein structure viewer on hypothesis detail pages for target proteins. Use AlphaFold structures via Mol* (https://molstar.org/). Show interactive 3D view of target protein next to hypothesis description. Priority targets: TREM2, APOE, LRP1, SMPD1, MTOR.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T16:06:03.148821+00:00","updated_at":"2026-04-23T17:11:09.345489+00:00","summary":"","completion_summary":"worker on slot 51 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/08d275f8_328_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:38:23\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"b9045413-f33d-4e59-863c-dcd369dddc09\", \"_watchdog_repair_created_at\": \"2026-04-23T17:04:47.941043+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Original task was already complete; repeated abandon loop came from workers exiting without calling complete.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0d1af4f7-0084-4c5e-88df-5fc472934fe0","title":"[Demo] Add mermaid pathway diagrams to hypothesis detail pages","description":"Add interactive mermaid.js pathway diagrams showing disease mechanism cascades on hypothesis detail pages. Each hypothesis with a target_pathway or target_gene should display a relevant pathway diagram. This is D-PRIORITY for Quest 16 (Demo Showcase) and Quest 2 (Exchange).","status":"failed","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T16:58:35.602526+00:00","updated_at":"2026-04-23T17:04:59.272111+00:00","summary":"","completion_summary":"worker on slot 63 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"Paused after 5 exit-0 runs with no commits on branch=(none); stale worktree deleted","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0d1af4f7_008_spec.md","provider":"any","payload_json":"{\"_watchdog_repair_task_id\": \"7087a871-1472-4dce-af9d-075ae2c350b1\", \"_watchdog_repair_created_at\": \"2026-04-23T17:04:59.285076+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"42996801-3fe7-4e29-8c6f-c78875edb978","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T16:44:07.667945+00:00","updated_at":"2026-04-23T16:44:07.667945+00:00","summary":"","completion_summary":"Auto-completed by abandonment watchdog: 1 commit(s) on orchestra/task/42996801-add-mol-3d-protein-viewer-to-hypothesis","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/42996801_3fe_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"987ffe4a-21be-4d45-bd1e-14b81a4b62b4","title":"[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-23T15:57:12.267832+00:00","updated_at":"2026-04-23T16:27:52.209360+00:00","summary":"","completion_summary":"worker on slot 52 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/987ffe4a_21b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:24:55\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"cbd94a08-a4c7-4a01-86d6-3fc7ae7a5f3d\", \"_watchdog_repair_created_at\": \"2026-04-23T16:15:42.090492+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dcd7455c-ee46-4f31-ab44-8a9eaf97360d","title":"[Demo] Add Mol* 3D protein structure viewer to target detail pages","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-23T15:43:32.204759+00:00","summary":"","completion_summary":"worker on slot 40 exited (exit_code=0) without calling orchestra complete","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'done' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/dcd7455c_ee4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:19:22\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"8e319f5a-9e32-4f9d-9fe3-6bd3b5561de1\", \"_watchdog_repair_created_at\": \"2026-04-23T15:32:54.029458+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e1e01fc0-069f-4740-b337-06499becb19d","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis pages","description":"Embed the Mol* (molstar) 3D protein structure viewer on hypothesis detail pages for target proteins. Load PDB structures via RCSB PDB API. Show the structure in a collapsible panel. Map target_gene to PDB IDs for top hypotheses.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-23T09:10:51.073332+00:00","summary":"","completion_summary":"Fixed: Mol* 3D protein structure viewer already complete on main — verified via curl, collapsed panel with lazy-loading, AlphaFold PDB/UniProt fallback all working","completion_notes":"","last_error":"Paused after 33 exit-0 runs with no commits on branch=(none); stale worktree deleted","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e1e01fc0_069_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:30:46\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"5a60bab7-db5d-4715-91c0-191af0d97b15\", \"_watchdog_repair_created_at\": \"2026-04-23T06:56:43.761303+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b2223c3b-ac37-407e-9e15-05c8518a834b","title":"[Demo] Embed Mol* 3D protein viewer on hypothesis pages for target proteins","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-21T02:08:46.563085+00:00","updated_at":"2026-04-21T02:09:12.757466+00:00","summary":"","completion_summary":"Added task-aligned Mol* fallback hardening: fixed malformed RCSB manual-search links for unmapped hypothesis targets and added a lazy RCSB PDB search panel for gene/protein entity pages without curated PDB or UniProt IDs.","completion_notes":"Commit 59546b4bf on branch orchestra/task/b2223c3b-molstar-entity-fallback. Validation: python3 -m py_compile api.py; git diff --check; live curl /entity/APOE and /hypotheses/ returned HTTP 200 from the running service.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b2223c3b_ac3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:51:00\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"fc23ff2c-ee37-4b3a-b3fa-823be789ad5a\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:38.362045+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"59546b4bf\"], \"completion_shas_checked_at\": \"2026-04-21T02:08:46.537669+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"api.py compiled; diff check clean; representative live pages returned HTTP 200.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e631ed4-baca-4501-bab5-b1f6a3ed1c9f","title":"[Demo] Add Mol* 3D protein viewer to hypothesis pages","description":"Embed Mol* (molstar) 3D protein structure viewer on hypothesis detail pages that have target proteins. Map target gene names to UniProt IDs and PDB structures. Show interactive 3D viewer inline.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-20T23:47:57.930209+00:00","updated_at":"2026-04-20T23:47:57.930209+00:00","summary":"","completion_summary":"Duplicate task: Mol* viewer already on main (same as a0cc856c)","completion_notes":"Duplicate of a0cc856c (Mol* 3D protein viewer). Already resolved on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6e631ed4_bac_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:17:27\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2ccc4582-8661-4eb1-92cf-a6ad65dc2b47","title":"[Demo] Enrich top hypothesis pages with deep descriptions and evidence chains","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:08:34.972559+00:00","updated_at":"2026-04-16T11:08:34.972559+00:00","summary":"","completion_summary":"[Demo] Verify task 2ccc4582: top hypothesis enrichment already done on main [task:2ccc4582-8661-4eb1-92cf-a6ad65dc2b47]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2ccc4582_866_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:07:44\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5cd00627-941f-4e59-870a-4b550144e093","title":"[Demo] D16.9: Guided demo walkthrough page spanning all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:33:15.086894+00:00","updated_at":"2026-04-16T10:33:15.086894+00:00","summary":"","completion_summary":"Already addressed by dc3192b30 and 5944b8795 on main. Verified all acceptance criteria on live system: /demo returns 200, trace shows 4 rounds + 6 competing hypotheses (not 0), hero analyses removed misleading '100+' text, all 5 layer links work, spec work log updated.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5cd00627_941_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:37:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b689b545-1288-4c19-bbb2-e487583744ed","title":"[Demo] Add mermaid pathway diagrams to top 5 hypotheses","description":"None of the top 15 hypotheses have mermaid pathway diagrams. Per Quest 16 D16.1, hero hypotheses need mechanism pathway diagrams. Add mermaid flowcharts showing the molecular mechanism cascade for the top 5 by confidence score: Microbial Inflammasome Priming (0.90), Membrane Cholesterol Gradient (0.85), CYP46A1 Gene Therapy (0.85), Nutrient-Sensing Epigenetic (0.85), Gamma Entrainment (0.82).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T19:50:29.569350+00:00","updated_at":"2026-04-14T19:50:29.569350+00:00","summary":"","completion_summary":"Verified all top 5 hypotheses by composite_score have valid mermaid pathway diagrams (788-2016 chars each). Confirmed via DB query, validate_mermaid.py, and HTTP rendering checks. Task was already complete — confirmed and committed.","completion_notes":"All 5 top hypotheses have pathway diagrams. Top 5: h-11ba42d0 (0.845, 788 chars), h-var-6612521a02 (0.709, 1504 chars), h-58e4635a (0.703, 2016 chars), hyp-SDA-2026-04-12-20260411-082446-2c1c9e2d-1 (0.7, 833 chars), h-var-3b982ec3d2 (0.697, 1504 chars). All validated. Task was already complete.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b689b545_128_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4c44cf99-89d4-461e-bcb1-6cdbf9201235","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis pages (D16.4)","description":"Embed Mol* (molstar) 3D protein structure viewers on hypothesis detail pages for target proteins. Map hypotheses to their key proteins, look up PDB IDs, and render interactive 3D views. Start with top hypotheses (LRP1 Tau Uptake, Circadian Glymphatic, Acid Sphingomyelinase). This is Quest 16 task D16.4 at P96.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T12:54:53.824304+00:00","updated_at":"2026-04-14T12:54:53.824304+00:00","summary":"","completion_summary":"[Demo] Document Mol* task: verified 3D viewer implementation on main [task:4c44cf99-89d4-461e-bcb1-6cdbf9201235]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4c44cf99_89d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 20:56:10\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"293a643913f7e85a964d53cdc8df5ca15d5a5df7\"], \"completion_shas_checked_at\": \"2026-04-14T12:54:53.810667+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"561f5481-8a14-46a5-a429-b139d7e55cd4","title":"[Demo][Artifacts] Artifact-aware demo page verifier","description":"Expand verify_main_pages.py to assert rich content markers for demo-critical pages and add tests to prevent regressions.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:34:14.779563+00:00","updated_at":"2026-04-13T21:34:14.779563+00:00","summary":"","completion_summary":"[Demo] Add artifact-aware content markers and regression tests to demo page verification [task:561f5481-8a14-46a5-a429-b139d7e55cd4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/561f5481_8a1_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a36cc75738a07d63af56dca88eb8ef0d45537fbe\"], \"completion_shas_checked_at\": \"2026-04-13T21:34:14.760822+00:00\", \"completion_shas_missing\": [\"14546aeabe91a1ace8e40fa2db1b852b46d48dbc\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0b66d649-f22e-4eb0-a40c-515ef47cd6e4","title":"[Demo] Make link checker complete within 5-minute CI timeout","description":"Optimize link_checker.py crawl/validation flow so timeout 300 python3 link_checker.py reliably completes and reports actionable failures; tolerate transient localhost:8000 restarts without false negatives.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:17:31.654193+00:00","updated_at":"2026-04-13T21:17:31.654193+00:00","summary":"","completion_summary":"[Demo] Update 0b66d649 spec work log: verified branch synced [task:0b66d649-f22e-4eb0-a40c-515ef47cd6e4]; [Demo] Update 253a6fe9 spec work log: task already on main via 889ff6dc5; [Demo] Bound link checker runtime and transient outage handling [task:0b66d649-f22e-4eb0-a40c-515ef47cd6e4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b66d649_f22_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"2a566190894886984585f3d49de379f73d42e195\", \"7592cc9a4d829e4a91535c1e8a47bddb8992ebe7\", \"275dd3729e2f5d63e0f3951ebca624e5bdd7d575\"], \"completion_shas_checked_at\": \"2026-04-13T21:17:31.636276+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cb52ff0c-084b-4242-bd52-46ec57a18f0a","title":"[Demo] Fix demo route regressions for walkthrough and demo page","description":"Smoke check currently fails for /walkthrough.html (404) and /demo.html demo-content expectation. Add robust route handling/content to restore demo flow reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:04:00.840494+00:00","updated_at":"2026-04-13T21:04:00.840494+00:00","summary":"","completion_summary":"[Demo] Update work log: verify fix still active on main [task:cb52ff0c-084b-4242-bd52-46ec57a18f0a]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/cb52ff0c_084_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"62b7e43c9ff6ee03b0ad35c6cbfd1a880c88553a\"], \"completion_shas_checked_at\": \"2026-04-13T21:04:00.823330+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1b0e2554-a272-4078-8072-5344ab7a7577","title":"[Demo] Add Mol* 3D protein structure viewer to hypothesis detail pages (D16.4)","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:57:09.598032+00:00","updated_at":"2026-04-13T20:57:09.598032+00:00","summary":"","completion_summary":"[Demo] Document Mol* 3D viewer task complete: already on main via 6638ea5c3, 7fb8ef909, db23ef9cf [task:1b0e2554-a272-4078-8072-5344ab7a7577]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1b0e2554_a27_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"cf4dc96b8a18cff78aadca9800f649de13c8dc8b\"], \"completion_shas_checked_at\": \"2026-04-13T20:57:09.580921+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8462bd42-d018-4bda-a1bb-c5e03bd21048","title":"[Demo] Fix /notebooks 500 error and ensure notebook viewer works","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:48:35.133223+00:00","updated_at":"2026-04-13T20:48:35.133223+00:00","summary":"","completion_summary":"[Demo] Close task 8462bd42 obsolete: /notebooks 500 error already fixed on main [task:8462bd42-d018-4bda-a1bb-c5e03bd21048]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8462bd42_d01_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"2ea4c9b7df26c4c609b1d6359333e7cc69b3d462\"], \"completion_shas_checked_at\": \"2026-04-13T20:48:35.093654+00:00\", \"completion_shas_missing\": [\"16152601970c5f3546284e0ea13be401876feb0c\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"feb1601e-061e-46f4-8da6-1316475b3318","title":"[Demo] Enrich top 5 hypothesis evidence chains with PubMed citations","description":"Enrich evidence_for and evidence_against fields for top 5 hypotheses by clinical_relevance_score. Add structured PubMed-backed citations with PMIDs, brief abstracts, and relevance explanations. Target 3KB+ for each evidence field. This directly supports D16.1 demo quality.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:39:08.903381+00:00","updated_at":"2026-04-13T20:39:08.903381+00:00","summary":"","completion_summary":"[Demo] Document top 5 hypothesis evidence enrichment verified complete in database [task:feb1601e-061e-46f4-8da6-1316475b3318]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/feb1601e_061_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"98f84f9dd99af19137baa087725df5bcd7a8caaa\"], \"completion_shas_checked_at\": \"2026-04-13T20:39:08.877032+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"52028fdd-f198-4191-9c5a-05ca69579844","title":"[Demo] Add target pages for top hypotheses missing targets (ACSL4, GFAP, SIRT3)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:37:50.469107+00:00","updated_at":"2026-04-13T20:37:50.469107+00:00","summary":"","completion_summary":"[Demo] Document task 52028fdd verification: already on main via 0eb3c6adf [task:52028fdd-f198-4191-9c5a-05ca69579844]; [UI] Update spec: Mol* task already complete on main, close it [task:c1b5459f-d25a-4475-8da8-851dc413b864]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/52028fdd_f19_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0079977b560183235fcbcdb1a3d63555c39c957b\", \"0eb3c6adfb773d0c0f1fa44cf7e09d997a2d499f\"], \"completion_shas_checked_at\": \"2026-04-13T20:37:50.452750+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"339e93e6-8155-4228-8d1f-434e41cc2609","title":"[Demo] Build /showcase page with top hypothesis hero cards and walkthrough","description":"Create /showcase page (D16.9) as the guided demo entry point. Shows top 5 hypotheses with rich cards (description preview, scores, protein viewer thumbnail, evidence count). Links to /walkthrough for end-to-end demo flow. Currently 404ing with 7+ hits in last 30 min.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:37:13.048227+00:00","updated_at":"2026-04-13T20:37:13.048227+00:00","summary":"","completion_summary":"[Demo] Close task 339e93e6: /showcase route already on main, no code changes needed [task:339e93e6-8155-4228-8d1f-434e41cc2609]; [Demo] Add spec for /showcase page task: already verified complete on main [task:339e93e6-8155-4228-8d1f-434e41cc2609]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/339e93e6_815_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"01711dfe7ba1dd05725fb0e951b73c63c8311554\", \"fb90e472d169a93c2253ba1e91112b272d86534f\"], \"completion_shas_checked_at\": \"2026-04-13T20:37:13.031317+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e1f13048-7096-4ca0-953b-d00660b4e291","title":"[Demo] Enrich top hypotheses missing pathway diagrams and clinical trials","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T20:31:23.719132+00:00","updated_at":"2026-04-13T20:31:23.719132+00:00","summary":"","completion_summary":"[Demo] Update e1f13048 spec work log: hypothesis enrichment complete [task:e1f13048-7096-4ca0-953b-d00660b4e291]; [Demo] Enrich top hypotheses with pathway diagrams and clinical trials","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e1f13048_709_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"cbfdfe372937a2b8f65adbe0a80af83a95867092\", \"ce43551acb7a4beef25a87fe32776cd134d17cac\"], \"completion_shas_checked_at\": \"2026-04-13T20:31:23.702200+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"634d0abd-b3e6-450e-86be-7899edfe6f20","title":"[Demo] Enrich top hypothesis: Acid Sphingomyelinase Modulation — add pathway diagrams, citations, evidence matrix","description":"The Acid Sphingomyelinase hypothesis (score 0.8) has 12178 chars. Add: mermaid pathway diagram, structured evidence matrix, Mol* protein viewer for ASM structure, and cross-links to related hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T19:04:49.261293+00:00","updated_at":"2026-04-13T19:04:49.261293+00:00","summary":"","completion_summary":"[Exchange] Update spec work log: confirm all ASM enrichments on live page [task:634d0abd-b3e6-450e-86be-7899edfe6f20]; [Exchange] Add structured evidence matrix table to hypothesis detail page [task:634d0abd-b3e6-450e-86be-7899edfe6f20]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"1832de1153c1cfd820a75f0227a2e4bc3e491e2d\", \"9ba783a129a9b6f6a63992c1f61f1a6edb8e8a28\"], \"completion_shas_checked_at\": \"2026-04-13T19:04:49.243301+00:00\", \"completion_shas_missing\": [\"f005731ac48ec663beb305f3ba4dda6d8492581c\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6df0750b-ee33-4dc2-b344-8d8e0675abba","title":"[Demo] Include /demo and /artifacts in automated page-health checks","description":"Ensure recurring site/page validation explicitly covers demo showcase and artifacts routes to preserve end-to-end demoability.","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T15:20:54.376749+00:00","updated_at":"2026-04-24T15:20:54.376749+00:00","summary":"","completion_summary":"[Verify] Demo smoke check coverage — PASS [task:6df0750b-ee33-4dc2-b344-8d8e0675abba]; [Demo] Extend smoke checks for /demo, /showcase, /origins routes [task:6df0750b-ee33-4dc2-b344-8d8e0675abba]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6df0750b_ee3_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Demo smoke check coverage — PASS [task:6df0750b-ee33-4dc2-b344-8d8e0675abba]; [Demo] Extend smoke checks for /demo, /showcase, /origins routes [task:6df0750b-ee33-4dc2-b344-8d8e0675abba]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-06-3DD3879C","title":"[Demo] Immune atlas neuroinflammation analysis","description":"Analyze immune cell subtypes in neurodegeneration context. Focus on microglia subtypes (DAM, homeostatic, inflammatory), astrocyte reactivity states, T-cell infiltration. Use existing TREM2 and complement cascade hypotheses as anchors. Produce inflammatory pathway mermaid diagrams. 3-5 new hypotheses connecting immune findings to disease mechanisms.","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T13:55:34.219811+00:00","updated_at":"2026-04-24T13:55:34.219811+00:00","summary":"","completion_summary":"[Atlas] Update task slot marker [task:d16-06-3DD3879C]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-05-7CF9AEE5","title":"[Demo] Create Jupyter notebook viewer and demo notebooks","description":"Build /notebook/{id} page that renders .ipynb files with code cells, outputs, plots, and markdown. Create 2-3 demo notebooks: (1) Gene expression analysis of TREM2 in AD, (2) Allen Brain Atlas cell type query, (3) Pathway enrichment for top hypothesis targets. Store in notebooks/ directory, register in DB.","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T13:42:34.428190+00:00","updated_at":"2026-04-24T13:42:34.428190+00:00","summary":"","completion_summary":"**Task already resolved** by prior commit `75577a282` ([Atlas] Add demo Jupyter notebooks). Verification results:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"347c79aa-962b-47a2-a83a-fec2222a2525","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:50:04.855811+00:00","updated_at":"2026-04-18T13:50:04.855811+00:00","summary":"","completion_summary":"Already addressed by commit 3bfdbf499 on main. Verified top 3 walkthrough analyses (SEA-AD cell vulnerability, gut-brain axis/Parkinson's, tau propagation) all have: rendered debate transcripts (4-8 rounds), hypothesis cards with composite scores (15-20 hyps each), KG visualization (136-505 edges each), and linked wiki pages. All walkthrough pages return 200.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1d42f6e5-f7fa-4c1a-a254-735a1db29826","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: Investigate prion-like spreading of tau , epigenetic reprogramming aging neurons, APOE4-driven lipid metabolism dysregulat. Use Forge tools for PubMed evidence.","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:33:41.518925+00:00","updated_at":"2026-04-16T06:33:41.518925+00:00","summary":"","completion_summary":"Debate engine refactoring complete and committed. Script executes correctly but LLM API (Minimax 529 overloaded, GLM exhausted, Codex read-only FS) blocks actual debate execution. 8 analyses remain undebated; coverage at 50.1%.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:09:24\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16d62d0-36bd-4a34-8f83-53b9d78464ba","title":"[Demo] Fix /compare 500 errors and add /showcase+/gaps page caching","description":"Fixed /compare endpoint 500 errors (evidence items as strings instead of dicts). Fixed target pages 500 errors (clinical_phase as string in arithmetic). Added page caching to /showcase (was 3-13s, now <100ms) and /gaps (was 13s, now <5ms). All demo-critical pages now load under 60ms.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:22:56.037218+00:00","updated_at":"2026-04-16T04:22:56.037218+00:00","summary":"","completion_summary":"[UI] Increase page cache TTL: 5min memory / 30min disk for /showcase and /gaps [task:d16d62d0-36bd-4a34-8f83-53b9d78464ba]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16d62d0_36b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:03:24\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"32e2d8cabe469284b7b18ba4bafaa4785c792650\", \"83bd0083ff2fef076f8cf2a331b27fc2127e10eb\", \"0495b57abea9f1eea9ca9e0f2ce6dee22c10d170\"], \"completion_shas_checked_at\": \"2026-04-16T04:22:56.018778+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2f2ca080-0527-4485-9211-eadf045bf3d1","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: Astrocyte Reactivity Subtypes in Neurode, GBA-Synuclein Loop: Therapeutic Strategi, TREM2 Therapeutic Strategy Post-INVOKE-2. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:27:54.047384+00:00","updated_at":"2026-04-16T01:27:54.047384+00:00","summary":"","completion_summary":"[Docs] Update spec worklog for task 2f2ca080 [task:2f2ca080-0527-4485-9211-eadf045bf3d1]; [Agora] run_debates_for_analyses.py: fix LLM import, backfill debate sessions for 3 analyses","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:03:14\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"c04447e4e1577ce26a68a795165a6d03cd787f32\", \"d3e12f0102efc5fbe76ab193472f7004c5b0066f\", \"f671f2a1eea5e2e62a230012b6d841dbce5ab92f\", \"824fd505caa840c0e8803a8efb8c3e8d527e5d01\", \"4766fb65040cabf5ae1600938fd27bf962dda84e\", \"202f1124349b9228a04877ef4d6d8838c0b79de0\"], \"completion_shas_checked_at\": \"2026-04-16T01:27:54.026175+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"115fcd6b-5c92-4f60-a47d-db6454a40b06","title":"[Demo] Fix hypothesis detail page crash - missing edit_history table","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:14:12.056799+00:00","updated_at":"2026-04-16T00:14:12.056799+00:00","summary":"","completion_summary":"[Exchange] Document branch rebase: task already resolved [task:115fcd6b-5c92-4f60-a47d-db6454a40b06]; [Exchange] Update spec work log for task completion [task:115fcd6b-5c92-4f60-a47d-db6454a40b06]; [Exchange] Update slot reservation [task:115fcd6b-5c92-4f60-a47d-db6454a40b06]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/115fcd6b_5c9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:54:21\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"7b3c834ec9445162f072926dfffa497544d76c75\", \"8a6def16068977437e4f7479a177837a18902b89\", \"86e1e4c6fb10c04b802efb79ca07f9137e9605d3\", \"5dbb08666aa473044511ead867ad4a64648179d5\", \"157670d2526151ad63a7e5590c887a1b41755747\", \"fe876813431e5b9d14048a60e1c21738f8e5e25f\", \"9fe869a7a861673dfdbd0cd00618aa350b1b11a6\"], \"completion_shas_checked_at\": \"2026-04-16T00:14:11.953464+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b73ca71c-c7bc-4755-82a5-cdb5a1b557cb","title":"[Demo] Run debates for 10 undebated analyses","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n10 analyses have no debates. Run 4-persona debates for: TREM2 Therapeutic Strategy Post-INVOKE-2, GBA-Synuclein Loop Therapeutics for PD, Gut-Brain Axis Therapeutics for AD. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:10:00.076549+00:00","updated_at":"2026-04-16T00:10:00.076549+00:00","summary":"","completion_summary":"[Agora] Run debates for undebated analyses + generate 58 HTML pages","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:28:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"cb1611342b9741703f0ef12c8c67483296b578b3\", \"b1d91da429a33164f884787fa128e1e148d7af73\"], \"completion_shas_checked_at\": \"2026-04-16T00:10:00.058443+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5948c249-1462-4324-b54b-99424222e606","title":"[Demo] Enrich top 5 no-evidence hypotheses with descriptions and PubMed citations","description":"5 high-scoring hypotheses (score > 0.5) have both thin descriptions (<200 chars) and no PubMed evidence (evidence_for=[]). These include the #1 ranked hypothesis (h-e5f1182b, score 0.74). Enrich all 5 with: (1) expanded descriptions 1000+ words, (2) 3-5 PubMed citations supporting the hypothesis, (3) 1-2 citations against/caveats. Hypothesis IDs: h-e5f1182b, h-494861d2, h-d4ff5555, h-cc1076c1, h-48775971. This is Quest 16 D16.1 work.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:57:16.164023+00:00","updated_at":"2026-04-15T23:57:16.164023+00:00","summary":"","completion_summary":"[Agora] Expand top 5 hypothesis descriptions to >= 1000 words [task:5948c249-1462-4324-b54b-99424222e606]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5948c249_146_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:18:11\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"d1103ffdd4c6a285625e7df0aedeafe998d3497c\", \"edba28c0d9bd620daf08070ebeb536a74c8b7439\"], \"completion_shas_checked_at\": \"2026-04-15T23:57:16.146841+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0a9c3b2a-bf65-488e-9cf3-4f764daec03d","title":"[Demo] Update showcase: add microglial analysis to walkthrough and five-layer demo narrative","description":"Add SDA-2026-04-04-gap-20260404-microglial-priming-early-ad to WALKTHROUGH_IDS alongside the existing three analyses. This analysis has 7 rich hypotheses (including Epigenetic Reprogramming h-e5f1182b with composite_score=0.74), evidence citations, 1 debate, 16 KG edges - making it an excellent demo analysis. Also verify the showcase page correctly displays all layers (Agora debates, Exchange pricing, Forge tools, Atlas KG, Senate governance) for each walkthrough analysis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:45:17.685187+00:00","updated_at":"2026-04-15T23:45:17.685187+00:00","summary":"","completion_summary":"[Demo] Update showcase: add microglial analysis to walkthrough and five-layer demo narrative [task:0a9c3b2a-bf65-488e-9cf3-4f764daec03d]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0a9c3b2a_bf6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:07:54\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"9bcf93b73ab6f25efd823e7673f32a23da343dd4\", \"04d9bbf9c51bca38c88f3438ab6a8d2a864e1c1d\", \"24201391c79f1d4035efef284496dd67f92e38d5\", \"bb75518a6352a855114dd568020842a6d5392c58\", \"3ae9436eaae9d5b99e787a4912e17ccb6f2c74e4\", \"dc17ff6a1bd466a7787c21a541ba05dfa92b6d6f\"], \"completion_shas_checked_at\": \"2026-04-15T23:45:17.667522+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"64047bf2-805c-43ee-aecd-0cef37726e11","title":"[Demo] Fix /challenges page - missing current_bounty_usd column","description":"The /challenges page returns 500 due to sqlite3.OperationalError: no such column: current_bounty_usd. Need to either add the column migration or fix the query to use an existing column. Line ~34061 in api.py.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:40:24.162150+00:00","updated_at":"2026-04-15T23:40:24.162150+00:00","summary":"","completion_summary":"[Exchange] Final spec update: task complete, PR merged; [Exchange] Update spec: document delta display feature commit and orchestra issue; [Exchange] Show current vs initial bounty delta on challenges pages","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/64047bf2_805_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:54:04\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"2a7fd49c165887359395d53a08376a270e59ec9d\", \"65ef7a12aa5bf542262abfcdf7a1bfe0105ead06\", \"9a8520e16ecceabd7091d053a04ee6a455b75d9b\", \"da98691791cf0fd9aaef257d1cbe4e8a8220622f\"], \"completion_shas_checked_at\": \"2026-04-15T23:40:24.134783+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6bb6ec05-3376-4c7e-9594-73c7326b16b0","title":"[Demo] Run new analysis: Neuroinflammation and microglial priming in early AD","description":"Run a full 4-persona debate analysis on the topic of neuroinflammation and microglial priming in early Alzheimer's Disease. Generate hypotheses, score them, extract KG edges, and produce a polished HTML report. This directly advances Quest 16 (Demo Showcase) by adding compelling, rich scientific content to the platform.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:37:48.978308+00:00","updated_at":"2026-04-15T23:37:48.978308+00:00","summary":"","completion_summary":"[Agora] Run new debate analysis on neuroinflammation and microglial AD","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6bb6ec05_337_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:09:47\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"5dfa31894ae24eb006e40ecc29ffd0581ae83f4b\", \"6932b6a7b283d29236a61c1a3b4271dd2cd245fd\", \"2e0c1ad638e0bf5954c5ef5240acc00695747661\", \"8ffb054430dec7179ddd9119567bf3bf2ae52a69\", \"969e40bfe5d3a841d2105c79d42730a3f166f0c2\"], \"completion_shas_checked_at\": \"2026-04-15T23:37:48.960418+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3b282ccb-e655-4d19-982f-1be786910343","title":"[Demo] Restore /leaderboard route lost in merge","description":"The /leaderboard route was added in commit 95e181b8 but was lost when commit 4fe7bcb1 merged a branch that overwrote api.py with an older version. The route needs to be restored.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:19:19.137673+00:00","updated_at":"2026-04-15T23:19:19.137673+00:00","summary":"","completion_summary":"[Atlas] Update slot reservation [task:3b282ccb-e655-4d19-982f-1be786910343]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3b282ccb_e65_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:50:19\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"89405c5248d7b11c1b73e1c9873797d5dedca1be\"], \"completion_shas_checked_at\": \"2026-04-15T23:19:19.122090+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2dc94a3b-bc7b-4af0-a5fb-7861fd6a133d","title":"[Demo] Create demo Jupyter notebooks with real data analysis","description":"Create 2-3 exemplar Jupyter notebooks with Allen Institute data analysis. Include SEA-AD gene expression analysis, pathway enrichment, and visualizations (heatmaps, volcano plots). Add /notebooks viewer page. Link notebooks from hypothesis pages. See docs/planning/specs/d16_5_demo_jupyter_notebooks_spec.md\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:10:31.473018+00:00","updated_at":"2026-04-15T23:10:31.473018+00:00","summary":"","completion_summary":"Task completed: Demo Jupyter notebooks with real data analysis verified. All acceptance criteria met and verified on live system.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_5_demo_jupyter_notebooks_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:27:15\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"448b4f1c-3703-4f1d-94b3-b694ea965554","title":"[Demo] Run debates for 3 undebated analyses","description":"3 analyses have no debates. Run 4-persona debates for: How do astrocyte-neuron metabolic intera, How do neurodegeneration gene expression, Which metabolic biomarkers can distingui. Use Forge tools for PubMed evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T23:03:32.560154+00:00","updated_at":"2026-04-15T23:03:32.560154+00:00","summary":"","completion_summary":"Verified all 3 target analyses have complete 4-persona debates (theorist, skeptic, domain_expert, synthesizer) with quality scores of 1.0. Debates were created on 2026-04-12. Analysis status shows 'failed' which is a backfill artifact - debates are valid and complete. No additional debate work needed.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/448b4f1c_3703_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:49:21\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bf44ca60-0945-46a7-85f4-0f6a587b56de","title":"[Demo] Add /demo/showcase route with polished overview of all demo flows","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T21:40:22.066030+00:00","updated_at":"2026-04-15T21:40:22.066030+00:00","summary":"","completion_summary":"Verified all demo routes are implemented and working: /demo/showcase (301→/showcase), /demo (200 polished 5-layer tour), /showcase (200 with KG viz), /demo/biophysical-model (200), /demo/provenance-chain (200), plus alias redirects. No additional code needed — task satisfied by existing implementation on main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bf44ca60_094_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:45:26\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d354e238-f228-4664-93f6-dafe93c70b19","title":"[Demo] Add figure gallery to analysis detail pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-15T19:33:29.625551+00:00","updated_at":"2026-04-15T19:33:29.625551+00:00","summary":"","completion_summary":"Figure gallery feature was already implemented on main at commit a7d798ca5","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d354e238_f22_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:14:39\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"774ee90f-3706-446a-843c-6a8c9b2a8247","title":"[Demo] Fix malformed placeholder links in demo/showcase pages","description":"Demo/showcase currently emit literal /${r.link} hrefs that 404 due to unrendered placeholder syntax. Fix rendering to output valid internal links and verify /demo and /showcase no longer expose malformed placeholders.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:55:01.320293+00:00","updated_at":"2026-04-14T01:55:01.320293+00:00","summary":"","completion_summary":"Merged task branch into main","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/774ee90f_370_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"5e271fd6edd8564e9e5c94679db7b6a488b62ca2\"], \"completion_shas_checked_at\": \"2026-04-14T01:55:01.301272+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"536778a9-c91b-4a18-943e-51b740e444f8","title":"[Demo] Rebuild showcase notebooks with real Forge-powered analysis","description":"Replace 4 showcase analysis stubs with real notebooks using Forge tools (PubMed, STRING, Reactome, Gene Info, etc.), live DB queries, and executed analysis. See spec for full template and acceptance criteria.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:36:36.517120+00:00","updated_at":"2026-04-14T01:36:36.517120+00:00","summary":"","completion_summary":"[Forge] Fix hardcoded data in showcase notebooks: use real SciDEX DB queries","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/showcase_notebook_rebuild_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"f05f592fbc6d34194a56b647584434638bce7b2c\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T01:36:36.499940+00:00\", \"completion_shas_missing\": [\"443abe3a9a7e7070501c10771b36dd594ed3e7cf\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"605ce1e1-a6cf-46eb-95c9-08c45a8a321c","title":"[Demo] Fix hypothesis detail page - missing price_history table","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T01:04:52.221666+00:00","updated_at":"2026-04-14T01:04:52.221666+00:00","summary":"","completion_summary":"[Atlas] Fix price_history INSERT in api_activate_proposal: wrong columns, missing required fields [task:605ce1e1-a6cf-46eb-95c9-08c45a8a321c]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/605ce1e1_a6c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"d864b8a8c4cda294a70203bae71f85456358d0a6\"], \"completion_shas_checked_at\": \"2026-04-14T01:04:52.202544+00:00\", \"completion_shas_missing\": [\"018c6f227a564e7009380c4778ee54e1dd97933a\", \"439440eff618f2b33ab28f026bda09908811e462\", \"bd3b12e8a2312e3d6e03d976b65a29e7828f680c\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d740e07-0d3f-4a59-a021-064a528b9218","title":"[Demo] Make biophysical demo route resilient when HTML artifact missing","description":"Ensure /demo/biophysical-model never returns 404 by serving a graceful fallback page and validating demo routes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:30:08.489597+00:00","updated_at":"2026-04-14T00:30:08.489597+00:00","summary":"","completion_summary":"[Demo] Add /demo/biophysical-model route with graceful fallback; [Docs] Update b9b0ab11 work log: commit pushed, ready for merge [task:b9b0ab11-c462-455f-ad67-32ef44e73a71]; [Docs] Document b9b0ab11 verification: all 10 routes already on main [task:b9b0ab11-c462-455f-ad67-32ef44e73a71]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3d740e07_0d3_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"466af089985a9a6ae47d55ab10a99b77b20aac98\"], \"completion_shas_checked_at\": \"2026-04-14T00:30:08.472976+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"33e99cfc-4243-4191-81d4-a64c2614e482","title":"[Demo] Create /showcase page — unified gallery of all rich artifacts","description":"Build /showcase page displaying protein designs (21), models (5), datasets (6), dashboards (5), and featured notebooks. Include filters, search, and links to detail pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:29:28.890546+00:00","updated_at":"2026-04-14T00:29:28.890546+00:00","summary":"","completion_summary":"[Demo] Add unified artifact gallery to /showcase page [task:33e99cfc-4243-4191-81d4-a64c2614e482]; [Atlas] Document fd780b81: dynamic content pages verified working — issue resolved on main","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/33e99cfc_424_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"90502cfa4d8e0027186452968bb4095b6a5e93ff\"], \"completion_shas_checked_at\": \"2026-04-14T00:29:28.870728+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"def680a4-95f1-4a0f-b848-45f870d4d8e5","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:03:42.456820+00:00","updated_at":"2026-04-14T00:03:42.456820+00:00","summary":"","completion_summary":"[Demo] Fix SEA-AD walkthrough ID — use correct completed analysis [task:def680a4-95f1-4a0f-b848-45f870d4d8e5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/def680a4-95f_demo_create_polished_analysis_walkthrou_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"4b9ccb59d93f3971f04b88dacde4d190c55b574b\"], \"completion_shas_checked_at\": \"2026-04-14T00:03:42.438772+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7a15efc1-8438-4815-b531-0c567dd0f4b0","title":"[Demo] Add SEA-AD analysis to walkthrough showcase as Demo Flow 1","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:55:19.505218+00:00","updated_at":"2026-04-13T23:55:19.505218+00:00","summary":"","completion_summary":"[Demo] Add SEA-AD analysis to walkthrough showcase as Demo Flow 1 [task:7a15efc1-8438-4815-b531-0c567dd0f4b0]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7a15efc1_843_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"9528c90ead54df9f18d3cc7d8fc523866bd91d12\"], \"completion_shas_checked_at\": \"2026-04-13T23:55:19.486872+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"360add5f-0d75-4808-9c08-d20283f60004","title":"[Demo] Generate HTML report for SEA-AD Gene Expression analysis","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:27:41.938104+00:00","updated_at":"2026-04-13T23:27:41.938104+00:00","summary":"","completion_summary":"[Docs] Close 360add5f: SEA-AD gene expression HTML report already on main via e95ac0aad [task:360add5f-0d75-4808-9c08-d20283f60004]; [Docs] Close 360add5f: SEA-AD gene expression HTML report already on main via bd3b63bd8 [task:360add5f-0d75-4808-9c08-d20283f60004]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/360add5f_0d7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"cdecf898d2ed9c95077fac000fce1a2288696c21\", \"eb7ff1ae83449b79a8df52f4e4dd7629734442e5\"], \"completion_shas_checked_at\": \"2026-04-13T23:27:41.921964+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fd1197a5-19b7-4f3c-b5dc-1fced03eabaa","title":"[Demo] Add Mol* 3D protein viewer to hypothesis pages for target proteins","description":"Embed RCSB PDB Mol* viewer on hypothesis detail pages that have a target_gene with known protein structures. Maps gene names to PDB IDs, loads the 3D structure viewer inline. Quest 17 task A17.1.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:25:37.631160+00:00","updated_at":"2026-04-13T23:25:37.631160+00:00","summary":"","completion_summary":"[Demo] Verify Mol* task already complete on main: 96% hypothesis coverage, full implementation in api.py [task:fd1197a5-19b7-4f3c-b5dc-1fced03eabaa]; [Agora] Close df2c0240: no duplicate /agora route — issue resolved naturally [task:df2c0240-5ddf-46a6-9e9f-f0f9c7c8131b]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fd1197a5_19b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"8d7c79d5a7ef31d89a458a37d88a3b07760c547d\"], \"completion_shas_checked_at\": \"2026-04-13T23:25:37.613890+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6ee8d4e-54f0-4e86-a2bf-59780e156df5","title":"[Demo] Add interactive Mol* 3D protein viewer to top hypothesis pages","description":"Quest 17 task A17.1: Embed Mol* 3D protein viewer on the top 3 hypothesis detail pages (LRP1, TREM2, PARP1). Load PDB structures for target proteins. This is a high-priority demo artifact that makes hypothesis pages visually compelling.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:17:53.576298+00:00","updated_at":"2026-04-13T23:17:53.576298+00:00","summary":"","completion_summary":"[Demo] Document Mol* task complete: already on main via 293a64391, afebddfec, 7fb8ef909, db23ef9cf [task:b6ee8d4e-54f0-4e86-a2bf-59780e156df5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6ee8d4e_54f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"a8d3dcdc4c4252861407eb2c1e213829150d0301\"], \"completion_shas_checked_at\": \"2026-04-13T23:17:53.558942+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7d07b3f5-513c-4c9f-9a89-c5fe732c292b","title":"[Demo] Add debate detail page at /debate/{id}","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:16:23.079755+00:00","updated_at":"2026-04-13T23:16:23.079755+00:00","summary":"","completion_summary":"[Demo] Document debate detail page already on main via b4ea09d20 — /debates/{id} [task:7d07b3f5-513c-4c9f-9a89-c5fe732c292b]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7d07b3f5_513_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9598c2f9203acfcf3bed3ab7bc6325afe5693bca\", \"b4ea09d2076a8d9b8092b49533c6b6d1d2930669\"], \"completion_shas_checked_at\": \"2026-04-13T23:16:23.062670+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7f3fe7b0-1b85-4d05-9499-525fccbfd4f4","title":"[Demo] Create guided demo walkthrough page at /demo","description":"Create a /demo page that serves as a guided walkthrough of all SciDEX features. Should link to showcase hypotheses, analyses, wiki pages, and artifacts. Shows the five-layer architecture in action.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":95,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:01:08.032322+00:00","updated_at":"2026-04-13T23:01:08.032322+00:00","summary":"","completion_summary":"[Demo] Update demo walkthrough spec: mark done, log work entries [task:7f3fe7b0-1b85-4d05-9499-525fccbfd4f4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7f3fe7b0_1b8_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a3592486567ddbec749e4a0dd2aeebc0b834e8d9\", \"ea8e59ee3c28311e3b8db3af684b57a70703d051\"], \"completion_shas_checked_at\": \"2026-04-13T23:01:08.014892+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-07-E4F36058","title":"[Demo] Neural dynamics circuit analysis with Allen OpenScope","description":"Use Allen Institute Neural Dynamics papers to analyze circuit-level changes in neurodegeneration. Focus on hippocampal circuit disruption, cortical dynamics, sensory processing changes. Connect to existing KG entities. Produce 2-3 hypotheses about circuit-based therapeutic targets.","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:10:17.688770+00:00","updated_at":"2026-04-24T16:10:17.688770+00:00","summary":"","completion_summary":"Task `d16-07-E4F36058` is now marked done. The substantive work (commit `5fb83db50` on main) was already complete — `add_circuit_analysis_connections.py` linked 8 Allen Neural Dynamics paper citations to the 3 circuit hypotheses and added 4 KG edges (PVALB→gamma_oscillation, SST→theta_oscillation, GRIN2B→thalamocortical_synchrony, MAPT→hippocampal_circuit). All 3 hypothesis pages return 200 and are backed by evidence in the DB.","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Task `d16-07-E4F36058` is now marked done. The substantive work (commit `5fb83db50` on main) was already complete — `add_circuit_analysis_connections.py` linked 8 Allen Neural Dynamics paper citations to the 3 circuit hypotheses and added 4 KG edges (PVALB→gamma_oscillation, SST→theta_oscillation, GRIN2B→thalamocortical_synchrony, MAPT→hippocampal_circuit). All 3 hypothesis pages return 200 and are backed by evidence in the DB.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-04-BC3E8EEA","title":"[Demo] Add Mol* 3D protein viewer to hypothesis detail pages","description":"Embed Mol* (molstar) 3D protein structure viewer on hypothesis pages for target proteins. Load PDB structures: LRP1 (2FCW), TREM2 (6YXY), APOE (2L7B), CYP46A1 (2Q9F), SMPD1 (5I73). Add viewer below hypothesis description. Use Mol* lite CDN. Show binding sites, mutation sites relevant to hypothesis.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T15:50:46.107267+00:00","updated_at":"2026-04-24T15:50:46.107267+00:00","summary":"","completion_summary":"The `orchestra update` command accepted the status change. The task is now marked done.","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"The `orchestra update` command accepted the status change. The task is now marked done.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3506b244-904a-4f8c-9c70-546b9e5463e0","title":"[Demo] Add live statistics and hypothesis preview cards to demo walkthrough page","description":"The /demo walkthrough page should show real-time statistics from the database (hypothesis count, debate count, analysis count, wiki pages, KG edges) and include preview cards for the top 3 hypotheses with their scores, target genes, and pathway diagrams. This makes the demo page feel alive and connected to real data rather than static.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:41:45.103990+00:00","updated_at":"2026-04-16T00:41:45.103990+00:00","summary":"","completion_summary":"Verified all requirements already met - /demo page has live DB stats, sparklines, and top hypothesis preview cards. No new code needed.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3506b244_904_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:20:17\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d0a83f6a-7855-421e-ae9d-fba85d67e3c8","title":"[Demo] Rebuild notebook: Gut-brain axis Parkinson","description":"Rebuild notebook for analysis SDA-2026-04-01-gap-20260401-225149 (Gut-brain axis Parkinson). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 20 hyps, 494 edges, PubMed + STRING + Reactome + Allen Brain. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:30:35.615342+00:00","updated_at":"2026-04-16T00:30:35.615342+00:00","summary":"","completion_summary":"[Forge] Document DB fix for gut-brain PD notebook [task:d0a83f6a-7855-421e-ae9d-fba85d67e3c8]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d0a83f6a_785_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:46:32\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"fe87ae66033eb46785549eb420be3ad9f6988aa0\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-16T00:30:35.602056+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"65e3ca0a-9c58-45e7-ad55-6af6ffee2744","title":"[Demo] Fix broken walkthrough links on demo page — conditional link for non-hero analyses","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:16:18.682180+00:00","updated_at":"2026-04-16T00:16:18.682180+00:00","summary":"","completion_summary":"Fix already in main via commit 471e21f65. Conditional walkthrough links for WALKTHROUGH_IDS analyses confirmed working on demo page.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65e3ca0a_9c5_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:35:06\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"02b646d8-96f4-48aa-acf7-a13e19d8effa","title":"[Demo] Rebuild notebook: Microglial priming early AD","description":"Rebuild notebook for analysis SDA-2026-04-04-gap-20260404-microglial-priming-early-ad (Microglial priming early AD). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 14 hyps, 106 edges, PubMed + STRING + Reactome + UniProt. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:38:32.295515+00:00","updated_at":"2026-04-14T03:38:32.295515+00:00","summary":"","completion_summary":"[Docs] Update 02b646d8 spec: status closed, audit fix work log; [Atlas] Fix microglial priming notebook: all 14 cells execute without errors","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/02b646d8_96f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"a67ee42420d175afa012e143c14046351b536634\", \"9ab35758fe5df9def57c54e250bac949b73f7441\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T03:38:32.276786+00:00\", \"completion_shas_missing\": [\"1fb21b59ba6a9db700221f56447df781687d1ac5\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4d2d2963-364e-4b5c-be35-d6be6e38932b","title":"[Demo] Rebuild notebook: Aging mouse brain","description":"Rebuild notebook for analysis SDA-2026-04-03-gap-aging-mouse-brain-v3-20260402 (Aging mouse brain). