{"quest":{"id":"8db4834c-51e","name":"Artifacts","description":"Rich artifacts & computational notebooks. Artifact lifecycle governance: git-like versioning (version_number, parent_version_id, changelog), lifecycle states (active/deprecated/cold/superseded), supersession chains with forward reference resolution, dependency tracking, never-delete policy. Deduplication agent scans for duplicates and produces merge recommendations for governance review.","layer":"Cross-cutting","priority":68,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-10T14:44:10.355870+00:00"},"tasks":[{"id":"2a81bb0d-6a2a-4630-bdba-761d5d6f17f5","title":"[Artifacts] Fix artifacts gallery crash from uninitialized caption variable","description":"Fix UnboundLocalError in api.py artifacts_gallery where caption may be referenced before assignment, causing /artifacts failures and API instability. Add safe initialization and verify demo pages load.\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":"open","priority":89,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 12:04:44","updated_at":"2026-04-13T10:14:01.859843+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: ORPHAN_BRANCH — 3 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2a81bb0d_6a2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"d271b465-bf6e-45bc-b22b-05349b863b4e","title":"[Artifacts] Add Mol* 3D protein structure viewer to entity pages (A17.1)","description":"REQUEUED — SPEC FILE MISSING: Spec file not found on disk. See original task description for context. Before doing work, verify the spec exists on main or create one.","status":"open","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:48:24.641419+00:00","updated_at":"2026-04-17T11:05:17.410434+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d271b465_bf6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"e27b4301-b99b-41ae-ad45-d29b603468c0","title":"[Artifacts] Enrich targets with PDB/UniProt IDs for Mol* protein viewer coverage","description":"Look up PDB IDs and UniProt IDs for the 159 targets currently missing protein structure data. Use RCSB PDB search API and UniProt REST API to populate pdb_id and uniprot_id columns. This enables Mol* 3D protein viewers on challenge detail pages for more challenges, advancing Q17 (Rich Artifacts).\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":"open","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:04:19.728893+00:00","updated_at":"2026-04-17T05:04:19.728893+00:00","summary":"","completion_notes":"","last_error":"worker_exit_unclean exit_code=0","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e27b4301_b99_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"4873cc51-d403-4726-b101-5143c6ddd918","title":"[Artifacts] Ensure all 18 spotlight notebooks have rich, executed content","description":"Query notebooks WHERE is_spotlight=1. Each must have: >50KB rendered HTML, real code cells with outputs, matplotlib/seaborn figures, proper title and description. Fix any that are stubs or have broken rendering.","status":"open","priority":76,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T07:33:56.145936+00:00","updated_at":"2026-04-17T20:30:01.216343+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"zombie_sweeper: no live slot (assigned='61'), stale heartbeat 2026-04-17 20:06:17.458658+00:00","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/visual_artifacts_quest_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"completion_shas\": [\"e812fe856d613f10bcd44234f9c2ed969c191f7e\", \"b3db0b5dbd834f92a2e05136b2c0ea6d527a074b\", \"e11689c32a32c7f89fab382e16dc3b6a5d1fdec3\"], \"completion_shas_checked_at\": \"2026-04-13T05:49:01.132316+00:00\", \"completion_shas_missing\": [\"975aaae7cf5d62da89ed68bedfc3c8bbfddd2bd2\", \"2628f9ef4a8521ebaae5c29493cd824329d4f4b3\", \"ae04acfa964bc406ab893ce192d0f6bf193a4f13\"]}"},{"id":"73ee83a5-c702-45de-8f3d-b41171c061a9","title":"[Artifacts] CI: Verify notebook coverage and generate summaries for recent analyses","description":"Recurring CI: scan for completed analyses without notebooks, generate notebook stubs for the top 3 missing, verify artifact pages load correctly, report coverage percentage.","status":"open","priority":62,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:00:08.159383+00:00","updated_at":"2026-04-17T15:00:08.159383+00:00","summary":"","completion_notes":"Auto-release: recurring task had no work this cycle","last_error":"","time_estimate_hours":0.0,"completion_count":1,"spec_path":"docs/planning/specs/73ee83a5_c70_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 