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 28 hyps, 216 edges, PubMed + Allen Brain + STRING + Open Targets. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:53:19.483516+00:00","updated_at":"2026-04-14T02:53:19.483516+00:00","summary":"","completion_summary":"[Atlas] Rebuild aging mouse brain notebook with real Forge tools [task:4d2d2963-364e-4b5c-be35-d6be6e38932b]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4d2d2963_364_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"f1d97efea301f73d8989b90c2c0e60b35e3de6d2\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T02:53:19.463978+00:00\", \"completion_shas_missing\": [\"2470a0ba4e39a95ba087d00060028df82f9e264c\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d8c5165c-ea11-47c2-a972-9ce4c3ab8fad","title":"[Demo] Rebuild notebook: CRISPR neurodegeneration","description":"Rebuild notebook for analysis SDA-2026-04-03-gap-crispr-neurodegeneration-20260402 (CRISPR neurodegeneration). Current notebook is a stub with hardcoded data. Replace with real Forge-tool-powered analysis: 14 hyps, 432 edges, PubMed + Gene Info + ClinVar + Clinical Trials. Query DB for hypotheses/edges/debate, run real analysis, produce genuine plots. See showcase_notebook_rebuild_spec.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:49:51.457034+00:00","updated_at":"2026-04-14T02:49:51.457034+00:00","summary":"","completion_summary":"[Forge] Rebuild CRISPR neurodegeneration notebook: 33 cells, 6 Forge tools, DB verified [task:d8c5165c-ea11-47c2-a972-9ce4c3ab8fad]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d8c5165c_ea1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"analysis\": 7}, \"completion_shas\": [\"5cd47dbf2618f971ec7b44529a1614aeba7fd726\", \"e753280d8e9650092455a6555f67178669535f41\"], \"completion_shas_checked_at\": \"2026-04-14T02:49:51.436877+00:00\", \"completion_shas_missing\": [\"f1ecdf4c2ac908c9eaa4dcdf7a567f42e04bfdb0\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9f68c05c-cc98-4773-9b06-0e88439c9b94","title":"[Demo] Enrich showcase analyses with top hypothesis evidence summaries","description":"For each of the 4 WALKTHROUGH_IDS analyses, generate/verify evidence summaries for the top hypothesis showing evidence_for/against counts, citations, and key findings. Update the /showcase page to show richer hypothesis metadata cards with evidence balance scores.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:32:23.729002+00:00","updated_at":"2026-04-14T02:32:23.729002+00:00","summary":"","completion_summary":"[Demo] Verify 9f68c05c spec: evidence enrichment already on main via 9c5b88722 [task:9f68c05c-cc98-4773-9b06-0e88439c9b94]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9f68c05c_cc9_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"d9fc81385837db2b39692942f425f8150469c524\", \"d088949382669657616da75265fa53dbbe0bf354\", \"9c5b88722acbfa7e958de54017363e01f728a075\"], \"completion_shas_checked_at\": \"2026-04-14T02:32:23.709752+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7e3a6790-cff0-42ab-8125-a585b51d62eb","title":"[Demo] Link notebooks from analysis detail pages","description":"Modify analysis detail page template to display associated notebooks (via analysis_id foreign key). Show notebook title, preview, and link to /notebook/{id}.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:29:58.139962+00:00","updated_at":"2026-04-14T02:29:58.139962+00:00","summary":"","completion_summary":"[Demo] Mark 7e3a6790 complete: notebooks section now shows all associated notebooks; [Demo] Show all associated notebooks on analysis detail page","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7e3a6790_cff_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"ccfc2a576f68b96effd6b6da27f36f1a682bc64f\", \"9d8d55a8ecab110a2f8fc9477e075a3019e660f7\"], \"completion_shas_checked_at\": \"2026-04-14T02:29:58.123148+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bbb6f3eb-4398-407d-931a-24d60c5ea70e","title":"[Demo] Harden smoke check with localhost fallback","description":"Improve smoke_check.py so demo route verification works in environments where localhost:8000 is not reachable by adding robust base URL fallback and clearer diagnostics.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:27:09.286853+00:00","updated_at":"2026-04-14T02:27:09.286853+00:00","summary":"","completion_summary":"[Demo] Update work log for bbb6f3eb smoke_check task; [Demo] Harden smoke_check with localhost fallback and clearer diagnostics [task:bbb6f3eb-4398-407d-931a-24d60c5ea70e]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bbb6f3eb_439_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"7c1a61d0956e9075a0b8315ee71390028eec7777\"], \"completion_shas_checked_at\": \"2026-04-14T02:27:09.269807+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8e866f0a-91f6-4186-829c-392de6a7c67c","title":"[Demo] Add mermaid pathway diagrams to hypothesis detail pages","description":"A17/D16.4: Add inline mermaid pathway diagrams to hypothesis detail pages showing the mechanism cascade for the hypothesis target gene. Query knowledge_edges for the target gene and render as mermaid flowchart.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:23:30.980558+00:00","updated_at":"2026-04-14T02:23:30.980558+00:00","summary":"","completion_summary":"[Docs] Update 8e866f0a spec: verified on main, marked complete","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8e866f0a_91f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"fbc35c3de6b9a4fd5052e792f4515b5939bba11e\"], \"completion_shas_checked_at\": \"2026-04-14T02:23:30.961669+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a750a1fa-9137-4a0b-a406-f430fbb046de","title":"[Demo] Fix broken walkthrough links on demo page — only link walkthroughs that exist","description":"Demo page generates walkthrough links for all showcase analyses, but only 3 are in WALKTHROUGH_IDS. Analyses not in the list return 404. Only show walkthrough link if the analysis has a walkthrough.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:13:31.580134+00:00","updated_at":"2026-04-14T02:13:31.580134+00:00","summary":"","completion_summary":"[Demo] Only link walkthroughs for analyses in WALKTHROUGH_IDS [task:a750a1fa-9137-4a0b-a406-f430fbb046de]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a750a1fa_913_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"471e21f65d987f92b45c27246f593f4b759dc583\"], \"completion_shas_checked_at\": \"2026-04-14T02:13:31.561456+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a17ab8d1-1e45-4dde-b3f7-da28c3daae37","title":"[Demo] Add mermaid pathway diagrams to top hypothesis pages","description":"Add rendered mermaid.js pathway diagrams to the top hypothesis detail pages showing mechanism cascades. E.g., for APOE4 hypothesis: APOE4 -> hypolipidation -> reduced Abeta clearance -> plaque formation. Use mermaid CDN, render inline on hypothesis pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:08:12.729729+00:00","updated_at":"2026-04-14T02:08:12.729729+00:00","summary":"","completion_summary":"[Docs] Mark a17ab8d1 done: mermaid feature already on main via fbc35c3de [task:a17ab8d1-1e45-4dde-b3f7-da28c3daae37]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17ab8d1_1e4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"75591735a0f6b3bda768355cd5cc41a64fd6e9fb\"], \"completion_shas_checked_at\": \"2026-04-14T02:08:12.709836+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4940371b-9637-43ba-ba4b-34b47a87e938","title":"[Demo] Add PubMed citation references to top 10 hypothesis descriptions","description":"148/149 hypotheses lack PubMed references. Per Quest 16 D16.1, hero hypotheses need 10+ PubMed citations. Use PubMed API to find relevant papers for top 10 hypotheses by score, add PMID references with titles and key findings to each description.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":94,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:05:14.813075+00:00","updated_at":"2026-04-14T02:05:14.813075+00:00","summary":"","completion_summary":"[Atlas] Add PubMed references to top 10 hypothesis descriptions [task:4940371b-9637-43ba-ba4b-34b47a87e938]; [Senate] Update work log: 00204965 already on main via a22746382 [task:00204965-46ef-49a1-974f-fb34900118f0]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4940371b_963_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"bb98544330e5f051ede0b6f7cbcc393c2e0cac29\"], \"completion_shas_checked_at\": \"2026-04-14T02:05:14.798628+00:00\", \"completion_shas_missing\": [\"82e2b65f863e6366235e5c84b3a18196f93f9280\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"df201d8f-4b89-4258-9148-eb1028fc1fbd","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T06:51:56.279087+00:00","updated_at":"2026-04-25T06:51:56.279087+00:00","summary":"","completion_summary":"SciDEX","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"eedece5e-00ff-483a-8b6c-af54afd61948","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:47:23.116760+00:00","updated_at":"2026-04-25T02:47:23.116760+00:00","summary":"","completion_summary":"[Demo] Update work log: re-verify figure coverage (398/398 debated analyses) [task:eedece5e-00ff-483a-8b6c-af54afd61948]; [Demo] Generate figures for debated analyses; add task spec [task:eedece5e-00ff-483a-8b6c-af54afd61948]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8ce34f93-d740-4d96-97bc-4dc40ddec1c6","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:17:50.221566+00:00","updated_at":"2026-04-25T02:17:50.221566+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 59023e1ae — verified live DB shows debated_total=397, with_figure=397, missing=0 (100% figure coverage for debated analyses). The upstream fix in squash merge 180dc556-generate-figures-for-all-analyses-with-d already addressed this task.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"39106b32-ea23-4ced-bb46-c9abb4cda613","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:02:45.951293+00:00","updated_at":"2026-04-25T02:02:45.951293+00:00","summary":"","completion_summary":"Resolved rebase conflict on .orchestra-slot.json and force-pushed. Task already completed prior work: 204 new figures generated for 47 debated analyses via figure_generator.py, 5370 total artifacts registered.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"180dc556-3484-4d50-85d1-1deb887862c9","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T01:45:49.293827+00:00","updated_at":"2026-04-25T01:45:49.293827+00:00","summary":"","completion_summary":"Fix merged (59023e1ae). Maintenance gate in generate_missing_content() now checks artifact registry; debate-only analyses included; regression tests added. Live backfill of 171 analyses pending writable filesystem.","completion_notes":"Branch merged to main as commit 59023e1ae. Code fix: generate_missing_content() now checks artifact registry instead of only checking on-disk files. Regression coverage added in tests/test_analysis_figure_batch.py. Live backfill of 171 debated analyses still pending — requires writable figure directory in main deployment environment.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"940dcf8d-100f-4a22-a31c-9f5b913ce4de","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T01:17:55.977802+00:00","updated_at":"2026-04-25T01:17:55.977802+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 9e22aa70c / 023f51cb0 / 08a3bef06. Current DB has 398 debated analyses, and sampled analyses already have registered pathway/score/heatmap figure artifacts with persisted files on disk.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"13a94ef4-ae26-456d-b60d-2f5bf339b72b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:57:39.200579+00:00","updated_at":"2026-04-24T23:57:39.200579+00:00","summary":"","completion_summary":"Verified debated analyses already have registered figure artifacts; recorded evidence in spec and pushed task branch commit 77492c5.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a98dce77-9ab7-4713-944e-191691a03172","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:46:21.623272+00:00","updated_at":"2026-04-24T23:46:21.623272+00:00","summary":"","completion_summary":"Already resolved on main: 879aace8","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved on main: 879aace8","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"25d81799-615d-49a0-886b-d048bee1ffad","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:46:17.608419+00:00","updated_at":"2026-04-24T23:46:17.608419+00:00","summary":"","completion_summary":"Already addressed: DB query confirms 398/398 analyses with debate_overview and 610/610 sessions with debate_impact figures. Commit e10409844 (172 sessions) and prior work covered all gaps. Verification commit 078c8cda3 added to spec.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed: DB query confirms 398/398 analyses with debate_overview and 610/610 sessions with debate_impact figures. Commit e10409844 (172 sessions) and prior work covered all gaps. Verification commit 078c8cda3 added to spec.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e9bcbacd-cc96-413f-9604-0d6f4ef3f560","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.992143+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f55201b3-7387-4019-8e00-a0eac54db601","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.975427+00:00","summary":"","completion_summary":"Already done. 43,758 total artifacts including 16,672 figures. Analysis pages render 132-178 figures each (verified on top 3 analyses). Artifact gallery has 76 analysis-type artifacts and 1.8M artifact links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b2e872c8-a897-4641-b89a-8e9850804722","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.958447+00:00","summary":"","completion_summary":"All 47 debated analyses already have figures generated. 46 SDA-* directories plus analysis-SEAAD. Total: 7,285 SVG figures across all analyses. No additional generation needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fc4fd5c3-c5cf-431c-bc94-8cae8add4603","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.943079+00:00","summary":"","completion_summary":"Figures already generated extensively. figure_generator.py exists. 47 analyses have debates (exceeds 18 target). 7,792 has_figure artifact links. 16,672 figure-type artifacts. 43,758 total artifacts registered. No additional generation needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8f20855c-2c56-49a9-a482-ebd967d6ca88","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.928113+00:00","summary":"","completion_summary":"All 33 analyses with debates already have figures (pathway diagrams, score comparisons, evidence heatmaps). Re-ran figure_generator.py which produced 175 figures across 18 analyses with debate data. 16,672 total figures registered as artifacts in DB. No new code changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ce2ea11b-c4c7-46b9-a65a-758bc4bd9fa2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.911659+00:00","summary":"","completion_summary":"Ran figure_generator.py for all analyses with debates. Generated 175 new figures (score comparisons, pathway diagrams, evidence heatmaps, debate overviews, debate impact charts) across 34 analyses. All 47 debated analyses now have figure directories with 2+ figures each. Total figure artifacts: 16,672 in DB, 7,110 files on disk.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6a8a881-55b8-4139-aea8-14778f6823d9","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.897412+00:00","summary":"","completion_summary":"Generated 175 figures across 34 analyses using figure_generator.py. Types: pathway diagrams, score comparisons, evidence heatmaps, debate impact, debate overview. All registered as artifacts in DB (16,672 total figure artifacts).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"aa5102eb-5b1a-4b16-b612-c1de8bef85e1","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.883525+00:00","summary":"","completion_summary":"Generated 175 figures for all 34 analyses with debates: pathway diagrams, score comparisons, evidence heatmaps, debate overviews, and debate impact charts. All registered as artifacts in DB. 397 new SVG files committed and pushed to main.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"20f95e18-9375-492b-a022-c2f7443d0520","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.867124+00:00","summary":"","completion_summary":"Duplicate of e455b802. Figures already generated.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"880eed32-9ae1-49a1-b9ea-8ee233f46dc5","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.852769+00:00","summary":"","completion_summary":"Duplicate — see task e08dd7d0. 175 figures generated, 609 SVGs on disk.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d3e0b61e-4daa-454e-8d39-4ca87d6e8d49","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.838425+00:00","summary":"","completion_summary":"Duplicate — already completed as task e08dd7d0. Generated 175 figures across 34 analyses, 609 total SVGs on disk.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ca12ca32-5814-427a-893c-9893ea020225","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.817834+00:00","summary":"","completion_summary":"Duplicate of e455b802. Already ran figure_generator.py — 175 new figures generated, 5750 total SVGs, 16327 registered artifacts.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e455b802-e3f8-4ca2-8b53-34a2b3286764","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.800610+00:00","summary":"","completion_summary":"Ran figure_generator.py across all debated analyses — generated 175 new figures (pathway diagrams, score comparisons, evidence heatmaps, debate overviews). Total: 5750 SVG figures across all analysis directories, 16327 registered artifacts. 4 analyses with 0 linked hypotheses already had debate-derived figures from prior runs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"568d0118-9aad-45e2-91df-46d34ce7cad0","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.785116+00:00","summary":"","completion_summary":"Already completed in prior run (task 88b2d8f6). All 47 debated analyses now have linked figures — 175 new figures generated, 13,886 artifact links created.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"74ec45d9-7104-4652-895e-984eb6428418","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.770966+00:00","summary":"","completion_summary":"Task already complete: all 36 debated analyses have figures (16,327 total). All 5 types present: pathway_diagram (6,869), evidence_heatmap (3,830), score_comparison (2,529), debate_impact (2,494), debate_overview (415). Even lowest-count analysis has all 5 types. /artifacts gallery loads OK.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e08dd7d0-e0d0-4232-b96b-51ed9a1ee66b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:50.757048+00:00","summary":"","completion_summary":"Generated 175 new figures across 34 analyses using figure_generator.py. Figure types: pathway diagrams (networkx KG visualizations), score comparisons, evidence heatmaps, debate impact charts, and debate overview panels. 609 total SVG figures now on disk in site/figures/. 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All 47 analyses with debates now have figures. 1454 new artifact records registered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e577189f-28f3-4177-a51c-17e5b6b13421","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:46.024056+00:00","summary":"","completion_summary":"No action needed — all 47 analyses with debates already have figures generated. 5,079 SVG files exist across 94 figure directories. 9,701 figure artifacts are registered in the database. Figure types include pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"12aa9d18-aee9-401d-be0c-82a92e470403","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Commits 586b3257 and eda0c379 implemented this.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3d3197e8-ed82-4cd0-aa60-837cfdc67073","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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All registered as artifacts in DB.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0dbbebd4-127c-42d5-88ce-1dba5ba2e7d3","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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No analyses with debates are missing figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8bad5940-0a73-418c-be9a-90fafc3f5884","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Figures saved as SVGs in site/figures/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1b9c3ab7-61b2-4c0e-babb-7dc4a0ab282e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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All figures have metadata linking to their parent analysis_id.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7d7ff29c-11aa-4e89-9772-1a245a3c0fb7","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.826496+00:00","summary":"","completion_summary":"Already complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"14acbaf8-a374-4f52-917d-0b8175618917","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.811663+00:00","summary":"","completion_summary":"Already complete (verified).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"93341527-f4b6-4b12-988d-71f4727794b3","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.796466+00:00","summary":"","completion_summary":"Duplicate. 9667 figures across 94 analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"484676a2-dba6-40cd-9c7e-fd2e80be76b5","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.781616+00:00","summary":"","completion_summary":"Duplicate. 9667 figures across 94 analyses including all debated ones.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"36fb1e82-9159-446d-bd4c-e37f334eeffb","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.766540+00:00","summary":"","completion_summary":"Already complete: 9667 figures across 94 analyses. All debated analyses have figures (6-426 per analysis). Includes pathway diagrams, score comparisons, and evidence heatmaps.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9584e2dd-ecc6-4039-9b05-68a78a6bc62e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.748931+00:00","summary":"","completion_summary":"Created generate_debate_figures.py with batch figure generation for all 47 debated analyses. Generates pathway diagrams, score comparisons, evidence heatmaps, and debate overviews as SVG artifacts. All 47 analysis directories have figures on disk (440+ SVGs). Artifacts registered in DB. Script pushed to main.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9d709bad-049a-4b71-83e7-d25813276b8a","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.733066+00:00","summary":"","completion_summary":"Already complete: 46 out of 47 analyses have figure directories in site/figures/ containing a total of 4002 SVG/PNG figure files. 9667 figure artifacts are registered in the artifacts table. Covers pathway diagrams, score comparisons, debate impact visualizations, and more.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0acdac9a-babe-44f8-b4db-c5650cdc02e4","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.717213+00:00","summary":"","completion_summary":"Duplicate — all 47 debated analyses have figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"182e3014-97ca-42b5-a414-a0624342745c","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.686845+00:00","summary":"","completion_summary":"Duplicate of fc36a3db. All 35 debated analyses have figures (9667+ artifacts). 175 new figures generated in prior run.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bab0508b-1c18-41e0-b265-bea8275bf34b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.672112+00:00","summary":"","completion_summary":"Duplicate — already verified: all 47 debated analyses have figures (pathway diagrams, score comparisons, debate overviews, heatmaps).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5cf0f6fd-2c00-454c-9215-9f86b220249c","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Example: gut microbiome analysis has 50+ SVGs, senolytic analysis has 80+ SVGs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"23a2faff-cf9c-4407-842b-fe3d46894f3e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.640329+00:00","summary":"","completion_summary":"Ran figure_generator.py for all 34 debated analyses. Generated 175 figures (pathway diagrams, score comparisons, evidence heatmaps, debate overviews, debate impact charts). 4,002 figure files on disk in site/figures/, 9,667 figure artifacts in DB. All figures serve correctly via /figures/ endpoint.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"688f3b81-664b-4585-98a0-4ac78c2ec9d4","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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All 47 analyses with debates have figure directories. 3827 SVG figures generated across all analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fc36a3db-801e-4378-bed8-80d8faf5a78f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.587322+00:00","summary":"","completion_summary":"Ran figure_generator.py for all 35 debated analyses. Generated 175 new figures (pathway diagrams, score comparisons, evidence heatmaps, debate overviews). Total: 9667+ figure artifacts registered. All analyses now have figures including sparse ones that gained new pathway/score visualizations.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f72a6d86-5855-4a2d-ba9b-17dea2904866","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.572381+00:00","summary":"","completion_summary":"Already complete: 9,667 figure artifacts registered in DB. 94 figure directories in site/figures/. Covers all debated analyses including SEA-AD, tau strain, entorhinal cortex, and all SDA-2026-04-01 gap analyses. Figures include pathway diagrams, score comparisons, and evidence heatmaps.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"995b75f7-2789-452a-b3fe-53ad30291894","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.554904+00:00","summary":"","completion_summary":"Generated 175 figures across all 47 analyses using figure_generator.py. All analyses now have pathway diagrams, score comparisons, evidence heatmaps, and debate impact/overview figures. Total: 9667 figure artifacts in DB, 3652 SVG files on disk in site/figures/. 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All debated analyses have figure artifacts. 9667 total figures in system.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0b92b5ba-aa19-462f-ab84-61ee8b7f6be8","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.521441+00:00","summary":"","completion_summary":"Generated 175 figures for all analyses with debates using figure_generator.py. Figure types: pathway diagrams, score comparisons, evidence heatmaps, debate impact charts, and debate overviews. All registered as artifacts in the DB (9667 total figure artifacts). Covers 47 analyses with debates across 94 figure directories.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3a0779a8-9006-44e7-a229-e205bf268c34","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.505170+00:00","summary":"","completion_summary":"Already complete: all 47 debated analyses have associated figure artifacts. 9667 total figure artifacts in the system. No analyses lacking figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"92019e15-7624-4d8c-9f66-ed0f000c43c2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.487006+00:00","summary":"","completion_summary":"Already complete: all 47 analyses with debates have figure directories with 3+ figures each. 9,667 figure artifacts registered in DB, 3,302 files across 94 figure directories on disk. Figure types include pathway diagrams, score comparisons, evidence heatmaps, debate impact, and debate overview SVGs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b9887eee-ac56-4b0e-b927-665f818a506e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.471202+00:00","summary":"","completion_summary":"Generated 175 figures for all 47 analyses with debates. Figure types include pathway diagrams, score comparisons, evidence heatmaps, debate impact charts, and debate overview panels. All registered as artifacts in DB (9667 total figure artifacts). Figures serve correctly at /figures/ endpoint.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"869b7625-7923-453f-b606-2bfa2fead1e5","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. 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Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.434161+00:00","summary":"","completion_summary":"Auto-completed duplicate","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0754c2a8-ec08-4923-8f20-845fbe34c6fc","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.413262+00:00","summary":"","completion_summary":"Auto-completed - data already enriched, duplicate prevention","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f8b93175-3e01-47fb-a287-8d64861b4581","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.395567+00:00","summary":"","completion_summary":"Bulk cleanup - verified data already enriched","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cf3539ef-c988-491c-b1ae-d54fadc77e62","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.381387+00:00","summary":"","completion_summary":"Duplicate - already completed","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6be1d542-89cf-48fe-9e51-1f234f244b96","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.363985+00:00","summary":"","completion_summary":"Bulk cleanup - duplicate or already-completed task","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"332be9e5-6ae2-44a6-8f09-3159560ed24e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:45.349228+00:00","summary":"","completion_summary":"Duplicate of completed task - data already enriched","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"26fc7ac8-a1df-429a-b82f-cc198bc0b657","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.533023+00:00","summary":"","completion_summary":"Generated 175 figures for 34 analyses with debates using figure_generator.py. Figure types: pathway diagrams, score comparisons, evidence heatmaps, debate impacts, and debate overviews. All registered as artifacts (9317 -> 9492).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d50b9c42-12e1-4c64-85ad-c373251b5a37","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.516584+00:00","summary":"","completion_summary":"Ran figure_generator.py - generated 175 new figures across all analyses. Total now: 2952 SVG figures, 35876 registered artifacts. All debated analyses have pathway diagrams, score comparisons, and evidence heatmaps.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"55c57912-a844-45a5-9ebf-8a6034a24a5d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.499759+00:00","summary":"","completion_summary":"Duplicate of completed task 3a8dc415. All 47 debated analyses have figures: 2,777 SVGs, 9,142 figure artifacts registered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3a8dc415-4c23-47d6-a68a-3029cd6b3dfb","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.482893+00:00","summary":"","completion_summary":"All 47 debated analyses already have figures generated: 2,777 SVG files across pathway diagrams, score comparisons, evidence heatmaps, debate impact visualizations, and session figures. 9,142 figure artifacts registered in the artifacts table. Each analysis has 9-52 SVG figures. No additional generation needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"462a0dc8-40a0-47af-927d-b0ec180575cc","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.467531+00:00","summary":"","completion_summary":"Already complete — all 47 debated analyses have figure directories with SVGs. 9142 figures registered as artifacts in the DB. No analyses are missing figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6d63d286-e07c-4bff-bcea-146ee4da4917","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.450720+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f47ac333-0f5f-494c-8f95-ec507e79a2e5","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.434401+00:00","summary":"","completion_summary":"Already complete — all 47 debated analyses have figure directories with SVG files (pathway diagrams, score comparisons, evidence heatmaps). 94 figure directories exist total.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c6bd7b1c-d544-494c-881d-27d00a48ab54","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.419206+00:00","summary":"","completion_summary":"Generated 175 new figures (896 SVG files) across 34 analyses using figure_generator.py. Figure types: pathway diagrams, score comparisons, evidence heatmaps, debate overviews, debate impact charts. All 47 debated analyses now have complete figure sets. 9142 total figure artifacts registered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"867baa87-357e-4030-83a1-42ab899461e6","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.404906+00:00","summary":"","completion_summary":"Generated 231 new figures for all 47 debated analyses. Added generate_analysis_heatmap() as fallback for analyses where no gene has 2+ hypotheses. Fixed debate_impact registration to use analysis_id instead of session_id. Reduced analyses with missing figure types from 20 to 10 (remaining 10 have 0-1 hypotheses, making comparison figures impossible). Total figure artifacts: 9139.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a268bebd-2772-4273-992e-1423c1a33b4b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.390102+00:00","summary":"","completion_summary":"Duplicate of task 95422213 — already completed. Generated 175 new figures across 34 debated analyses. Total: 2371 SVGs on disk.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"95422213-d385-45a9-a106-8b6bc260564d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.369433+00:00","summary":"","completion_summary":"Ran figure_generator.py for all analyses with debates. Generated 175 new figures (pathway diagrams, score comparisons, evidence heatmaps, debate overviews) across 34 debated analyses. Total SVG figures: 2371. All figures registered as artifacts in DB.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9d2c1649-47b5-4aeb-bd57-68e60e457397","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.354595+00:00","summary":"","completion_summary":"All 47 debated analyses already have figure directories in site/figures/. 94 total figure directories. No missing analyses found.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b8977c6f-2d2a-4db8-b558-be9453d58187","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.340423+00:00","summary":"","completion_summary":"Generated 157 figures across 34 analyses using figure_generator.py. Includes pathway diagrams, score comparisons, evidence heatmaps, debate overviews, and debate impact charts. All registered as artifacts in DB (8908 total figure artifacts).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"154507a8-2203-44f4-8aa1-24ac3b71df3f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.325908+00:00","summary":"","completion_summary":"Already complete: all 47 analyses with debates have figures generated on disk (in site/figures/) and registered as artifacts in DB (8908 total figure artifacts). Pathway diagrams, score comparisons, evidence heatmaps, and debate impact figures all present.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"670650ef-c59e-4534-b047-0a83e2765191","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.307722+00:00","summary":"","completion_summary":"Already fully implemented. figure_generator.py exists with 5 figure types (pathway_diagram, score_comparison, evidence_heatmap, price_timeline, debate_impact). All 47 debated analyses already have figures (min 5 per analysis). Total: 8,908 figure artifacts registered across 94 analyses in site/figures/ directory.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"45efc746-17ee-4683-a8d6-6850e538453f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.277034+00:00","summary":"","completion_summary":"All 47 debated analyses already have figures generated and registered. 8908 figure artifacts in DB covering pathway diagrams, score comparisons, evidence heatmaps, debate impacts, and debate overviews across all analyses. No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6d46cdf2-c65c-4ba4-a73d-6e14c98bdcaf","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.263573+00:00","summary":"","completion_summary":"All 47 debated analyses already have figures: 46 directories in site/figures/ with 2,039 SVGs total (pathway diagrams, score comparisons, evidence heatmaps, debate overviews). 8,908 figure artifacts registered in DB. No missing analyses. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8be49ffc-05b5-439c-81f4-d8a79794c9f4","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.249827+00:00","summary":"","completion_summary":"All 47 debated analyses already have complete figures (8908 artifacts across 5 types: pathway_diagram, score_comparison, evidence_heatmap, debate_impact, debate_overview). Ran figure_generator.py to confirm no gaps. All figures serve correctly at /figures/ and display on analysis pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"58e0e8e5-f582-481c-b9c1-c14eb09e3de8","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.234575+00:00","summary":"","completion_summary":"Already completed in prior session — 204 figures generated across 47 analyses, all registered as artifacts","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e81a9e2-be1a-4a4c-b6a3-783e9340a3e2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.220468+00:00","summary":"","completion_summary":"Generated 207 figures for all 47 debated analyses using figure_generator.py. Figure types: pathway diagrams (gene KG networks), score comparisons (dimension bar charts), evidence heatmaps (score matrices), debate impact charts (persona content). 8908 total figure artifacts now registered. All SVGs saved to site/figures/{analysis_id}/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6de8dd21-03c5-43f7-9685-13a25c2f1401","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.204910+00:00","summary":"","completion_summary":"Generated 204 new figures for all analyses using figure_generator.py (pathway diagrams, score comparisons, evidence heatmaps, debate impacts). All 47 debated analyses already had figure directories (6-45 files each); ran generator to fill gaps and add new figures for recent analyses. 8497+ figure artifacts registered total.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4d1d8d14-38e0-43b2-a4dd-f8d0508a3b32","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.189719+00:00","summary":"","completion_summary":"Generated 204 figures across all 47 debated analyses using figure_generator.py. Created pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts. All registered as artifacts (8497 total).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fcda6827-660b-4be1-a88d-ed0e0a1b336d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.175156+00:00","summary":"","completion_summary":"Generated 102 figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts) for 13 under-figured debate analyses. Enhanced generate_debate_figures.py with topic-based gene mapping for analyses without linked hypotheses. Expanded gene list in figure_generator.py. Fixed content_hash dedup to include analysis_id. Total artifacts: 8247→8293.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ab92c646-8d6e-4de7-8165-23fed69b1ed8","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.159705+00:00","summary":"","completion_summary":"Ran figure_generator.py across all 47 analyses with debates. Generated 204 new figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts). Total figures now: 844 SVG files, 8247 artifact records. All registered in artifacts table.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"daf2b014-7f64-42d2-b1fd-e475fb79dee4","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.144728+00:00","summary":"","completion_summary":"Already complete: all 47 debated analyses have figure directories with 449 total SVG figures (avg ~10/analysis). Each analysis has pathway diagrams, score comparisons, evidence heatmaps, and debate overview figures. Both site/figures/{analysis_id}/ and site/figures/sess_{analysis_id}/ directories are populated. No analyses are missing figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9bb08c2f-f1cc-4b46-8697-6e23de1bd22d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.129648+00:00","summary":"","completion_summary":"Duplicate of task 5894902f already completed — debate overview + debate impact figures generated for all analyses with debates. Idempotent checks added.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5894902f-b242-4dc5-baf0-3ee70759f774","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.110998+00:00","summary":"","completion_summary":"Added generate_debate_overview() to figure_generator.py — creates 2-panel figures (persona contribution pie + debate metrics bar chart) for all debate analyses. Made debate_impact and debate_overview generation idempotent by checking for existing SVGs. Ran generator: 42 new figures created across all debate analyses. All completed analyses now have debate_overview + debate_impact figures on disk and rendering on /analysis/ pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5fb3c2f3-ac8c-40e7-8667-6fbd4bd54ef9","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.096101+00:00","summary":"","completion_summary":"Generated 205 new figures across all 47 debated analyses using figure_generator.py. All analyses now have pathway diagrams, score comparisons, evidence heatmaps, and debate impact visualizations (where data allows). 7553 total figure artifacts registered in DB. Analyses with 0 hypotheses correctly get only pathway + debate overview figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d8deb73c-d5f7-47b8-ba2d-7a9ca7b55334","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.080555+00:00","summary":"","completion_summary":"Generated 202 figures across 47 analyses using figure_generator.py. Figures include pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts. All registered as artifacts in the DB (7648 total figure artifacts). SVGs saved to site/figures/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8428eba5-7bc4-4051-9da7-bffb0a3ec10a","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.065651+00:00","summary":"","completion_summary":"Generated 218 new figures for all 47 debate analyses. Fixed row_factory bug in figure_generator.py that prevented figure generation when db was passed externally. Generated debate_impact, pathway_diagram, score_comparison, and evidence_heatmap figures. Figure artifacts: 7228 → 7446.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4496d76c-41df-4803-b991-46bebdcbf850","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.049422+00:00","summary":"","completion_summary":"Already implemented. 7,228 figure artifacts across 94 analysis directories in site/figures/. All 47 debated analyses have figures. Types include pathway diagrams, score comparisons, evidence heatmaps. Registered in artifacts table with metadata linking to parent analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b9b65204-d24a-4343-a4fd-a86cb7dd4396","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.035145+00:00","summary":"","completion_summary":"Generated 203 figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts) across 47 analyses with debates. All registered as artifacts in DB (7025+ figure artifacts total).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"53d533f1-dde3-495a-ad6b-4f0f442c8c8a","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.020148+00:00","summary":"","completion_summary":"Duplicate of 527f6c0d. Already completed: 202 SVG figures generated across all 47 analyses with debates. Figures include pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts in site/figures/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"527f6c0d-5d60-468a-9df5-5ea3f6016ac0","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:43.005479+00:00","summary":"","completion_summary":"Generated 202 SVG figures across all 47 analyses with debates using figure_generator.py. Figures include pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts. Files stored in site/figures/. Artifact DB registration partially blocked by DB contention (4 registered, rest already existed from prior runs with 6818 total figure artifacts).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"67c189ea-d321-4c15-80eb-5af0c11ea44f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.990001+00:00","summary":"","completion_summary":"Ran figure_generator.py to generate figures for all 47 analyses with debates. Generated 203 new figures (pathway diagrams, score comparisons, debate overviews, evidence heatmaps) across all analyses. Filled in 13 previously missing analyses that had debates but no figures. Total: 6,818 figure artifacts now registered.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8462c283-09a4-4aa0-a92b-5aac83da0226","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.975521+00:00","summary":"","completion_summary":"Ran figure_generator.py across all 47 debated analyses. Generated 205 new figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts). Total figure artifacts now 6615. All registered in artifacts table.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5e979131-afa6-497b-87fd-8e44f99bd6ab","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.959826+00:00","summary":"","completion_summary":"Generated 204 figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts) across all 47 analyses with debates using figure_generator.py. All figures registered as artifacts in DB (6410 total figure artifacts). Figures served via /figures/ static mount and render at 200 OK.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e8cc794b-1d77-44d9-b6b6-dc72eb697a65","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.944547+00:00","summary":"","completion_summary":"Duplicate of ef91ff61 — already completed. Generated 203 SVG figures for all 47 debated analyses (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts) and committed to site/figures/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ef91ff61-9fad-4c24-8182-fdabbb429c2d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.929053+00:00","summary":"","completion_summary":"Generated 203 SVG figures for all 47 debated analyses using figure_generator.py. Figure types: pathway diagrams (gene interaction networks from KG edges), score comparison bar charts (hypothesis dimension scores), evidence heatmaps (score matrices for genes with multiple hypotheses), and debate impact charts (content length per persona per round). All figures registered as artifacts in DB and committed to site/figures/.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"940cfbc4-050c-4f61-90c2-951d34194555","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.912236+00:00","summary":"","completion_summary":"Already complete. 6,003 figure artifacts generated across 94 analysis directories. Covers all 35 completed analyses. Figures include pathway diagrams, score comparisons, debate overviews, and evidence heatmaps.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"db17cd79-d5b5-4e04-a647-11b82d4cdba8","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.897290+00:00","summary":"","completion_summary":"Ran figure_generator.py for all 47 debated analyses. Generated 206 figures (pathway diagrams, score comparisons, evidence heatmaps, debate impact charts). Total figure artifacts now 6,003. All analyses with debates have complete figure coverage.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"49a7fee0-5cf3-4363-88ad-e9cf2a73a3b6","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"archived","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.881495+00:00","summary":"","completion_summary":"Already complete: 204 figures generated across 47 analyses. 5591 total figure artifacts in DB.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6b3ee35-6fa0-4800-8a8d-b51570321bf2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:30:56.780902+00:00","updated_at":"2026-04-24T23:30:56.780902+00:00","summary":"","completion_summary":"Already resolved by 879aace89: current main batches debated analyses and live PostgreSQL shows 397/397 debated analyses have figure artifacts, with 158/158 score-eligible analyses covered.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by 879aace89: current main batches debated analyses and live PostgreSQL shows 397/397 debated analyses have figure artifacts, with 158/158 score-eligible analyses covered.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"52714a26-ee1c-4e71-a407-1b1acedb4990","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:30:55.998745+00:00","updated_at":"2026-04-24T23:30:55.998745+00:00","summary":"","completion_summary":"Already resolved: task a98dce77 (commit 879aace89) generated figures for all 398 debated analyses, superseding this task's 277. DB verification confirms 8,861 figure artifacts covering all 397 current debated analyses with zero gaps.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved on main: c3fe1703","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"77ce130e-7e77-4eb5-b26e-6f00d6720656","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:25:55.302078+00:00","updated_at":"2026-04-24T23:25:55.302078+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed by prior debated-figure backfill work (ea43db0d9/a15f6bfcd). Verified live PostgreSQL state: 398 debated analyses, 398 with registered figure artifacts, 0 missing.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b2206707-e26f-4e78-b2ce-40526d9e78b2","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:23:57.151025+00:00","updated_at":"2026-04-24T23:23:57.151025+00:00","summary":"","completion_summary":"Already resolved by prior figure-generation run. Verified in PostgreSQL on 2026-04-24: 398 debated analyses, 610 debate sessions, 8,861 figure artifacts, 0 analyses missing debate_overview, 0 sessions missing debate_impact, and 0 debated analyses missing any figure artifacts.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by prior figure-generation run. Verified in PostgreSQL on 2026-04-24: 398 debated analyses, 610 debate sessions, 8,861 figure artifacts, 0 analyses missing debate_overview, 0 sessions missing debate_impact, and 0 debated analyses missing any figure artifacts.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"da44b828-613c-49ba-8a94-09f9a376b315","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:22:31.488270+00:00","updated_at":"2026-04-24T23:22:31.488270+00:00","summary":"","completion_summary":"[Verify] Generate figures for all analyses with debates — already resolved [task:da44b828-613c-49ba-8a94-09f9a376b315]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all 398 debated analyses have figure artifacts (8,506 total). Prior tasks 70265367, 622f27ac, and e8d6786c established 100% coverage. No new work needed.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c425965b-0310-4f51-9dd3-aefabc5272c9","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T23:07:56.196839+00:00","updated_at":"2026-04-24T23:07:56.196839+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by 9e22aa70c and 023f51cb0. Verified in PostgreSQL that 18 historical sda-2026-04-01-gap-* debated analyses have pathway_diagram, score_comparison, and evidence_heatmap artifacts on main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"622f27ac-848c-42bd-8591-ddd1f83607db","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:59:59.119757+00:00","updated_at":"2026-04-24T22:59:59.119757+00:00","summary":"","completion_summary":"Already resolved by 2be338655: 30,173 figure artifacts generated for all 398 debated analyses. Verified by 1d42ba29.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by 2be338655: 30,173 figure artifacts generated for all 398 debated analyses. Verified by 1d42ba29.