01:14:05\", \"completion_shas\": [\"33c273e72a089a74b1ee0197797af50bf23b9b0d\", \"ad9bf94a2ce832f8cf9ff532e1bb768a204cf7f4\", \"c49d36d582f324341cca8cc3962b44e280ed091d\"], \"completion_shas_checked_at\": \"2026-04-12T23:52:54.817452+00:00\", \"completion_shas_missing\": [\"582657caecc19b6ef14454f179660c13838ded3e\", \"dd5d1a8352639df2b1b2b796825603cbea7ed4c1\", \"15742b176648b8c20b685ff198eea20c72e4b662\", \"9e28ff2900f928a7f4b79161c283690209ddbab1\", \"fc16c2c5502564182d81f41b95c888393c5b9d38\", \"fa68b788621fd797735429b75788eace82188817\", \"f2e61f69b4a32c8e451a7bb5662c53aa51e5c214\", \"bcbdb6b03c66b146c2b7a4252bf3917909783329\", \"eb45d1beecc6b2c6203e118d696414b4f04ee59b\", \"e8c872a67c65141019f330204d64399060edc62a\", \"57b6ed1fc7f414ee003ef67d32ff731959548acf\", \"fc7fbf64569e688d00b1bc4094bb01bd9fe2ec0d\", \"b949eafe79b9d2acb6444e4554bb11131e1b62a7\", \"daad56e4fdb9b3d01805d8943b89973a469ba7e9\", \"8e893dbe5c497e7c1e971d27eb19f57697b93f03\", \"7d1532d1796feec4a4507b8c30c6b8947e2b0030\", \"5c5255413c79977fd2deb4118939a8d188b02dc0\", \"37bcd6cef547ce03f2ef02ffd8fc566538e41700\", \"ea169f27b906c14400a1e49c12490c185e0b5141\", \"362921c2ff7379023e6c5767cb4307da64ef9db1\", \"9bcd004998c98494dcc1217f1c0b2abdf856ae87\", \"36ebb41506fdb48a1808cd6853c1219c71961a82\", \"9c56a7d8abf48f00a0f7229208573c7cd6f8e4fa\", \"391d16428c4354dd61a8a108349ccb985af769a7\", \"463143363bf7d22b73fd99d493e8935c9ce0c2a0\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"967e8646-8d4d-4102-907f-9575922abdd2","title":"[Artifacts] Review notebook links from analysis pages — fix any that lead to stubs","description":"Visit the top 20 analyses at /analyses/. Click each notebook link. Verify the notebook page shows real content (code cells, outputs, figures) not a stub or \"Not Rendered Yet\" message. For stubs: regenerate from analysis data. For missing: create the notebook.","status":"open","priority":60,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:01:49.314959+00:00","updated_at":"2026-04-17T15:01:49.314959+00:00","summary":"","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/967e8646_8d4d_artifacts_review_notebook_links_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"completion_shas\": [\"1f09a4461075fcc7ee1d482a24e6ce6941755317\", \"4bde3cc30a850a997224ceb6a44e0e1aa54276a2\", \"281e68478265280a6150cf58e66cc737e12d8576\", \"51beaac2c7099ce87d015c16d5608b2f8d54e5b0\", \"301dc7d80d5bc97bb13a11f6ed337d065866f8c8\", \"75e45b23e817673ebfc3558ef2aa4ba3a8d4cc6f\", \"9c92d5fe657b5010e976496ebdff2ed270ab3f3b\", \"c67f106a3641d534cc9bdcdaa3b032ce071d11a2\"], \"completion_shas_checked_at\": \"2026-04-13T05:56:20.452449+00:00\", \"completion_shas_missing\": [\"5e74199190afcd99c6ecd47e38b9b3a29c6a11ee\", \"f3aa31837f1f4d6533f9faed51f365b8e15e8300\", \"094853ec54fcaae83aaadc6924c131042c018462\", \"00569539cbeab3789863e5a19f51e21ae4642367\", \"a9af5a683bc2c9705bf3864fb04db1c75308a809\", \"c1e874dbf8c27624a7f25d99e33c235e1baa27b8\", \"8172eb0256a5ebfb1f457d31a3ac9e0e30952d81\", \"34954b59f4811985fba4e64bc6783b90c1c0e045\", \"a6d4e0d4459cb483a72397f4b465b20ed8e6627e\", \"bdbbb26e46335cce9d25c1d153f7d2b92a289a76\", \"2e0fdba86844e0149c37ecf9871d24362950f4ce\"]}"},{"id":"0186b1eb-d645-412d-873b-f30541d5f159","title":"[Artifacts] Audit all 67 stub notebooks (<10KB) and regenerate with real content","description":"Query notebooks table for entries where rendered HTML is <10KB. For each: check if the associated analysis has debate transcripts/hypotheses. If yes, regenerate the notebook using the create_notebooks.py or generate_nb pattern (see scripts/generate_nb_sea_ad_001.py as template). If no analysis data exists, mark the notebook as draft or archive it. Target: zero <10KB stubs.","status":"open","priority":58,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:07:22.056066+00:00","updated_at":"2026-04-17T15:07:22.056066+00:00","summary":"","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/showcase_notebook_rebuild_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"423f7b9a7f0b1da4a2ef83203a56fc29ff804539\", \"bea421f35b2b0a3d2ecb0092735473a03fa119a0\", \"7ce82743d9106fe1956315f13e3b3c278baf2d56\", \"0142faa373d2268ba9a5c02b542bb80588004fec\"], \"completion_shas_checked_at\": \"2026-04-13T05:35:04.906665+00:00\", \"completion_shas_missing\": [\"fc93b936824eecaccb34f0778f4165734c1a692b\", \"d91c87b69e2dc239e04d9cc906c1fb4ed240635d\", \"3b0c15fb438a787d93307cba8e2dd5f9f076f99b\"]}"},{"id":"c684ec5f-d8af-4d47-97b3-4a0aca40a76b","title":"[Artifacts] Add Mol* 3D protein viewer to hypothesis pages","description":"Embed interactive Mol* protein structure viewers on hypothesis pages for target proteins (TREM2, APOE, LRP1, etc.). Detect proteins in descriptions, load PDB structures, provide interactive rotation/zoom.