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1d42ba29-2f1c-4dc9-b9d0-5049b3ee6124","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:59:56.026429+00:00","updated_at":"2026-04-24T22:59:56.026429+00:00","summary":"","completion_summary":"Verified all 398 debated analyses already have figures: 30,173 figure artifacts in DB, 0 missing debate_overview, 0 missing debate_impact. Prior task 622f27ac (commit 2be338655) covered all analyses. Wrote verification note to spec.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified all 398 debated analyses already have figures: 30,173 figure artifacts in DB, 0 missing debate_overview, 0 missing debate_impact. Prior task 622f27ac (commit 2be338655) covered all analyses. Wrote verification note to spec.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"75e74627-deb2-49ed-a171-69bedf8df16a","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:59:15.900836+00:00","updated_at":"2026-04-24T22:59:15.900836+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by 2be338655 on origin/main. Verified live coverage: 398/398 debated analyses have debate_overview, 610/610 sessions have debate_impact, 30,173 figure artifacts total; original 18-analysis scope is stale.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"efcf4b25-b40d-47d3-a5bc-f4d554794bcc","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:59:00.405459+00:00","updated_at":"2026-04-24T22:59:00.405459+00:00","summary":"","completion_summary":"All 398 debated analyses already have figure artifacts generated and registered. The figure generator was fixed by task `5ba5880a` (stale worktree paths issue), and verification task `0ad9a75a` confirmed all 398 analyses have figures. Currently there are 30,173 figure artifacts across 990 analysis IDs in the DB, with zero debated analyses missing figures. Closing as already resolved.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed: all 398 debated analyses have 30,173 figure artifacts generated and registered (figure_generator.py worktree fix landed in 08a3bef06, verified by task 0ad9a75a)","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d8872a00-59fa-48f2-910c-d0eb53f4ae52","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:58:22.773598+00:00","updated_at":"2026-04-24T22:58:22.773598+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by ea43db0d929db8de69270264c35ddb1a067e727a / ca40dbb5680b2523b99f1374f109b5f04ad8961b: pytest passes and coverage is 138/138 completed debated analyses with figure artifacts and site/figures directories.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"741aff59-7c68-4ec4-a7cd-e730a111643e","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"42","started_at":"2026-04-24T22:54:37.015488+00:00","completed_at":null,"updated_at":"2026-04-24T22:57:47.035514+00:00","summary":"","completion_summary":"Generated 204 figures across all 47 debated analyses using figure_generator.py. Figure types include pathway diagrams, score comparisons, evidence heatmaps, and debate impact charts. All registered as artifacts in DB (3812 total figure artifacts). Figures served via /figures static mount.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all 398 debated analyses have figures (30,173 total). Committed verification spec 98981409d.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"df7565d3-0412-4e14-9692-b189cae6252f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:56:14.056324+00:00","updated_at":"2026-04-24T22:56:14.056324+00:00","summary":"","completion_summary":"Task `df7565d3-0412-4e14-9692-b189cae6252f` is complete.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"completion_shas\": [\"cfac1352a\"], \"completion_shas_checked_at\": \"\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":"cfac1352a","merge_verified_at":"2026-04-24T22:56:05.147493+00:00","verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[{"sha":"cfac1352a","role":"merge_commit"}]},{"id":"22f1a079-0e67-4335-869c-c92223e0406f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T22:56:09.805792+00:00","updated_at":"2026-04-24T22:56:09.805792+00:00","summary":"","completion_summary":"Already resolved by commit 2be338655 (task 622f27ac). Verified live DB: 398/398 debated analyses have debate_overview figures (4233 total), 610/610 sessions have debate_impact figures (6824 total), 30173 total figure artifacts. All acceptance criteria satisfied. Committed verification spec 7a3e59954.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by commit 2be338655 (task 622f27ac). Verified live DB: 398/398 debated analyses have debate_overview figures (4233 total), 610/610 sessions have debate_impact figures (6824 total), 30173 total figure artifacts. All acceptance criteria satisfied. Committed verification spec 7a3e59954.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7df89fb0-061d-46a5-b973-1f1ebccb507f","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:44:48.102603+00:00","updated_at":"2026-04-24T16:44:48.102603+00:00","summary":"","completion_summary":"Task completed. The work was already done by commit 2be338655 (\"[Demo] Generate figures for all 398 debated analyses; create task spec\") which generated pathway diagrams, score comparisons, and evidence heatmaps for all 398 analyses with debates and registered them as artifacts in the database. My branch fast-forwarded to the latest main which includes this commit.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"54f47fe9-d948-44a9-b402-e1bffd89d196","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:43:13.536849+00:00","updated_at":"2026-04-24T16:43:13.536849+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"fail","verification_notes":"Blocked on read-only filesystem: cannot write /home/ubuntu/scidex/site/figures or create git index.lock in this worktree. Implemented stale-figure repair logic and regression tests locally, but could not regenerate figures or commit from this slot.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"32c20782-e6cf-4497-8faa-09bee9edf316","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:43:08.439418+00:00","updated_at":"2026-04-24T16:43:08.439418+00:00","summary":"","completion_summary":"Task completed successfully.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"aaca84bb-90a2-4edd-9aab-b8474177a9a3","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:41:55.413048+00:00","updated_at":"2026-04-24T16:41:55.413048+00:00","summary":"","completion_summary":"Task completed successfully.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Generated 707 new figures (pathway diagrams, score comparisons, evidence heatmaps) for 226 debated analyses. All 397 debated analyses now have 100% figure coverage (30,173 total figure artifacts). Figures written to site/figures/ and registered as artifacts in PostgreSQL. No code changes required — operational work via figure_generator.py.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e33bcd4c-8b1e-4bef-a6c1-8c29cc7ef629","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:41:48.083617+00:00","updated_at":"2026-04-24T16:41:48.083617+00:00","summary":"","completion_summary":"Merged task branch into main","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"36a4ddfb-a2b9-463d-a93c-00344b727edd","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:41:47.929990+00:00","updated_at":"2026-04-24T16:41:47.929990+00:00","summary":"","completion_summary":"The task is already resolved. Here's what I found:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b8cc65de-d641-4720-953e-a9a52d538025","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:41:21.959619+00:00","updated_at":"2026-04-24T16:41:21.959619+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: e649e37ec. Verified on 2026-04-24 that debated_analyses_total=398, debated_analyses_with_any_figure=398, missing_ids=[] from PostgreSQL; no new figure generation needed.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a0529674-1418-4e33-9721-22cee4e33f05","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:39:56.845622+00:00","updated_at":"2026-04-24T16:39:56.845622+00:00","summary":"","completion_summary":"**Closing statement:** The task is already satisfied on main. Commits `08a3bef06` and `a9c79506c` generated 698+ SVG figures for 138+ debated analyses and registered them as artifacts; `023f51cb0` fixed the root cause by making `figure_generator.py` resolve `FIGURE_DIR` to `/home/ubuntu/scidex/site/figures` from any worktree. The site/figures directory on disk contains 569 subdirectories with figures physically present and served correctly. No new work needed.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed by 08a3bef06/a9c79506c/9e22aa70c: 698+ figures generated for 138+ debated analyses and registered as artifacts. Site/figures directory verified with 569 subdirectories on disk. Root cause fix (worktree-safe FIGURE_DIR) merged via 023f51cb0.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"70265367-3ea1-45ee-a888-3585a13b3bc6","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:39:52.124608+00:00","updated_at":"2026-04-24T16:39:52.124608+00:00","summary":"","completion_summary":"[Demo] Generate figures for 260 debated analyses; 1644 new artifacts registered [task:70265367-3ea1-45ee-a888-3585a13b3bc6]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ae236294-0072-4c3a-8b64-31f5f8eb4619","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:38:58.618691+00:00","updated_at":"2026-04-24T16:38:58.618691+00:00","summary":"","completion_summary":"Task completed. The figure generation for all debated analyses was already done by a prior agent. Verification confirmed 30,083 figure artifacts registered across all 398 debated analyses, with full coverage of pathway diagrams, score comparisons, evidence heatmaps, debate overviews, and debate impact figures.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed: figures already generated for all 398 debated analyses (verified by task 0ad9a75a in commit 476ad1655). 30,083 figure artifacts registered. Rebased to main HEAD; no additional changes needed.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a55645d8-b51d-42b1-8ae7-1f0b425f4c44","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:33:17.708594+00:00","updated_at":"2026-04-24T16:33:17.708594+00:00","summary":"","completion_summary":"The work for this task was already completed by prior agents. My verification confirmed:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Ran figure_generator.py — 1167 figures generated. DB query shows 989 analyses have figure artifacts registered. All 18 BIOMNI debated analyses have figure files on disk (3-5 per analysis) and artifact registrations (14-32 each). Coverage is complete.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5ba5880a-a3ea-4a82-ae1a-2e9bb76cb699","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:33:10.847610+00:00","updated_at":"2026-04-24T16:33:10.847610+00:00","summary":"","completion_summary":"Task closed. The work was already complete on main from prior commits (`023f51cb0` + `08a3bef06`): 27,805 figure artifacts registered in DB, 398 debated analyses fully covered with pathway diagrams, score comparisons, evidence heatmaps, and debate overview figures, and the `FIGURE_DIR` root-cause fix in `scidex/agora/figure_generator.py` ensures figures always write to the main checkout path regardless of which worktree calls it.","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Task closed. The work was already complete on main from prior commits (`023f51cb0` + `08a3bef06`): 27,805 figure artifacts registered in DB, 398 debated analyses fully covered with pathway diagrams, score comparisons, evidence heatmaps, and debate overview figures, and the `FIGURE_DIR` root-cause fix in `scidex/agora/figure_generator.py` ensures figures always write to the main checkout path regardless of which worktree calls it.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6886d74d-3dbe-4568-aef2-4fb1d8923100","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:32:13.613915+00:00","updated_at":"2026-04-24T16:32:13.613915+00:00","summary":"","completion_summary":"Task completed. Figures for all 398 debated analyses were already generated by prior tasks (`5ba5880a`, `8261beb1`, `0ad9a75a`). I verified by running the figure generator myself — it produced 1162 additional figures to fill any gaps, resulting in 9513 total SVGs on disk and 27003 figure artifacts registered in the DB. All 398 debated analyses now have complete figure coverage (pathway diagrams, score comparisons, evidence heatmaps, and debate overviews).","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: figures generated for all 398 debated analyses. Verified by running generate_analysis_figures() — produced 1162 additional figures (9513 total on disk, 27003 figure artifacts in DB). All 398 analyses confirmed with figures. Prior tasks 5ba5880a and 8261beb1 already completed this work on main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0ad9a75a-0f8e-4ec1-87f9-ed98b1002ed7","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:31:03.429664+00:00","updated_at":"2026-04-24T16:31:03.429664+00:00","summary":"","completion_summary":"[Verify] 0ad9a75a — figures already generated for all 398 debated analyses [task:0ad9a75a-0f8e-4ec1-87f9-ed98b1002ed7]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: figures already generated for all 398 analyses with debates. DB has 27,005 figure artifacts across 5 main types (pathway_diagram: 8,619, debate_impact: 5,929, evidence_heatmap: 5,061, score_comparison: 3,519, debate_overview: 3,376). Verified via direct DB query. Committed 3ea1d80ca to task branch.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8261beb1-a260-4a1b-95fc-ab7b9624a2da","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:30:35.477921+00:00","updated_at":"2026-04-24T16:30:35.477921+00:00","summary":"","completion_summary":"[Verify] Confirm debate figure backfill state [task:8261beb1-a260-4a1b-95fc-ab7b9624a2da]; [Demo] Repair debated figure artifact backfill [task:8261beb1-a260-4a1b-95fc-ab7b9624a2da]; [Demo] Backfill debate impact figure artifacts [task:8261beb1-a260-4a1b-95fc-ab7b9624a2da]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"338e1957-9fcf-4f6e-8c73-571e585955c4","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:29:24.693294+00:00","updated_at":"2026-04-24T16:29:24.693294+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: ea43db0d929db8de69270264c35ddb1a067e727a. Verified current main has the batch figure-generation fix in post_process.create_analysis_figures() and PostgreSQL shows 397 analyses with debate_sessions, 988 analysis_ids with figure artifacts, and 0 debated analyses missing any figure artifacts.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"51ea8bdd-be45-49c4-b97a-d6cc1297b10c","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:26:48.504827+00:00","updated_at":"2026-04-24T16:26:48.504827+00:00","summary":"","completion_summary":"Task already resolved by e8d6786c: all 138 completed debated analyses have figure dirs (569 subdirs) and DB artifacts (24,160 figures). Verified coverage via DB query and filesystem check.","completion_notes":"Verified: e8d6786c already generated figures for all 138 completed debated analyses (commit ea43db0d9 on main). 138/138 have figure dirs and DB artifacts. site/figures/ has 569 subdirs with SVG files. 24,160 figure artifacts in DB. No additional work needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3988dfbb-f89a-402f-a091-9065cdfbd9bb","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:24:41.466949+00:00","updated_at":"2026-04-24T16:24:41.466949+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: ea43db0d9. Verified origin/main contains the batch fix, tests pass, and coverage is 138/138 completed debated analyses with figure dirs and figure artifacts. Git commit of the verification-note spec edit was blocked in this sandbox by a read-only index.lock path.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"244425ca-4332-4d69-af53-fc6f57731370","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:24:16.449208+00:00","updated_at":"2026-04-24T16:24:16.449208+00:00","summary":"","completion_summary":"**Closing statement:** Verified via direct DB query that all 398 analyses with `debate_sessions` rows already have registered figure artifacts (7,838 pathway diagrams, 5,297 debate impacts, 4,552 evidence heatmaps, 3,134 score comparisons, 2,771 debate overviews across 988 total analyses with figures). Zero debated analyses lack figures. No new figures needed — marked as already resolved and completed.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-08-7273E0A5","title":"[Demo] Enrich top 20 wiki pages with mermaid diagrams and cross-links","description":"Add pathway diagrams (mermaid), infoboxes, cross-links to hypotheses/analyses for: TREM2, APOE, tau-propagation, neuroinflammation, microglia, autophagy, AD-cascade, alpha-synuclein, BBB, glymphatic, mitochondria, PARP1, LRP1, SMPD1, CYP46A1, complement-system, senescence, epigenetic-clocks, GBA, TDP43. Each should have at least one mermaid diagram and links to relevant hypotheses.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:22:38.828735+00:00","updated_at":"2026-04-24T16:22:38.828735+00:00","summary":"","completion_summary":"[Atlas] Reconcile latest remote task tip [task:d16-08-7273E0A5]; [Atlas] Reconcile rebased task branch [task:d16-08-7273E0A5]; [Atlas] Record gate-fix retry verification [task:d16-08-7273E0A5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ed9ab56a-6fe7-4ff4-87b5-636aa7394d42","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:21:05.936380+00:00","updated_at":"2026-04-24T16:21:05.936380+00:00","summary":"","completion_summary":"Task `ed9ab56a-6fe7-4ff4-87b5-636aa7394d42` is complete and verified as already resolved on main.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"02e5eb39-9592-451b-8561-bafe0c66e27b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:20:27.450296+00:00","updated_at":"2026-04-24T16:20:27.450296+00:00","summary":"","completion_summary":"Already resolved: all 397 analyses with debate sessions have figure artifacts (23,620 total figure artifacts in DB). Work completed by prior tasks e8d6786c and 2df0bbef. Committed verification spec at 6621682b8 and pushed branch.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all 397 analyses with debate sessions have figure artifacts (23,620 total figure artifacts in DB). Work completed by prior tasks e8d6786c and 2df0bbef. Committed verification spec at 6621682b8 and pushed branch.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e02f1e77-4a3b-4fa8-b1eb-3e1653441b7d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:20:24.935569+00:00","updated_at":"2026-04-24T16:20:24.935569+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by ea43db0d9 (merge of task e8d6786c on 2026-04-24). Verified on 2026-04-24: create_analysis_figures() on main includes debate-only analyses, and current state has 138/138 completed debated analyses with figure directories under site/figures and figure artifacts in PostgreSQL; task record had no spec_path to update.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"62c92478-5537-42ec-88fa-e75e61369d89","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:16:37.792539+00:00","updated_at":"2026-04-24T16:16:37.792539+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by ea43db0d9. Verified 138 completed debated analyses have figure directories, 0 completed debated analyses are missing figure artifacts, and the earlier fix landed via task e8d6786c. Local verification spec exists at docs/planning/specs/62c92478_generate_figures_for_all_analyses_with_debates_spec.md but could not be committed because this sandbox mounts the worktree gitdir read-only.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"53762ad0-f9a4-4ba3-befb-5f5cebad768b","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:16:01.989424+00:00","updated_at":"2026-04-24T16:16:01.989424+00:00","summary":"","completion_summary":"Task `53762ad0` completed as already resolved. Prior tasks (squash merges for e8d6786c, 8afebaa6) already generated figures for all 398 debated analyses. DB has 21,566 figure artifacts with 100% coverage across all figure types (pathway_diagram, score_comparison, evidence_heatmap, debate_impact, debate_overview). The rejected spec-only commit was removed and the branch reset to match main. No new code changes were needed.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: prior tasks (squash merges for task IDs e8d6786c, 8afebaa6) generated figures for all 398 debated analyses. DB has 21,566 figure artifacts with 100% coverage (0 missing analyses). All figure types present: pathway_diagram (218 analyses), score_comparison (203), evidence_heatmap (144), debate_impact (985 sessions), debate_overview (398). API endpoint /api/artifacts?artifact_type=figure returns 200 with figures browsable. Branch reset to match main - no new code changes needed.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"217e01ad-7aad-4dc5-9236-cb9bc3cd8452","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:15:53.609674+00:00","updated_at":"2026-04-24T16:15:53.609674+00:00","summary":"","completion_summary":"Already resolved: all 398 analyses with debate_sessions have registered figure artifacts (pathway diagrams, score comparisons, evidence heatmaps, debate overviews). Previous task 2df0bbef completed this work (squash merged as 88005dccf). Verified via DB query 398/398 covered. Committed verification spec as c76411104.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all 398 analyses with debate_sessions have registered figure artifacts (pathway diagrams, score comparisons, evidence heatmaps, debate overviews). Previous task 2df0bbef completed this work (squash merged as 88005dccf). Verified via DB query 398/398 covered. Committed verification spec as c76411104.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3b7a6677-003c-42c3-a1f3-4097e485c6ea","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:14:14.490951+00:00","updated_at":"2026-04-24T16:14:14.490951+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: ca40dbb56. Verified on origin/main that create_analysis_figures includes debate-only analyses and current worktree coverage is 138/138 completed debated analyses with figure directories.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2df0bbef-e95e-4078-9383-45e0da7b4178","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:13:00.815294+00:00","updated_at":"2026-04-24T16:13:00.815294+00:00","summary":"","completion_summary":"[Verify] Generate figures for all debated analyses — already resolved [task:2df0bbef-e95e-4078-9383-45e0da7b4178]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all 398 analyses with debates have figure artifacts registered (7,458 pathway diagrams, 4,300 evidence heatmaps, 2,943 score comparisons, 2,326 debate overviews, 536 debate impacts). 0 analyses missing coverage. Verified by direct DB query on 2026-04-24; spec committed at c99499def.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6525749d-f927-4614-a623-b605104afaa0","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:11:55.771534+00:00","updated_at":"2026-04-24T16:11:55.771534+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 90cf03064 / ea43db0d9. Verified on 2026-04-24 that 138 completed debated analyses have 138 figure directories and 138 registered figure artifacts; batch selector includes debate-only analyses.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6cb86654-167a-4f6b-b3df-f73c5841ab3d","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:08:13.659653+00:00","updated_at":"2026-04-24T16:08:13.659653+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved by ea43db0d929db8de69270264c35ddb1a067e727a. Verified post_process.create_analysis_figures() now includes debate-session analyses without the old recent/top-100 or multi-hypothesis exclusion, PostgreSQL shows figure artifacts for all 149 non-archived debated analyses, and all 138 completed debated analyses already have SVG directories in site/figures/.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"270849a9-22dd-4508-91db-fa8b8f391a72","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:04:29.854794+00:00","updated_at":"2026-04-24T16:04:29.854794+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: ea43db0d929db8de69270264c35ddb1a067e727a. Verified current main includes the figure-generation fix and PostgreSQL shows 138 completed debated analyses with 138 figure-artifact-covered analyses, zero missing.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2996c642-29aa-4ab1-9f52-6ce47419f6b1","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:01:45.861787+00:00","updated_at":"2026-04-24T16:01:45.861787+00:00","summary":"","completion_summary":"Task `2996c642-29aa-4ab1-9f52-6ce47419f6b1` is already resolved. Commits `ea43db0d9` (squash merge of `e8d6786c-generate-figures-for-all-analyses-with-d`) and `216cfbee0` already ran the `figure_generator.py` script against all 18 debated analyses from commit `b5ddddb51` (the 14 gap-debate analyses from 04-11/04-12 plus the 4 frontier analyses from 04-16). The worktree was rebased onto main which pulled in those commits — no additional code changes were needed. The 18 analyses now have 88 figure","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed by ea43db0d9: task e8d6786c-generate-figures-for-all-analyses-with-d ran figure_generator.py for all 18 debated analyses (14 gap + 4 frontier). 88 figure artifacts registered (pathway_diagram: 12, debate_overview: 58, debate_impact: 18). No code changes needed — work already on main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"517b1698-59b8-45b8-b3e4-4ed32312f190","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T16:01:44.925592+00:00","updated_at":"2026-04-24T16:01:44.925592+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: ea43db0d929db8de69270264c35ddb1a067e727a. Verified current main contains the batch figure-generation fix and PostgreSQL shows figure artifacts for all 18 debated analyses named by this task (rows=18, missing=0).","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e8d6786c-52f1-4238-8877-0ecc9d7faf92","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T15:57:32.206564+00:00","updated_at":"2026-04-24T15:57:32.206564+00:00","summary":"","completion_summary":"[Demo] Backfill figures for debated analyses [task:e8d6786c-52f1-4238-8877-0ecc9d7faf92]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already addressed by pushed task-branch commit ca40dbb56: exact post_process.py, scidex/agora/figure_generator.py, spec, and test diff present; verified PYTHONPATH=. pytest -q tests/test_analysis_figure_batch.py passes and completed debated-analysis figure coverage is 138/138 in this checkout.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8afebaa6-1823-40a5-a85d-7291dd419b96","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-24T15:56:08.811366+00:00","updated_at":"2026-04-24T15:56:08.811366+00:00","summary":"","completion_summary":"[Agora] Generate figures for all 149 debated analyses; register as artifacts [task:8afebaa6-1823-40a5-a85d-7291dd419b96]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5722c169-9e5f-42f9-9f3d-4f96d64f1ba6","title":"[Demo] Enrich 10 thin hypothesis descriptions to 1000+ words","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n29 hypotheses have <500 char descriptions. Expand with mechanisms, evidence, clinical relevance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:27:50.319227+00:00","updated_at":"2026-04-18T15:27:50.319227+00:00","summary":"","completion_summary":"[Agora] Add hypothesis enrichment script to expand thin descriptions to 1000+ words [task:5722c169-9e5f-42f9-9f3d-4f96d64f1ba6]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"12bd92f9-109b-4727-a558-d56762df7f8f","title":"[Demo] Fix /demo.html smoke-check content assertion","description":"Resolve smoke_check failure for /demo.html missing expected demo marker while preserving page behavior.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T14:08:07.864031+00:00","updated_at":"2026-04-18T14:08:07.864031+00:00","summary":"","completion_summary":"Fix already in remote branch: commit 84e973580 handles None composite_score to prevent TypeError on /demo page [task:12bd92f9-109b-4727-a558-d56762df7f8f]","completion_notes":"The fix for the /demo 500 error (None composite_score causing TypeError) was already committed in 84e973580 and pushed to origin/orchestra/task/12bd92f9-demo-html-smoke-check-content-assertion. Verified the branch is up-to-date and contains the correct fix.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/12bd92f9_109_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"84e97358077f77ddf23ae5ac0d0f01bffb775207\"], \"completion_shas_checked_at\": \"2026-04-18T14:08:07.845433+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cafef3bf-932b-4bcf-9bda-6946de13a573","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T14:06:48.322822+00:00","updated_at":"2026-04-18T14:06:48.322822+00:00","summary":"","completion_summary":"[Demo] Migrate figure_generator.py from sqlite3 to get_db() for PostgreSQL compat; generate figures for all 18 debated analyses [task:cafef3bf-932b-4bcf-9bda-6946de13a573]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b1c46945-4466-4a28-84f9-5e4cef3dce87","title":"[Demo] Harden demo smoke checks with internal CTA link validation","description":"Quest 16/17 reliability: extend scripts/demo_smoke_check.py to validate key internal links discovered on /demo and /showcase (status, latency, size), add explicit reporting, and verify script passes on localhost.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:57:55.907225+00:00","updated_at":"2026-04-18T13:57:55.907225+00:00","summary":"","completion_summary":"[Verify] Demo smoke check CTA link validation — OBSOLETE [task:b1c46945-4466-4a28-84f9-5e4cef3dce87]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b1c46945_446_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Demo smoke check CTA link validation — OBSOLETE [task:b1c46945-4466-4a28-84f9-5e4cef3dce87]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"87cc5967-a187-4e03-ad40-5f1de4981034","title":"[Demo] Generate figures for all analyses with debates","description":"Use figure_generator.py to create pathway diagrams, score comparisons, and evidence heatmaps for all 18 debated analyses. Register as artifacts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:46:19.762961+00:00","updated_at":"2026-04-18T13:46:19.762961+00:00","summary":"","completion_summary":"Verified figure coverage is complete. 8,569 figure files tracked in git, 12,510 figure artifacts in DB. 233 of 246 analyses with debates have figures. The 13 missing analyses have empty debate sessions (0 hypotheses, 0 rounds) and cannot generate figures. All analyses with sufficient data have complete figure coverage.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/87cc5967-a18_demo_generate_figures_for_all_analyses_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Confirmed 8,569 SVG figure files in site/figures/ tracked on main (commit 700e194d0). 12,510 figure artifacts registered in artifacts table. 233/246 analyses with debates have figures. 13 analyses without figures all have 0 hypotheses and 0 debate rounds — insufficient data. Figure generation attempted for all 13 and confirmed no figures possible.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a0102e96-cdf6-4f11-ae1f-07d26eeb7008","title":"[Demo] Add evidence matrix table to hypothesis pages with citation quality scoring","description":"Quest 17 A17.6: Add a structured evidence matrix table to hypothesis detail pages showing all citations with quality x relevance scoring. Display evidence_for and evidence_against items in a tabular format with strength ratings, source journals, year, and PMID links. Replaces plain bullet list with a rich, sortable evidence matrix.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:45:47.680588+00:00","updated_at":"2026-04-18T13:45:47.680588+00:00","summary":"","completion_summary":"[Atlas] Update evidence matrix spec: mark done, log consolidation [task:a0102e96-cdf6-4f11-ae1f-07d26eeb7008]; [Atlas] PostgreSQL JSON field compatibility for hypothesis detail + exchange in api.py; update evidence matrix spec work log [task:a0102e96-cdf6-4f11-ae1f-07d26eeb7008]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a0102e96_cdf_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0628f2ea-1b8e-42c8-97f8-b199b3a766fa","title":"[Demo] Harden link checker timeout handling to always emit partial report","description":"Ensure link_checker writes logs/link-check-latest.json and exits cleanly when close to runtime deadline by skipping expensive LLM analysis/task creation under low remaining budget.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:36:20.298721+00:00","updated_at":"2026-04-18T13:36:20.298721+00:00","summary":"","completion_summary":"[Demo] Update spec work log: verify and implement link checker timeout hardening [task:0628f2ea-1b8e-42c8-97f8-b199b3a766fa]; [Demo] Add llm_analysis_skipped and llm_skip_reason to link checker reports [task:0628f2ea-1b8e-42c8-97f8-b199b3a766fa]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0628f2ea_1b8_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"217b0e36-849a-4eed-bbcb-a6a1c7baf80a","title":"[Demo] Add guided five-layer quickstart rail on demo page","description":"Improve /demo with an explicit start-here quickstart rail linking the five layers and primary walkthrough entry points for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:33:21.949614+00:00","updated_at":"2026-04-18T13:33:21.949614+00:00","summary":"","completion_summary":"Already addressed by 03b2dc687 (squash-merged): quickstart rail present in site/demo.html with 5-layer links, walkthrough section, and working demo page render.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/217b0e36_849_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8ee4c367-46a4-4dd9-a242-27b3c0ff5637","title":"[Demo] Create /forge page showing tool registry and usage","description":"Build /forge page displaying all 48 registered tools from skills table. Show tool name, type, times_used, and examples of analyses using each tool.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:31:36.551692+00:00","updated_at":"2026-04-18T13:31:36.551692+00:00","summary":"","completion_summary":"Already done on main. /forge page (api.py:48683-49220) displays all tools from skills table with name, type, times_used, per-tool usage examples from tool_calls, featured demos, analytics dashboard, tool chains, and PubMed pipeline. Page returns 200. Prior commits 6e50abf22/113e9b058/ba6ffd444 were on orphan branches but features landed on main via squash merge.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8ee4c367_46a_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4ac1f8b5-dd8b-4822-a1a4-4fd3a8c8b48c","title":"[Demo] Repair missing top-nav links for demo surfaces","description":"Audit top navigation links on core demo pages and fix broken/incorrect href targets to improve end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T13:30:36.462537+00:00","updated_at":"2026-04-18T13:30:36.462537+00:00","summary":"","completion_summary":"Already addressed by b898ff319, c31ca2f28, d9fd2a7ef: All /analysis/ href links on demo surfaces have been fixed to use /analyses/ canonical URLs. No remaining href=\"/analysis/ links found in api.py.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4ac1f8b5_dd8_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"06d4e19e-1782-4768-b233-864dfc787fe9","title":"[Demo] Add structured evidence matrix with citation quality scores to hypothesis pages","description":"Quest 17 task A17.6: Build a structured evidence matrix component on hypothesis detail pages. Show citations in a table with columns: citation title, PMID link, relevance score, quality score, evidence type (supporting/opposing). Replace the current plain-text evidence lists with a rich, sortable table. This makes hypothesis pages much more compelling for demos.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:59:41.306805+00:00","updated_at":"2026-04-16T00:59:41.306805+00:00","summary":"","completion_summary":"[Atlas] Update slot reservation for evidence matrix task [task:06d4e19e-1782-4768-b233-864dfc787fe9]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/06d4e19e_178_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:25:48\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"89c6c50ca6b7a22226c395012f6f9fbb489d77bd\"], \"completion_shas_checked_at\": \"2026-04-16T00:59:41.284620+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"68ae1f33-6182-43f5-9b40-ab7cd333faec","title":"[Demo] Expand Mol* 3D protein viewer PDB mappings for top 20 hypothesis targets","description":"\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:53:56.010477+00:00","updated_at":"2026-04-16T00:53:56.010477+00:00","summary":"","completion_summary":"[Atlas] Update spec work log for mol-3d-protein-viewer task; [Atlas] Expand PDB/UniProt mapping for molecular 3D protein viewer","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/68ae1f33_618_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:24:12\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"727de71f8e353a593a35cc83d1fdf33f8bc2ccc2\"], \"completion_shas_checked_at\": \"2026-04-16T00:53:55.989948+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0e962abd-b625-43d5-8515-20631cf736e9","title":"[Demo] Build analysis walkthrough page at /walkthrough/{id}","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:45:59.966196+00:00","updated_at":"2026-04-16T00:45:59.966196+00:00","summary":"","completion_summary":"[Atlas] Update spec work log for task 0e962abd [task:0e962abd-b625-43d5-8515-20631cf736e9]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0e962abd_b62_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 03:56:31\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"788144ddf07b4b022f3cbccbca698931449be190\", \"2b1ffee5583d8a3a4f611a6f7514001572bc065e\"], \"completion_shas_checked_at\": \"2026-04-16T00:45:59.947039+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"90ca80d5-bc47-4ab9-9d8c-fd81b4cc3c10","title":"[Demo] Generate figures for top 20 analyses to populate artifact gallery","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T05:15:19.824434+00:00","updated_at":"2026-04-14T05:15:19.824434+00:00","summary":"","completion_summary":"[Demo] Add figure generation spec: 422 figures for top analyses [task:90ca80d5-bc47-4ab9-9d8c-fd81b4cc3c10]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/90ca80d5_bc4_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"b2dc83e44d7b023058ac2e754e7fb415daed3799\"], \"completion_shas_checked_at\": \"2026-04-14T05:15:19.807225+00:00\", \"completion_shas_missing\": [\"349e8dd8e83856c20787a25725be7d3c5d27e50a\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"89109399-28f5-4815-9b25-40c88874900f","title":"[Demo] Protein design gallery with 3D viewer integration","description":"Create /protein-designs page showing all 21 designs. Integrate TREM2 3D viewer for designs with PDB structures. Display sequences, mutations, stability scores, binding affinities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:48:25.154195+00:00","updated_at":"2026-04-14T04:48:25.154195+00:00","summary":"","completion_summary":"[Demo] Add /protein-designs gallery with 3D viewer for all 21 TREM2 designs [task:89109399-28f5-4815-9b25-40c88874900f]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/89109399_28f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"5e3a118b5f8fc6ae5bc2f91cdfce8e197d4e5803\"], \"completion_shas_checked_at\": \"2026-04-14T04:48:25.137137+00:00\", \"completion_shas_missing\": [\"13c4ea62eac64e7d63f219fed36644a493aee0ff\"]}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6d25ffd0-fb79-451a-b3cd-ddb1baff286c","title":"[Demo] Expand walkthroughs to 5 hero analyses — add sleep disruption, digital biomarkers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T04:19:14.921071+00:00","updated_at":"2026-04-14T04:19:14.921071+00:00","summary":"","completion_summary":"[Docs] Update 6d25ffd0 spec work log: added 7 analyses note [task:6d25ffd0-fb79-451a-b3cd-ddb1baff286c]; [Demo] Add sleep disruption and digital biomarkers to hero walkthroughs [task:6d25ffd0-fb79-451a-b3cd-ddb1baff286c]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6d25ffd0_fb7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"1093901bfee47ef2326b517abe69f7d49596d2b4\", \"59566c540ebfdc5ad429ffd56b1dac02dcde6ca2\", \"242b5b9a8829072ec776c18e12968ee67fea1702\"], \"completion_shas_checked_at\": \"2026-04-14T04:19:14.901735+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a4dfe11e-dd75-43d8-aeac-5456932ce199","title":"[Demo] Build guided demo walkthrough page at /demo","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:40:27.716133+00:00","updated_at":"2026-04-14T03:40:27.716133+00:00","summary":"","completion_summary":"[Docs] Document a4dfe11e task: /demo guided tour already complete on main [task:a4dfe11e-dd75-43d8-aeac-5456932ce199]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a4dfe11e_dd7_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0752e93c5a15eceb4945a4fc322edf84caebe75b\"], \"completion_shas_checked_at\": \"2026-04-14T03:40:27.698061+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e6265b0c-1c60-42f9-8550-06fd21b68f48","title":"[Demo] Add featured discoveries carousel to home page","description":"Add a 'Featured Discoveries' section to the home page showing top 3 hypotheses with scores, pathway diagrams, and linked analyses. This gives visitors an immediate sense of the platform's scientific depth.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:36:09.148697+00:00","updated_at":"2026-04-14T03:36:09.148697+00:00","summary":"","completion_summary":"[Demo] Add Featured Discoveries carousel to home page [task:e6265b0c-1c60-42f9-8550-06fd21b68f48]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e6265b0c_1c6_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"cc0451cd3d6c5fbd3241628cd91185aa0f566c68\"], \"completion_shas_checked_at\": \"2026-04-14T03:36:09.129708+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5c2c16ad-76c1-4fd3-a75d-b9a721a0196e","title":"[Demo] Generate HTML renderings for all 39 analysis notebooks","description":"Convert all .ipynb notebooks in site/notebooks/ to HTML for web viewing. Many notebooks exist but lack HTML counterparts. Run jupyter nbconvert for all missing HTML files.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:28:04.887060+00:00","updated_at":"2026-04-14T03:28:04.887060+00:00","summary":"","completion_summary":"[Docs] Verify 5c2c16ad task complete: 406 notebooks have HTML counterparts; [Docs] Update 5c2c16ad work log: all 406 notebooks already have HTML [task:5c2c16ad-76c1-4fd3-a75d-b9a721a0196e]; [Docs] Update work log: CRISPR analysis verified complete on origin/main [task:20032895-acb8-4035-8c1d-9a94fab2c5ae]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5c2c16ad_76c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"4a2d232eb8c7a876523fa313d5f7830e67856212\", \"be3c6a25051dfaea94b822f819187619ecb755f3\", \"b84035ff3a5a1b6f31324c9c1c9ce7e7258d02a3\"], \"completion_shas_checked_at\": \"2026-04-14T03:28:04.870717+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0a9b1fd7-3ea6-431e-8944-d671068548c9","title":"[Demo] Create /walkthrough demo tour page linking all five layers","description":"D16.9: Build an end-to-end demo walkthrough page at /walkthrough that guides visitors through SciDEX's five layers with showcase content. Links to best hypotheses, debates, tools, KG, and governance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:23:15.043759+00:00","updated_at":"2026-04-14T03:23:15.043759+00:00","summary":"","completion_summary":"[Docs] Update 0a9b1fd7 spec work log: /walkthrough now redirects to /demo [task:0a9b1fd7-3ea6-431e-8944-d671068548c9]; [Demo] Redirect /walkthrough to /demo five-layer tour [task:0a9b1fd7-3ea6-431e-8944-d671068548c9]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0a9b1fd7_3ea_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0147141b5d95fcee96825099bba7d0c2bb362122\", \"a253cbb2779dcc8620bf6a886aa6fac4f3f56af6\"], \"completion_shas_checked_at\": \"2026-04-14T03:23:15.025482+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-26-DDSH0001","title":"[Demo] Create live dashboard: Knowledge Growth Monitor","description":"Build a dashboard artifact that shows real-time SciDEX knowledge growth: paper count, KG edge count, hypothesis count, and trend sparklines. Data sources: sql_query against scidex.db metrics tables. Dashboard auto-refreshes every 5 minutes. Embed it in the demo authored paper to show a living document. Demonstrates: dashboard creation, data source binding, auto-refresh, embedding in papers. Depends on: a17-28-DASH0001, a17-30-DREF0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:14:28.857683+00:00","updated_at":"2026-04-14T03:14:28.857683+00:00","summary":"","completion_summary":"[Docs] Update d16-26-DDSH0001 work log: document render_dashboard bug fix; [Atlas] Fix render_dashboard using wrong DB_PATH for SQL queries","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-26-DDSH0001_dashboard_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"2aaccb2fa74cb2ff59459bcb80cb813a525bcd00\", \"8b9af1467b299dcf82c365d8fd95cded16d468d7\", \"47f7bb0ed24fca6b9646a07efa2652326896161c\", \"3c6b6be639cd27545e8b3991aa170f209cff19bd\"], \"completion_shas_checked_at\": \"2026-04-14T03:14:28.838018+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-20-AVER0001","title":"[Demo] Versioned artifact demo: create protein design with 3 iterations","description":"Register a protein design artifact (e.g. an engineered TREM2 variant for AD) with 3 successive versions showing iterative refinement: v1 (initial design from AlphaFold prediction), v2 (stability-optimized via mutations), v3 (binding-affinity tuned). Each version has different metadata (mutations, predicted_stability, binding_affinity). Show version timeline and diff on the artifact page. Exercises: artifact versioning, protein_design type, version browser UI. Depends on: a17-18-VERS0001, a17-19-TYPE0001, a17-20-VAPI0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:09:42.731411+00:00","updated_at":"2026-04-14T03:09:42.731411+00:00","summary":"","completion_summary":"[Docs] Update work log for d16-20-AVER0001 bug fix [task:d16-20-AVER0001]; [Atlas] Fix get_version_history to walk forward through children [task:d16-20-AVER0001]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-20-AVER0001_versioned_protein_design_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"b05ae0e344158622934e32dec372b9f6a94e7597\", \"8dc7cfd7fa9e3913a219208b9a8f6a7267687518\", \"3ed28a8ea3eed4800e33c0749bd2398b315c2aa3\", \"e9e0997c789d373ea5b286e8ceb127bf75619aec\"], \"completion_shas_checked_at\": \"2026-04-14T03:09:42.712185+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-24-PROV0001","title":"[Demo] End-to-end provenance demo: trace reasoning chain from paper to model","description":"Create a showcase provenance walkthrough: Paper (PubMed) -> KG edges (extracted) -> Hypothesis (generated) -> Dataset (referenced) -> Analysis (executed) -> Model (built) -> Figure (produced). Display the full DAG with artifact versions pinned at each step. Demonstrate verify_reproducibility() showing all inputs are intact. This is the capstone demo for the artifact versioning system. Depends on: a17-24-REPR0001, d16-23-BMOD0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T02:55:24.707966+00:00","updated_at":"2026-04-14T02:55:24.707966+00:00","summary":"","completion_summary":"[Docs] Mark d16-24-PROV0001 acceptance criteria complete; [Docs] Update d16-24-PROV0001 spec work log: verify_reproducibility implemented, demo page added; [Forge] End-to-end provenance demo: verify_reproducibility, /api/analyses/{id}/provenance, /demo/provenance-chain","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-24-PROV0001_end_to_end_provenance_demo_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"524da90d0754a2e8bb249a8d935807f866cb43f6\", \"a418f9b55766709979138f5972b2574b9e500049\", \"c8c5b62caf3ee43be0f122c7aef0f630b2807664\"], \"completion_shas_checked_at\": \"2026-04-14T02:55:24.689630+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"200534d6-ef24-4358-b7bb-6b8017abd45e","title":"[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages","description":"Add interactive 3D molecular structure viewer (Mol* / PDBe Molstar) to hypothesis detail pages for target proteins. Query RCSB PDB for structures by gene name, embed viewer via PDBe Molstar web component. Priority: top 10 hypotheses by composite_score. This is D16.4 from Quest 16.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T03:48:37.677911+00:00","updated_at":"2026-04-25T03:48:37.677911+00:00","summary":"","completion_summary":"Replaced the hypothesis detail iframe-based structure viewer with a lazy-loaded PDBe Mol* plugin viewer and merged it to main in 37e6facef43d12f2a5434a947960a709f3b04367 via PR #31.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/200534d6_ef2_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"670a14f8-347a-4f23-ac41-63c2d4a1e272","title":"[Demo] End-to-end discovery walkthrough page with guided tour","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:25:29.211849+00:00","updated_at":"2026-04-25T02:25:29.211849+00:00","summary":"","completion_summary":"Task closed as already resolved. The demo walkthrough page with the \"Follow One Discovery\" guided tour is live at `/demo` with all five layers (Agora, Exchange, Forge, Atlas, Senate) present and returning HTTP 200. Prior implementation landed in commit `e83befca7`. No additional work needed.","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/670a14f8_347_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: demo walkthrough page live at /demo with Follow One Discovery guided tour, verified 200 response with all five layers present. Prior work landed in e83befca7.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"620f67ae-3e36-4fbf-a687-979a6931d2d3","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all features","description":"","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:16:46.404924+00:00","updated_at":"2026-04-25T02:16:46.404924+00:00","summary":"","completion_summary":"The task is already resolved on main. The `/demo` page exists at HTTP 200 with comprehensive content:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/620f67ae_3e3_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-09-7924D488","title":"[Demo] End-to-end demo walkthrough page","description":"Create /demo or /tour page that guides visitors through: (1) Start at a hypothesis, (2) See the debate that produced it, (3) Explore the evidence and tools used, (4) Navigate the knowledge graph, (5) Check governance/quality metrics. Interactive guided tour with highlights and arrows. This is the entry point for new visitors.","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T02:02:19.830139+00:00","updated_at":"2026-04-25T02:02:19.830139+00:00","summary":"","completion_summary":"[Verify] Demo walkthrough — already resolved on main [task:d16-09-7924D488]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 967cae164. Verified live /demo contains Start Guided Tour, Follow One Discovery, and Senate quality section; recorded evidence in task spec.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8aba1c2f-6223-4836-bbd8-e0c02e958a44","title":"[Demo] Add Mol* 3D protein viewers to walkthrough pages","description":"The walkthrough pages (our primary demo pages) don't have inline Mol* 3D protein structure viewers. The challenge detail pages already have this. We need to add inline Mol* viewers for key target genes in the walkthrough protein section, using the existing PDB mapping in api.py. This will significantly improve the demo quality for Quest 16.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:02:40.572198+00:00","updated_at":"2026-04-16T10:02:40.572198+00:00","summary":"","completion_summary":"[Demo] Update spec work log: rebase preserved all changes [task:8aba1c2f-6223-4836-bbd8-e0c02e958a44]; [Demo] Restore inline Mol* 3D protein viewers to walkthrough pages","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8aba1c2f_622_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"completion_shas\": [\"0235fc86ff953a59eecc61f0907d2ecef4f37723\", \"1650d2174064e836a7a3232d04ce447284749de2\", \"3c90807e76c2375592959842f830baef0aa09ab0\", \"afebddfeca53bdebe896a36fd63d532b3d2559fa\"], \"completion_shas_checked_at\": \"2026-04-16T10:02:40.553931+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b0e67854-a3ef-4c1e-ae00-970b9d5d7e10","title":"[Demo] Add multi-hypothesis radar chart to analysis detail pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:46:14.376347+00:00","updated_at":"2026-04-16T09:46:14.376347+00:00","summary":"","completion_summary":"Radar chart feature implemented in api.py (lines 33147-33210). Adds Chart.js radar chart comparing top 3 hypotheses' 8-dimension scores on analysis detail pages. Code committed (bd9f82a5b), PR previously merged to main (37dff6822). Git push blocked - no credentials available.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b0e67854_a3e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d9ad02ce-6e8f-45ae-ba0e-94924a0bceaf","title":"[Demo] Add /search and /pitch to demo smoke coverage","description":"Expand scripts/demo_smoke_check.py route coverage to include /search and /pitch; validate command output and keep timeout-safe usage.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:36:30.870754+00:00","updated_at":"2026-04-16T09:36:30.870754+00:00","summary":"","completion_summary":"Added /search route to demo smoke check coverage. /pitch was already present. Smoke check validates both routes return 200 OK.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d9ad02ce_6e8_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0ef6d46de\"], \"completion_shas_checked_at\": \"2026-04-16T09:36:30.852017+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"896b24fa-9055-4834-8b6e-c4374165f200","title":"[Demo] Audit and repair demo page route regressions","description":"Slot 3 batch task: run targeted demo page health checks, fix any route/template regressions, and verify core demo pages return healthy status codes.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:27:05.583533+00:00","updated_at":"2026-04-16T09:27:05.583533+00:00","summary":"","completion_summary":"Demo page route audit complete: all 22 demo-critical routes return healthy HTTP status codes (200/301/302/307). Spec file is on origin/main with complete work log. No regressions found. Task was previously completed but flagged as ORPHAN_BRANCH due to commit burial via squash merge — content is on main.","completion_notes":"Verified 18 demo routes (/, /exchange, /gaps, /graph, /analyses/, /atlas.html, /how.html, /demo, /demo/walkthrough, /demo/showcase, /entity/TREM2, /hypothesis, /forge, /senate, /market, /api/health, /api/status, /atlas). All returned acceptable HTTP codes. Task content (spec file) is on origin/main at docs/planning/specs/896b24fa_905_spec.md. Individual task commits (ca4377558, 0f51a649c) exist in refs/check/fd26f10d0ea6 — not as direct main-branch commits due to squash merge path, but the work is verified on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/896b24fa_905_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Demo page route audit complete: all 22 demo-critical routes return healthy HTTP status codes (200/301/302/307). Spec file is on origin/main with complete work log. No regressions found. Task was previously completed but flagged as ORPHAN_BRANCH due to commit burial via squash merge — content is on main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"73f5ece2-7342-463e-b45c-b716b9599287","title":"[Demo] Validate key demo routes and fix render/content regressions","description":"Check /demo, top hypothesis pages, and top analyses for status/content quality; fix any regressions in routing or rendering and document results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:21:29.866519+00:00","updated_at":"2026-04-16T09:21:29.866519+00:00","summary":"","completion_summary":"Validated all demo-critical routes: /demo (200, 125KB, live stats), top 5 hypothesis pages (all 200, 213-517KB), top 3 analysis pages (301/307 redirects to /analyses/ as expected, resolve to 200 with content). No regressions found. Spec updated with current verification evidence.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/73f5ece2_734_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Validated all demo-critical routes: /demo (200, 125KB, live stats), top 5 hypothesis pages (all 200, 213-517KB), top 3 analysis pages (301/307 redirects to /analyses/ as expected, resolve to 200 with content). No regressions found. Spec updated with current verification evidence.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bb26a052-4f82-4156-bebc-133afaeb9e9f","title":"[Demo] Versioned artifact demo: create protein design with 3 iterations","description":"Create a showcase protein design artifact (TREM2 variant) with 3 successive versions demonstrating iterative refinement and the version browser UI.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:15:53.524146+00:00","updated_at":"2026-04-16T09:15:53.524146+00:00","summary":"","completion_summary":"Verified: 3-version TREM2 protein design lineage exists and all acceptance criteria pass. Version history API returns all 3 versions (v1→v2→v3), diff API shows 5 accumulated mutations and 7x binding improvement, artifact page renders version timeline with stability-opt/binding-opt tags, and 5 related artifacts linked (2 hypotheses + 3 protein designs). Work was completed in commit 74864dee1 which landed on origin/main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-20-AVER0001_versioned_protein_design_demo_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"74864dee1\"], \"completion_shas_checked_at\": \"2026-04-16T09:15:53.507047+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5d834fd8-c5f0-4e2e-9fd5-686c6f76ae44","title":"[Demo] Add supporting evidence panel to hypothesis pages","description":"The evidence_for/evidence_against columns store JSON arrays with pmid, claim, source, year, strength. Add a 'Supporting Evidence' section to /hypothesis/{id} pages showing top 5 evidence_for papers and top 3 evidence_against papers with their claims and journal/year. This makes hypothesis quality visible to demo viewers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:13:52.607987+00:00","updated_at":"2026-04-16T09:13:52.607987+00:00","summary":"","completion_summary":"Supporting evidence panel already on main — verified on live site (30 ev-card elements on h-58e4635a, evidence summary banner, sortable matrix). Previous agent implementation landed on main but task was audited as NO_COMMITS due to branch state.","completion_notes":"Verified feature already present on main at origin/main (commit 9a3b0cb53). No new commits needed. The work was done previously and is live.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5d834fd8_c5f_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9a3b0cb53\"], \"completion_shas_checked_at\": \"2026-04-16T09:13:52.587815+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Feature verified working: curl http://localhost:8000/hypothesis/h-58e4635a returned 200 with 30 ev-card elements and evidence summary showing citation counts.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"65eb10aa-aef7-4d0e-84b4-77a6dae0af1a","title":"[Demo] Exclude non-HTML CTA assets from demo smoke quality checks","description":"scripts/demo_smoke_check.py should not fail on .ipynb/.json/static asset links extracted from /demo and /showcase CTAs; validate only page-like internal routes for content-size/latency checks.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:11:32.107715+00:00","updated_at":"2026-04-16T09:11:32.107715+00:00","summary":"","completion_summary":"Task already complete. Implementation from ecba66083 (NON_PAGE_SUFFIXES, is_page_like_path filtering for demo smoke check) is on main at scripts/archive/oneoff_scripts/demo_smoke_check.py (file was archived after task completion at commit 1178a0c46). Audit ORPHAN_BRANCH flag was a false positive — commit is verifiable on main via merge-base --is-ancestor.","completion_notes":"Verified: commit ecba66083 IS on main (merge-base --is-ancestor returns true). The file was later archived from scripts/demo_smoke_check.py → scripts/archive/oneoff_scripts/demo_smoke_check.py at commit 1178a0c46. The NON_PAGE_SUFFIXES and is_page_like_path filtering logic is present in the archived file on main. Audit ORPHAN_BRANCH flag appears to be a false positive — the implementation landed on main correctly.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65eb10aa_aef_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ef614bb0-06d7-43f1-bae5-4a900eca8d7b","title":"[Demo] Fix broken internal links on showcase and dashboard pages","description":"Targeted demo-link quality pass: replace stale senate.html/hypothesis links that 404 with live routes or remove dead CTAs; verify affected pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:09:34.397913+00:00","updated_at":"2026-04-16T09:09:34.397913+00:00","summary":"","completion_summary":"Task already complete — all ef614bb0 commits verified in origin/main, 20/20 smoke check passes","completion_notes":"Task was already complete. All ef614bb0 commits (17c11d39f, 7e21443f2, f451f8025, 5cd677a2a) are in origin/main. The audit's NO_COMMITS flag was a false positive — the work landed correctly on main before this branch was created. smoke_check.py 20/20 pass, no broken links remain. Branch already pushed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ef614bb0_06d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Confirmed all commits present in origin/main: 17c11d39f, 7e21443f2, f451f8025, 5cd677a2a. smoke_check.py 20/20 pass. No broken links. Audit NO_COMMITS was false positive — work pre-dates this branch.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6e95afff-d644-4e03-93f8-0c6591bd0ae0","title":"[Demo] Repair demo page readiness issues discovered by CI sweep","description":"Quest 16 batch: run targeted demo page verification, fix concrete rendering/content/link defects, validate health checks, and document completion.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:05:55.624356+00:00","updated_at":"2026-04-16T09:05:55.624356+00:00","summary":"","completion_summary":"[Demo] Fix demo.html stats showing '—' for missing API fields","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6e95afff_d64_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"9a3b0cb53e6e880f24abdb50031e32dd3858020c\"], \"completion_shas_checked_at\": \"2026-04-16T09:05:55.607745+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"068b7689-7035-4c49-9e5c-402c17d6ab5b","title":"[Demo] Fix walkthrough route 500 for hero analyses","description":"walkthrough_detail has mis-indented analysis lookup causing UnboundLocalError for hero walkthrough IDs; patch route and verify /demo linked walkthrough pages return 200\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:04:36.353893+00:00","updated_at":"2026-04-16T09:04:36.353893+00:00","summary":"","completion_summary":"Verified all walkthrough routes return 200 - issue already resolved on main","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/068b7689_703_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9aa0e113-0dc6-4e3a-ad2a-4261b7b42093","title":"[Demo] Add deterministic demo route smoke check script","description":"Build a bounded-time smoke-check script for demo-critical routes with status code, latency, and key content assertions to improve end-to-end demo reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:49:26.734143+00:00","updated_at":"2026-04-16T08:49:26.734143+00:00","summary":"","completion_summary":"[Demo] Add deterministic demo route smoke check script [task:9aa0e113-0dc6-4e3a-ad2a-4261b7b42093]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9aa0e113_0dc_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"7410645d23e86c7b756826c5e1bdd9f12ddda677\", \"ea4405dd868ef331ea9c4d2e4de16383b2914864\", \"3e0845faa7cc2fee2f7af0f19479fc1a5caddc4c\"], \"completion_shas_checked_at\": \"2026-04-16T08:49:26.582292+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a3909fdc-d626-4d68-91b4-15442f1dc1c7","title":"[Demo] Fix /agora /agents /missions /experiments 500 errors: create missing DB tables","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:43:25.243937+00:00","updated_at":"2026-04-16T08:43:25.243937+00:00","summary":"","completion_summary":"Fix already on main in fc79f50fa. All 4 pages (/agora, /agents, /missions, /experiments) return 200. The fix created missing DB tables (agent_personas, missions, experiments) via squash-merged commit — audit incorrectly flagged as orphan branch.","completion_notes":"Verified all 4 pages return 200. The fix (commit fc79f50fa) landed on main via squash merge from this branch — audit incorrectly flagged as ORPHAN_BRANCH. The tables `agent_personas`, `missions`, `experiments` exist in scidex.db and the pages work.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a3909fdc_d62_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"91ebb28f-f2af-4453-86f3-38f130fa9c4d","title":"[Demo] Harden scidex status when scidex.db is malformed","description":"Make scidex CLI status resilient to sqlite DatabaseError so service health checks still work during DB corruption incidents; add clear warning and continue reporting service status.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:42:57.269638+00:00","updated_at":"2026-04-16T08:42:57.269638+00:00","summary":"","completion_summary":"Verified: commits 110475ed1 and 257298335 ARE on origin/main. Work is done. Task was incorrectly flagged as orphan — the 2 commits are present on main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/91ebb28f_f2a_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"be2ac004-f698-490b-ac2d-b223d13dab90","title":"[Demo] Fix broken internal links on hero showcase pages","description":"Run targeted link audit for top demo routes, repair broken internal links in generated/hand-authored pages, and verify key routes return 200.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:42:26.455468+00:00","updated_at":"2026-04-16T08:42:26.455468+00:00","summary":"","completion_summary":"[Demo] Fix broken internal links in walkthrough.html: replace SDA-2026-04-01-gap-013 (0 edges, case mismatch bug) with SDA-2026-04-03-gap-seaad-v4-20260402065846 (53 nodes, 198 edges) for dynamic graph and evidence API calls","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/be2ac004_f69_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"14d91db42a576c98da76af475318d11fce6fbdde\"], \"completion_shas_checked_at\": \"2026-04-16T08:42:26.434617+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8b5bbc06-590a-4cde-abf4-c80484380bbb","title":"[Demo] One-shot: verify demo pages and repair regressions","description":"Run immediate demo page health checks for /demo plus top hypotheses/analyses pages, fix concrete regressions, and document verification results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:41:19.524652+00:00","updated_at":"2026-04-16T08:41:19.524652+00:00","summary":"","completion_summary":"Verified all demo pages - zero regressions found. /demo (200), top 5 hypotheses (all 200), top 5 analyses (all 200), key pages (/exchange, /gaps, /graph, /atlas.html, /wiki all 200). Services healthy. Site is demo-ready.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8b5bbc06_590_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified on 2026-04-16 via slot-73 worktree. All pages return 200/301 (redirects are correct). The task was previously done but had an orphan branch issue (no commits found referencing task ID on current branch). Re-created spec and verified system health.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6f8c69c-cda3-4e92-8154-5736c86a3f6e","title":"[Demo] Restore missing QUESTS.md roadmap document","description":"Create and commit QUESTS.md roadmap index so autonomous agents can prioritize Quest 16/17 when no tasks are eligible.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:32:39.971399+00:00","updated_at":"2026-04-16T08:32:39.971399+00:00","summary":"","completion_summary":"QUESTS.md already on main with 17-quest roadmap; Quest 16 (Demo Showcase, P99) and Quest 17 (Rich Artifacts, P90) marked as top priorities. No additional work needed.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6f8c69c_cda_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d704027d-ddd8-41c9-8871-344d769f7618","title":"[Demo] Add missing QUESTS.md roadmap source-of-truth","description":"Create canonical QUESTS.md defining all 17 SciDEX quests and current priorities (Quest 16 Demo Showcase, Quest 17 Rich Artifacts), since self-improve workflow references it but file is missing.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:30:58.217682+00:00","updated_at":"2026-04-16T08:30:58.217682+00:00","summary":"","completion_summary":"Verified QUESTS.md already exists on origin/main with all 17 quests documented, Quest 16/17 correctly marked as highest priorities (P99/P90). No commits with this task ID exist in git history — previous agent did not complete the commit. File content was already correct; updated spec work log with verification notes.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d704027d_ddd_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"QUESTS.md exists at repo root, contains all 17 quests (Quest 1-17), Quest 16 (Demo Showcase) and Quest 17 (Rich Artifacts) marked as highest priorities with P99/P90. File is identical to origin/main. No code changes were needed.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d2687802-e7d9-487b-ba9d-0dd83f5de578","title":"[Demo] Create deep hypothesis showcase with rich evidence","description":"Build /demo page with 3-5 exemplar hypotheses showing: multi-round debates, rich evidence arrays (10+ papers per hypothesis), price history charts, threaded discussions (when WS1 delivers), linked analyses. Goal: demonstrate full SciDEX capability to visitors. Supports Quest 16 (Demo Showcase).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:26:40.876492+00:00","updated_at":"2026-04-16T08:26:40.876492+00:00","summary":"","completion_summary":"Verified: /demo page already on main. Built with 5 hypothesis showcase cards featuring evidence strength badges (high/medium/low), mechanism previews from pathway diagrams, debate quality scores, and multi-layer narrative sections. /showcase page also live with interactive KG widgets. No new code needed — prior agent work delivered the showcase functionality.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d2687802_e7d_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Audit confirmed: /demo at line 53670 in api.py shows 5 hypothesis cards with rich evidence arrays, pathway previews, debate links, and layer-narrative sections. /showcase at line 55046 shows interactive KG widgets and analysis cards. Both pages serve live DB data. Work was delivered by prior agents but without [task:d2687802] tag in commits.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4d604c9d-daf7-4508-b54b-9ba741a6219b","title":"[Demo] Render 4 unrendered Jupyter notebooks to HTML","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:01:32.996600+00:00","updated_at":"2026-04-16T08:01:32.996600+00:00","summary":"","completion_summary":"Already done — commits ec79ae4ab and 43ab73f67 on origin/main confirm 3 notebooks rendered (aging-mouse-brain-v2, aging-mouse-brain-v3, seaad), 4 others pre-existed. 830 notebooks on main verified.","completion_notes":"Work already landed on origin/main in squash merges ec79ae4ab (3 notebooks) and 43ab73f67 (spec update). Verified: origin/main has 830 notebooks, worktree has 818. No SHA check needed — work confirmed on main.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4d604c9d_daf_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e439a9e3-5c45-4484-887c-63565849eae5","title":"[Demo] Create end-to-end demo walkthrough page at /demo/walkthrough","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:44:57.254048+00:00","updated_at":"2026-04-16T06:44:57.254048+00:00","summary":"","completion_summary":"[UI] Add push-blocked note to spec work log [task:e439a9e3-5c45-4484-887c-63565849eae5]; [UI] Mark spec complete for /demo/walkthrough [task:e439a9e3-5c45-4484-887c-63565849eae5]; [UI] Update spec work log for /demo/walkthrough route [task:e439a9e3-5c45-4484-887c-63565849eae5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e439a9e3_5c4_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e28b00dc14b187700aabd945594235cf4d6d2651\"], \"completion_shas_checked_at\": \"2026-04-16T06:44:57.232009+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"09e54732-0825-4969-8b78-d8e726a7ea0e","title":"[Demo] Add evidence strength badges and structured display on hypothesis pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:42:36.333582+00:00","updated_at":"2026-04-16T06:42:36.333582+00:00","summary":"","completion_summary":"Squash merge: orchestra/task/1ca8a93a-broken-links-in-api-http-0-7-links (1 commits)","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/09e54732_082_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"5de825ad2378a26fd68d493843e0cc111ab25b24\"], \"completion_shas_checked_at\": \"2026-04-16T06:42:36.316005+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6f2c4d26-b2c3-44bf-b59d-b74d1bcd3d08","title":"[Demo] Build demo walkthrough page — guided tour of all 5 layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:25:45.142653+00:00","updated_at":"2026-04-16T06:25:45.142653+00:00","summary":"","completion_summary":"[UI] Final work log update — demo walkthrough verified HTTP 200, pushed [task:6f2c4d26-b2c3-44bf-b59d-b74d1bcd3d08]; [UI] Update demo walkthrough spec work log [task:6f2c4d26-b2c3-44bf-b59d-b74d1bcd3d08]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6f2c4d26_b2c_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"158e4032b706bdd1c236666aaa4164372affcd47\", \"f7992f71458b343ebef4f3a5b7a3c9171a8410ba\"], \"completion_shas_checked_at\": \"2026-04-16T06:25:45.121964+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3ea6ec71-baa7-4e53-a14d-461e754ee78c","title":"[Demo] Enhance demo walkthrough with live data links and five-layer tour","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T06:02:48.392301+00:00","updated_at":"2026-04-16T06:02:48.392301+00:00","summary":"","completion_summary":"Enhanced demo.html with live data from APIs; all acceptance criteria verified; pushed to worktree branch","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3ea6ec71_baa_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4e2211c5-77bb-4260-9ec6-d49a07f75086","title":"[Demo] Add 3D protein structure viewers (Mol*) to hypothesis detail pages","description":"Embed Mol* (molstar) 3D protein viewers on hypothesis pages for target proteins. Use PDB IDs mapped to target genes. Show the actual protein structures that hypotheses discuss, making the science tangible and visual. Ref: QUESTS D16.4.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:43:38.747549+00:00","updated_at":"2026-04-16T05:43:38.747549+00:00","summary":"","completion_summary":"Task already complete: Mol* 3D protein viewers implemented on main via squash merge 4c49eed29. Feature includes 150+ PDB IDs, 190+ UniProt IDs for AlphaFold fallback, lazy-loaded collapsible viewer on hypothesis/entity/challenge pages (not on /showcase).","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4e2211c5_77b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8124130e-1e43-47e7-b1f9-d4d9c8d28bb2","title":"[Demo] Expand walkthrough whitelist with richest new analyses (CRISPR, SEA-AD, BBB)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:31:47.102975+00:00","updated_at":"2026-04-16T05:31:47.102975+00:00","summary":"","completion_summary":"[Demo] Expand WALKTHROUGH_IDS with BBB transport and Circuit-level analyses (richest at 49 hyps) [task:8124130e-1e43-47e7-b1f9-d4d9c8d28bb2]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8124130e_1e4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"782273432d87f90d791fea8e5d90e5d1b337a6c8\"], \"completion_shas_checked_at\": \"2026-04-16T05:31:47.066419+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b6fcaf88-1609-49a2-9602-def144d9a422","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all features","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:05:27.287578+00:00","updated_at":"2026-04-16T05:05:27.287578+00:00","summary":"","completion_summary":"[UI] Sync demo.html walkthrough IDs with api.py; fix hero card links [task:b6fcaf88-160]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b6fcaf88_160_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e0e83d83981bd54e2db2c636e8277df4b12b93dc\"], \"completion_shas_checked_at\": \"2026-04-16T05:05:27.255067+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0b543336-d96a-4c4d-a4cf-fbd48ffc57ca","title":"[Demo] D16.9: Create end-to-end demo walkthrough page — guided tour linking all features","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:01:09.909179+00:00","updated_at":"2026-04-16T05:01:09.909179+00:00","summary":"Duplicate - walkthrough pages already exist for top 3 analyses","completion_summary":"Demo walkthrough page with guided tour already exists on main — implemented via task branches 29cf4473 and 1bb03794. Verified: /demo route at api.py:53391, 8-step tour overlay with backdrop dimming, progress bar, keyboard nav, scenario cards all present.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b543336_d96_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1bb03794-fbab-4637-bde4-b0dd09090666","title":"[Demo] Build end-to-end demo walkthrough page at /demo","description":"Create a guided tour page at /demo that walks visitors through all 5 SciDEX layers with links to the best content. Show: hero hypotheses with rich evidence -> debates that produced them -> tools that gathered data -> KG connections -> governance tracking. D16.9 from QUESTS.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:01:02.807767+00:00","updated_at":"2026-04-16T04:01:02.807767+00:00","summary":"","completion_summary":"[Atlas] Mark task 1bb03794 complete - /demo walkthrough already implemented","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1bb03794_fba_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"84e35e6807583844b1329239ab4b2f90e96b87ed\"], \"completion_shas_checked_at\": \"2026-04-16T04:01:02.788346+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"29cf4473-c50f-4d6a-a6f9-c480d9d875c7","title":"[Demo] End-to-end demo walkthrough page — guided tour linking all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:26:55.200581+00:00","updated_at":"2026-04-16T03:26:55.200581+00:00","summary":"","completion_summary":"Verified complete: demo.html already implemented with guided tour for all 5 layers, verified on main","completion_notes":"VERIFIED ALREADY DONE. Work merged to main in commit 67f0cfc75 and squash-merged in 04e1d688d. site/demo.html (125KB) serves HTTP 200 with all required elements. Audit was false-positive: NO_COMMITS search matched zero commits because task ID search was against partial hash.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/29cf4473_c50_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"de4c85a0-f841-4b71-80e7-97513a4ce3b0","title":"[Demo] Enrich demo walkthrough page with rich embedded content and guided tour","description":"D16.9: Transform minimal demo.html into a polished guided tour with embedded hero hypothesis cards, live stats, figure gallery, and notebook links. Show all 5 layers with real data snippets.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T03:04:26.737465+00:00","updated_at":"2026-04-16T03:04:26.737465+00:00","summary":"","completion_summary":"[Demo] Update spec work log - task already on main [task:de4c85a0-f841-4b71-80e7-97513a4ce3b0]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/de4c85a0_f84_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"0dcd7be1447e236ae6b11f258f0d7651c2fa41c6\", \"a6d9ab65d5bc97a70dddce7e41de143faa01a387\", \"1ddf2d98779c7a0e50011cff4355ec70ae25badb\"], \"completion_shas_checked_at\": \"2026-04-16T03:04:26.716908+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"91161be1-97c2-4cc1-a2d1-2c8cce0625ba","title":"[Demo] Add hypothesis detail page — deep dive view with evidence, pathway diagrams, and debate links","description":"Create /hypothesis/{id} detail page that renders the full hypothesis with: description, evidence_for/against with citations, linked experiments, debate sessions, pathway diagrams. This is the hero page that demo visitors click into from /exchange.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:36:46.908630+00:00","updated_at":"2026-04-16T02:36:46.908630+00:00","summary":"","completion_summary":"Verified hypothesis detail page at /hypothesis/{id} is fully functional with: description, evidence_for/against citations, linked experiments, debate sessions with persona perspectives, pathway diagrams, market/price history, clinical trials, linked papers, 3D protein viewer, dependency graph, Elo ratings, radar chart. Exchange page correctly links to hypothesis detail as the hero page for demo visitors.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/91161be1_97c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"292ab415-360f-4243-8672-0bbc163f9f5c","title":"[Demo] Build end-to-end demo walkthrough page (D16.9)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:31:12.780167+00:00","updated_at":"2026-04-16T02:31:12.780167+00:00","summary":"","completion_summary":"[Demo] Verify and document end-to-end demo walkthrough D16.9 [task:292ab415-360f-4243-8672-0bbc163f9f5c]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/292ab415_360_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"e6b40dbdd88492343b8abd99ac2939eaac59df25\"], \"completion_shas_checked_at\": \"2026-04-16T02:31:12.759655+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0e838b9d-3237-4c95-9c55-6c7bd318d30a","title":"[Demo] End-to-end demo walkthrough page — guided tour of all five layers","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:30:59.209473+00:00","updated_at":"2026-04-16T02:30:59.209473+00:00","summary":"","completion_summary":"Verified /demo walkthrough page has all required features already implemented on main: sticky step navigation, section anchors for deep linking, Follow One Discovery trace section with live hypothesis data, and smooth scroll/active highlighting JavaScript. Updated spec work log to reflect completion.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0e838b9d_323_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"52dd0d6b-23a5-461e-b769-3fde52a2d777","title":"[Demo] End-to-end demo walkthrough page — guided tour of all 5 layers","description":"Create /demo page: a guided walkthrough tour linking all 5 SciDEX layers (Agora, Exchange, Forge, Atlas, Senate). Shows the platform's capabilities with links to best content in each layer. Quest D16.9.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T02:26:19.253652+00:00","updated_at":"2026-04-16T02:26:19.253652+00:00","summary":"","completion_summary":"[Demo] Update work log - verify merged demo walkthrough page [task:52dd0d6b-23a5-461e-b769-3fde52a2d777]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/52dd0d6b_23a_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"c668b285b7b47d64246559c0450f0274566500be\"], \"completion_shas_checked_at\": \"2026-04-16T02:26:19.232556+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-23-BMOD0001","title":"[Demo] Build simple biophysical model from KG-derived parameters","description":"Build a demo biophysical model: a minimal ODE model of microglial activation in AD (e.g. Ab accumulation -> microglial response -> cytokine release). Derive initial rate constants from KG edge weights and literature values. Run parameter fitting against the demo tabular dataset. Register as versioned model artifact linked to source hypothesis, dataset, and analysis. Show model outputs (time-course plots) as figure artifacts. Exercises: model building, biophysical template, artifact versioning, provenance chains. Depends on: frg-mb-02-BIOP, d16-22-TABD0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-14T10:43:55.460681+00:00","updated_at":"2026-04-14T10:43:55.460681+00:00","summary":"","completion_summary":"[Forge] Microglial model: add KG query + fix artifact registration [task:d16-23-BMOD0001]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-23-BMOD0001_biophysical_model_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"completion_shas\": [\"028007a8f87fff63e5801b95c850a86bb8ac07f6\"], \"completion_shas_checked_at\": \"2026-04-14T10:43:55.440037+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-21-DSET0001","title":"[Demo] Register Allen Brain Cell Atlas as external dataset artifact","description":"Register the SEA-AD Allen Brain Cell Atlas as an external dataset artifact with full metadata: source=allen_brain, URL, description, schema summary (cell types, gene expression columns, donor metadata). Link it to existing SEA-AD hypotheses and analyses via artifact_links. Show that browsing the dataset surfaces related KG entities and hypotheses. Exercises: external dataset references, artifact linking. Depends on: a17-21-EXTD0001.","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T00:29:44.414521+00:00","updated_at":"2026-04-26T00:29:44.414521+00:00","summary":"","completion_summary":"[Verify] SEA-AD dataset already registered, verified on main [task:d16-21-DSET0001]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-21-DSET0001_allen_brain_external_dataset_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"completion_shas\": [\"ef4c0312d\"], \"completion_shas_checked_at\": \"\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified already complete; SEA-AD dataset registered at commit 1955f024a with correct artifact ID dataset-allen_brain-SEA-AD-MTG-10x, 14 outgoing links (5 hypotheses, 4 analyses, 5 KG entities), GET /api/datasets working.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"822b6a6a-187f-45ea-9180-d79a2c40cb86","title":"[Demo] Harden link checker against transient localhost timeout storms","description":"Make link_checker resilient when localhost:8000 intermittently times out by adding per-URL circuit-breaking/fallback so CI demo verification can complete within timeout 300.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:28:09.611256+00:00","updated_at":"2026-04-16T11:28:09.611256+00:00","summary":"","completion_summary":"[Demo] Update spec work log for task 822b6a6a reopen and re-implementation [task:822b6a6a-187f-45ea-9180-d79a2c40cb86]; [Demo] Harden link checker: circuit breaker + bounded retries for timeout resilience","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/822b6a6a_187_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8dc2011f-aeb6-4863-a752-778d779a4833","title":"[Demo] Register Allen Brain Cell Atlas as external dataset artifact","description":"Register the Allen Brain Cell Atlas SEA-AD dataset as an external dataset artifact in SciDEX. Creates a traceable reference that analyses can link to.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:05:23.753279+00:00","updated_at":"2026-04-16T11:05:23.753279+00:00","summary":"","completion_summary":"[Atlas] Register Allen Brain Cell Atlas SEA-AD as external dataset artifact [task:8dc2011f-aeb6-4863-a752-778d779a4833]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-21-DSET0001_allen_brain_external_dataset_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a07bd425-88a8-4e0d-a299-928cd04a1797","title":"[Demo][UI] Add /demos alias redirect to /demo","description":"Create a compatibility route so /demos redirects to /demo, preventing 404s in demo links and improving end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:00:15.048357+00:00","updated_at":"2026-04-16T11:00:15.048357+00:00","summary":"","completion_summary":"Already done in commits 4a58dc22a/f145f504e: /demos redirect to /demo with query param preservation exists at api.py:53403-53406 on origin/main","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a07bd425_88a_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"29acf921-068b-4ec3-bded-73eb128356b7","title":"[Demo] Fix broken walkthrough links on demo landing page","description":"Audit /demo internal links for 404s and patch route/data selection so all showcased walkthrough CTAs resolve.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:58:35.419041+00:00","updated_at":"2026-04-16T10:58:35.419041+00:00","summary":"","completion_summary":"Already done: commits 86aa6e251 + 7866a6720 on origin/main harden demo hero walkthrough selection. Verified all 3 walkthrough links on /demo and all 9 on /showcase return 200. No new code changes needed.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/29acf921_068_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"39fdaefa-c95b-441a-8f22-14cc243d5df0","title":"[Demo] Harden key page links and rendering checks","description":"Run bounded render/link verification on core demo pages, fix any discovered broken internal links or template regressions, and verify service health.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:56:05.360627+00:00","updated_at":"2026-04-16T10:56:05.360627+00:00","summary":"","completion_summary":"Already addressed by prior commits 2cf4dd491 and f1439b5d6: api.py fix gates empty analysis_id links; all core pages return 200/302/307","completion_notes":"Verified: prior commits 2cf4dd491 (api.py fix) and f1439b5d6 (spec) are on auth/main/direct-origin/main branches and incorporated into current HEAD=cbdf735d7 which matches origin/main. Fixes are live in api.py lines 30578-30765 (analysis_id gating for empty /analyses/ links). All core routes healthy (200/302/307). Only uncommitted change is .orchestra-slot.json (slot breadcrumb, not task-related).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/39fdaefa_c95_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d98b5ffb-2c11-4c15-bf73-aff5b7d2a5fb","title":"[Demo] Add remaining 8 analysis notebooks to complete full coverage","description":"8 analyses still lack notebooks. Create .ipynb + .html for: gut-brain axis PD, mitochondrial transfer v2, protein cross-seeding v2, sleep-neurodegeneration x2, aging mouse brain v1-v4, SEA-AD v1-v2. Use hypothesis data from related analyses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:55:44.243275+00:00","updated_at":"2026-04-16T10:55:44.243275+00:00","summary":"","completion_summary":"[Demo] Update work log: aging mouse brain v4 notebook created, 7/8 already on main [task:d98b5ffb-2c11-4c15-bf73-aff5b7d2a5fb]; [Atlas] Add aging mouse brain v4 notebook: complete v1-v4 coverage [task:d98b5ffb-2c11-4c15-bf73-aff5b7d2a5fb]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d98b5ffb_2c1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d2b6209f-bde5-404e-8cd1-c8208d8594a2","title":"[Demo] Add structured evidence matrix table to hypothesis detail pages","description":"Replace simple evidence bullet lists with structured evidence matrix tables showing: claim, source journal, year, PMID link, strength badge (high/medium/low with color coding), and evidence type (for/against). Sortable columns. This is A17.6 from Quest 17 (Rich Artifacts).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":91,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:26:40.439195+00:00","updated_at":"2026-04-16T10:26:40.439195+00:00","summary":"","completion_summary":"Already implemented: structured evidence matrix table was added to hypothesis detail pages by task 634d0abd ([Exchange] Add structured evidence matrix table) — confirmed on origin/main at api.py:28612. Contains claim, source journal, year, PMID, strength badge (high/medium/low with color coding), evidence type (for/against), sortable columns, and expandable abstracts. Working on main (curl verified).","completion_notes":"Task already implemented on main via task 634d0abd ([Exchange] Add structured evidence matrix table). Evidence matrix at api.py:28612-28776 renders on hypothesis pages with claim, source, year, PMID link, strength badge (high/medium/low), evidence type (for/against), quality score, and expandable abstracts. Sortable columns via JavaScript. Confirmed working via curl. Closing as duplicate.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d2b6209f_bde_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"61c555a10\"], \"completion_shas_checked_at\": \"2026-04-16T10:26:40.401125+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-22-TABD0001","title":"[Demo] Tabular dataset demo: gene expression matrix linked to KG entities","description":"Create a demo tabular dataset artifact from SEA-AD differential expression results (gene, cell_type, log_fold_change, p_value). Map gene column to KG gene entities, cell_type column to KG cell-type entities. Show cross-references: clicking a gene shows its KG neighborhood + expression data, clicking cell type shows related genes from the table. Exercises: tabular datasets, column-to-entity linking, KG cross-referencing. Depends on: a17-22-TABL0001, d16-21-DSET0001.","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T04:59:04.068200+00:00","updated_at":"2026-04-25T04:59:04.068200+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-22-TABD0001_tabular_gene_expression_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 229399f5349bfa68d65f932fde9dcd4440d25658. Verified live artifact page returns 200 and renders SEA-AD tabular dataset schema; remaining Related Datasets/KG coverage UI is tracked by atl-ds-02-XREF_dataset_kg_crossref_spec.md.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"54d41c1a-ba60-4a14-90dc-7694c802d937","title":"[Demo] Enrich top 5 demo hypotheses with PubMed citations and mechanism details","description":"Find the top 5 hypotheses by composite score, fetch additional PubMed citations for each using the tools.py search functions, update their citations_count and evidence_for fields, and verify hypothesis pages render correctly with rich evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-20T13:12:05.302781+00:00","updated_at":"2026-04-20T13:12:05.302781+00:00","summary":"","completion_summary":"Verification confirms all 5 top hypotheses enriched with PubMed citations. DB has rich evidence arrays. Push blocked by missing GitHub credentials.","completion_notes":"Verification confirmed all 5 hypotheses enriched. DB state: h-var-55da4f915d (50 total), h-var-58e76ac310 (50), h-var-6612521a02 (65), h-var-3b982ec3d2 (55), SDA-2026-04-16-hyp-e5bf6e0d (11). All HTTP 200 on /hypothesis/{id}. Individual /api/hypotheses/{id} returns full evidence arrays. Push failed due to missing GitHub credentials — needs supervisor to merge.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/54d41c1a_ba6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"23f2dc149\"], \"completion_shas_checked_at\": \"2026-04-20T12:40:41.685796+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"DB confirmed: all 5 top hypotheses have ef/ea counts matching citations_count. Individual endpoint returns full evidence. Commit e86d93623 pushed to branch but push to GitHub failed (no credentials).","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c1284dcd-a41c-4993-83ab-b1cf4843448a","title":"[Demo] Seed 7 rich TREM2 hypotheses for DAM microglia analysis","description":"Seed 7 curated, LLM-enriched hypotheses for analysis SDA-2026-04-01-gap-001 (TREM2 agonism vs antagonism in DAM microglia). Each hypothesis gets a 1200-1600 word scientific description, evidence for/against citations, and a Mermaid pathway diagram. Advances Quest 16 D16.1: Deep enrichment of top demo hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:33:02.173784+00:00","updated_at":"2026-04-18T16:33:02.173784+00:00","summary":"","completion_summary":"7 rich TREM2 hypotheses verified in DB; data seeded 2026-04-16, branch was reset before merge but data persisted. Quest D16.1 complete.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c1284dcd_a41_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"7 rich TREM2 hypotheses verified in DB; data seeded 2026-04-16, branch was reset before merge but data persisted. Quest D16.1 complete.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7f3e9aaf-cd7a-4c70-a3eb-bc224938d08a","title":"[Demo] Tighten local demo smoke validation for notebook artifact links","description":"Improve demo smoke validation to catch broken notebook artifact links in local runs and keep Quest 16/17 demo surfaces stable.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:32:45.556897+00:00","updated_at":"2026-04-18T16:32:45.556897+00:00","summary":"","completion_summary":"[Verify] Tighten local demo smoke validation — PASS [task:7f3e9aaf-cd7a-4c70-a3eb-bc224938d08a]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7f3e9aaf_cd7_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Tighten local demo smoke validation — PASS [task:7f3e9aaf-cd7a-4c70-a3eb-bc224938d08a]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e625ca06-3329-4549-acfb-0d9d34099d40","title":"[Demo] Verify end-to-end demo pages and repair any render blockers","description":"Run demo-critical page checks (home, analyses, exchange, atlas, graph, gaps, how), fix any render/link blockers found, and record results.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:31:13.353858+00:00","updated_at":"2026-04-18T16:31:13.353858+00:00","summary":"","completion_summary":"13/15 demo pages pass; /api/graph and /demo fail due to pre-existing DB corruption (2026-04-17 incident)","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e625ca06_332_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"partial","verification_notes":"13/15 demo pages pass; /api/graph and /demo fail due to pre-existing DB corruption (2026-04-17 incident)","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0b58e9eb-493c-4abc-bd92-b4d86e0c00de","title":"[Demo] Harden link checker readiness for demo/showcase routes","description":"Add explicit readiness probes for /demo and /showcase in link_checker.py so demo-critical route outages are detected before crawl, with clear logging for transient restart diagnosis.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:29:59.450225+00:00","updated_at":"2026-04-18T16:29:59.450225+00:00","summary":"","completion_summary":"[Verify] Demo/showcase readiness probes — already resolved on main [task:0b58e9eb-493c-4abc-bd92-b4d86e0c00de]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0b58e9eb_493_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: probes for /demo and /showcase were already present in both link_checker.py files on main (landed in 700e194d0). All 5 acceptance criteria verified. No code changes needed — committed verification note to spec.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"686511ea-8998-4843-ab91-ac1a9972e94e","title":"[Demo] Strengthen demo smoke check API readiness assertions","description":"Extend scripts/demo_smoke_check.py to validate key API endpoints and include clearer failure diagnostics for demo readiness.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:26:30.322298+00:00","updated_at":"2026-04-18T16:26:30.322298+00:00","summary":"","completion_summary":"[Demo] Update spec work log for task rebase — clean push [task:686511ea-8998-4843-ab91-ac1a9972e94e]; [Demo] Extend smoke check with API readiness assertions [task:686511ea-8998-4843-ab91-ac1a9972e94e]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/686511ea_899_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"a635337ac\"], \"completion_shas_checked_at\": \"2026-04-16T15:38:33.199953+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Restored scripts/demo_smoke_check.py (ORPHAN_BRANCH fix) — commit a635337ac pushed","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4732ae38-3b59-4a79-95e3-07bca1eeb8be","title":"[Demo] Add guided walkthrough page linking all five layers","description":"Create a polished /demo walkthrough page with explicit five-layer flow and add clear entry links from existing navigation surfaces for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:25:38.878384+00:00","updated_at":"2026-04-18T16:25:38.878384+00:00","summary":"","completion_summary":"Demo walkthrough CTAs verified present on origin/main (5 locations: homepage, exchange, analyses, showcase, demo page). Accept criteria complete.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4732ae38_3b5_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Demo walkthrough CTAs verified present on origin/main (5 locations: homepage, exchange, analyses, showcase, demo page). Accept criteria complete.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c442133c-b269-4ecd-9c97-81fc1a49b857","title":"[Demo] CI: Add /forge and /notebooks to demo smoke-check route list","description":"The demo smoke check (scripts/demo_smoke_check.py) verifies that key routes load correctly. The /forge and /notebooks pages were recently fixed to use disk-backed caching (fixing 18-21s load times). The smoke check already checks /notebooks (under Artifacts), but the latency threshold check could be tightened. Task: Review the smoke check's route list and required_tokens, verify all 5 layers have health checks, and ensure the disk cache warm-up after restart is fast enough to pass 2s latency budget consistently.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:25:11.723824+00:00","updated_at":"2026-04-18T16:25:11.723824+00:00","summary":"","completion_summary":"[Verify] Smoke check route list — already resolved on main [task:c442133c-b269-4ecd-9c97-81fc1a49b857]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c442133c_b26_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"All acceptance criteria already satisfied on main via commit 700e194d0: /forge content markers, /agora route, 8s retry logic, 5-layer coverage, 31 routes total. Spec updated with verification evidence.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ec5b21dc-88de-41b5-b619-99cc2ca51d61","title":"[Demo] Add guided five-layer walkthrough page and homepage entrypoint","description":"Implement a polished demo walkthrough page spanning Agora, Exchange, Forge, Atlas, Senate with direct links and verification checks for end-to-end demoability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:23:59.349296+00:00","updated_at":"2026-04-18T16:23:59.349296+00:00","summary":"","completion_summary":"[Verify] Guided five-layer walkthrough page — already resolved [task:ec5b21dc-88de-41b5-b619-99cc2ca51d61]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ec5b21dc_88d_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"All 5 acceptance criteria verified: (1) /demo exists with comprehensive five-layer guided walkthrough, (2) homepage and /vision have prominent CTA entrypoint, (3) all key demo routes exist with handlers, (4) syntax compiles cleanly, (5) spec work log updated with verification evidence.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2e0e2408-151e-4b19-8276-2955a87f2adf","title":"[Demo] Improve transient outage diagnostics in link checker","description":"When link_checker detects restart cascades, report concise actionable diagnostics and persist summary fields in JSON without counting transient retries as opaque failures.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:23:10.045905+00:00","updated_at":"2026-04-18T16:23:10.045905+00:00","summary":"","completion_summary":"[Verify] Transient outage diagnostics already resolved [task:2e0e2408-151e-4b19-8276-2955a87f2adf]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2e0e2408_151_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved in dee11bae2: build_transient_diagnostics() returns structured fields, generate_report() includes transient_diagnostics in JSON, and transient cascade log is actionable.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8ac5df2e-b561-4661-814d-a6b5b94d95b1","title":"[Demo] Populate /targets with drug target data from hypotheses — page shows 0 targets","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:19:44.648910+00:00","updated_at":"2026-04-18T16:19:44.648910+00:00","summary":"","completion_summary":"[Docs] Update spec work log for task 8ac5df2e rebase — clean push [task:8ac5df2e-b561-4661-814d-a6b5b94d95b1]; [Docs] Update spec work log for task 8ac5df2e push resolution [task:8ac5df2e-b561-4661-814d-a6b5b94d95b1]; [Demo] Populate /targets from hypotheses when targets table is empty — add _derived_targets_from_hypotheses fallback in api.py [task:8ac5df2e-b561-4661-814d-a6b5b94d95b1]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8ac5df2e_b56_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f2165a12-fb1b-4340-8fc0-12b1e143d2ca","title":"[Demo] CI: Validate core demo routes and fix first failing endpoint","description":"Run demo route checks on port 8000, identify the first failing endpoint in the core demo flow, implement a fix, and verify all critical pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:18:37.239601+00:00","updated_at":"2026-04-18T16:18:37.239601+00:00","summary":"","completion_summary":"All 30 demo routes pass; /demo 500 fixed with None score handling","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f2165a12_fb1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"All 30 demo routes pass; /demo 500 fixed with None score handling","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4e386ba7-cecc-48fa-b746-68e5d056fd34","title":"[Demo] Stabilize link checker API readiness probe","description":"Fix false-negative API readiness timeouts in link_checker.py so CI checks run reliably for demo validation.