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:15:48.178066+00:00","updated_at":"2026-04-17T09:37:39.891682+00:00","summary":"","completion_notes":"","last_error":"Paused after 13 exit-0 runs with no commits on branch=(none)","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_4_molstar_protein_viewer_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:43:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"9883da7a-92f7-43b1-863c-25de7e15ccf6\", \"_watchdog_repair_created_at\": \"2026-04-17T09:27:33.707733+00:00\"}"},{"id":"05a277d6-f4cc-4439-ae7a-71806332e313","title":"[Artifacts] Add Mol* 3D protein viewer to hypothesis pages","description":"Embed interactive 3D protein structure viewers using Mol* (molstar.org) on hypothesis pages. Load PDB structures for target proteins mentioned in hypotheses. Add viewer to hypothesis detail page template. Support PDB ID input and automatic structure loading. See docs/planning/specs/d16_4_molstar_protein_viewer_spec.md\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:31:42.601903+00:00","updated_at":"2026-04-17T08:33:22.395107+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d16_4_molstar_protein_viewer_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:34:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"72fb121c-6f2f-44d6-9fb0-d0fe0999e3ef\", \"_watchdog_repair_created_at\": \"2026-04-17T08:26:34.971694+00:00\"}"},{"id":"12d70cee-d20c-4d91-b250-eafba8eae3e7","title":"[Artifacts] Demo notebook registry filters and showcase highlighting","description":"Add demo-focused filtering/sorting on /notebooks so Allen/SEA-AD/aging showcase artifacts are easier to discover; include metadata chips and a spotlight section for top demo notebooks.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T22:59:38.590452+00:00","updated_at":"2026-04-15T22:59:38.590452+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/12d70cee_d20_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 00:34:41\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"34b59c35-bc0c-4ea5-99e7-f33ad51cf10e","title":"[Artifacts] Add Mol* 3D protein viewer to hypothesis detail pages","description":"Embed Mol* (molstar) 3D protein structure viewer on hypothesis detail pages. For hypotheses with a target_gene, look up the corresponding PDB structure and embed an interactive 3D viewer. This is A17.1 from Quest 17.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-15T20:02:07.114968+00:00","updated_at":"2026-04-15T20:02:07.114968+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/34b59c35_bc0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:31:20\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"738203e4-01b0-400f-bfbb-d3cb9fdb3e1b","title":"[Artifacts] Add version tracking schema to artifacts table","description":"Add versioning columns (version_number, parent_version_id, version_tag, changelog, is_latest) to the artifacts table. Foundation for all reproducible analysis chains and artifact lineage tracking.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:43:53.625563+00:00","updated_at":"2026-04-14T00:43:53.625563+00:00","summary":"","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/a17-18-VERS0001_version_tracking_schema_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"b9a46968c35d93f349e684e36b3eec490580c0b8\", \"856422caf086c0ee29416c1922ff68e62f547f6c\"], \"completion_shas_checked_at\": \"2026-04-14T00:43:53.605384+00:00\"}"},{"id":"ffb99f3d-6ab5-4efe-be3c-9d33714b5da1","title":"[Artifacts] Implement resolve_embeds() engine — replace {{artifact:ID}} markers with rendered HTML previews","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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T00:41:31.588945+00:00","updated_at":"2026-04-14T00:41:31.588945+00:00","summary":"","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/a17-29-EMBD_artifact_embed_rendering_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7}, \"completion_shas\": [\"84e32e5a5e412fdae6fc38d0f1981c0139be017f\", \"fe6e3e7f0934f33ee4b6be391888ce2bf67a8117\"], \"completion_shas_checked_at\": \"2026-04-14T00:41:31.569373+00:00\"}"},{"id":"f205405e-e160-4ce4-bcc1-aace4d3c10d1","title":"[Artifacts] A17.6: Evidence matrix component on hypothesis pages","description":"Add structured evidence matrix table to hypothesis detail pages showing citations with quality scores, relevance ratings, and evidence type. Mol* viewer already exists so pivoting to next highest-value Quest 17 artifact.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T23:08:45.823207+00:00","updated_at":"2026-04-13T23:08:45.823207+00:00","summary":"","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/f205405e_e16_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"completion_shas\": [\"fb122fe7b8a517dd9825bb3898a7ced0842b9203\"], \"completion_shas_checked_at\": \"2026-04-13T23:08:45.803212+00:00\"}"},{"id":"a17-01-9150F369","title":"[Artifacts] Embed Mol* protein viewer component","description":"Create reusable Mol* (molstar.org) viewer component. CDN: https://molstar.org/mol-star/molstar.js. Load PDB structures by ID. Show in iframe or div. Add to hypothesis detail pages where target_gene has a known PDB structure. Map gene names to PDB IDs for top 20 targets.