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:15:17.295693+00:00","updated_at":"2026-04-18T16:15:17.295693+00:00","summary":"","completion_summary":"Fixed false-negative abort in link_checker.py. The caller of wait_for_api_ready() was breaking out of the crawl loop when readiness probes returned False, despite the probe function logging \"proceeding with guarded crawl.\" Removed the early-exit break so the link checker continues with transient-suppressed crawling instead of skipping the run entirely. Prior commits (f4415a57d, 498b55ea5) never merged to main; this is a clean fix on current main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4e386ba7_cec_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Fixed false-negative abort in link_checker.py. The caller of wait_for_api_ready() was breaking out of the crawl loop when readiness probes returned False, despite the probe function logging \"proceeding with guarded crawl.\" Removed the early-exit break so the link checker continues with transient-suppressed crawling instead of skipping the run entirely. Prior commits (f4415a57d, 498b55ea5) never merged to main; this is a clean fix on current main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"63263427-d9ea-4f0d-a25b-b8e3120c8109","title":"[Demo] Add Mol* protein viewer + score radar chart to challenge detail pages","description":"Challenge detail pages (/challenge/{id}) lack visual richness. Add: (1) auto-link challenges to relevant targets by parsing gene symbols from title/description, (2) embed Mol* 3D protein viewer for linked targets with known PDB IDs, (3) show a visual score radar chart for the 5 scoring dimensions (gap_importance, therapeutic_potential, existing_investment, urgency, landscape). This directly advances Quest 16 (Demo Showcase) by proving the Atlas+Exchange layers in a single compelling view.\n\nIMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:08:02.749576+00:00","updated_at":"2026-04-18T16:08:02.749576+00:00","summary":"","completion_summary":"Already resolved: code in origin/main at api.py:67260-67427. Verified live on /challenge/ch-trem2-dam-001 — Detected Targets, 3D Protein Structure (Mol*), and SVG radar chart all present. Original work squash-merged from prior task branch.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/63263427_d9e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: code in origin/main at api.py:67260-67427. Verified live on /challenge/ch-trem2-dam-001 — Detected Targets, 3D Protein Structure (Mol*), and SVG radar chart all present. Original work squash-merged from prior task branch.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"de03c8da-9a93-47f7-b9d5-5da9fddc4236","title":"[Demo] Seed challenges table from knowledge gaps for /challenges page","description":"The /challenges page exists and was recently fixed (DB migrations added) but the challenges table is empty. Seed it with 10-15 high-quality scientific challenges derived from knowledge_gaps, hypotheses, and analyses. Each challenge should have a title, question, description, domain, bounty, scores, and linked analysis/hypothesis IDs. This makes /challenges demoable as part of Quest 16 (Demo Showcase).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:05:47.199894+00:00","updated_at":"2026-04-18T16:05:47.199894+00:00","summary":"","completion_summary":"[Exchange] Update spec work log for reimplementation of challenges enrich endpoint [task:de03c8da-9a93-47f7-b9d5-5da9fddc4236]; [Exchange] Add POST /api/challenges/enrich endpoint to populate question, domain, analysis_id from linked analyses in api.py [task:de03c8da-9a93-47f7-b9d5-5da9fddc4236]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/de03c8da_9a9_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"09052e66-1f0b-48e8-9a6f-ce9843edb414","title":"[Demo] Tabular dataset demo: gene expression matrix linked to KG entities","description":"Create a demo showing tabular gene expression matrix from Allen data linked to KG entities (genes, brain regions). Demonstrates the tabular dataset artifact type.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:58:04.228512+00:00","updated_at":"2026-04-18T15:58:04.228512+00:00","summary":"","completion_summary":"[Verify] Tabular dataset demo — already resolved [task:09052e66-1f0b-48e8-9a6f-ce9843edb414]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-22-TABD0001_tabular_gene_expression_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}, \"completion_shas\": [\"2f55baa1a\", \"66a0801ba\", \"c09f7c483\"], \"completion_shas_checked_at\": \"2026-04-16T15:01:12.723574+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: tabular_dataset-b3889491-fc25-440e-863d-bc96f9d33c51 exists in DB with 5-column schema, 128 rows, gene/cell_type entity links, derives_from link to parent SEA-AD dataset.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e14242a4-9256-4b3d-9c3b-b02d3d6960ba","title":"[Demo] Add Allen Institute data analysis examples","description":"Create 2-3 analysis pages using Allen Institute datasets (Brain Atlas, single-cell RNA-seq, etc.). Show tool usage, KG integration, debate-driven insights. Link from /demo. Demonstrates Forge layer capabilities. Supports Quest 16.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:55:33.848658+00:00","updated_at":"2026-04-18T15:55:33.848658+00:00","summary":"","completion_summary":"[Verify] Allen Institute demo pages — already resolved [task:e14242a4-9256-4b3d-9c3b-b02d3d6960ba]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e14242a4_925_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6b8e7ec5-4806-4c72-9a0d-94341117bef4","title":"[Demo] Verify and polish demo walkthrough pages (/demo, /showcase, /origins)","description":"Ensure all demo routes render correctly with rich content. Fix any 404s/500s. Add missing content cards.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:53:10.961760+00:00","updated_at":"2026-04-18T15:53:10.961760+00:00","summary":"","completion_summary":"[Verify] Demo walkthrough pages — PASS [task:6b8e7ec5-4806-4c72-9a0d-94341117bef4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6b8e7ec5_demo_walkthrough_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Demo walkthrough pages — PASS [task:6b8e7ec5-4806-4c72-9a0d-94341117bef4]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"19e6d400-1bda-4bf7-81b7-2362d8c212b9","title":"[Demo] Provenance visualization UI for artifacts","description":"Build interactive provenance graph visualization using /api/artifacts/{id}/provenance-graph. Show parent artifacts, processing steps, and derivation chains. Use D3.js or similar.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:50:19.921427+00:00","updated_at":"2026-04-18T15:50:19.921427+00:00","summary":"","completion_summary":"All components already on main: D3 provenance graph in artifact detail pages, /api/artifacts/{id}/provenance-graph endpoint, and standalone /provenance-example demo page.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19e6d400_1bd_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified: artifact_provenance_graph_html() produces D3 force-directed SVG; artifact_registry.get_provenance_graph() returns nodes/edges; site/provenance-example.html (359 lines, Cytoscape.js) serves at /provenance-example; artifact detail page embeds provenance graph at api.py:23432; API endpoint at api.py:20878.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"74c44af2-13fc-4728-a8b1-04773fb19185","title":"[Demo] Generate HTML reports for 5 recent completed analyses missing reports","description":"5 recent completed analyses (epigenetic reprogramming, SEA-AD v3/v4, senescent clearance, EV biomarkers) have debate JSON but no HTML reports. Run post_process.py report generation for each.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:30:36.183722+00:00","updated_at":"2026-04-18T15:30:36.183722+00:00","summary":"","completion_summary":"Already done: all 5 HTML reports verified present on main (de47d06db) with proper debate content","completion_notes":"Re-verified all 5 analyses have HTML reports on origin/main (de47d06db). Reports: epigenetic reprogramming (9 hypotheses), SEA-AD v3 (full debate), SEA-AD v4 (full debate), senescent clearance (full debate), EV biomarkers (0 hypotheses). No new work needed — confirmed existing reports on main contain proper debate content.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/74c44af2_13f_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"de47d06db\"], \"completion_shas_checked_at\": \"2026-04-18T15:30:36.165003+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d22c9050-8d19-411d-8abd-b449c9743868","title":"[Demo] Add /clinical-trials listing page aggregating all trial data","description":"D16 demo completeness: Build /clinical-trials page showing all clinical trials extracted from hypothesis enrichment. Aggregated view with phase distribution, status breakdown, linkback to hypotheses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:26:14.435707+00:00","updated_at":"2026-04-18T15:26:14.435707+00:00","summary":"","completion_summary":"Already resolved: /clinical-trials listing page and /clinical-trials/{nct_id} detail page exist on origin/main (api.py:36385-36776). Includes phase distribution, status breakdown, search/filter, hypothesis linkbacks, stat cards, OG meta tags. Prior commits 375e9a0b5 and c912989ee landed this work.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d22c9050_8d1_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"375e9a0b5\"], \"completion_shas_checked_at\": \"2026-04-16T13:35:54.274658+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: /clinical-trials listing page and /clinical-trials/{nct_id} detail page exist on origin/main (api.py:36385-36776). Includes phase distribution, status breakdown, search/filter, hypothesis linkbacks, stat cards, OG meta tags. Prior commits 375e9a0b5 and c912989ee landed this work.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3bf7293b-c2d4-46bc-8dbb-bd8a2b2cf8a2","title":"[Demo] Add top hypothesis showcase cards to demo page","description":"Add a 'Featured Hypotheses' section to the /demo page showcasing the top 3 highest-scored hypotheses with their evidence counts, debate quality scores, and direct links. This gives demo visitors an immediate path to the richest content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T15:13:30.941970+00:00","updated_at":"2026-04-18T15:13:30.941970+00:00","summary":"","completion_summary":"Already resolved: code for Featured Hypotheses showcase cards is fully present on origin/main. Verified /api/featured-hypotheses endpoint at api.py:2898, CSS at demo.html:94, HTML section at demo.html:315-368, JavaScript at demo.html:887-910. Original commit 2500e07d9 merged via squash (not direct ancestor). Pushed verification commit aebdd7701.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3bf7293b_c2d_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: code for Featured Hypotheses showcase cards is fully present on origin/main. Verified /api/featured-hypotheses endpoint at api.py:2898, CSS at demo.html:94, HTML section at demo.html:315-368, JavaScript at demo.html:887-910. Original commit 2500e07d9 merged via squash (not direct ancestor). Pushed verification commit aebdd7701.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d16-25-DPAP0001","title":"[Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review","description":"Write an authored paper artifact that reviews microglial activation in AD, embedding live artifacts: the TREM2 protein design (version timeline), the biophysical model (time-course figure), the SEA-AD differential expression table, and KG subgraph for TREM2. Paper uses {{artifact:ID}} markers that render inline. Demonstrates: authored papers, artifact embedding, internal origin tracking, versioned documents. Depends on: a17-27-APAP0001, a17-29-EMBD0001, d16-20-AVER0001.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:21:05.218011+00:00","updated_at":"2026-04-16T11:21:05.218011+00:00","summary":"","completion_summary":"[Demo] Re-implement SEA-AD authored paper demo (ORPHAN_BRANCH recovery) [task:d16-25-DPAP0001]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-25-DPAP0001_dynamic_paper_demo_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c19610c7-3d34-4fed-814b-dd9ebc50ae97","title":"[Demo] Enrich top hypothesis: Closed-loop tACS targeting EC-II SST interneurons — full mechanistic description and evidence","description":"Deeply enrich the highest-scored hypothesis: \"Closed-loop tACS targeting EC-II SST interneurons\" (h-var-3b982e, score=0.990, 3 debates) with full mechanistic details and clinical evidence.\n\nSteps:\n1. Fetch hypothesis: `SELECT * FROM hypotheses WHERE id LIKE 'h-var-3b982e%' OR title ILIKE '%tACS%SST%'`\n2. Expand description to 2000+ characters covering:\n - EC-II (entorhinal cortex layer II) SST interneuron dysfunction in AD\n - tACS (transcranial alternating current stimulation) closed-loop mechanism\n - 40Hz gamma oscillation restoration approach\n - Patient selection criteria and biomarker indicators\n3. Add >= 10 PubMed citations: tACS in AD, SST interneurons in memory, gamma oscillations in neurodegeneration\n4. Add falsifiable predictions to the description\n5. Create a visual schematic of the closed-loop tACS circuit using image_generator.py\n6. Add evidence_against entries covering: stimulation parameter uncertainty, penetrance limitations\n\nAcceptance criteria:\n- Description >= 2000 chars with mechanistic detail \n- >= 10 citations in evidence_for\n- pathway_diagram or equivalent image generated\n- evidence_against has >= 2 entries\n- Hypothesis page renders correctly","status":"done","priority":89,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T04:30:48.424726+00:00","updated_at":"2026-05-16T04:12:40.706507+00:00","summary":"","completion_summary":"Task `c19610c7-3d34-4fed-814b-dd9ebc50ae97` completed. The hypothesis `h-var-3b982ec3d2` (\"Closed-loop tACS targeting EC-II SST interneurons to block tau propagation and restore perforant-path gamma gating in AD\") is now fully enriched:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Legacy done-evidence audit pass 2 backfill: preserved historical done state with administrative/no-merge evidence from completion summary. Original summary: Task `c19610c7-3d34-4fed-814b-dd9ebc50ae97` completed. The hypothesis `h-var-3b982ec3d2` (\"Closed-loop tACS targeting EC-II SST interneurons to block tau propagation and restore perforant-path gamma gating in AD\") is now fully enriched:","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dfa76dd9-7f75-4d1e-9706-46d6213abb5e","title":"[Demo] Enrich top hypothesis: TREM2-Dependent Astrocyte-Microglia Cross-talk — add full pathway diagram, citations, and clinical context","description":"Deeply enrich the TREM2-Dependent Astrocyte-Microglia Cross-talk hypothesis (h-var-de1677, composite_score=0.990, 4 debates) to demo quality with a complete pathway diagram, rich citations, and clinical context.\n\nSteps:\n1. Fetch the hypothesis: `SELECT * FROM hypotheses WHERE id = 'h-var-de1677'` or search by title\n2. Add a detailed pathway diagram description in pathway_diagram field covering:\n - TREM2 activation on microglia → DAP12 signaling → phagocytosis and cytokine release\n - Astrocyte-microglia crosstalk via IL-33, CXCL10, C1q\n - Disease context: TREM2 R47H variant in AD/PD\n3. Expand description to 2000+ characters with: molecular mechanism, TREM2 variants (R47H, Y38C), clinical GWAS evidence, proposed therapeutic strategies\n4. Add >= 10 citations to evidence_for covering: TREM2 structural biology, GWAS studies, mouse models, clinical trials\n5. Add 2 substantive counterarguments to evidence_against \n6. Generate a visual pathway diagram image using image_generator.py\n7. Verify /hypothesis/h-var-de1677 renders with all enriched content\n\nAcceptance criteria:\n- Description >= 2000 chars\n- >= 10 citations in evidence_for (PubMed PMIDs)\n- pathway_diagram image generated and saved\n- evidence_against has >= 2 substantive entries\n- Page renders at HTTP 200 with full content","status":"done","priority":89,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T04:34:19.485612+00:00","updated_at":"2026-04-28T04:34:19.485612+00:00","summary":"","completion_summary":"Task complete. Here's a summary of what was done:","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Description 2097 chars (≥2000 ✓), evidence_for 36 entries (≥10 ✓), pathway_diagram Mermaid text present + AI image artifact registered (✓), evidence_against 18 entries (≥2 ✓), HTTP 200 with AI Visual Card rendered (✓).","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"0e92acb2-4839-47aa-950b-fc68b34f4c00","title":"[Demo] Enrich 5 analyses with complete evidence chains and figures to make them showcase-ready","description":"Identify 5 completed analyses that would make strong showcase examples, and enrich them with complete evidence chains, visualizations, and polished content.\n\nTarget: analyses with compelling scientific questions but thin metadata (short descriptions, no figures, few citations in related hypotheses).\n\nSteps:\n1. Find candidate analyses: `SELECT id, title, question, domain, report_url FROM analyses WHERE status='completed' ORDER BY completed_at DESC LIMIT 20`\n2. Select 5 with the most compelling scientific questions (avoid duplicates with already-showcased ones)\n3. For each:\n - Write a 500+ word narrative summary of the analysis findings\n - Add 5+ PubMed citations supporting the key claims\n - Link to or generate a visual figure (using matplotlib or image generator)\n - Verify the analysis page at /analysis/{id} renders with rich content\n - Add the analysis to the showcase listing if not already there\n4. Tag enriched analyses with quality_verified=true\n\nAcceptance criteria:\n- 5 analyses enriched with 500+ word summaries\n- Each has >= 5 citations \n- Each has a figure (pathway diagram, chart, or schematic)\n- All 5 render at /analysis/{id} with HTTP 200 and rich content\n- quality_verified=true set for all 5","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T05:28:15.138288+00:00","updated_at":"2026-04-28T05:28:15.138288+00:00","summary":"","completion_summary":"Task closed as **pass**. All 5 analyses were already enriched and verified on main via PR #1036 (squash merge `583465659`):","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Task closed as **pass**. All 5 analyses were already enriched and verified on main via PR #1036 (squash merge `583465659`):","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c3889cdf-757b-4997-b2c3-059576b9af33","title":"[Demo] Harden local health checks against localhost redirect false negatives","description":"Update local health checks to avoid false failures from nginx localhost redirects by checking FastAPI directly (localhost:8000) or following redirects where appropriate; update related docs and verification behavior.","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T07:02:09.501685+00:00","updated_at":"2026-04-26T07:02:09.501685+00:00","summary":"","completion_summary":"[Verify] Harden local health checks — PASS [task:c3889cdf-757b-4997-b2c3-059576b9af33]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c3889cdf_757_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"561612b9a\"], \"completion_shas_checked_at\": \"\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Harden local health checks — PASS [task:c3889cdf-757b-4997-b2c3-059576b9af33]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9c045da5-42fd-4fe0-ab6f-3229089716c3","title":"[Demo] Add structured evidence matrix to hypothesis pages","description":"A17.6: Replace the simple evidence list on hypothesis detail pages with a structured evidence matrix table. Show each evidence item in a row with: claim, strength badge (strong/moderate/weak), source journal, year, PMID link, and evidence type categorization (mechanistic/clinical/genetic/epidemiological). Add a summary bar showing evidence balance. This makes hypothesis pages more professional and demo-ready.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-21T04:16:38.294689+00:00","updated_at":"2026-04-21T04:16:38.294689+00:00","summary":"","completion_summary":"[Demo] Harden hypothesis evidence matrix citation parsing [task:9c045da5-42fd-4fe0-ab6f-3229089716c3]","completion_notes":"Normalized raw evidence strings for matrix rows to extract embedded PMIDs, years, and strength words; mapped strong/moderate/weak aliases into high/medium/low evidence buckets. Tested py_compile and local hypothesis page HTTP 200 on port 8018.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9c045da5_42f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"fc359ad6bbc2c0a8681862dd9a817102dfe1b446\"], \"completion_shas_checked_at\": \"2026-04-21T04:16:38.254213+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"python3 -m py_compile api.py; curl http://127.0.0.1:8018/hypothesis/h-var-58e76ac310 returned 200 and rendered Evidence Matrix/Evidence Types/PMID links.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"591dc8b3-8580-433d-9c41-c0e4b2061d6c","title":"[Demo] Add hypothesis comparison feature — side-by-side view of top hypotheses","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-21T00:32:50.944645+00:00","updated_at":"2026-04-21T00:32:50.944645+00:00","summary":"","completion_summary":"Already resolved: hypothesis comparison feature /compare route at api.py:32246 confirmed live (HTTP 200, radar chart + score bars + evidence). Verification note committed to spec.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/591dc8b3_858_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1fcd8ef5-a0e1-4606-b714-7407eeb22a32","title":"[Demo] Add regression guard for markdown-free demo hypothesis snippets","description":"Prevent raw markdown artifacts from reappearing in /demo hypothesis snippets by adding an automated CI smoke check and documenting acceptance criteria.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:47:59.974031+00:00","updated_at":"2026-04-19T01:47:59.974031+00:00","summary":"","completion_summary":"[Demo] Add snippet-level markdown regression guard in demo smoke check","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1fcd8ef5_a0e_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"57503d6f-cc7c-47c8-b487-02b99a2b1857","title":"[Demo] Enrich 10 thin hypothesis descriptions to 1000+ words","description":"IMPORTANT: Before implementing, verify this work hasn't already been done. Check api.py routes, git log, and the live site. If already implemented, mark complete with summary explaining what already exists.\n\n141 hypotheses have <500 char descriptions. Expand with mechanisms, evidence, clinical relevance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:36:52.974137+00:00","updated_at":"2026-04-19T01:36:52.974137+00:00","summary":"","completion_summary":"[Verify] Task 57503d6f: 10 thin hypotheses enrichment verified complete","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/57503d6f_cc7c_enrich_10_thin_hypotheses_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7559b983-6027-4abd-b087-67f0246034f2","title":"[Demo] Suppress transient link-checker false positives after successful revalidation","description":"Link checker should not emit systematic issues in final JSON/report when sampled affected links are healthy after retry checks; reduce demo CI noise and avoid misleading route-missing diagnoses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:36:24.773003+00:00","updated_at":"2026-04-19T01:36:24.773003+00:00","summary":"","completion_summary":"Already resolved: a9cd57835. _filter_recovered_links() in generate_report filters recovered links from transient_outage_links, preserving them in revalidated_links for audit.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7559b983_602_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified on origin/main (bdd7c0ea7): link_checker.py contains _filter_recovered_links() at line 708, suppress_resolved_issues() at line 1067, revalidated_links in generate_report at line 1225. The commit a9cd57835 landed the fix. Acceptance criteria: [x] link_checker.py filters out transiently resolved issues before final report/task-creation; [x] timeout 300 python3 link_checker.py completes and no longer reports stale transient issue titles; [x] Work log records implementation and validation results.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"372abf40-6d00-4db3-96f0-aef54b6095f3","title":"[Demo] Harden link-check API readiness to avoid false startup timeouts","description":"Reduce false API readiness failures in link_checker.py by probing lightweight health endpoint with bounded retry/backoff and preserving transient-outage classification behavior for demo CI reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:33:41.215303+00:00","updated_at":"2026-04-19T01:33:41.215303+00:00","summary":"","completion_summary":"Already resolved: 01dfbce01. Confirmed via py_compile syntax check and code review — lightweight /api/health probe with exponential backoff (2s base, 15s cap, 8 attempts) already present in origin/main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/372abf40_6d0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: 01dfbce01. Confirmed via py_compile syntax check and code review — lightweight /api/health probe with exponential backoff (2s base, 15s cap, 8 attempts) already present in origin/main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"61c9215e-27c0-4745-a755-2eabce5a9bf9","title":"[Demo] Use canonical /analyses links in demo walkthrough cards","description":"Replace legacy /analysis links in /demo analysis cards with canonical /analyses paths to remove redirect hops and improve demo page performance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:32:28.094068+00:00","updated_at":"2026-04-19T01:32:28.094068+00:00","summary":"","completion_summary":"Already addressed: commits a4dd7d0cb and 91ddf898b on main canonicalized /demo analysis links to /analyses. Verified 0 legacy /analysis/[0-9] hrefs remain.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/61c9215e_27c_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7db32f89-29f3-438c-bc3a-dd5fb5e37a0a","title":"[Demo] Verify core demo routes and fix one blocking render issue","description":"Run demo-critical page/API health checks, identify a concrete blocking issue if present, implement fix, and verify end-to-end demo route health.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:30:14.129326+00:00","updated_at":"2026-04-19T01:30:14.129326+00:00","summary":"","completion_summary":"[Verify] Core demo routes health check — PASS [task:7db32f89-29f3-438c-bc3a-dd5fb5e37a0a]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7db32f89_29f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Core demo routes health check — PASS [task:7db32f89-29f3-438c-bc3a-dd5fb5e37a0a]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3face9c1-54f4-4a14-8620-acb4ae1e9d55","title":"[Demo] Link orphan hypotheses to relevant challenges","description":"212 hypotheses exist but are not linked to any challenge. Match hypotheses to relevant challenges using keyword/target/disease matching. This enriches challenge pages from 2 hypotheses to 10+ per challenge, dramatically improving demo quality (Q16 D16.1).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:23:36.392237+00:00","updated_at":"2026-04-19T01:23:36.392237+00:00","summary":"","completion_summary":"[Demo] Update spec work log: rebase fix for URL corruption [task:3face9c1-54f4-4a14-8620-acb4ae1e9d55]; [Demo] Update spec work log: re-link orphan hypotheses to challenges [task:3face9c1-54f4-4a14-8620-acb4ae1e9d55]; [Demo] Add script to link orphan hypotheses to challenges via keyword matching [task:3face9c1-54f4-4a14-8620-acb4ae1e9d55]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3face9c1_54f_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"4c6c454d9\"], \"completion_shas_checked_at\": \"2026-04-19T01:23:17.568038+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c0bd88ac-0ecc-4413-8269-b7070b80f3f1","title":"[Demo] Expand demo smoke check to validate walkthrough detail pages","description":"Extend scripts/demo_smoke_check.py to detect walkthrough detail links from /showcase and verify each page status, latency, and content-size quality to improve Quest 16 demo reliability.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:16:02.589484+00:00","updated_at":"2026-04-19T01:16:02.589484+00:00","summary":"","completion_summary":"Re-implemented walkthrough detail validation in demo_smoke_check.py — discovers walkthrough URLs from /showcase, validates HTTP/latency/size with retries [task:c0bd88ac-0ecc-4413-8269-b7070b80f3f1]","completion_notes":"Re-implemented walkthrough detail validation in scripts/demo_smoke_check.py. The implementation: (1) parses /showcase HTML to discover /walkthrough/ links via WALKTHROUGH_PATTERN regex; (2) validates each walkthrough detail page with HTTP status, latency budget (2s), and minimum body-size (5KB) checks; (3) includes retry logic (2 attempts) for transient failures; (4) reports discovery count and walkthrough-specific failures separately. Pushed to orchestra/task/c0bd88ac-expand-demo-smoke-check-to-validate-walk and force-pushed to update stale branch state. Spec updated with work log and verification block.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c0bd88ac_0ec_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"426e8eb9f\"], \"completion_shas_checked_at\": \"2026-04-19T01:16:02.565733+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Implementation verified: collect_walkthrough_targets() parses /showcase for href=/walkthrough/ links, dedicated validation loop checks HTTP status (200/3xx), latency budget (2s), and minimum body size (5KB). Retry logic handles retryable status codes and slow responses. Syntax validated with py_compile.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"15706b67-6ffa-4318-9641-573f762dfa3b","title":"[Demo] Fix invalid escape sequence warnings in api.py UI scripts","description":"Eliminate Python SyntaxWarning invalid escape sequence issues in embedded JS/HTML strings in api.py to improve demo-page reliability and startup cleanliness.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:11:29.454322+00:00","updated_at":"2026-04-19T01:11:29.454322+00:00","summary":"","completion_summary":"[Demo] Update spec work log for reopened task attempt [task:15706b67-6ffa-4318-9641-573f762dfa3b]; [Demo] Fix invalid escape sequence SyntaxWarnings in api.py wiki page JS","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/15706b67_6ff_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ce861697-6110-4e75-a6f2-54536e88b1bc","title":"[Demo] Repair broken demo-route links from health sweep","description":"Run bounded page/link verification on demo-critical routes, fix broken internal links/templates, and verify 200/3xx responses for demo pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:10:36.348177+00:00","updated_at":"2026-04-19T01:10:36.348177+00:00","summary":"","completion_summary":"[Demo] Update spec work log: fix /graph?node= corruption [task:ce861697-6110-4e75-a6f2-54536e88b1bc]; [Demo] Fix /graph?node= corruption in wiki and walkthrough pages [task:ce861697-6110-4e75-a6f2-54536e88b1bc]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ce861697_611_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bd76fdd5-4eea-42e1-a654-8e91bfb279a5","title":"[Demo] Fix scidex CLI startup when optional auth/webhook modules are missing","description":"Make cli.py resilient when auth.py/webhooks.py are unavailable so status/site/db commands still run from minimal deployments and main checkout.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:04:41.088390+00:00","updated_at":"2026-04-19T01:04:41.088390+00:00","summary":"","completion_summary":"[Verify] CLI resilient fix already on main — task resolved [task:bd76fdd5-4eea-42e1-a654-8e91bfb279a5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bd76fdd5_4ee_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: commit f3605c7a0 on origin/main implements the lazy-load fix. Verification commit 74f08512c added to spec.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"686b564a-2980-40fe-adf1-c73dcd60d42e","title":"[Demo] Harden link checker partial-timeout reporting","description":"Ensure link_checker.py always emits logs/link-check-latest.json and avoids long LLM analysis when run under timeout 300, so CI runs are actionable.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:04:33.604879+00:00","updated_at":"2026-04-19T01:04:33.604879+00:00","summary":"","completion_summary":"[Verify] link_checker hardening — PASS, all criteria met on main [task:686b564a-2980-40fe-adf1-c73dcd60d42e]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/686b564a_298_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c72ce6ef-aad8-4695-9fab-e339a7e96dd7","title":"[Demo] Harden demo smoke check with latency budgets and showcase/artifact routes","description":"Expand scripts/demo_smoke_check.py to validate core demo+artifact routes and fail when route latency exceeds configured budget (default 2s) to enforce demoability quality bar.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:04:04.345850+00:00","updated_at":"2026-04-19T01:04:04.345850+00:00","summary":"","completion_summary":"[Demo] Update spec work log: re-apply smoke check after revert [task:c72ce6ef-aad8-4695-9fab-e339a7e96dd7]; [Demo] Harden demo smoke check with latency budgets and artifact routes [task:c72ce6ef-aad8-4695-9fab-e339a7e96dd7]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c72ce6ef_aad_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"82b3b55b-a2f4-4ec1-bf86-8fd3c5f15bd8","title":"[Demo] Make link checker worktree-safe (remove hardcoded main paths)","description":"Fix link_checker.py to use repository-relative paths for report/context/task DB access so runs from worktrees produce stable reports and accurate context; verify report freshness and task creation behavior.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:02:10.674821+00:00","updated_at":"2026-04-19T01:02:10.674821+00:00","summary":"","completion_summary":"Already resolved: link_checker.py has MAIN_REPO_ROOT/_resolve_main_repo_root worktree-safe paths on origin/main. Verification confirmed no hardcoded main paths in runtime code.","completion_notes":"Fix already landed on origin/main (verified via git show). This task was reopened because audit couldn't find the original commits. Worktree detection correctly resolves to /home/ubuntu/scidex for DB and report paths. Only change was adding verification entry to spec.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/82b3b55b_a2f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"36c90c341\", \"4e740d41a\", \"f7ed8eb9b\", \"3c34f8284\"], \"completion_shas_checked_at\": \"2026-04-16T16:55:07.117120+00:00\", \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"19519ab7-8d0d-45f6-b01a-51a434bf75c6","title":"[Demo] Fix link checker retry handling for relative URLs","description":"Prevent invalid URL retries on relative internal links during demo CI link checks by normalizing/reusing resolved absolute URLs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:01:17.663918+00:00","updated_at":"2026-04-19T01:01:17.663918+00:00","summary":"","completion_summary":"Already resolved: 988f6cf9b — relative URL retry normalization via urljoin(BASE_URL, ...) is in place on main; link_checker.py line 385 confirms fix","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19519ab7_8d0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"988f6cf9bffda13239536efafb726b18c7060be3\", \"8310bd85699ec68f0bff25d425d8282f2fe3a343\"], \"completion_shas_checked_at\": \"2026-04-19T01:01:17.643215+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f4d205ba-3770-4792-91bc-b1e7dde1a29b","title":"[Demo] Harden guided demo route checks and repair broken path references","description":"Recurring demo validations miss legacy path variants; add robust demo route coverage and fix discovered broken demo links/routes so walkthrough pages return 200/3xx.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T01:00:57.060742+00:00","updated_at":"2026-04-19T01:00:57.060742+00:00","summary":"","completion_summary":"[Demo] Correct commit SHA in spec work log [task:f4d205ba-3770-4792-91bc-b1e7dde1a29b]; [Demo] Fix None-type score formatting in api.py demo walkthrough [task:f4d205ba-3770-4792-91bc-b1e7dde1a29b]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f4d205ba_377_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5d65f0ff-9d7c-444a-bcce-4065e346391e","title":"[Demo] Fix broken /demo/showcase deep link","description":"Audit found /demo/showcase returns 404 while /demo exists. Add a stable route/redirect for showcase deep links and verify demo/artifact pages render.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T00:58:39.187489+00:00","updated_at":"2026-04-19T00:58:39.187489+00:00","summary":"","completion_summary":"[Verify] /demo/showcase fix confirmed on main [task:5d65f0ff-9d7c-444a-bcce-4065e346391e]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5d65f0ff_9d7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"979153bd-7b65-4fce-9917-904373cc6e2b","title":"[Demo] Add /demo-showcase alias route to avoid 404","description":"Create a one-shot fix so /demo-showcase resolves to the existing demo experience instead of returning 404. Include route handling, page validation, and spec work log.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T00:58:06.162077+00:00","updated_at":"2026-04-19T00:58:06.162077+00:00","summary":"","completion_summary":"Already resolved: /demo-showcase route exists at api.py:60311, validated by smoke_check.py. Branch up to date with origin/main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/979153bd_7b6_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1b983b0f-02b6-4f19-8b6c-17b727e376f2","title":"[Demo] Add protein 3D structure section to demo/showcase pages","description":"The Mol* 3D protein viewer is now active on 12 target pages (TREM2, APOE, SNCA, BACE1, BRD4, etc.) but the demo walkthrough and showcase pages don't mention or link to it. Add a protein structure section to /demo and /showcase highlighting the interactive Mol* viewer feature with direct links to key targets.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T00:55:00.698005+00:00","updated_at":"2026-04-19T00:55:00.698005+00:00","summary":"","completion_summary":"[Verify] Mol* 3D protein structure sections on demo and showcase pages — already resolved [task:1b983b0f-02b6-4f19-8b6c-17b727e376f2]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1b983b0f_02b_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1ceb5f3b-b413-40a6-88d0-15e563c9d3a9","title":"[Demo] Harden demo route smoke check with explicit five-layer coverage","description":"Add/upgrade a lightweight demo smoke check script that validates all five-layer routes and returns non-zero on failures; include timeout-safe usage and document in spec.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T00:51:27.026315+00:00","updated_at":"2026-04-19T00:51:27.026315+00:00","summary":"","completion_summary":"[Demo] Restore five-layer demo smoke check script [task:1ceb5f3b-b413-40a6-88d0-15e563c9d3a9]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1ceb5f3b_b41_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bb4412a7-ec41-4083-8fbc-67086cec0614","title":"[Demo] Populate drug targets table with top AD/neurodegeneration targets","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T00:50:07.428183+00:00","updated_at":"2026-04-19T00:50:07.428183+00:00","summary":"","completion_summary":"Already resolved: all deliverables (185 targets, agent_personas, hypothesis_debates, uniprot_id column, int() phase conversion) verified on main at 8f3785dce","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/bb4412a7_ec4_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: all deliverables (185 targets, agent_personas, hypothesis_debates, uniprot_id column, int() phase conversion) verified on main at 8f3785dce","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"48a272c0-940a-43ee-956b-bf893d23ebae","title":"[Demo] Hypothesis detail pages: add rich content panels (evidence, debates, price history)","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:44:56.707635+00:00","updated_at":"2026-04-18T17:44:56.707635+00:00","summary":"","completion_summary":"Task resolved via orphan branch rebase: tabbed rich content panels (Evidence/Debates/Market/Clinical Trials/Papers/Notebooks/Arenas tabs) already present on branch after rebase onto origin/main. All 3 prior commits (0d725bfbc, 5cf5cda15, 99077a84c) now in branch history.","completion_notes":"Audit found 3 orphaned commits (0d725bfbc tabbed panels, 5cf5cda15 knowledge_edges fix, 99077a84c evidence cards) tagged with this task but not merged to main. Rebased worktree onto origin/main, which pulled the orphaned commits into history (they share common ancestry with current main HEAD c25d53234). Feature confirmed present: grep returns ~15 matches for hypSwitchTab/hyp-tab-btn/hyp-tab-panel. Branch pushed via push-token remote.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/48a272c0_940_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"248445f3a\"], \"completion_shas_checked_at\": \"2026-04-18T17:44:56.688198+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6ce00da3-a400-410b-a982-65d291ba0051","title":"[Demo] Fix walkthrough analysis pages returning 500","description":"Diagnose and fix /walkthrough/{analysis_id} server errors so demo deep-link walkthroughs render successfully.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:44:12.558362+00:00","updated_at":"2026-04-18T17:44:12.558362+00:00","summary":"","completion_summary":"Already addressed: fix landed in 2757cb9e7 and 4f823e886, is_curated refactor confirmed on main at line 64074, all WALKTHROUGH_IDS pages return 200","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6ce00da3_a40_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified: walkthrough pages for all WALKTHROUGH_IDS return 200 (SDA-2026-04-03-gap-seaad-v4-20260402065846, sda-2026-04-01-gap-013, SDA-2026-04-04-gap-tau-prop-20260402003221). Fix (is_curated refactor, `a = db.execute(...)` moved outside `if not is_curated:` block) is at api.py:64074 confirmed by grep. Original task ID SDA-2026-04-01-gap-20260401-225155 is not a curated walkthrough and correctly returns 404, not 500.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f840df44-9012-4580-a754-b7da2621f23a","title":"[Demo] Harden link checker for redirect-aware demo verification","description":"Make link_checker robust to local redirect topology (301/302), add non-LLM fast mode, and ensure CI-style checks finish within timeout windows.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:41:50.508236+00:00","updated_at":"2026-04-18T17:41:50.508236+00:00","summary":"","completion_summary":"[Verify] link_checker hardening — PASS, all criteria met on main [task:f840df44-9012-4580-a754-b7da2621f23a]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f840df44_901_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] link_checker hardening — PASS, all criteria met on main [task:f840df44-9012-4580-a754-b7da2621f23a]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b726f64c-41e5-456b-81ff-ff806a53066c","title":"[Demo] Fix health-check endpoint assumptions for HTTPS host routing","description":"Update SciDEX health-check guidance/scripts to avoid localhost false negatives under HTTPS+Host routing; validate against scidex.ai/Host header patterns.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:39:39.226196+00:00","updated_at":"2026-04-18T17:39:39.226196+00:00","summary":"","completion_summary":"smoke_check.py HTTPS+Host routing fix verified PASS — code correct on main, 502 on scidex.ai is infra issue","completion_notes":"Verification PASS: code-level check confirms fix is correct and merged on main. Live test returned 502 (infrastructure issue, not code defect). Fix properly handles HTTPS+Host routing via auto-extracted Host header.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b726f64c_41e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"smoke_check.py HTTPS+Host routing fix verified PASS — code correct on main, 502 on scidex.ai is infra issue","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9b158072-664c-412e-a3a9-d296819d32c9","title":"[Demo] Dashboard browser page","description":"Create /dashboards page listing all 5 dashboard artifacts. Show live dashboard embeds or previews with refresh timestamps.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:39:06.582882+00:00","updated_at":"2026-04-18T17:39:06.582882+00:00","summary":"","completion_summary":"[Verify] /dashboards page already on main — task resolved [task:9b158072-664c-412e-a3a9-d296819d32c9]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/9b158072_664_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: /dashboards endpoint exists at api.py:21887 on main (SHA 2809ee453). Prior orphan commits 943907452/667e5f116 did the work; implementation verified and spec updated.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a59e422a-c3d6-4027-b048-910cb00c4be7","title":"[Demo] Fix /showcase 500 when hypothesis confidence is null","description":"Resolve TypeError in showcase_top_analyses caused by comparing null confidence values to float thresholds; keep showcase rendering for sparse hypothesis rows and verify route returns 200.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:36:20.539726+00:00","updated_at":"2026-04-18T17:36:20.539726+00:00","summary":"","completion_summary":"[Verify] /showcase null confidence fix — already resolved on main [task:a59e422a-c3d6-4027-b048-910cb00c4be7]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a59e422a_c3d_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: NULL confidence guards (or 0 fallback) present on origin/main at lines 62843, 63203, 63247 in showcase_top_analyses(). Original commits 26a2715af/259c7cacd were orphan/never-merged; equivalent fix independently landed on main via commits 5568c47d6/49d97dd67.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a48fe1f1-4bcf-43a2-bdf1-c93821159eee","title":"[Demo] Ensure /demo hero analyses render with fallback content","description":"Make /demo resilient when no analyses meet strict richness thresholds by adding deterministic fallback selection and preserving polished card metadata.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:27:01.481550+00:00","updated_at":"2026-04-18T17:27:01.481550+00:00","summary":"","completion_summary":"Fix already in main via commit 9c5929459: WHERE a.status='completed' filter at line 61062 in demo_walkthrough_page()","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a48fe1f1_4bc_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"760d6b61-f157-4ebf-b3f7-b74e184b5012","title":"[Demo] Fix broken walkthrough links on demo page — only show for valid walkthrough IDs","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T17:22:04.410166+00:00","updated_at":"2026-04-18T17:22:04.410166+00:00","summary":"","completion_summary":"[Verify] Fix broken walkthrough links — already resolved on main [task:760d6b61-f157-4ebf-b3f7-b74e184b5012]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/760d6b61_f15_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d9f9c0d1-d1b8-4965-8c59-feab3993175a","title":"[Demo] Evidence matrix component with quality scores on hypothesis pages","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-18T16:46:30.597576+00:00","updated_at":"2026-04-18T16:46:30.597576+00:00","summary":"","completion_summary":"Evidence matrix component already on main (api.py:32906). Implemented by task 06d4e19e in commit a52f93353. Confirmed on current main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d9f9c0d1_d1b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"a46d75008\"], \"completion_shas_checked_at\": \"2026-04-18T16:46:30.572639+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Verified on main: `_build_evidence_matrix_html` at api.py:32906. Evidence tab on hypothesis pages includes sortable quality scores (Strength, Year, Quality columns) with color coding.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"68757880-1652-41e4-997a-9bb9f0c4b483","title":"[Demo] Build per-disease landing page: Alzheimer's Disease — curated hypotheses, analyses, and mechanistic narrative","description":"Enrich the Alzheimer's Disease landing page with curated, showcase-ready content mirroring the quality of the PD page.\n\nSteps:\n1. Check the AD landing page state: `curl -s 'http://localhost:8000/disease/alzheimer' | head -200` or equivalent URL\n2. Identify the top 10 AD-relevant hypotheses by composite_score (filter by title/description ILIKE '%alzheimer%' OR '%AD%' OR '%amyloid%' OR '%tau%')\n3. Find the 5 best completed AD analyses\n4. Find the 3 most substantive AD debate sessions\n5. Write a curated narrative (500+ words) covering:\n - Amyloid-tau-neuroinflammation triangle\n - Key genetic risk factors (APOE4, TREM2, CLU)\n - Most valuable SciDEX hypotheses about AD\n - Open questions with highest-priority analyses\n6. Update the AD disease page with this content\n7. Cross-link to PD page for shared mechanisms\n\nAcceptance criteria:\n- AD landing page has narrative text >= 500 words\n- Page lists >= 5 curated AD hypothesis links\n- Page lists >= 3 analysis links\n- All linked entities return HTTP 200\n- PD-AD cross-mechanism link present","status":"done","priority":87,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T05:49:40.992985+00:00","updated_at":"2026-04-28T05:49:40.992985+00:00","summary":"","completion_summary":"Already resolved on main: 3560cb45, fd86e808","completion_notes":"Auto-release: work already on origin/main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved on main: 3560cb45, fd86e808","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"79fef48d-d455-46a1-a5aa-1fcecd171332","title":"[Demo] Build per-disease landing page content: Parkinson's Disease — key hypotheses, open questions, and leading analyses","description":"Enrich the Parkinson's Disease landing page with curated, showcase-ready content linking to the best hypotheses, analyses, and debates.\n\nContext: A per-disease landing page was recently added (commit d734ea71d). The PD page needs rich curated content beyond basic statistics.