\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":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 10:09:27","updated_at":"2026-04-02 09:43:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"a17-18-VERS0001","title":"[Artifacts] Add version tracking schema to artifacts table","description":"Add versioning columns to the artifacts table: version_number INTEGER DEFAULT 1, parent_version_id TEXT (self-referencing FK), version_tag TEXT (e.g. v1.0, draft), changelog TEXT, is_latest BOOLEAN DEFAULT TRUE. Create index on (artifact_type, entity_ids, is_latest). Add migration in Orchestra/migrations/. This is the foundation for all reproducible analysis chains.","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 23:33:20","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-18-VERS0001_version_tracking_schema_spec.md","provider":"claude","payload_json":"{}"},{"id":"b072f27c-d29a-4681-a40c-fc58a6b069e9","title":"[Artifacts] Extend artifact_type to include figure, code, model, protein_design, dataset","description":"Extend the artifact_type enum to support new artifact categories: figure, code_script, biophysical_model, protein_design, external_dataset. Required by Demo protein design and dataset registration tasks.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:43:28.391730+00:00","updated_at":"2026-04-16T00:43:28.391730+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-19-TYPE0001_extend_artifact_types_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 02:36:55\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"a17-19-TYPE0001","title":"[Artifacts] Extend artifact_type to include figure, code, model, protein_design, dataset","description":"Extend the artifact registry to accept new artifact_type values: figure, code, model, protein_design, dataset, tabular_dataset. Update artifact_registry.py register_artifact() validation. Add type-specific metadata schemas: figure (format, resolution, source_notebook), code (language, entrypoint, dependencies), model (architecture, framework, parameter_count, training_config), protein_design (pdb_id, sequence, method), dataset (source_url, format, row_count, schema). Can run in parallel with a17-18.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T00:13:29.776344+00:00","updated_at":"2026-04-16T00:13:29.776344+00:00","summary":"","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/a17-19-TYPE0001_extend_artifact_types_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 01:52:59\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"023b47dedb7228eeb00837bb0de3a3178d71f51f\"], \"completion_shas_checked_at\": \"2026-04-16T00:13:29.760465+00:00\"}"},{"id":"5a22b3a8-3aaa-4edc-abeb-59ba7a0a61b4","title":"[Artifacts] Add evidence matrix component to hypothesis detail pages","description":"Replace the plain evidence lists (for/against) on hypothesis detail pages with a structured evidence matrix table. Show claim, source journal, year, PMID link, strength badge (high/medium/low), and expandable abstract. Sortable by strength and year. This is A17.6 from Quest 17.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:13:19.728493+00:00","updated_at":"2026-04-16T01:13:19.728493+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5a22b3a8_3aa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 04:03:14\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"58309097-1f15-4cb6-bc6c-74f05410ed10","title":"[Artifacts] Version-aware artifact registry API: create_version, get_history, diff","description":"Implement the API endpoints and database functions for version-aware artifact management: creating versions, retrieving history, diffing versions.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:09:33.162648+00:00","updated_at":"2026-04-16T01:09:33.162648+00:00","summary":"","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/a17-20-VAPI0001_version_aware_api_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 05:11:25\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"c762f241a65d4b552993ab783f9fa4cca4f784d4\", \"6aca5e819a01043c8ff07ad6dc4f88a16e7ea1f5\"], \"completion_shas_checked_at\": \"2026-04-16T01:09:33.144324+00:00\"}"},{"id":"7a734b93-e895-4917-a9b7-878bba4d6976","title":"[Artifacts] General-purpose artifact origin tracking (origin_type, origin_url)","description":"Add origin_type (internal/external/derived) and origin_url fields to artifacts. Track where every artifact came from — internal agent output, external dataset, or derived from other 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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T01:08:39.153311+00:00","updated_at":"2026-04-16T01:08:39.153311+00:00","summary":"","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/a17-26-ORIG0001_artifact_origin_tracking_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 04:54:05\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"6eb8b6752dc7208cfec2550099d835a5f52a6cf4\", \"b441705e2909c6674237bb549b1b57818ce2c80f\", \"771e32318954a906453adfb3e5fac7a691cf2803\", \"254fbdb0334598281c83ab9169638737c84cac5f\"], \"completion_shas_checked_at\": \"2026-04-16T01:08:39.137740+00:00\"}"},{"id":"4059a75a-0c3d-4987-a476-89e3674589ec","title":"[Artifacts] Add Mol* 3D protein viewer to enriched hypothesis pages","description":"Embed Mol* (molstar) viewer for target proteins on hypothesis detail pages. Start with TREM2 (PDB: 5UD7), LRP1 (PDB: 1CR8), ASM (PDB: 5I85). Use the mol* CDN embed approach.