\n\nSteps:\n1. Check the current PD landing page: `curl -s 'http://localhost:8000/disease/parkinson' | head -200` or similar\n2. Identify the top 10 PD-relevant hypotheses by composite_score\n3. Identify the 5 best completed analyses for PD (from analyses table)\n4. Find the 3 most substantive PD debate sessions\n5. Write a curated narrative (500+ words) about the PD research landscape on SciDEX:\n - Key mechanistic themes (lysosomal, mitochondrial, neuroinflammatory)\n - Open research questions with highest-scoring hypotheses\n - Most valuable completed analyses\n6. Update the disease page data structure to include this curated content\n7. Verify the page renders at HTTP 200 with rich content\n\nAcceptance criteria:\n- PD landing page has narrative text >= 500 words\n- Page lists >= 5 curated hypothesis links\n- Page lists >= 3 analysis links\n- Page lists >= 1 debate link\n- All linked entities return HTTP 200 on their own pages","status":"done","priority":87,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-28T05:24:54.625720+00:00","updated_at":"2026-04-28T05:24:54.625720+00:00","summary":"","completion_summary":"[Atlas] Retry-2 verification note: all acceptance criteria confirmed [task:79fef48d-d455-46a1-a5aa-1fcecd171332]; [Atlas] PD disease landing page: curated narrative, pinned links, fix debate URL (api.py) [task:79fef48d-d455-46a1-a5aa-1fcecd171332]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"completion_shas\": [\"d87f0c25d\"], \"completion_shas_checked_at\": \"\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":"d87f0c25d","merge_verified_at":"2026-04-28T05:15:51.353586+00:00","verification_result":"pass","verification_notes":"Confirmed: git show --stat d87f0c25d shows disease_curated_content.py (Added) and api.py (Modified). All 6 hypothesis, 5 analysis, 3 debate URLs verified HTTP 200.","task_type":"one_shot","pr_links":[],"commit_links":[{"sha":"d87f0c25d","role":"merge_commit"}]},{"id":"d16-27-ORIG0001","title":"[Demo] Origin tracking showcase: internal vs external artifact provenance","description":"Already resolved on main: repo code contains the /origins provenance showcase and /demo/origins redirect; verified via code inspection and TestClient. Local localhost:8000 is stale because scidex-api restart is blocked in this sandbox.","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T04:16:42.223948+00:00","updated_at":"2026-04-26T04:16:42.223948+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16-27-ORIG0001_origin_tracking_demo_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved on main: /origins provenance showcase and /demo/origins redirect are present in repo code and verified with TestClient; localhost:8000 still serves the older page because scidex-api was not refreshed here.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4c5f9f52-3a67-462d-8621-b166fb79df6f","title":"[Demo] Add /leaderboard route and fix /challenges 500 error","description":"Nav links point to /leaderboard (404) and /challenges (500). Add the /leaderboard page (top hypothesis leaderboard with sparklines) and fix the /challenges 500 error. These are broken links on the main nav visible to all visitors.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T05:03:54.023377+00:00","updated_at":"2026-04-19T05:03:54.023377+00:00","summary":"","completion_summary":"[Exchange] Fix /leaderboard filter URL and /challenges 500 error in api.py [task:4c5f9f52-3a67-462d-8621-b166fb79df6f]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4c5f9f52-3a67-462d-8621-b166fb79df6f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fbe2795d-545f-4348-9a89-2595dab26374","title":"[Demo] Replace 0-Experiments stat on demo page with Notebooks count","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:49:03.225075+00:00","updated_at":"2026-04-19T04:49:03.225075+00:00","summary":"","completion_summary":"[Verify] Replace 0-Experiments stat on demo page — already resolved [task:fbe2795d-545f-4348-9a89-2595dab26374]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fbe2795d_545_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b97b6c81-c302-4ff4-b7d0-6752e85b4b80","title":"[Demo] Harden link checker against transient API restarts","description":"Improve link_checker reliability during temporary localhost:8000 connection refusals so demo CI checks complete within timeout and avoid false failures.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:44:56.620262+00:00","updated_at":"2026-04-19T04:44:56.620262+00:00","summary":"","completion_summary":"Already resolved: 436c06dc3 — link checker fully hardened against transient API restarts. Verified acceptance criteria met (CircuitBreaker, wait_for_api_ready, RETRYABLE_STATUSES={0,502,503,504}, transient_candidate, reconcile_transient_failures). link_checker.py identical to origin/main (0 diff).","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b97b6c81_c30_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ab24f3c1-399a-4184-8583-a2e923ebb94d","title":"[Demo] Fix disk cache SQLite contention on entity pages","description":"Entity page disk cache writes fail under concurrent load (SQLite lock timeout). The _set_cached_page() function uses sqlite3.connect with timeout=2 but under CI smoke checks with 50+ concurrent entity requests, writes fail silently. Fix: increase busy_timeout, add WAL checkpoint optimization, or use write serialization via a threading.Lock to prevent concurrent writers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:43:29.823108+00:00","updated_at":"2026-04-19T04:43:29.823108+00:00","summary":"","completion_summary":"Already resolved: fix present in api_shared/cache.py — _DISK_CACHE_WRITE_LOCK serializes writes, daemon thread avoids blocking, WAL mode on each connection","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab24f3c1_399_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\", \"completion_shas\": [\"54d7ce5ec\"], \"completion_shas_checked_at\": \"2026-04-19T04:43:29.808303+00:00\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5b1fa594-9751-4e1d-9a90-60f85cecac36","title":"[Demo] Add transient outage diagnostics to link checker report","description":"Extend link_checker JSON output with explicit transient outage metadata (counts, classification, and source context) so demo CI can distinguish real broken links from restart cascades.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:42:00.058898+00:00","updated_at":"2026-04-19T04:42:00.058898+00:00","summary":"","completion_summary":"Already resolved: f1d12004b (landed via squash merge e3519edc5). build_transient_diagnostics() and transient_diagnostics in report confirmed on origin/main.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5b1fa594_975_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: f1d12004b (landed via squash merge e3519edc5). build_transient_diagnostics() and transient_diagnostics in report confirmed on origin/main.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6a5b47da-270e-4a8f-b9ea-d931fa03cb6f","title":"[Demo] Add live growth metrics section to /demo page","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:39:17.252394+00:00","updated_at":"2026-04-19T04:39:17.252394+00:00","summary":"","completion_summary":"[Demo] Fix SQLite compatibility in live growth metrics SQL queries in api.py [task:6a5b47da-270e-4a8f-b9ea-d931fa03cb6f]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/demo_live_growth_metrics_spec.md","provider":"any","payload_json":"{\"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c4b55a70-b39f-4174-aeb5-b9efb2d6cd6e","title":"[Demo] Harden link-check readiness to avoid transient outage cascades","description":"Strengthen link_checker preflight so full crawl only starts after sustained API readiness; reduce transient false-failure cascades during demo CI.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:37:09.975695+00:00","updated_at":"2026-04-19T04:37:09.975695+00:00","summary":"","completion_summary":"Already resolved on main via 700e194d0 — all 6 acceptance criteria verified: READINESS_CONFIRMATION_STEPS env var, wait_for_api_ready() confirmation window, abort-on-failure logic, transient suppression preserved, py_compile passes","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c4b55a70_b39_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4225e413-8095-4223-a793-6cccd095b3c5","title":"[Demo] Fix /demo/origins route returning 404","description":"Demo smoke checks show /demo/origins returns 404 while /demo is 200. Ensure route is registered and page renders with origin stats/provenance content; add regression test coverage for demo routes where feasible.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-19T04:25:25.007698+00:00","updated_at":"2026-04-19T04:25:25.007698+00:00","summary":"","completion_summary":"[Verify] Audit and confirm /demo/origins fix already on main — resolved [task:4225e413-8095-4223-a793-6cccd095b3c5]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4225e413_809_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_reset_note\": \"This task was reset after a database incident on 2026-04-17.\\n\\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\\ncorruption. Some work done during Apr 16-17 may have been lost.\\n\\n**Before starting work:**\\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\\n\\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\\nSCIDEX_DB_BACKEND=postgres env var.\", \"_reset_at\": \"2026-04-18T06:29:22.046013+00:00\", \"_reset_from_status\": \"done\"}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2afefff3-4df7-498a-bbe4-8962ca2b0ebf","title":"[Demo] Enrich 5 top-scoring hypotheses with full evidence narratives and PubMed citations","description":"Select top 5 hypotheses by composite_score. For each: (1) fetch supporting papers from hypothesis_papers and paper_corpus_cache, (2) write a 300+ word evidence_for narrative citing specific papers with PMIDs, (3) populate evidence_against with known counter-evidence, (4) ensure mechanistic_plausibility_score, druggability_score, and clinical_relevance_score are all set, (5) set epistemic_status to 'supported'. Acceptance: 5 hypotheses with evidence_for >300 chars, ≥3 linked papers, all 10 dimension scores non-zero.","status":"done","priority":80,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T15:04:09.367682+00:00","updated_at":"2026-04-26T15:04:09.367682+00:00","summary":"","completion_summary":"[Agora] Enrich top 5 hypotheses with evidence narratives and PubMed citations [task:2afefff3-4df7-498a-bbe4-8962ca2b0ebf]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fe71613c-8335-4b41-8005-19466e9ad4df","title":"[Demo] Create showcase analysis for TREM2 in Alzheimer's Disease with linked hypothesis tree","description":"TREM2 is a flagship Alzheimer's target. Create a high-quality showcase analysis: (1) check if a TREM2/Alzheimer analysis exists in analyses table; if not, create one via POST /api/analyses, (2) ensure at least 5 hypotheses are linked to this analysis with hypothesis_type diversity (mechanistic, therapeutic, diagnostic), (3) add 10+ supporting KG edges from kg_edges linking TREM2 to its known interactors, (4) link the 3 most cited papers (pmid lookup) to the analysis, (5) add a debate session with synthesizer output. Acceptance: analysis exists, 5+ linked hypotheses, 10+ KG edges, debate session present.","status":"done","priority":78,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T15:03:14.028676+00:00","updated_at":"2026-04-26T15:03:14.028676+00:00","summary":"","completion_summary":"[Agora] Build TREM2 AD showcase analysis with linked hypotheses and debate [task:fe71613c-8335-4b41-8005-19466e9ad4df]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b44f99bd-7f7a-4978-9a29-47ce28bd422d","title":"[Demo] Add summary statistics widget to site homepage — hypothesis/evidence/paper counts","description":"The homepage should show live counts of the platform's knowledge. In api.py, add a /api/stats/summary endpoint that returns: {hypotheses: count, hypotheses_with_evidence: count, papers: count, wiki_pages: count, kg_edges: count, active_markets: count, debates_run: count}. Then integrate these stats into the main homepage HTML template (index page). Cache the stats for 5 minutes via page_cache. Acceptance: curl /api/stats/summary returns valid JSON with all 7 fields, and the homepage HTML displays the live counts.","status":"done","priority":75,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T15:24:49.579996+00:00","updated_at":"2026-04-26T15:24:49.579996+00:00","summary":"","completion_summary":"[Atlas] Add wiki_pages, hypotheses_with_evidence, active_markets to homepage stats widget [task:b44f99bd-7f7a-4978-9a29-47ce28bd422d]; [Atlas] Add /api/stats/summary endpoint with 5-min cache — returns hypotheses/papers/wiki/kg_edges/active_markets/debates counts [task:b44f99bd-7f7a-4978-9a29-47ce28bd422d]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ab05482c-8248-49bb-9b67-57303ad81cf4","title":"[Demo] Harden route health check for demo-critical pages","description":"Add/verify a reusable route-health check that includes /demo, /artifacts, /walkthrough, /entity, and /analyses with timeout handling and clear failure diagnostics for demo readiness.","status":"done","priority":70,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-25T23:51:30.984886+00:00","updated_at":"2026-04-25T23:51:30.984886+00:00","summary":"","completion_summary":"[Verify] Site health check — PASS [task:ab05482c-8248-49bb-9b67-57303ad81cf4]; [Demo] Fix /walkthrough (302) and /agents (301) in smoke check [task:ab05482c-8248-49bb-9b67-57303ad81cf4]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab05482c_824_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"[Verify] Site health check — PASS [task:ab05482c-8248-49bb-9b67-57303ad81cf4]; [Demo] Fix /walkthrough (302) and /agents (301) in smoke check [task:ab05482c-8248-49bb-9b67-57303ad81cf4]","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"884376c0-3d22-4804-b394-fd2ab39fb626","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"done","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T06:26:49.984928+00:00","updated_at":"2026-04-26T06:26:49.984928+00:00","summary":"","completion_summary":"No commits on iteration 1/3; requeuing","completion_notes":"Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"api.py already contains curated WALKTHROUGH_IDS, showcase links, non-hero Back to Showcase navigation, and the wiki_html fallback rebuild. Runtime checks on 2026-04-25 PT: /showcase plus /walkthrough/SDA-2026-04-03-gap-seaad-v4-20260402065846, /walkthrough/SDA-2026-04-01-gap-20260401-225149, and /walkthrough/SDA-2026-04-04-gap-tau-prop-20260402003221 returned 200 and included Executive Summary, Debate Transcript, Hypotheses, Knowledge Graph, Linked Wiki Pages, and More Walkthroughs.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"08826160-8c56-46ed-a9f9-ef889db063cb","title":"[Demo] Create guided demo walkthrough page at /demo","description":"Build a single page that walks visitors through all 5 SciDEX layers: start with a hypothesis -> show the debate that produced it -> tools used -> KG connections -> governance tracking. Include links to real content at each step.","status":"done","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T06:15:21.795952+00:00","updated_at":"2026-04-26T06:15:21.795952+00:00","summary":"","completion_summary":"Already resolved: /demo page exists on origin/main at api.py:68148 with all 5 layers (Agora, Exchange, Forge, Atlas, Senate), live stats, hero analysis cards, Follow One Discovery trace, and guided tour overlay. Verified HTTP 200 and all section IDs present. Prior commit 396e0424a was initial creation; expanded by subsequent tasks.","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":"pass","verification_notes":"Already resolved: /demo page exists on origin/main at api.py:68148 with all 5 layers (Agora, Exchange, Forge, Atlas, Senate), live stats, hero analysis cards, Follow One Discovery trace, and guided tour overlay. Verified HTTP 200 and all section IDs present. Prior commit 396e0424a was initial creation; expanded by subsequent tasks.","task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ea332662-aabf-41e2-b750-1c3329e10615","title":"[Demo] Build guided demo walkthrough page at /demo","description":"Create a polished /demo page that guides visitors through all 5 SciDEX layers with curated links to the best content. Show: top hypothesis with 3D viewer -> debate that produced it -> Forge tools used -> KG connections -> Senate quality tracking. Include stats, screenshots-like sections, and a compelling narrative about how multi-agent AI accelerates scientific discovery. This is D16.9 from QUESTS.md.","status":"done","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":"2026-04-26T06:02:12.464519+00:00","updated_at":"2026-04-26T06:02:12.464519+00:00","summary":"","completion_summary":"[Verify] Demo walkthrough already resolved — spec work log updated [task:ea332662-aabf-41e2-b750-1c3329e10615]","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ea332662_aab_spec.md","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5810fbef-2526-43d7-a14c-6e5d19b1dcca","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.866966+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6a14cfb2-4763-481a-aff4-15894217a19f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.852466+00:00","summary":"","completion_summary":"Already done (duplicate). Top 3 analyses are polished hero content with debate transcripts, 7 ranked hypotheses, 200-400 KG edges, pathway diagrams, and 132-178 figures each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"cdcb3856-505d-44b9-bc1d-41c2f2f9bb29","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.835921+00:00","summary":"","completion_summary":"Duplicate of task 433022a3. Already verified: all 3 hero walkthroughs (Gut-brain PD, CRISPR neurodegeneration, Senolytics) fully polished with debate transcripts, hypothesis cards, KG visualizations, wiki links, and all other sections. Also fixed raw JSON leaking in synthesizer output.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e758f674-f950-45a1-a98c-9e66423bfc68","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.819809+00:00","summary":"","completion_summary":"Top 3 analyses are already hero content: (1) Gut microbiome-PD: 5 debate rounds, 7 hypotheses, 400 KG edges, 132 figures, mermaid diagrams, wiki links. (2) CRISPR neurodegeneration: 3 rounds, 7 hyps, 346 edges, 138 figs. (3) Senolytic therapy: 3 rounds, 7 hyps, 287 edges, 178 figs. All pages 175-199KB with polished rendering.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"433022a3-9347-4b97-899c-76817f05743c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.804497+00:00","summary":"","completion_summary":"Verified all 3 hero analysis walkthroughs are fully polished and working. Each walkthrough (Gut-brain axis PD, CRISPR neurodegeneration, Senolytic therapy) has all required components: rendered 4-persona debate transcripts with expand/collapse, hypothesis cards scored across 11 dimensions, interactive D3 KG visualization (400/346/287 edges), 16-20 linked wiki pages, executive summary, key findings, evidence deep dive, clinical trials, pathway diagrams, figure gallery, papers, TOC navigation, reading guide, methodology section, and related walkthroughs. Showcase page links to all 3. All rendering at 200 OK in <0.5s.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6356cde6-17e9-46f6-a194-070d1c3ee877","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.788367+00:00","summary":"","completion_summary":"Top 3 analyses are fully polished hero content: (1) Gut-brain axis/PD (7 hyps, 400 KG edges, debate, mermaid, wiki), (2) CRISPR neurodegeneration (7 hyps, 346 edges, full transcript), (3) Senolytic therapy (7 hyps, 287 edges, mermaid). All render at /analysis/{id} with scores, debates, wiki links. Showcase page at /showcase features them.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c1aca3e3-9018-4ce5-b2b4-a99a9c49128b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.772079+00:00","summary":"","completion_summary":"Verified all 3 hero analysis walkthroughs are fully polished. /showcase has comparison table, KG widgets, debate previews, hypothesis cards with dimension bars, wiki links, figures, and paper references for all 3 analyses (Gut Microbiome-PD with 400 edges/136 papers, CRISPR Neurodegeneration with 346 edges/42 papers, Senolytic Therapy with 287 edges/180 papers). Each /walkthrough/ detail page includes: progress bar, sticky TOC with active highlighting, analysis journey timeline, executive summary, full debate transcript (expand/collapse), 7 hypothesis cards with 11 dimension score bars, score comparison chart, evidence deep dive with PubMed links, gene expression context, per-hypothesis Mermaid pathway diagrams, clinical trials with NCT links, target proteins with entity links, interactive KG visualization, categorized figure gallery, wiki page links, related walkthroughs cross-links, and print/share functionality. Code sections for Why These Three and Average Dimension Scores are in main but require server restart to appear.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e9c01743-49c2-43b8-9193-e43a3e65a509","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.757597+00:00","summary":"","completion_summary":"Polished walkthrough pages for top 3 hero analyses (Gut-PD, CRISPR, Senolytic). Added 3 additional score dimensions (Competition, Data Availability, Clinical Relevance) to hypothesis cards, hypothesis type badges, disease/pathway metadata, and Copy Link share button. All 3 walkthroughs verified working with debate transcripts, KG viz, wiki links, figures, and papers.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"077d4f5f-3136-48e0-838d-b074d9a4daff","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.742900+00:00","summary":"","completion_summary":"Duplicate — completed as 38c8ec84.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bb664746-8a90-4d45-8932-b75fee0a49fa","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.727522+00:00","summary":"","completion_summary":"All 3 hero walkthrough analyses already fully implemented with polished content: SDA-2026-04-01-gap-20260401-225155 (Gut microbiome & PD, 400 edges, 136 papers), SDA-2026-04-02-gap-crispr-neurodegeneration-20260402 (CRISPR neurodegeneration, 346 edges), SDA-2026-04-01-gap-013 (Senolytic therapy, 287 edges, 180 papers). Each walkthrough page includes: executive summary, key findings, multi-agent debate transcript with expand/collapse, hypothesis cards with 8-dimension score bars, score comparison chart, evidence deep dive with PubMed links, gene expression context, pathway diagrams (Mermaid), clinical trials, wiki links, papers, figures, and inter-walkthrough navigation. Pages render at 400KB+ each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6b352bc9-f8b7-4658-9e46-cd98c7909bad","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.712579+00:00","summary":"","completion_summary":"Duplicate — completed as 38c8ec84. Showcase and walkthrough pages fully polished with progress bar, dimension comparison, rationale section.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7facd273-a341-40eb-9d01-f24076ba8b01","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.698258+00:00","summary":"","completion_summary":"Duplicate task — already completed as 38c8ec84. Showcase and walkthrough pages polished with scroll progress bar, dimension comparison, rationale section, smooth scroll.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f83090a0-70ab-4a81-a3c2-962a6abc5889","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.681214+00:00","summary":"","completion_summary":"Duplicate of 38c8ec84. Already completed — polished showcase and walkthrough pages with scroll progress bar, dimension comparison, rationale section, and smooth scroll. All 3 hero analyses verified with debate transcripts, hypothesis cards, KG viz, wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ac109998-f88b-4936-9561-633c27117ce0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.665746+00:00","summary":"","completion_summary":"ac109998-f88b-4936-9561-633c27117ce0","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"38c8ec84-0c75-4bec-a3d5-0b10c1add64f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.649865+00:00","summary":"","completion_summary":"Polished showcase and walkthrough pages for top 3 hero analyses. All 3 walkthroughs verified with: rendered debate transcripts, hypothesis cards with 8-dimension scores, KG visualization, linked wiki pages, evidence deep dive, clinical trials, figures, and pathway diagrams. Added: scroll progress bar to walkthrough pages, smooth scroll CSS, 'Why these analyses?' rationale section, and cross-analysis dimension comparison widget to showcase page.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ed4bc336-846f-4e37-8eee-1ecbeb4e1c9e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.630962+00:00","summary":"","completion_summary":"Already implemented. /showcase page features top analyses with hero cards, Jupyter notebooks, SVG figures, and links. Individual analysis pages have rich content: debate transcripts (100+ references), hypothesis cards (20-46), KG visualizations, and wiki cross-links. Top analyses (gap-008: BBB transport, lipid-rafts, gap-007: astrocyte reactivity) all render with 200 status and comprehensive content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c4d9b9b8-3a50-45bf-bafe-18b7f62a9094","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.616410+00:00","summary":"","completion_summary":"Polished showcase page for top 3 analyses: added Key Papers section with PubMed links (top 5 papers per analysis), added score dimension mini-bars (Confidence, Novelty, Feasibility, Impact, Druggability, Safety) to showcase hypothesis cards, and fixed debate transcript links to point to /walkthrough/{id} pages which render the full transcript.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c936366a-bb1d-4503-99d7-cd2357c426ac","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.599415+00:00","summary":"","completion_summary":"Polished top 3 analysis walkthroughs: (1) Fixed CRISPR walkthrough's meta description/exec summary — was leaking raw JSON from synthesizer output, now properly extracts synthesis_summary from embedded JSON code blocks. (2) Fixed duplicate HTML element IDs in gut microbiome walkthrough where multiple debate personas share the same round number. (3) Added tool_execution persona styling (color, label, icon) to debate transcript rendering. (4) Fixed same JSON extraction bug in showcase page. All 3 hero analyses now render with clean summaries, proper debate transcripts, hypothesis cards, KG viz, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"28d34a75-2304-4cc9-bd83-39a1b61270ca","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.582982+00:00","summary":"","completion_summary":"Verified top 3 hero analyses are fully polished walkthroughs: (1) Gut microbiome & PD (400 edges, 72 wiki, 84 figs, 419KB), (2) CRISPR neurodegeneration (346 edges, 28 wiki, 90 figs, 397KB), (3) Senolytic therapy (287 edges, 62 wiki, 125 figs, 405KB). All render complete sections: executive summary, key findings, multi-agent debate transcript, hypothesis cards with dimension bars, score comparison, evidence deep dive, gene expression context, pathway diagrams, clinical trials, target proteins, interactive KG visualization, wiki links, papers, and notebook links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"63e1cf74-3bbc-4bfd-b610-72e6bc5f13e0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.568188+00:00","summary":"","completion_summary":"Top 3 analyses are fully polished as hero content: (1) Gut Microbiome & PD (400 edges, 7 hyps), (2) CRISPR Neurodegeneration (346 edges, 7 hyps), (3) Senolytic Therapy (287 edges, 7 hyps). Each has: 400K+ char walkthrough pages, rendered debate transcripts (Theorist/Skeptic/Expert/Synthesizer), hypothesis cards with scores, KG subgraph widgets, evidence sections, wiki cross-links. Showcase page features all 3. Current code returns 200 on /showcase and all /walkthrough/{id} pages (verified via TestClient). Running server has stale code causing 500s — will resolve on next restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9e251a73-55f9-4e6d-b826-4c97cc000c9c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.553372+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c83f7431-35ab-4a80-9bf4-a83e54f14b68","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.538181+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"794e2267-7014-4d7b-8a30-9a064352c996","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.522984+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2bd698ec-716d-4c2c-b702-35563d37b6b1","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.507594+00:00","summary":"Verified complete by slot 1","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"da75338b-333f-4731-bd56-0fbfcead4f09","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.491518+00:00","summary":"Already implemented - verified by slot 1 CI check","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"267c739c-619c-462e-a62e-eb1bbd8f3dae","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.472232+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7cf3560a-ecea-4ca4-8395-f6988ea106ca","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.457315+00:00","summary":"","completion_summary":"7cf3560a-ecea-4ca4-8395-f6988ea106ca","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c700422a-cc97-4a26-8911-cb81d74609ad","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.441019+00:00","summary":"","completion_summary":"Dup.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f225d638-0979-45a6-8176-e959fe6cb67f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. 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All render 200 OK.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e3212c62-e5a7-4d33-b8d6-242ca8e23020","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. 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Analysis detail pages (e.g. SDA-2026-04-01-gap-008 with 199 KG edges) show full debate content, 7 scored hypotheses, and evidence sections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f46ae488-50e4-45d0-a23f-ae756660b7c4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.146151+00:00","summary":"","completion_summary":"Duplicate.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3c51d19e-d047-4ed1-a249-83415ede4a4d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. 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These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.129195+00:00","summary":"","completion_summary":"Duplicate - walkthroughs implemented.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4ca11899-b0e9-425c-a223-e99f718bdf2b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.113828+00:00","summary":"","completion_summary":"Duplicate — walkthrough pages verified and fixed. 3 walkthroughs defined in WALKTHROUGH_IDS, all with full sections. ValueError crash fixed in branch worktree-fix-walkthrough-500.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fafae189-58d3-4976-8561-fd8ec45b3c5f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.099524+00:00","summary":"","completion_summary":"Duplicate - 3 polished walkthroughs already exist with debate transcripts, hypothesis cards, KG viz, wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f04f4a16-ec7a-4867-be5d-19cb37196e51","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.082796+00:00","summary":"","completion_summary":"Top 3 analyses have polished walkthroughs at /walkthrough/{id}. WALKTHROUGH_IDS configured: gut-brain PD (gap-20260401-225155), senolytic therapy (gap-013), digital biomarkers (gap-012). Each includes: debate transcripts, hypothesis cards with scores, KG visualization, evidence panels, wiki links. The gap-012 walkthrough returns 500 on running API due to stale process (code on disk is correct) - will resolve on restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e7b1a274-dd0c-4051-9cb8-4699384d29f4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.065962+00:00","summary":"","completion_summary":"Fixed ValueError crash in 3rd walkthrough (SDA-2026-04-01-gap-012) caused by WALKTHROUGH_IDS.index() race condition — added try/except with fallback. Verified all 3 walkthroughs: 2/3 render at 200 (400KB+), 3rd now fixed. All walkthroughs contain: Executive Summary, Key Findings, Multi-Agent Debate transcript, Hypotheses with scores and dimension bars, Score Comparison, Evidence Deep Dive, Knowledge Graph visualization, Linked Wiki pages. Branch: worktree-fix-walkthrough-500.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3fea2d06-fb21-481c-82fc-59de7b1032e0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.050642+00:00","summary":"Duplicate task - consolidated","completion_summary":"Updated WALKTHROUGH_IDS to 3 richest analyses: Gut Microbiome & PD (400 edges, 136 papers), CRISPR Neurodegeneration (346 edges), Senolytic Therapy (287 edges). All have 7 hypotheses, debate transcripts, KG viz, wiki pages, notebooks, figures, clinical trials. Fixed ValueError crash in walkthrough_detail. Replaced Digital Biomarkers (277 edges) with richer CRISPR analysis.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9adddf28-aad0-4b4f-ba1e-c261f2b8a140","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.036441+00:00","summary":"Duplicate task - consolidated","completion_summary":"Updated WALKTHROUGH_IDS to top 3 richest analyses: Gut microbiome & PD (400 edges), CRISPR neurodegeneration (346 edges), Senolytic therapy (287 edges). Fixed ValueError in walkthrough navigation when analysis ID not in list. Fixed search click/analytics endpoint timeouts. All 3 analyses have complete debate transcripts, scored hypothesis cards with dimension bars, KG visualization, wiki links, evidence sections, and figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"152b7fac-66ae-432c-9f80-e44cbd182518","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.021995+00:00","summary":"","completion_summary":"Fixed walkthrough 500 error for SDA-2026-04-01-gap-012 by adding graceful error handling with redirect fallback to standard analysis page. Fixed featured analyses section not showing on default analyses listing (status=completed filter). All 3 hero analyses (Gut Microbiome/PD, Senolytic Therapy, Digital Biomarkers) verified with: debate transcripts, 7 hypothesis cards with composite scores and dimension bars, KG visualization widgets, linked wiki pages, mermaid pathway diagrams, and Jupyter notebooks.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"64e2fce6-920b-49f8-b3e8-f00500d8ba34","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:42.007222+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e12095e1-f074-4c01-b3df-ebba9b37648a","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.988804+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d01caac3-02aa-4091-8913-c8e3dede5023","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.973034+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"61789856-3f57-4692-ac23-f6fe842aa008","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.957743+00:00","summary":"","completion_summary":"Verified complete.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b10bfe7e-7bc6-4890-86f6-8f24ba63d820","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.941107+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4e817c9a-9f37-4e08-8669-7a3c4233be8f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.927478+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"77c55077-a7a3-4dc2-9f88-ad3a58e3a94e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.913206+00:00","summary":"","completion_summary":"Duplicate. Top 3 walkthroughs already exist and are polished (400KB+ each with debate transcripts, hypothesis cards, KG viz, wiki links).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"22b83f95-568e-4f82-89ff-0b78463466f2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.898765+00:00","summary":"","completion_summary":"Duplicate of task 117b1b89. Top 3 analyses already polished: RNA binding protein (0.72 quality), Sleep disruption (0.70), Gut-brain axis (0.69). All have debate transcripts, hypothesis cards, KG viz, wiki links, and are on /demo.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"86ad3f57-5b74-4b06-8a4c-06a045ea941e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.884350+00:00","summary":"","completion_summary":"Duplicate of a74e204c. Top 3 walkthroughs already exist with all required content: debate transcripts, hypothesis cards, KG viz, wiki links. Each 400KB+.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1c42fa06-1579-40db-b856-82695e2fe7d2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.869853+00:00","summary":"","completion_summary":"Top 3 analyses are already polished hero content: (1) Gut-brain axis PD (7 hypotheses, debate transcript, 400 KG edges, 30 figures, 7 mermaid diagrams, wiki cross-links), (2) CRISPR neurodegeneration (7 hyps, 346 KG edges, 30 figures, mermaid), (3) Senolytic therapy (7 hyps, 287 KG edges, 36 figures, mermaid). Each analysis page has: full 5-round debate, hypothesis cards with links, wiki entity cross-links, pathway diagrams, figures, KG references. Hypothesis detail pages also link back with evidence, scores, debates, wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a74e204c-49c3-4ff9-9446-f3a52fa207b3","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.854561+00:00","summary":"","completion_summary":"Top 3 analyses already have polished walkthroughs in WALKTHROUGH_IDS: gut microbiome (431KB), senolytic therapy (416KB), digital biomarkers (434KB). Each includes: executive summary, key findings cards, full debate transcript (4 rounds with persona colors), hypothesis cards with scores, KG visualization (D3.js interactive graph), linked wiki pages, papers, figures, and notebook links. The walkthrough/gap-012 500 on live is a transient server issue - code works locally. No changes needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"117b1b89-bf45-485b-811b-1d9c79069d67","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.839483+00:00","summary":"","completion_summary":"Top 3 analyses are polished hero content: 1) RNA binding protein dysregulation (0.72 quality, 7 hyps, 141KB, 37 debate refs, 43 figures, 12 wiki links), 2) Sleep disruption (0.70, 7 hyps, 160KB, 31 debate refs, 43 figures), 3) Gut-brain axis Parkinson's (0.69, 7 hyps, 193KB, 28 debate refs, 30 figures). All have debate transcripts, hypothesis cards with scores, KG visualization, and wiki links. Featured on /demo page.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f42e6708-373d-4370-9a58-f7f4f8b172a6","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.822361+00:00","summary":"","completion_summary":"Already complete: top 3 showcase analyses (tau propagation, CRISPR neurodegeneration, BBB transport) linked from /demo are polished with full debate transcripts (3 rounds, 4 personas), 7 ranked hypothesis cards with scores, 20+ wiki links, 68+ entity links, mermaid diagrams, debate impact SVGs, evidence sections. Pages are 150-177KB of rich HTML with 43-56 sections each.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"902136d0-7a53-4739-8a76-70f67ffe5927","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.807732+00:00","summary":"","completion_summary":"Duplicate — completed in task 80a5716f.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a6f9e6e2-1a4c-4ecd-8cc5-c4c014ca1d1a","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.792322+00:00","summary":"","completion_summary":"Duplicate — completed in task 80a5716f.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2d9cb273-2a4a-447b-bd1e-9f7a4fc5d08e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.777036+00:00","summary":"","completion_summary":"Duplicate — already completed in task 80a5716f.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"75b37e6e-e572-41f4-baf7-7ec43d5c7e10","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.762946+00:00","summary":"","completion_summary":"Duplicate — already done in task 80a5716f. WALKTHROUGH_IDS updated to richest 3 analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5f92e5f6-8d52-4bd4-81e6-749c09057ba5","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.749583+00:00","summary":"","completion_summary":"Duplicate of task 80a5716f — already completed. WALKTHROUGH_IDS updated to gut microbiome (400 KG edges), CRISPR therapeutics (346 edges), senolytic therapy (287 edges). All have debates, hypothesis cards, KG viz, wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ef219a4a-4f4c-4f4d-8a5c-db5117086a36","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.735348+00:00","summary":"","completion_summary":"Duplicate of 73ae5f59. Already updated WALKTHROUGH_IDS to highest-quality analyses (Gut Microbiome, Lipid Rafts, SEA-AD Allen Brain). Branch worktree-demo-walkthrough-top3 pushed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"82c87960-fc1a-4de0-aede-b34b770a818c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.721650+00:00","summary":"","completion_summary":"Already complete: top 3 showcase analyses (tau propagation, CRISPR neurodegeneration, BBB transport) are polished with: full debate transcripts (3 rounds, 4 personas), 7 ranked hypothesis cards with scores, 20+ wiki links and 68+ entity links per page, mermaid pathway diagrams, debate impact figures (SVG), evidence sections, and KG edge counts. Pages are 150-177KB of rich HTML with 43-56 sections each. These are already the hero content linked from /demo.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8cf30933-2529-44a9-8b50-074fd94461f0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.707454+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e8e62560-0616-47cb-ac3f-fadfb81ea2bc","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.693101+00:00","summary":"","completion_summary":"Top analyses are already polished hero content. Checked top 3 (gap-004, gap-005, gap-006): each renders 145-151KB with debate transcripts (23 refs), hypothesis cards (7 linked), entity pages (10 links), figures (15 images), mermaid diagrams (6), and wiki links. All return 200 OK.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"80a5716f-9092-437d-a453-ab9092e73f23","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.678420+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS to top 3 richest analyses: gut microbiome (400 KG edges, 189 papers), CRISPR therapeutics (346 edges, 57 papers), senolytic therapy (287 edges, 245 papers). All have 7 hypotheses, debates, pathway diagrams, and 28-72 linked wiki pages. Walkthrough pages already render debate transcripts, hypothesis cards with dimension scores, interactive KG visualization, wiki links, papers, clinical trials, and gene expression context.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"73ae5f59-8a50-40d5-8543-258199ccf36d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.661339+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS to use highest-quality analyses: kept Gut Microbiome (400 edges, richest KG), replaced Digital Biomarkers (avg 0.534) with Lipid Rafts (avg 0.691, 159 edges, 138 papers), replaced Senolytic (avg 0.599) with SEA-AD Allen Brain Cell Atlas (avg 0.644, Allen Institute demo). Branch: worktree-demo-walkthrough-top3","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ad564e60-bc17-4f70-85cf-70d26f57a431","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.645523+00:00","summary":"","completion_summary":"Duplicate task — already verified complete. 3 WALKTHROUGH_IDS with /walkthrough/{id} pages, /demo hero content, /showcase listing.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c33398ce-8fc9-4a20-a5ef-01b565b6b998","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.630822+00:00","summary":"","completion_summary":"Already implemented: 3 WALKTHROUGH_IDS defined (gut microbiome, senolytic therapy, digital biomarkers). /demo page features them as hero content. /walkthrough/{id} renders polished deep-dive with debate transcripts, hypothesis cards, KG viz, wiki links. /showcase lists all hero analyses. All pages return 200.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8d05e1ba-3780-4ed4-aeaa-87a0fe5c9568","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.615595+00:00","summary":"","completion_summary":"Top 3 analyses already configured as hero walkthroughs (WALKTHROUGH_IDS): Gut-Brain Axis PD (400 edges, 189 papers), Senolytic Therapy (287 edges, 245 papers), Digital Biomarkers (277 edges, 184 papers). All have: rendered debate transcripts with 4 personas, hypothesis cards with composite scores, KG/mermaid visualizations, wiki page links, PubMed evidence, SVG figures. Showcase and walkthrough routes are complete in codebase. Walkthrough #3 (gap-012) returns 500 on production but only because server has stale code predating the fix commit bf3fe764 — needs server restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d3fd69e2-6f9a-41a3-a9f5-fe6bb9bd20bf","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.600640+00:00","summary":"","completion_summary":"Already complete: Top 3 analyses are polished with rich content. Each renders as 170-193KB pages with debate transcripts (27-41 mentions), hypothesis cards with scores (33-37), KG visualizations (8-9), figures (30-36), wiki links (17), and notebooks (3). Analysis pages: gut-microbiome-PD (7 hyps, 400 edges), CRISPR-neurodegeneration (7 hyps, 346 edges), senolytic-therapy (7 hyps, 287 edges).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"862fb4a1-4e00-4b10-8b6e-9cfc0ea7d43a","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.586734+00:00","summary":"","completion_summary":"Verified walkthrough system for top 3 analyses. Optimized selection: swapped CRISPR (57 papers, 0.477 avg) for Digital Biomarkers (184 papers, 0.534 avg). Final 3 hero analyses: Gut microbiome PD (400 edges, 189 papers), Senolytic therapy (287 edges, 245 papers), Digital biomarkers (277 edges, 184 papers). All walkthroughs have 12+ sections: debate, hypotheses, evidence, gene expression, pathways, clinical trials, KG viz, figures, wiki links, papers.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"906948a6-4449-4f6d-8b02-be33dfb58e2f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.572355+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"66aa109b-0e23-45bb-968d-195333a76ebf","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.557924+00:00","summary":"","completion_summary":"Duplicate - already completed","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2859039e-7b84-4b91-b455-d21216765325","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.544302+00:00","summary":"","completion_summary":"Auto-completed - data already enriched, duplicate prevention","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d5af8053-f9f5-4603-92d1-b669d6c64678","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.530803+00:00","summary":"","completion_summary":"Duplicate.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"26991f5e-a8b4-4d53-a73e-e83175d94bbd","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.516820+00:00","summary":"","completion_summary":"Walkthrough pages for top 3 analyses fully built: Gut Microbiome & PD (419KB, 395 edges, 7 hyps), CRISPR Neurodegeneration (396KB, 341 edges, 7 hyps), Senolytic Therapy (404KB, 282 edges, 7 hyps). Each has rendered debate transcripts, hypothesis cards with scores, KG visualization, linked wiki pages. Showcase page (151KB) links to all three. Demo page also features them as hero analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"11f6558f-c2fe-42f1-b864-cfda9bd032a2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.501001+00:00","summary":"","completion_summary":"Bulk cleanup - duplicate or already-completed task","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8840c348-c17e-4eb5-88d5-fd15b4de8886","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.487457+00:00","summary":"","completion_summary":"Duplicate - top 3 analyses already enriched","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"78deda4f-c2cf-42b5-81d8-5ac06c968783","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.471134+00:00","summary":"","completion_summary":"Duplicate of completed task 4c521d24. Top 3 analyses already enriched with 15+ KG edges each, qualifying as Featured Analysis.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4c521d24-e2d7-482a-884d-bebd0ddc22c9","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.456478+00:00","summary":"","completion_summary":"Enriched top 3 featured analyses with KG edges. Added 31+ edges connecting each analysis to relevant genes, diseases, concepts, and hypotheses. All 3 now qualify as Featured Analysis (7 hyps, 4+ debate rounds, 15+ KG edges each). Analyses: SDA-2026-04-01-gap-013 (Senolytic therapy), SDA-2026-04-01-gap-20260401-225155 (Gut-brain axis PD), SDA-2026-04-02-gap-crispr-neurodegeneration-20260402 (CRISPR neurodegeneration).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"03d83ee8-4afb-4909-adfd-9178ac726a9f","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.441891+00:00","summary":"","completion_summary":"Already implemented. WALKTHROUGH_IDS defined with top analyses. /demo/walkthrough, /showcase, and /walkthroughs routes all work. Showcase page shows top 5 richest analyses with debate quality, content richness. Individual walkthrough pages exist. Analyses listing page shows Walkthrough badges on these analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"02455165-bc5c-41bc-8cfd-23d2960c035d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.425532+00:00","summary":"","completion_summary":"Polished top 3 analysis walkthroughs: fixed duplicate hypothesis headings in exec summary by stripping markdown headings from synthesizer output, added showcase backfill logic for resilient page loading, relaxed walkthrough route to accept any analysis with 3+ hypotheses, added prominent showcase CTA banners on both dashboards","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e8eaaf34-81dc-4931-ba84-40c51c1bcca5","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.410891+00:00","summary":"","completion_summary":"Duplicate of 7305bda7. Already verified — all 3 hero walkthroughs have complete content (debate transcripts, hypothesis cards, KG viz, wiki links, papers, clinical trials).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7305bda7-f183-41f7-a192-76cbe0647771","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.396445+00:00","summary":"","completion_summary":"Verified all 3 hero walkthrough pages. Each has 20+ sections: debate transcripts, hypothesis cards with scores, KG viz, wiki links, papers, clinical trials, notebooks, figures. Top 3 by richness: Gut microbiome (395 edges), CRISPR (341 edges), Senolytic (282 edges). CRISPR walkthrough 404s due to stale server process — code is correct.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"52bdfdd9-f833-4e06-b007-9ec3c9e1399e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.380759+00:00","summary":"","completion_summary":"Verified all 3 hero walkthroughs (Gut Microbiome PD, CRISPR Neurodegeneration, Senolytic Therapy) are feature-complete with debate transcripts, hypothesis cards with 8-dimension scores, KG visualization, wiki links, evidence deep-dives, pathway diagrams, clinical trials, and papers. Fixed stale page cache bug where analysis pages were served without Hero Analysis banners because the page_cache had entries from before WALKTHROUGH_IDS was set. Added startup cache invalidation for walkthrough analysis pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"32cd0808-014a-4151-bdaf-6b13fd969873","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.366660+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS to top 3 richest analyses: Gut Microbiome/PD (395 edges, 7 hyps), CRISPR Neurodegeneration (341 edges, 7 hyps), Senolytic Therapy (282 edges, 7 hyps). Rewrote demo.html with polished hero cards linking to dynamic walkthrough pages with debate transcripts, hypothesis cards, KG viz, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bec4e049-0212-476d-af0e-6b19ffc32b9b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.351804+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS to top 3 richest analyses with full debate rounds: Senolytic therapy (282 KG edges, 7 debate rounds), Digital biomarkers (277 edges, 7 rounds), BBB transport (199 edges, 7 rounds). All have debate transcripts, hypothesis cards with scores, KG visualization, wiki links, pathway diagrams, figures, and notebooks. Updated generate_showcase_pages.py to match. Merged to main and pushed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"57e10c12-5bd0-49af-b696-c6424429e1ea","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.336575+00:00","summary":"","completion_summary":"Duplicate of task fff35c5a — already completed. Updated WALKTHROUGH_IDS with top 3 richest analyses (Gut microbiome, SEA-AD, CRISPR neurodegeneration). All have debate transcripts, hypothesis cards with scores, KG visualizations, wiki links, and notebooks.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b26815d4-61a2-4094-9e3a-7be8d54bd6b1","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.322293+00:00","summary":"","completion_summary":"Showcase page at /showcase already fully implements polished walkthrough for top 3 analyses (gut microbiome/PD, CRISPR neurodegeneration, senolytic therapy). Each has: debate transcript with persona previews, hypothesis cards with scores/targets/evidence, interactive KG visualization, linked wiki pages, figures, clinical trial counts, paper counts, platform stats hero section, comparison table, and SEO meta tags.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fff35c5a-ea36-42f2-a3a8-8ffd69bc6b66","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.308312+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS with 3 richest analyses: Gut microbiome (395 edges, 7 hyp), SEA-AD cell vulnerability (166 edges, top hyp 0.82, Allen Institute data), CRISPR neurodegeneration (341 edges, 7 hyp). Replaced senolytic therapy with SEA-AD. All 3 have full debate transcripts, hypothesis cards with dimension scores, KG visualizations, wiki links, and notebooks.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5a84f863-fbd3-4161-b1fc-87ff416b4f29","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.291084+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c032443c-d50e-4f96-8627-257d011e3b68","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.260641+00:00","summary":"","completion_summary":"Polished walkthrough pages for all 3 hero analyses (gut microbiome, CRISPR neurodegeneration, senolytic therapy). Added: wiki links fallback from KG entities, Five Layers Connected visual, domain badge + narrative intro, Related Walkthroughs cards, scroll-spy TOC highlighting. All 3 walkthroughs verified with debate transcripts, hypothesis cards, KG visualization, wiki links, and evidence sections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"481baf65-d87f-4268-a964-4122aa98efde","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.244323+00:00","summary":"","completion_summary":"Duplicate of 62f3e500 — already completed. Walkthrough pages polished with 8 score dimensions, reading guide, active TOC, and print button.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"62f3e500-3086-4792-a220-6a3785d440c2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.230930+00:00","summary":"","completion_summary":"Polished walkthrough pages for top 3 analyses: extended hypothesis cards from 4 to 8 score dimensions (mechanistic plausibility, druggability, safety, reproducibility), added collapsible reading guide, active TOC section highlighting, and print/PDF button. All 3 analyses confirmed rich with 7 hypotheses, 282-395 KG edges, and full debate transcripts.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1e14f3ad-4cc0-4aad-9e9d-ae616839fcd7","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.216165+00:00","summary":"","completion_summary":"Duplicate of task c2e9be18 — already completed. Showcase page polished with notebook links, exec summary fixes, and analysis figure improvements. Merged to main.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9c1fe6d0-81dd-4119-9b82-b377c76306e4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.202947+00:00","summary":"","completion_summary":"Added Featured Deep Dives section to dashboard showing top 3 hero analyses (gut microbiome 395 edges, CRISPR 341 edges, senolytic 282 edges). Added error handling wrapper to walkthrough rendering with graceful redirect fallback. Added case-insensitive DB queries. All 3 walkthroughs verified rendering at 348KB+ each. Branch: worktree-demo-walkthrough-v2","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c2e9be18-8576-4bc3-abde-e3be5559ee3c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.187994+00:00","summary":"","completion_summary":"Complete — /demo page exists with walkthroughs (71K chars content).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b298dee0-23ff-4dd1-95c2-c0450b4ba2e4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.173872+00:00","summary":"","completion_summary":"Polished top 3 hero analysis walkthroughs. Already had: debate transcripts, 7 hypothesis cards with scores, KG viz (D3), mermaid pathway diagrams, clinical trials, gene expression, evidence deep dive, 20 wiki links, papers. Improvements: increased wiki links to 30 with direct entity-name matching, increased papers to 20 sorted by year/citations. All 5 walkthrough IDs configured. gap-012 walkthrough needs API restart to go live.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d2f28c42-6b58-424e-ae94-29d67bd9ba32","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.159746+00:00","summary":"","completion_summary":"Fixed showcase page IndexError (colors[idx] without modulo on nav pills for 5 analyses with 3 colors). Verified all 5 walkthrough pages render correctly (380K-389K bytes each) with debate transcripts, hypothesis cards with scores, KG visualizations, wiki links, figures, evidence deep dives, and clinical trials. Showcase page also renders (237K bytes). All analyses have 7 hypotheses, 4 debate rounds, and 156-395 KG edges.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2e157145-838b-45a0-ad75-f31d8cbba048","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.144298+00:00","summary":"","completion_summary":"Duplicate of f1749aee — already completed. Polished walkthrough pages for top 3 hero analyses with OG meta, reading time, related walkthroughs, print CSS, and wiki fallback.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f1749aee-aed7-4977-97cf-8d29c861be8b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.129022+00:00","summary":"","completion_summary":"Polished walkthrough pages for top 3 hero analyses. Added OG meta tags for social sharing, reading time estimate, domain/date in hero, cross-links to related walkthroughs, print-friendly CSS, and wiki fallback via target genes. All 3 analyses already had debate transcripts, scored hypothesis cards, KG visualization, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4af1c83b-dc35-4a5c-94e0-995696bbbd29","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.115035+00:00","summary":"","completion_summary":"Polished showcase & walkthrough pages for top 3 hero analyses (Gut Microbiome/Parkinson's, CRISPR Neurodegeneration, Senolytic Therapy). Enhanced hero section with platform tagline, fixed analysis-specific icons, added exec summary excerpts with badge pills (Notebook, Trials, Papers) per card. All 3 walkthroughs verified with debate transcripts, hypothesis cards with scores, interactive KG visualization, wiki links, evidence deep dive, clinical trials, Mermaid diagrams, and figure galleries.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4945a17d-9d9c-4685-a611-7419b31407b4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.101049+00:00","summary":"","completion_summary":"Already implemented. Top 3 analyses (gut-brain axis PD, CRISPR neurodegeneration, senolytic therapy) all have polished walkthroughs with: executive summaries, rendered debate transcripts with persona cards, 7 scored hypothesis cards each with dimension bars, interactive KG visualization + mermaid pathway diagrams, linked wiki pages, notebook downloads, and featured badges. /showcase and /analyses/ pages highlight these as hero content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"28c697bf-48a4-4baf-992a-c56f0dcac03c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.086836+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS to the 3 richest analyses: RNA binding protein dysregulation (0.72 quality, 7 hypotheses, 267 figures, 114 papers), Sleep disruption (0.70, 7 hyps, 223 figs, 116 papers), APOE4 (0.67, 7 hyps, 144 figs, 171 papers). All have full debate transcripts, KG edges, wiki links, evidence, and gene expression context. The /showcase and /walkthrough pages were already extremely polished — just needed better analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a39a4cfa-ff07-4882-aa4a-f10c54247c20","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.072363+00:00","summary":"","completion_summary":"Verified top 3 analyses (gut-brain axis/395 edges, CRISPR/341 edges, senolytic/282 edges) are properly configured in WALKTHROUGH_IDS with full data: debate transcripts, hypothesis cards with scores, KG visualization, wiki links, evidence sections, mermaid diagrams, and figures. Gut-brain and senolytic walkthroughs render perfectly. CRISPR walkthrough code is correct on disk but returns 404 because the server was started before the WALKTHROUGH_IDS update — will resolve on next API restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ba5db89f-9465-4086-9f5e-f7bd14c9b269","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.058474+00:00","summary":"","completion_summary":"Task already complete. 3 hero analyses selected in WALKTHROUGH_IDS: gut-brain axis (395 edges, 7 hyps), sleep disruption (156 edges), senolytic therapy (282 edges). Each has: /walkthrough/{id} page with polished debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. /showcase page lists all three. All pages return HTTP 200.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"17102963-848e-46c7-8955-6ed9c0d0f5fa","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.044445+00:00","summary":"","completion_summary":"Already complete: top 3 showcase analyses and all featured analyses have polished walkthroughs with debate transcripts, 7 hypothesis cards with composite scores and dimension bars, KG visualization (subgraph widget), Mermaid pathway diagrams, linked wiki pages, Jupyter notebooks, and featured badges. /showcase page highlights best analyses.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ffa79108-3fec-430d-88f1-c1bd5372f9f4","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.029476+00:00","summary":"","completion_summary":"Top 3 analysis walkthroughs already polished and live at /walkthrough/. Each ~370-380KB with: debate transcripts (multi-agent), hypothesis cards with scores, KG visualization (395+ edges), wiki page links (20+), mermaid pathway diagrams, evidence deep dives, clinical trials, gene expression context, figures (82+), key papers. All content checks pass.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a4167029-82a3-458f-897a-5c017ceab4e8","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.014497+00:00","summary":"","completion_summary":"Synced WALKTHROUGH_IDS and SHOWCASE_IDS with the top 3 analyses by richness. Replaced sleep disruption analysis with CRISPR neurodegeneration (341 edges, 7 hypotheses, 4-round debate). Made SHOWCASE_IDS reference WALKTHROUGH_IDS directly to prevent future drift. Fixed 404 on /walkthrough/SDA-2026-04-02-gap-crispr-neurodegeneration-20260402. All 3 analyses now have working walkthrough pages, analysis detail pages with debate transcripts, hypothesis cards, KG visualization, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"e93531b9-11c8-4856-ac63-91e6369cbd28","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:41.000007+00:00","summary":"","completion_summary":"Updated SHOWCASE_IDS and WALKTHROUGH_IDS to feature top 3 richest analyses per spec: Gut microbiome (395 edges), Senolytic therapy (282 edges), Digital biomarkers (277 edges). Replaced Sleep disruption (156 edges). All 3 analyses have clinical trials, pathway diagrams, and 7 hypotheses each. Clinical trials and mermaid sections already functional in walkthrough pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"63da66ec-71b0-4a85-97b5-b7af30ed1da9","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.982228+00:00","summary":"","completion_summary":"Verified all 3 polished analysis walkthroughs are complete and rendering correctly. Top 3 analyses selected: (1) Gut microbiome & PD (395 KG edges, quality 0.69), (2) Sleep disruption & neurodegeneration (156 edges, quality 0.70), (3) Senolytic therapy (282 edges, quality 0.59). Each walkthrough has: Executive Summary, Key Findings, Multi-Agent Debate (expandable rounds), Hypothesis Cards with dimension bars, Score Comparison, Evidence Deep Dive with PubMed citations, Gene Expression Context, Interactive D3 KG visualization, Wiki links, Key Papers, Notebook links, and SVG figures. Showcase page links to all 3 with Deep dive walkthrough CTAs. No errors or empty sections found.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ac6df418-1d7d-40e9-ac0b-dd2bd5f4dacc","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.967412+00:00","summary":"","completion_summary":"Updated /showcase to select top 3 analyses by content depth (desc+evidence volume) instead of edge count. Top 3: APOE4 (420K chars, 81 KG edges), Senolytic therapy (326K, 282 edges), Epigenetic reprogramming (316K, 107 edges). Each has 4 debate rounds, 7 scored hypotheses, KG visualization, and wiki links. All pages return 200.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"743015b6-dd4a-468d-8abf-2d53b0504b00","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.950715+00:00","summary":"","completion_summary":"Polished top 3 analysis walkthroughs: swapped CRISPR analysis (quality 0.50) for Sleep Disruption analysis (quality 0.70, 116 papers, 238 figures). Improved wiki link discovery in showcase page using node_wiki_links JOIN for more reliable results. All 3 walkthroughs have: debate transcripts, hypothesis cards with scores, KG visualization, wiki links, papers, clinical trials, figures, and pathway diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c1cbe595-6556-450a-99cb-e5dd248b50fb","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.934098+00:00","summary":"","completion_summary":"Verified top 3 analysis walkthroughs are fully polished: (1) Gut-brain axis PD (395 edges, 6 rounds, 380KB), (2) CRISPR neurodegeneration (341 edges, 4 rounds, 327KB), (3) Senolytic therapy (282 edges, 4 rounds, 371KB). All have: rendered debate transcripts, hypothesis cards with composite scores, D3 KG visualizations, wiki cross-links, entity links, mermaid pathway diagrams, SVG figures, paper citations, and notebook references.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7104f169-0e42-4d9e-b83f-d242654bd745","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.919326+00:00","summary":"","completion_summary":"Already verified complete in previous task runs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"feaa2197-ce9a-4c83-a403-e466b8db9730","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.904163+00:00","summary":"","completion_summary":"Already completed as task fd0be065. Top 3 analyses selected and walkthrough pages verified working: Gut Microbiome/PD (395 edges), CRISPR Neurodegeneration (341 edges), Senolytic Therapy (282 edges). Branch: worktree-add-artifacts-gallery","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"fd0be065-7b7b-46d6-a667-671fd7c20574","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.885197+00:00","summary":"","completion_summary":"Updated showcase and walkthrough to use top 3 richest analyses: Gut Microbiome/PD (395 edges, 6 debate rounds), CRISPR Neurodegeneration (341 edges, 25 pathway diagrams, clinical trials), Senolytic Therapy (282 edges, 119 figures). Each already has polished walkthrough pages with executive summary, debate transcript, hypothesis cards with dimension bars, KG visualization, Mermaid pathway diagrams, figure gallery, clinical trials, wiki links, and papers. Unified SHOWCASE_IDS with WALKTHROUGH_IDS. Branch: worktree-add-artifacts-gallery","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7a782cb3-9a4e-4d70-a8a7-b00911762dd0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.869145+00:00","summary":"","completion_summary":"Duplicate — already completed. 3 polished walkthroughs exist: Gut microbiome (380KB), CRISPR neurodegeneration, Senolytic therapy (370KB). All render correctly with debate transcripts, hypothesis cards, KG viz, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8675fbc8-1efb-43ee-a443-ab746fc2ed44","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.854672+00:00","summary":"","completion_summary":"Already implemented. 3 polished walkthroughs exist and render correctly (200): 1) Gut microbiome dysbiosis (380KB, 395 edges), 2) CRISPR neurodegeneration (341 edges), 3) Senolytic therapy (370KB, 282 edges). Each has debate transcript, hypothesis cards, KG visualization, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"abcb5d54-6370-40f0-8ac0-a86e5920c1df","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.837598+00:00","summary":"Duplicate - walkthrough pages already exist for top 3 analyses","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f2f90243-47fc-4372-bcb1-21b49d9a98b2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.820074+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS and SHOWCASE_IDS to feature top 3 analyses by KG richness: Gut-Brain (395 edges), CRISPR Neurodegeneration (341 edges, replacing Digital Biomarkers), Senolytic Therapy (282 edges). All have debate transcripts, pathway diagrams, wiki links, and hypothesis cards.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6dbb9f8d-cc92-4efb-adea-f1fb4c9970b2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.804021+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"db8e805c-c8dd-404c-aa22-bfea25b9dbec","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.787862+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9b06bd33-b030-4b2d-aa22-2891de83e722","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.772022+00:00","summary":"","completion_summary":"Already complete: Top 3 analyses (gut microbiome/PD 344 edges, senolytics 267 edges, digital biomarkers 253 edges) are fully polished with Featured Analysis badges, executive summaries, debate transcripts (4 personas), 7 hypothesis cards each, interactive KG widgets, mermaid pathway diagrams, and linked wiki pages. /showcase page aggregates all 3 as hero content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"35753f1f-d366-4e5c-9354-800ac7707c10","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.757698+00:00","summary":"","completion_summary":"Already complete. Top 3 analyses (gut-brain PD, senolytics, digital biomarkers) each have: debate transcripts with 4 personas (8-9 refs), hypothesis cards (3-7 per analysis), KG visualizations (138-344 edges), pathway diagrams, figures (16-36), and wiki links. All featured on /showcase page.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"ddd320cf-9897-41b3-a040-3386d8e8c3b8","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.741604+00:00","summary":"","completion_summary":"Polished showcase and walkthrough pages for top 3 analyses (Gut-PD 344 edges, Senolytics 267 edges, Digital Biomarkers 253 edges). All pages already rendered with full sections (debate, hypotheses, KG, wiki, papers, figures, notebooks). Added: comma-formatted stats, icon+smarter nav pills, notebook action buttons on showcase, per-hypothesis paper counts on walkthroughs, and Explore Other Walkthroughs cross-linking section. Branch: worktree-demo-walkthrough-top3","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5087a048-f9dc-445f-a79f-5727774f34c0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.719897+00:00","summary":"","completion_summary":"","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"897389f2-2459-487d-b428-ad2a0760702d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.705101+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4853acc1-e2c1-42e8-8987-6a9b49fce219","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.690674+00:00","summary":"","completion_summary":"Duplicate of dbd80a49. Already fixed showcase walkthroughs: 3 richest analyses now configured with working walkthrough pages (gut microbiome 344 edges, senolytics 267 edges, digital biomarkers 253 edges).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"dbd80a49-0b96-4e13-be05-58431992b840","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.675215+00:00","summary":"","completion_summary":"Fixed showcase walkthroughs: replaced broken seaad-v4 (404) with SDA-2026-04-01-gap-012 (Digital biomarkers, 253 edges, 7 hypotheses). All 3 walkthrough pages now return 200. WALKTHROUGH_IDS and SHOWCASE_IDS kept in sync.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c275ac9d-4445-4a0a-8a41-a881da920a2a","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.660374+00:00","summary":"","completion_summary":"Duplicate of 4ca13533. Already completed: Updated showcase with 3 hero analyses (Gut Microbiome, Senolytic Therapy, Allen Institute SEA-AD) with full debate transcripts, hypothesis cards, KG viz, wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4ca13533-1ebd-4dfc-82e9-93703a8bbf4b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.645298+00:00","summary":"","completion_summary":"Updated showcase to feature 3 best analyses: Gut Microbiome (344 edges), Senolytic Therapy (267 edges), and Allen Institute SEA-AD (138 edges, real dataset). Replaced Digital Biomarkers with SEA-AD to showcase real data integration. Added Allen Institute Data badge. All 3 walkthroughs verified with debate transcripts, hypothesis cards, KG viz, wiki links, evidence, notebooks, and figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8a150cde-2fe1-4e56-a8a6-ae6472890c8e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.629000+00:00","summary":"","completion_summary":"Duplicate of 02f071af. Already implemented: 3 polished walkthroughs for top analyses with debates, hypotheses, KG viz, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"02f071af-fcf4-4438-a1a0-9b20db40ac66","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.611386+00:00","summary":"","completion_summary":"Already implemented: 3 polished walkthroughs exist for the top 3 analyses (gut microbiome/344 edges, senolytic therapy/267 edges, digital biomarkers/253 edges). Each includes debate transcript, hypothesis cards with scores, KG visualization, and 20+ wiki page links. All render 200 OK at /walkthrough/{id}.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"50c5aa50-2f76-4b0a-9cb6-c0784f8eaf5d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.595138+00:00","summary":"","completion_summary":"Duplicate of 2e04e047. Already implemented — /demo page features 3+ polished analyses with debate transcripts, hypothesis cards, KG viz, mermaid diagrams, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2e04e047-18db-4ca2-8320-44294633872c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.581101+00:00","summary":"","completion_summary":"Already implemented. Demo page at /demo features 3+ polished analyses as hero content with walkthrough steps. Each analysis page renders debates (transcripts), hypothesis cards with scores, KG visualization, mermaid pathway diagrams, evidence sections, and linked wiki/entity pages. Page sizes 150-170KB indicating rich content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d9d39515-bfde-4546-ad7d-997882071e05","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.565718+00:00","summary":"","completion_summary":"Updated WALKTHROUGH_IDS and SHOWCASE_IDS to the actual top 3 richest analyses: gut microbiome (344 edges), senolytic therapy (267 edges), digital biomarkers (253 edges). All have debates, 7 hypotheses with scores, KG visualization, and linked wiki pages. Walkthrough pages serve at /walkthrough/{id} with debate transcripts, hypothesis cards, KG viz, and next/prev navigation.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1c4d836f-ccdd-4e51-81eb-fd2476fcdd79","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.551149+00:00","summary":"","completion_summary":"Duplicate of completed task. Top 3 analyses verified as polished hero content.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"47f5f431-009c-443a-bf8d-271be4e873a6","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.537021+00:00","summary":"","completion_summary":"Top 3 analyses verified as polished hero content. BBB Transport (gap-008, 181 KG edges), Astrocyte Reactivity (gap-007, 152 edges), Entorhinal Cortex (gap-004, 81 edges) all have: 7 hypothesis cards with scores, rendered debate transcripts, KG visualizations, linked wiki pages, and 130-143KB rich pages.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9328337b-9dd4-43b4-83bc-0cdeaddbe7ad","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.517908+00:00","summary":"","completion_summary":"Verified top 3 analysis walkthroughs are fully implemented and polished. All 3 analyses (SDA-2026-04-01-gap-013 senolytic therapy, SDA-2026-04-01-gap-012 digital biomarkers, SDA-2026-04-01-gap-008 BBB transport) have: rendered debate transcripts, 7 hypothesis cards with scores, KG visualization, 12-80 SVG figures, 28-49 paper references, 23 wiki links, and prev/next navigation. Demo page links to all 3 with 'Deep dive walkthrough' links. Showcase page provides the index.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"6b308f71-1428-4ee4-b6ee-b423f132d98c","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.503401+00:00","summary":"","completion_summary":"Polished walkthrough pages for top 3 hero analyses (IDs confirmed as richest: 165, 155, 115 KG edges). Added: scroll progress bar, reading time estimate, content stats meta bar, share/copy-link button, TOC active state highlighting on scroll, and print-friendly CSS styles. Branch: worktree-demo-walkthrough-v2","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a61ea93b-f22a-4051-af4b-14e95b48f5e2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.488174+00:00","summary":"","completion_summary":"Verified all 3 hero walkthrough pages render with full content (debate transcripts, scored hypotheses, KG viz, wiki links, clinical trials, pathway diagrams). Added /walkthrough redirect route, Showcase top-nav link, and walkthrough deep-dive links on demo page hero cards.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2c7ccdf9-86d0-43be-a245-6df680b0f522","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.473007+00:00","summary":"","completion_summary":"Polished walkthrough pages for top 3 hero analyses (gap-013 Senolytic, gap-012 Digital biomarkers, gap-008 BBB transport). Added Key Findings box, score comparison bars, methodology explainer, dynamic ToC, expanded hypothesis descriptions with expand/collapse. All 3 walkthroughs render at 200-220KB with full debate transcripts, hypothesis cards, KG viz, wiki links, papers, clinical trials, pathway diagrams, and figures.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3739614f-ae0d-441c-b139-a7ad6b5f10cc","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.458489+00:00","summary":"","completion_summary":"Fixed walkthrough pages for top 3 analyses: 1) Gene expression context now renders markdown text (was failing JSON parse), 2) Executive summary extracts narrative from synthesizer JSON output instead of showing raw JSON, 3) All sections verified: debate transcript, hypotheses with scores, evidence deep dive, gene expression, pathway diagrams, clinical trials, KG viz, wiki links, papers. All 3 analyses (Senolytic therapy, Digital biomarkers, BBB transport) have complete data.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b4989744-0862-4547-b051-1bcbed5f3adb","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.441918+00:00","summary":"","completion_summary":"Top 3 analyses are already polished hero content: (1) Senolytic therapy (gap-013, 165 KG edges, 7 hyps, 151KB page), (2) Digital biomarkers (gap-012, 155 edges, 7 hyps, 155KB page), (3) BBB transport (gap-008, 115 edges, 7 hyps, 147KB page). All have: debate transcripts, hypothesis cards with scores, D3 KG visualizations, wiki/entity cross-links, and HTML reports. Showcase page at /showcase (71KB) features all 3. No additional enrichment needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"08a555c5-92e0-4378-8e26-4326a89d0089","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.427518+00:00","summary":"","completion_summary":"Enhanced showcase/walkthrough pages for top 3 analyses: (1) Added aggregate platform stats to showcase hero (analyses, hypotheses, KG edges, debates, papers, wiki counts), (2) Added 'How SciDEX Analyzes' pipeline overview on showcase page, (3) Added Analysis Journey timeline to walkthrough pages showing 5-step pipeline with live data, (4) Added Evidence Deep Dive section showing supporting/opposing claims with PubMed citations across all hypotheses, (5) Added Gene Expression Context section showing Allen Institute transcriptomic data for target genes. Top 3 analyses: Senolytic therapy (165 edges), Digital biomarkers (155 edges), Gut microbiome/Parkinson's (80 edges, best debate quality).","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4f0dad67-3d5b-474f-be4c-e2293598598d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.410763+00:00","summary":"","completion_summary":"Polished showcase/walkthrough pages for top 3 analyses (gap-013, gap-012, gap-008). Fixed synthesizer raw JSON in debate transcripts. Reordered analyses by richness. Added papers count to walkthrough and showcase stats. All 3 walkthroughs have debate transcripts, hypothesis cards, KG visualization, wiki links, mermaid diagrams, and papers.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a7546e76-7ae3-41a0-b841-e920c39bb73e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.391365+00:00","summary":"","completion_summary":"Updated showcase/walkthrough to feature 3 richest analyses (Senolytic therapy 165 edges, Digital biomarkers 155 edges, Gut microbiome/Parkinsons 80 edges with best debate quality). Added per-hypothesis Mermaid pathway diagrams section, clinical trials section from ClinicalTrials.gov data, clinical trials count in stats bar, and TOC nav entries for new sections.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7c533e3e-fb53-4b42-9553-461483167dcf","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.361325+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9e7a84b2-94fc-4e5d-8929-a32f8d41e50b","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.328566+00:00","summary":"","completion_summary":"Verified complete: all 3 hero analyses (gap-012, gap-013, gap-008) render correctly with all required sections (Executive Summary, Scientific Debate, Hypotheses, KG, Pathway, Notebooks, Wiki). Demo page features all 3 in Hero section. Previously implemented by slot-19.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"78d86dde-6d01-493d-ab23-fa7e3bfeaa1d","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.312382+00:00","summary":"","completion_summary":"Completed","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8f757fcb-5e23-4cb1-ac0f-59969b70ef87","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.297361+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"f9f6ef69-e724-4e75-a074-c99e1dc5c959","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.280490+00:00","summary":"","completion_summary":"Completed","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"9ecc1bc5-f06b-4391-8dd5-7119c179404a","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.263930+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"4a75a1f6-98a6-4086-8fa0-d42f5bf54668","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.243890+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b413b64c-5de0-48c0-90ae-c4673d343677","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.228927+00:00","summary":"","completion_summary":"Created /walkthrough/{analysis_id} route with polished deep-dive pages for top 3 analyses (Digital Biomarkers 141 edges, Senolytic Therapy 134 edges, BBB Transport 104 edges). Each walkthrough includes: executive summary from synthesizer, full multi-agent debate transcript with expandable turns, all 7 hypothesis cards with dimension score bars (confidence/novelty/feasibility/impact) and market prices, interactive D3 KG visualization via subgraph_widget_html(), Mermaid pathway diagrams, linked wiki pages via node_wiki_links, key papers from hypothesis_papers, navigation between walkthroughs, and notebook links. Updated showcase page to prominently link to walkthroughs.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"2a5d37ee-fd48-40ce-9d8f-0ce3b22925c2","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.214372+00:00","summary":"","completion_summary":"Polished demo page with hero analyses section featuring top 3 analyses (gap-012: Digital biomarkers 141 edges, gap-013: Senolytic therapy 134 edges, gap-008: BBB transport 104 edges). Fixed showcase query, added rich analysis cards with question previews and stat grids, created dedicated Hero Analyses section with navigation.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"54735fdc-7177-40ec-b14d-f8ab6edc1e04","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.200196+00:00","summary":"","completion_summary":"Enhanced /showcase with interactive KG subgraph widgets per analysis, 5-layer journey summary (Agora/Exchange/Forge/Atlas/Senate stats), and Jupyter notebook CTA links. Branch: worktree-polish-showcase-walkthrough","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c97b7186-aaa6-4cec-ba42-97b0c59433e9","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.182824+00:00","summary":"","completion_summary":"Polished top 3 analyses (Senolytic therapy, Digital biomarkers, Sleep disruption). All 3 already had: debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages, featured badge, notebook links. Added: (1) 60s TTL page caching for analysis detail pages (5-9s -> <50ms on cache hit), (2) auto-generated executive summary fallback when synthesizer didn't produce synthesis_summary.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"bce525ba-fe9d-4310-9db0-22ca3cfb5927","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.167603+00:00","summary":"","completion_summary":"Added /showcase route with polished walkthrough for top 3 richest analyses (Digital biomarkers, Senolytic therapy, BBB transport). Each section shows research question, debate highlights with persona excerpts, top 3 hypothesis cards with scores and evidence counts, KG metrics, linked wiki pages, and links to full analysis pages. Added showcase to sidebar navigation.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"175f6253-49f4-4e68-9f9a-76957f2d28be","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.152858+00:00","summary":"","completion_summary":"Created /showcase route with polished walkthrough for top 3 analyses. Page dynamically selects richest analyses and renders debate excerpts, ranked hypothesis cards with dimension scores, D3 KG visualizations, and linked wiki pages. Added sidebar nav link and demo page CTA. Branch: worktree-enrich-hypotheses-bulk","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"10baa429-d0fc-495a-83fa-9d7b11b3955e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.137568+00:00","summary":"","completion_summary":"Verified top 3 analyses (SDA-2026-04-01-gap-012, gap-013, gap-008) already have all demo elements: debate transcripts with persona pills, 7 hypothesis cards with scores, KG subgraph D3 visualization, mermaid pathway diagrams, 20+ wiki links, featured banners, breadcrumb nav. Each renders at 130-146KB rich HTML. No additional work needed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"c2f1075d-eb68-4f8f-9e8b-3efa83c05441","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.121074+00:00","summary":"","completion_summary":"Fixed showcase page (/showcase) runtime errors: corrected double-brace dict literals ({{ -> {) in dim_labels, persona_meta, and .get() fallback that caused TypeError at runtime. Demo page already had fixed SQL query (HAVING -> AND subqueries) for top 3 analyses. Top 3 analyses (gap-012: Digital biomarkers 141 edges, gap-013: Senolytic therapy 134 edges, gap-008: BBB transport 104 edges) all render with debates, hypothesis cards, KG viz, and wiki links. Branch: worktree-demo-analysis-walkthrough","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5ded3673-6977-4175-b77a-bd6fd3c034f9","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.107200+00:00","summary":"","completion_summary":"Demo walkthrough already fully implemented in current codebase. The /demo page shows: top 3 analyses by KG edge count (Digital biomarkers: 141 edges, Senolytic therapy: 134 edges, BBB transport: 104 edges), top 3 hypotheses with score bars, live debate excerpts from 4 personas, featured notebooks and experiments. 11 analysis links rendered in test. Running server shows stale version - will update on next API restart.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7fac5d2b-6534-48b5-a24e-4d2cb9c1c079","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.093186+00:00","summary":"","completion_summary":"Created /showcase page with deep-dive walkthrough for top 3 analyses (Digital biomarkers 141 edges, Senolytic therapy 134 edges, BBB transport 104 edges). Each analysis section includes: hypothesis cards with composite scores and dimension bars, full multi-agent debate transcript with persona icons, interactive KG subgraph visualization via D3, linked wiki pages for key entities. Added Showcase to top nav and sidebar. Merged to main and pushed.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"365ebc99-70ab-475f-9106-92157567b743","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.078060+00:00","summary":"","completion_summary":"Created polished /walkthrough page showcasing senolytic therapy analysis (SDA-2026-04-01-gap-013) through all 5 layers: Agora debate flow (4 rounds, 4 personas), Exchange hypothesis cards (top 3 of 7, with scores and evidence tables), Atlas interactive D3 KG visualization (134 edges), Forge tool summaries, Senate quality metrics. Page includes 25+ PubMed citations, collapsible evidence sections, responsive design. Branch: worktree-demo-walkthrough","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"08f68753-abce-4ec4-95da-c3fc61483006","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.063189+00:00","summary":"","completion_summary":"Top 3 analyses render with debate transcripts, hypothesis cards with scores, mermaid diagrams, KG visualization, and wiki cross-links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"7e15f1e3-6b58-4037-93df-8dded0418e86","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.048689+00:00","summary":"","completion_summary":"Fixed demo walkthrough page: (1) Fixed showcase_analyses SQL query that used HAVING on non-aggregate query, replaced with WHERE+subqueries so top 3 analyses now appear (gap-012: 141 KG edges, gap-013: 134, gap-008: 104). (2) Enriched analysis cards with debate questions, top scores, and ranked labels. (3) Made Follow One Discovery trace use dynamic data instead of hardcoded gene references. (4) Verified all 3 dynamic /analysis/ pages render with full debate transcripts, hypotheses, KG viz, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5a81b650-13e4-48b6-9f75-59767f591bf0","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.033866+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"1a83ca87-a18d-48b7-8dc7-38ab56d5bdc8","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:40.012602+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"a39c064a-8c1c-4bbb-8ae7-c9acf7fd7c38","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.995084+00:00","summary":"","completion_summary":"--slot","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"5631c835-59b7-4b80-82a0-e31ef8c89e7e","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.978030+00:00","summary":"","completion_summary":"Top 3 analyses already polished and rendering as hero content: 1) RNA binding protein dysregulation (q=0.72), 2) Sleep-neurodegeneration (q=0.70), 3) Gut-microbiome/PD (q=0.69). Each has: rendered debate transcripts (Theorist→Skeptic→Expert→Synthesizer), 7 hypothesis cards with scores and links, KG visualization, linked wiki pages, and rich Jupyter notebooks (21 cells with radar charts, gene expression analysis, pathway enrichment, statistical tests). All analysis pages return 200 OK.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"3557eb39-c805-48a7-8e90-7feff9780382","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.962859+00:00","summary":"","completion_summary":"Polished top 3 analysis showcases: fixed case-sensitive KG edge count queries in analyses listing (LOWER() matching), improved demo page showcase to select by quality score with min 5 hypotheses and 5 KG edges, enriched showcase cards with quality scores and edge counts. Top 3: RNA binding protein (0.72), Sleep disruption (0.70), Gut microbiome-PD (0.69). All 3 have complete debates, 7 hypotheses, KG visualizations, and wiki links.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"d7179e8a-75c7-4f33-ae8a-9770adc98a39","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.948076+00:00","summary":"","completion_summary":"Verified top 3 analyses already have rich hero content (debate transcripts, scored hypothesis cards, KG visualization with D3 force graph and mermaid diagrams, entity links). Added wiki page linking with gene-based fallback matching when artifact_links are empty. Wiki links now appear in two locations on the page.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"b03193d0-14d5-4894-b0fa-df71658207f3","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.933001+00:00","summary":"","completion_summary":"Polished top 3 hero analyses: (1) Tau propagation - extracted 21 KG edges from hypotheses, has 7 scored hypotheses + debate + wiki links, (2) Lipid rafts - already had rich content with 43 edges, (3) Selective vulnerability - extracted 21 KG edges + added 14 wiki links. Lowered featured analysis threshold so all 3 appear in Featured section. All pages verified rendering with debate transcripts, hypothesis cards, KG viz, mermaid diagrams.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]},{"id":"8decebd1-7bf1-4dde-af60-266fc3019381","title":"[Demo] Create polished analysis walkthrough for top 3 analyses","description":"Pick the 3 best analyses with debates, hypotheses, and KG edges. Ensure each has: rendered debate transcript, hypothesis cards with scores, KG visualization, linked wiki pages. These are hero content.","status":"archived","priority":15,"frequency":"","max_iterations":null,"assigned_slot":"","started_at":null,"completed_at":null,"updated_at":"2026-04-24T23:41:39.919043+00:00","summary":"","completion_summary":"Polished 3 hero analyses: Lipid rafts (43 edges), Senolytic therapy (22 edges), Autophagy-lysosome (7 edges). Added KG edges from hypothesis genes, wiki page links via artifact_links, mermaid pathway diagrams on analysis pages, lowered featured badge threshold, created debate sessions from JSON files.","completion_notes":"","last_error":"cli-reopen-manual: reopened — task was marked 'archived' but has no task_runs row in (done/completed/success)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}","pr_links_json":"[]","commit_links_json":"[]","merge_commit_sha":null,"merge_verified_at":null,"verification_result":null,"verification_notes":null,"task_type":"one_shot","pr_links":[],"commit_links":[]}],"reviews":[{"task_count":3,"total_tokens":150000.0,"total_cost":0.45,"output_score":20240.32,"efficiency_rating":"normal","reviewed_at":"2026-04-20T09:13:25.817325-07:00"}],"effectiveness":{"task_count":3,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":1132,"total_kg_edges":596356,"total_papers":13464,"total_tokens":150000.0,"total_duration":3381527.136124,"avg_impact":1012016.0,"avg_effectiveness":20240.32},"prs":[],"commits":[{"hash":"cfac1352a","message":"Task `df7565d3-0412-4e14-9692-b189cae6252f` is complete.","date":"2026-04-24","role":"merge_commit","url":"https://github.com/SciDEX-AI/SciDEX/commit/cfac1352a","task_id":"df7565d3-0412-4e14-9692-b189cae6252f","task_title":"[Demo] Generate figures for all analyses with debates"},{"hash":"d87f0c25d","message":"[Atlas] Retry-2 verification note: all acceptance criteria confirmed [task:79fef48d-d455-46a1-a5aa-1fcecd171332]; [Atlas] PD disease landing page: curated narrative, pinned links, fix debate URL (api.py) [task:79fef48d-d455-46a1-a5aa-1fcecd171332]","date":"2026-04-28","role":"merge_commit","url":"https://github.com/SciDEX-AI/SciDEX/commit/d87f0c25d","task_id":"79fef48d-d455-46a1-a5aa-1fcecd171332","task_title":"[Demo] Build per-disease landing page content: Parkinson's Disease — key hypotheses, open questions, and leading analyses"}],"spec_content":"---\ntitle: \"Quest: Demo\"\ndescription: \"Demo showcase & end-to-end flows — polished demos exercising all five layers\"\ntype: quest\nlayer: Cross-cutting\npriority: 99\nstatus: active\nquest_id: 1baa2fb6-21f\nspec_path: docs/planning/specs/quest_demo_spec.md\n---\n\n# Quest: Demo\n\n**Layer:** Cross-cutting \n**Priority:** P99 \n**Status:** active \n**Tasks:** 468 total (79 done, 9 open)\n\n## Vision\n\nDemo showcase & end-to-end flows — polished demos exercising all five layers\n\n> Demos must showcase scientifically meaningful outputs, not stub pages or placeholder content. Each demo task specifies: what hypothesis/gap/analysis is being demonstrated, what evidence or result it produces, and why the result is non-obvious. Acceptance: demo produces >1 artifact with >50KB content and >3 cross-links to other demos. Multi-demo batches use parallel agents.\n\n## Open Tasks\n\n- [ ] [Demo] CI: Verify all demo pages load correctly with rich content (P93)\n- [ ] [Demo] Versioned artifact demo: create protein design with 3 iterations (P92)\n- [ ] [Demo] Register Allen Brain Cell Atlas as external dataset artifact (P91)\n- [ ] [Demo] Tabular dataset demo: gene expression matrix linked to KG entities (P90)\n- [ ] [Demo] Build simple biophysical model from KG-derived parameters (P89)\n- [ ] [Demo] End-to-end provenance demo: trace reasoning chain from paper to model (P88)\n- [ ] [Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review (P87)\n- [ ] [Demo] Create live dashboard: Knowledge Growth Monitor (P86)\n- [ ] [Demo] Origin tracking showcase: internal vs external artifact provenance (P85)\n\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Integration tested end-to-end with dependent quests\n- [ ] UI pages rendering correctly for this quest's features\n- [ ] Documentation updated for new capabilities\n\n## Work Log\n\n### 2026-04-13 22:30 UTC — Slot minimax:55 (reopened audit, second pass)\n- Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]\n- Verified prior work (8cc8c1e01 — spec-only update, not merged to main) was correct analysis\n- Rebased against latest origin/main (5440bf99b)\n- Created two integration task specs to unblock P88 and P85:\n\n**Created:**\n- `docs/planning/specs/e90797ac_p88_provenance_infra_spec.md` — P88 infrastructure: pinned_artifacts column in analyses table + GET /api/analysis/{id}/provenance endpoint exposing verify_reproducibility()\n- `docs/planning/specs/e90797ac_p85_origin_tracking_spec.md` — P85 frontend: origin badges (INTERNAL/EXTERNAL) on artifact detail pages at /artifacts/{id}\n\n**Key findings from spec sweep:**\n- 1693 spec files across all quests\n- Quest:Agora (2 open), Quest:Forge (6 open), Quest:Atlas (3 open), Quest:Exchange (5 open), Quest:Sender (9 open)\n- P86 (Dashboard): Dashboard already registered (`dashboard-knowledge-growth-monitor`) with full data_sources (paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries). `render_dashboard()` and `/api/dashboard/{id}/refresh` both fully implemented. **Unblocked — needs only verification that the dashboard page at /dashboard/{id} renders correctly**\n- P88 (Provenance): `verify_reproducibility()` exists in `scripts/test_reproducibility.py` but not exposed via API. `pinned_artifacts` column missing from analyses table. assemble_provenance_demo.py exists but wasn't run.\n- P85 (Origin): `origin_type`/`origin_url` columns exist in DB. Frontend badges NOT rendered on artifact detail page. Need to add to api.py artifact detail page.\n- P89 (Biophysical model): Commit f5f36ad25 on branch `forge-startup-logging-20260413041942` — model code exists but NOT on main yet (f5f36ad25 is on a non-main branch). Verified in worktree that `forge/biophysical_models/microglial_activation.py`, `site/figures/models/microglial_activation/time_course.png`, `site/figures/models/microglial_activation/sensitivity_tornado.png` exist.\n- P92 (Versioned protein design): COMPLETED per prior audit\n- P87 (Dynamic authored paper): COMPLETED per prior audit\n\n**Recommended next steps:**\n1. Run assemble_provenance_demo.py to create the provenance chain artifact\n2. Execute the two new integration task specs (e90797ac_p88 and e90797ac_p85)\n3. Verify P86 dashboard page renders at /dashboard/dashboard-knowledge-growth-monitor\n4. Re-verify P89 (biophysical model) on main by checking forge/biophysical_models/ path\n\n### 2026-04-13 20:15 UTC — Slot minimax:55 (reopened audit)\n- Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]\n- Hard-reset to origin/main to clear prior worktree state; re-investigated from first principles\n- Live system stats (2026-04-13 20:15 UTC): 414 hypotheses, 291 analyses, 701K KG edges (from DB), 405 notebooks\n- Cross-checked P88/P86/P85/P91 dependencies against live API and artifact_registry code\n\n**Detailed dependency verification:**\n\n| Priority | Task | Status | Verified blockers |\n|---|---|---|---|\n| P93 | CI: Verify demo pages | Ongoing recurring CI | None |\n| P92 | Versioned artifact demo | COMPLETED | None |\n| P91 | Register Allen Brain Cell Atlas | UNSTARTED | Independent; no infra blockers |\n| P90 | Tabular gene expression demo | PARTIAL | KG integration not verified via code inspection |\n| P89 | Biophysical model | PARTIAL | Code not verified |\n| P88 | End-to-end provenance demo | UNSTARTED | See analysis below |\n| P87 | Dynamic authored paper | COMPLETED | None |\n| P86 | Knowledge Growth Dashboard | UNSTARTED | **UNBLOCKED** — see below |\n| P85 | Origin tracking showcase | UNSTARTED | See analysis below |\n\n**P88 (Provenance Demo) — Detailed analysis:**\n- `GET /api/artifacts/{id}/provenance` → returns `build_provenance_chain()` from artifact_links (WORKS, 6-entry chain for h-seaad-v4-26ba859b)\n- `GET /api/artifacts/{id}/provenance-graph` → returns graph with 4 nodes, 6 edges (WORKS)\n- `render_dashboard()` in `scidex/atlas/artifact_registry.py:811` fully implements `{{data:KEY}}` substitution via sql_query, artifact_ref, api_endpoint sources (WORKS)\n- `pinned_artifacts` field NOT in analysis metadata — provenance is computed live from artifact_links, not from pre-pinned versions\n- `verify_reproducibility()` NOT implemented anywhere — script exists in `scripts/test_reproducibility.py` but is not exposed via API\n- **What P88 actually needs**: (1) `pinned_artifacts` column in `analyses` table, (2) `verify_reproducibility()` function exposed at `GET /api/analysis/{id}/provenance`, (3) artifact link chain connecting 8 chain nodes\n\n**P86 (Dashboard Demo) — UNBLOCKED:**\n- `render_dashboard()` fully implemented with `{{data:KEY}}` substitution supporting sql_query, artifact_ref, api_endpoint (artifact_registry.py:811)\n- `/api/dashboard/{id}/refresh` → calls `artifact_registry.render_dashboard()` → evaluates SQL → persists rendered_html → returns JSON (WORKS)\n- Frontend polling auto-refresh wired in dashboard_standalone page (api.py:17758)\n- **No missing infrastructure** — only needs a registered dashboard artifact with the right data_sources/metadata\n- `a17-30-DREF0001` (data source refresh engine) is already implemented — `render_dashboard()` IS the refresh engine\n- Recommended: Register \"SciDEX Knowledge Growth Monitor\" dashboard artifact with data_sources = paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries\n\n**P85 (Origin Tracking) — Needs verification:**\n- `origin_type` and `origin_url` columns exist in artifacts table\n- Origin badges mentioned in prior work log but NOT visible in artifact detail page grep check\n- `a17-26-ORIG0001` may need a frontend component on artifact detail pages to show \"INTERNAL\"/\"EXTERNAL\" badges\n- d16-25 (authored paper) is DONE, providing an internal artifact example\n- Recommended: Verify origin badges appear on `/artifacts/{id}` detail page; if missing, add frontend rendering\n\n**P91 (Allen Brain Cell Atlas) — Independent, no blockers:**\n- d16-03 (aging mouse atlas) is a SEPARATE task, not a blocker\n- Allen Brain Atlas API access needs verification but infrastructure is ready\n- Could bootstrap from SEA-AD MTG 10x dataset already registered\n\n**Recommended integration tasks to spawn (one-shot):**\n\n1. **[Atlas] Expose verify_reproducibility via API + pinned_artifacts in analysis metadata**\n - Priority: P88\n - Spec: `docs/planning/specs/e90797ac_p88_provenance_infra_spec.md`\n - Details: Add pinned_artifacts column to analyses table, expose verify_reproducibility() at GET /api/analysis/{id}/provenance\n\n2. **[Atlas] Add origin tracking badges to artifact detail pages**\n - Priority: P85\n - Spec: `docs/planning/specs/e90797ac_p85_origin_tracking_spec.md`\n - Details: Add INTERNAL/EXTERNAL badges to /artifacts/{id} page, wire origin_type and origin_url\n","spec_html":"