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:10:14.056296+00:00","updated_at":"2026-04-14T03:10:14.056296+00:00","summary":"","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}, \"completion_shas\": [\"4ced97f44c5aedcb2c997799c84c1d6eca654bec\"], \"completion_shas_checked_at\": \"2026-04-14T03:10:13.983649+00:00\"}"},{"id":"a17-02-87C1C845","title":"[Artifacts] Jupyter notebook template for Allen Brain analysis","description":"Create template .ipynb notebook for Allen Brain data analysis. Include: AllenSDK setup, brain-map.org API queries, gene expression extraction, basic visualization (matplotlib/seaborn), differential expression with scipy, pathway enrichment with enrichr API. Save as template in notebooks/.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:48:17","updated_at":"2026-04-02 09:43:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"a17-20-VAPI0001","title":"[Artifacts] Version-aware artifact registry API: create_version, get_history, diff","description":"Add to artifact_registry.py: create_version(parent_artifact_id, **kwargs) creates new artifact row with incremented version_number, links to parent via parent_version_id, sets previous version is_latest=FALSE. get_version_history(artifact_id) returns all versions ordered by version_number. diff_versions(v1_id, v2_id) returns metadata/content diff. pin_version(artifact_id, version_tag) sets human-readable tag. Also add GET /api/artifact/{id}/versions and GET /api/artifact/{id}/versions/{version} endpoints to api.py. Depends on: a17-18-VERS0001.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:48:21","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-20-VAPI0001_version_aware_api_spec.md","provider":"any","payload_json":"{}"},{"id":"a17-26-ORIG0001","title":"[Artifacts] General-purpose artifact origin tracking (origin_type, origin_url)","description":"Add origin tracking to every artifact: origin_type (internal/external) and origin_url (canonical location). Internal artifacts are created by SciDEX agents/users. External artifacts are pre-existing resources referenced by URL/DOI. Origin info stored in metadata._origin for backwards compatibility. Already implemented in artifact_registry.py — this task covers migration to promote _origin fields to top-level columns and backfill existing artifacts.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:49:49","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-26-ORIG0001_artifact_origin_tracking_spec.md","provider":"any","payload_json":"{}"},{"id":"f16462d7-3ab9-40dd-aed4-390eaca63b38","title":"[Artifacts] Harden demo smoke check coverage for rich artifact routes","description":"Extend scripts/demo_smoke_check.py to verify rich artifact and notebook routes used in demo/showcase flows, with explicit pass/fail output and bounded execution.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:47:21.811276+00:00","updated_at":"2026-04-16T09:47:21.811276+00:00","summary":"","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/f16462d7_3ab_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"79e2c68f70a93339b6a1136c5d4ec07c404817fa\", \"7d4d66ae0caf97f0dd89cecab13704f79bedb38b\", \"9cea61ab59b50a7edd883604ff0f3a31d59a5be8\"], \"completion_shas_checked_at\": \"2026-04-16T09:47:21.792625+00:00\"}"},{"id":"ab00507c-36db-40a1-bdb8-9e5cb666b60a","title":"[Artifacts] Register existing notebooks in DB — /notebooks page shows 0 despite 150+ files","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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T09:02:27.401762+00:00","updated_at":"2026-04-16T09:02:27.401762+00:00","summary":"","completion_notes":"Fix was re-applied: cherry-picked ff8b7fc3e which existed in repo history and was ancestor of origin/main but whose changes were lost during previous conflict resolution. Resolved 2 conflicts. Verified: /api/notebooks returns 390, /notebooks renders 389+ cards, /api/status healthy. Pushed to origin.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab00507c_36d_spec.md","provider":"any","payload_json":"{}"},{"id":"65e848db-dec0-43e5-acb5-10419b94b17a","title":"[Artifacts] Bootstrap artifacts table and register existing hypotheses/analyses as artifacts","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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:48:23.218892+00:00","updated_at":"2026-04-16T08:48:23.218892+00:00","summary":"","completion_notes":"Work verified on origin/main: artifacts table created (38,200 rows), /artifacts returns HTTP 200. No additional changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/65e848db_dec_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"4957920ef63f6d9d08f91cfe4b4aa38b8de0e16e\"], \"completion_shas_checked_at\": \"2026-04-16T08:48:23.197903+00:00\"}"},{"id":"7c4b96ac-86f2-4190-91af-4146439e2ef4","title":"[Artifacts] Add evidence matrix to hypothesis detail pages","description":"Quest 17 A17.6: add structured evidence matrix table (stance, claim, PMID, strength, relevance, source/year) to /hypothesis/{id}, with robust parsing and graceful fallback for sparse evidence 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":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T08:25:31.043937+00:00","updated_at":"2026-04-16T08:25:31.043937+00:00","summary":"","completion_notes":"Evidence matrix was already implemented in api.py (lines 28557-28721) as verified by testing h-e12109e3 (19 evidence rows, all sorting/abstract features present). Branch only needed spec file which was created and committed. No code changes needed - task was completed by previous agent but never committed/pushed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/7c4b96ac_86f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"5b6097a8-f06c-4582-a9cb-08677fd010a3","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and 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":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T05:15:14.660600+00:00","updated_at":"2026-04-16T05:15:14.660600+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5b6097a8-f06_artifacts_build_artifact_gallery_page_a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"a17-21-EXTD0001","title":"[Artifacts] External dataset references: track datasets like we track papers","description":"Create external dataset tracking using artifacts with type=dataset. Fields in metadata: source (zenodo, figshare, geo, allen_brain, etc.), external_id, url, license, description, schema_summary, last_checked_at. Implement register_dataset(source, external_id, metadata) similar to register_paper(). Add periodic freshness check. Do NOT download or host data -- just track references and metadata. Link datasets to KG entities via artifact_links. Depends on: a17-19-TYPE0001.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:15:25","updated_at":null,"summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-21-EXTD0001_external_dataset_references_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}}"},{"id":"ad284a00-a73c-44bc-aaee-e902586bd313","title":"[Artifacts] Build git-backed artifact catalog with immutable blob references","description":"Design and implement a git-backed artifact catalog with immutable blob-addressed references for large data, models, notebooks, and figures.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:04:32.860553+00:00","updated_at":"2026-04-16T11:04:32.860553+00:00","summary":"","completion_notes":"The git-backed artifact catalog with immutable blob references was fully implemented and is present on origin/main. Verification shows: artifact_catalog.py (59KB), artifact_catalog_integration.py (32KB), docs/artifact_storage_guide.md, and forge/runtime_capture.py all exist on main. HEAD is synchronized with origin/main at 38b298467.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/git_backed_artifact_catalog_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 7, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"codex\", \"_stall_requeued_at\": \"2026-04-11 03:33:17\", \"completion_shas\": [\"c0d3bd637\", \"e7a64da66\", \"b0e21e959\", \"1056eb307\", \"c99d5c0a2\"], \"completion_shas_checked_at\": \"2026-04-16T11:04:32.837330+00:00\", \"completion_shas_missing\": [\"b0e21e959abf1d20d71a1be9130e6a5a2b1f6f2f\", \"1056eb30790389f5045e4ab1d966314b4fecc06a\", \"c0d3bd637f0e99051b9f25979eeb1d414b220e2d\", \"c99d5c0a20a05369cd735c94008a8cee358b3899\", \"618c4e70e145be1b1c58e01c49db0719cc003ca3\", \"de02bf2240ec71ebf9a0bcce65fb3c77471a00fe\", \"8e3f2167c5e862e88bfaef1b9282e79c88e3abf9\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"c564df47-04c7-4560-a923-f63709029ae1","title":"[Artifacts] Build interactive notebook viewer page at /notebooks","description":"Create a page that lists available Jupyter notebooks (5 exist in site/notebooks/) and renders them inline with code cells, outputs, and plots. Use nbconvert HTML output or a lightweight JS viewer.