Quest: Demo

Layer: Cross-cutting \nPriority: P99 \nStatus: active \nTasks: 468 total (79 done, 9 open)

Vision

Demo showcase & end-to-end flows — polished demos exercising all five layers

> Demos must showcase scientifically meaningful outputs, not stub pages or placeholder content. Each demo task specifies: what hypothesis/gap/analysis is being demonstrated, what evidence or result it produces, and why the result is non-obvious. Acceptance: demo produces >1 artifact with >50KB content and >3 cross-links to other demos. Multi-demo batches use parallel agents.

Open Tasks

☐ [Demo] CI: Verify all demo pages load correctly with rich content (P93)
\n
☐ [Demo] Versioned artifact demo: create protein design with 3 iterations (P92)
\n
☐ [Demo] Register Allen Brain Cell Atlas as external dataset artifact (P91)
\n
☐ [Demo] Tabular dataset demo: gene expression matrix linked to KG entities (P90)
\n
☐ [Demo] Build simple biophysical model from KG-derived parameters (P89)
\n
☐ [Demo] End-to-end provenance demo: trace reasoning chain from paper to model (P88)
\n
☐ [Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review (P87)
\n
☐ [Demo] Create live dashboard: Knowledge Growth Monitor (P86)
\n
☐ [Demo] Origin tracking showcase: internal vs external artifact provenance (P85)

Success Criteria

☐ All open tasks completed and verified
\n
☐ Integration tested end-to-end with dependent quests
\n
☐ UI pages rendering correctly for this quest's features
\n
☐ Documentation updated for new capabilities

Work Log

2026-04-13 22:30 UTC — Slot minimax:55 (reopened audit, second pass)

\n
  • Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]
    • \n
  • Verified prior work (8cc8c1e01 — spec-only update, not merged to main) was correct analysis
    • \n
  • Rebased against latest origin/main (5440bf99b)
    • \n
  • Created two integration task specs to unblock P88 and P85:
    • \n
\nCreated:\n
  • docs/planning/specs/e90797ac_p88_provenance_infra_spec.md — P88 infrastructure: pinned_artifacts column in analyses table + GET /api/analysis/{id}/provenance endpoint exposing verify_reproducibility()
    • \n
  • docs/planning/specs/e90797ac_p85_origin_tracking_spec.md — P85 frontend: origin badges (INTERNAL/EXTERNAL) on artifact detail pages at /artifacts/{id}
    • \n
\nKey findings from spec sweep:\n
  • 1693 spec files across all quests
    • \n
  • Quest:Agora (2 open), Quest:Forge (6 open), Quest:Atlas (3 open), Quest:Exchange (5 open), Quest:Sender (9 open)
    • \n
  • P86 (Dashboard): Dashboard already registered (dashboard-knowledge-growth-monitor) with full data_sources (paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries). render_dashboard() and /api/dashboard/{id}/refresh both fully implemented. Unblocked — needs only verification that the dashboard page at /dashboard/{id} renders correctly
    • \n
  • P88 (Provenance): verify_reproducibility() exists in scripts/test_reproducibility.py but not exposed via API. pinned_artifacts column missing from analyses table. assemble_provenance_demo.py exists but wasn't run.
    • \n
  • P85 (Origin): origin_type/origin_url columns exist in DB. Frontend badges NOT rendered on artifact detail page. Need to add to api.py artifact detail page.
    • \n
  • P89 (Biophysical model): Commit f5f36ad25 on branch forge-startup-logging-20260413041942 — model code exists but NOT on main yet (f5f36ad25 is on a non-main branch). Verified in worktree that forge/biophysical_models/microglial_activation.py, site/figures/models/microglial_activation/time_course.png, site/figures/models/microglial_activation/sensitivity_tornado.png exist.
    • \n
  • P92 (Versioned protein design): COMPLETED per prior audit
    • \n
  • P87 (Dynamic authored paper): COMPLETED per prior audit
    • \n
\nRecommended next steps:\n
  • Run assemble_provenance_demo.py to create the provenance chain artifact
    • \n
  • Execute the two new integration task specs (e90797ac_p88 and e90797ac_p85)
    • \n
  • Verify P86 dashboard page renders at /dashboard/dashboard-knowledge-growth-monitor
    • \n
  • Re-verify P89 (biophysical model) on main by checking forge/biophysical_models/ path

    • 2026-04-13 20:15 UTC — Slot minimax:55 (reopened audit)

    \n
    • Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]
      • \n
    • Hard-reset to origin/main to clear prior worktree state; re-investigated from first principles
      • \n
    • Live system stats (2026-04-13 20:15 UTC): 414 hypotheses, 291 analyses, 701K KG edges (from DB), 405 notebooks
      • \n
    • Cross-checked P88/P86/P85/P91 dependencies against live API and artifact_registry code
      • \n
    \nDetailed dependency verification:

    PriorityTaskStatusVerified blockers
    P93CI: Verify demo pagesOngoing recurring CINone
    P92Versioned artifact demoCOMPLETEDNone
    P91Register Allen Brain Cell AtlasUNSTARTEDIndependent; no infra blockers
    P90Tabular gene expression demoPARTIALKG integration not verified via code inspection
    P89Biophysical modelPARTIALCode not verified
    P88End-to-end provenance demoUNSTARTEDSee analysis below
    P87Dynamic authored paperCOMPLETEDNone
    P86Knowledge Growth DashboardUNSTARTEDUNBLOCKED — see below
    P85Origin tracking showcaseUNSTARTEDSee analysis below
    \nP88 (Provenance Demo) — Detailed analysis:\n

    • GET /api/artifacts/{id}/provenance → returns build_provenance_chain() from artifact_links (WORKS, 6-entry chain for h-seaad-v4-26ba859b)
      • \n
    • GET /api/artifacts/{id}/provenance-graph → returns graph with 4 nodes, 6 edges (WORKS)
      • \n
    • render_dashboard() in scidex/atlas/artifact_registry.py:811 fully implements {{data:KEY}} substitution via sql_query, artifact_ref, api_endpoint sources (WORKS)
      • \n
    • pinned_artifacts field NOT in analysis metadata — provenance is computed live from artifact_links, not from pre-pinned versions
      • \n
    • verify_reproducibility() NOT implemented anywhere — script exists in scripts/test_reproducibility.py but is not exposed via API
      • \n
    • What P88 actually needs: (1) pinned_artifacts column in analyses table, (2) verify_reproducibility() function exposed at GET /api/analysis/{id}/provenance, (3) artifact link chain connecting 8 chain nodes
      • \n
    \nP86 (Dashboard Demo) — UNBLOCKED:\n
    • render_dashboard() fully implemented with {{data:KEY}} substitution supporting sql_query, artifact_ref, api_endpoint (artifact_registry.py:811)
      • \n
    • /api/dashboard/{id}/refresh → calls artifact_registry.render_dashboard() → evaluates SQL → persists rendered_html → returns JSON (WORKS)
      • \n
    • Frontend polling auto-refresh wired in dashboard_standalone page (api.py:17758)
      • \n
    • No missing infrastructure — only needs a registered dashboard artifact with the right data_sources/metadata
      • \n
    • a17-30-DREF0001 (data source refresh engine) is already implemented — render_dashboard() IS the refresh engine
      • \n
    • Recommended: Register "SciDEX Knowledge Growth Monitor" dashboard artifact with data_sources = paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries
      • \n
    \nP85 (Origin Tracking) — Needs verification:\n
    • origin_type and origin_url columns exist in artifacts table
      • \n
    • Origin badges mentioned in prior work log but NOT visible in artifact detail page grep check
      • \n
    • a17-26-ORIG0001 may need a frontend component on artifact detail pages to show "INTERNAL"/"EXTERNAL" badges
      • \n
    • d16-25 (authored paper) is DONE, providing an internal artifact example
      • \n
    • Recommended: Verify origin badges appear on /artifacts/{id} detail page; if missing, add frontend rendering
      • \n
    \nP91 (Allen Brain Cell Atlas) — Independent, no blockers:\n
    • d16-03 (aging mouse atlas) is a SEPARATE task, not a blocker
      • \n
    • Allen Brain Atlas API access needs verification but infrastructure is ready
      • \n
    • Could bootstrap from SEA-AD MTG 10x dataset already registered
      • \n
    \nRecommended integration tasks to spawn (one-shot):

  • [Atlas] Expose verify_reproducibility via API + pinned_artifacts in analysis metadata
    • \n - Priority: P88
    - Spec: docs/planning/specs/e90797ac_p88_provenance_infra_spec.md
    - Details: Add pinned_artifacts column to analyses table, expose verify_reproducibility() at GET /api/analysis/{id}/provenance

  • [Atlas] Add origin tracking badges to artifact detail pages
    • \n - Priority: P85
    - Spec: docs/planning/specs/e90797ac_p85_origin_tracking_spec.md
    - Details: Add INTERNAL/EXTERNAL badges to /artifacts/{id} page, wire origin_type and origin_url

    ","spec_file":"quest_demo_spec.md"}