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:12:56.296518+00:00","updated_at":"2026-04-16T10:12:56.296518+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a17-22-TABL0001","title":"[Artifacts] Tabular dataset support: schema tracking, column metadata, linkage to KG","description":"Support tabular datasets as first-class artifacts. Store column schemas (name, dtype, description, linked_entity) in metadata JSON. Implement register_tabular_dataset(title, columns, source, row_count) that creates artifact with type=tabular_dataset. Add ability to link individual columns to KG entities (e.g. column gene_symbol maps to entity type gene). Tabular datasets contribute to the world model by providing structured observations that complement graph edges. Depends on: a17-19-TYPE0001, a17-21-EXTD0001.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:49:44","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-22-TABL0001_tabular_dataset_support_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}}"},{"id":"a17-27-APAP0001","title":"[Artifacts] Authored paper artifact type: dynamic documents that embed other artifacts","description":"Add authored_paper as a new artifact type for papers/reports written within SciDEX. Unlike imported papers (PubMed), authored papers have editable HTML/Markdown content, can embed live references to other artifacts via {{artifact:ID}} markers, and evolve through versions. Similar to notebooks in management but focused on narrative scientific writing. Supports draft/review/published workflow states.","status":"done","priority":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:53:06","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-27-APAP0001_authored_paper_type_spec.md","provider":"any","payload_json":"{}"},{"id":"f0d7afba-9261-489c-83f0-bf48ad8f4103","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T04:52:49.684469+00:00","updated_at":"2026-04-17T04:52:49.684469+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"232f22e3-0eb5-493f-9bac-eeea6c6bd6e4","title":"[Artifacts] Repair notebook coverage CI gaps for demo readiness","description":"Run notebook coverage CI, identify concrete coverage/render gaps that affect demoability, implement targeted fixes, and verify pages/services remain healthy.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:44:14.971643+00:00","updated_at":"2026-04-16T15:44:14.971643+00:00","summary":"","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/232f22e3_0eb_spec.md","provider":"any","payload_json":"{}"},{"id":"a37790f5-1872-4065-9128-7d7a3fbcaa69","title":"[Artifacts] Auto-repair stale notebook references in coverage CI","description":"Update notebook coverage CI to detect and repair stale notebook paths for analyses using nearest existing notebook artifacts, then persist updates to analysis_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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:41:28.881707+00:00","updated_at":"2026-04-16T15:41:28.881707+00:00","summary":"","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/a37790f5_187_spec.md","provider":"any","payload_json":"{}"},{"id":"b2970616-7309-47ee-81e6-58e7e1d5f991","title":"[Artifacts] Persist notebook coverage summary artifact for demo ops","description":"Add persistent markdown summary output to ci_notebook_coverage.py so Quest 17 notebook coverage checks produce inspectable artifacts in site/notebooks and logs 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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:40:10.169550+00:00","updated_at":"2026-04-16T15:40:10.169550+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b2970616_730_spec.md","provider":"any","payload_json":"{}"},{"id":"d16d84eb-a445-4576-823d-3fc89fdd262b","title":"[Artifacts] Repair stale notebook references flagged by coverage CI","description":"Fix stale analyses.notebook_path and broken notebook links identified by ci_notebook_coverage.py so strict notebook coverage improves and notebook links 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:38:31.872443+00:00","updated_at":"2026-04-16T15:38:31.872443+00:00","summary":"","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/d16d84eb_a44_spec.md","provider":"any","payload_json":"{}"},{"id":"e482bf04-6d1d-4888-affa-1341dbedf7f5","title":"[Artifacts] Make notebook coverage CI self-healing by default","description":"Quest 17 follow-up: ensure ci_notebook_coverage registers generated notebook stubs by default in recurring runs and document behavior in spec/worklog.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:37:45.266708+00:00","updated_at":"2026-04-16T15:37:45.266708+00:00","summary":"","completion_notes":"Verification on origin/main (commit 7853deedc):\n- Commit b7e7afcce IS ancestor of origin/main (verified via git merge-base --is-ancestor)\n- ci_notebook_coverage.py lines 940-948 contain self-healing mode output\n- registration_mode = \"enabled (self-healing default)\" when --register (default)\n- stale_repair_mode = \"enabled (self-healing default)\" when --repair-stale (default)\n- JSON report output includes registration_mode and stale_repair_mode fields\n- --no-register and --no-repair-stale provide explicit opt-out\n- All acceptance criteria from spec are satisfied","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e482bf04_6d1_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"b7e7afcce\"], \"completion_shas_checked_at\": \"2026-04-16T15:37:44.923713+00:00\"}"},{"id":"bb734dee-a584-42a7-9ba4-feb35272b818","title":"[Artifacts] Fix notebook coverage CI site-root resolution in worktrees","description":"Make ci_notebook_coverage.py resolve notebook files against the canonical SciDEX site root when running from worktrees, eliminating false stale/missing notebook reports.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:33:42.277889+00:00","updated_at":"2026-04-16T15:33:42.277889+00:00","summary":"","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/bb734dee_a58_spec.md","provider":"any","payload_json":"{}"},{"id":"a7e4e7da-e730-42a3-b6e7-311493cac49c","title":"[Artifacts] Improve notebook coverage report for recent analyses","description":"Add richer coverage diagnostics for recent analyses (missing, stale, and quality metadata) and emit a clearer CI summary 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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:31:25.852296+00:00","updated_at":"2026-04-16T15:31:25.852296+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a7e4e7da_e73_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"d6b092bc-1eec-4bed-80b3-dfc13bf608bc","title":"[Artifacts] Emit machine-readable notebook coverage CI report","description":"Add JSON report output to ci_notebook_coverage.py with coverage and stale-ref metrics for Demo/Artifacts monitoring.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:29:17.007103+00:00","updated_at":"2026-04-16T15:29:17.007103+00:00","summary":"","completion_notes":"Verification complete: JSON report functionality already on main at commit e17e455f3. Worktree rebased and matches origin/main. Only spec work log update was needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d6b092bc_1ee_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}, \"completion_shas\": [\"e17e455f3\", \"11a850d0c\"], \"completion_shas_checked_at\": \"2026-04-16T15:29:16.993778+00:00\"}"},{"id":"539bba81-9ab2-4667-8abd-75a3aa8ab179","title":"[Artifacts] Strengthen smoke check coverage for notebook and experiment pages","description":"Extend demo smoke checks to validate artifact routes and content richness for /notebooks and /experiments, then verify with bounded 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:26:23.987563+00:00","updated_at":"2026-04-16T15:26:23.987563+00:00","summary":"","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/539bba81_9ab_spec.md","provider":"any","payload_json":"{}"},{"id":"421caac9-b82d-4467-a6b8-36a65ae5de6c","title":"[Artifacts] Harden notebook coverage CI and surface actionable missing-artifact report","description":"Improve notebook coverage verification to produce actionable output for recent analyses and reduce false-positive pass states 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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:25:45.960096+00:00","updated_at":"2026-04-16T15:25:45.960096+00:00","summary":"","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/421caac9_b82_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"8f2d138c-4da7-4201-a2b2-acf55fa8b0a1","title":"[Artifacts] Surface linked notebooks on hypothesis detail pages","description":"Expose notebook artifacts associated with a hypothesis/analysis directly on /hypothesis/{id} to improve demo-ready rich artifacts navigation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:24:25.008285+00:00","updated_at":"2026-04-16T15:24:25.008285+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8f2d138c_4da_spec.md","provider":"any","payload_json":"{}"},{"id":"c2677437-af87-469b-abad-df89046580dc","title":"[Artifacts] Backfill missing notebook stubs for completed analyses","description":"Generate and verify notebook/html stubs for completed analyses missing artifacts, then validate site endpoints and services.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:24:04.104837+00:00","updated_at":"2026-04-16T15:24:04.104837+00:00","summary":"","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/c2677437_af8_spec.md","provider":"any","payload_json":"{}"},{"id":"6b07e5d1-9d70-492a-a1f6-39357ec85a95","title":"[Artifacts] Harden notebook registry tag filter URL and JS escaping","description":"Fix /notebooks tag filter and sort controls to safely encode query params and prevent reflected XSS from unescaped tag values in href/onchange HTML.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:21:54.157355+00:00","updated_at":"2026-04-16T15:21:54.157355+00:00","summary":"","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/6b07e5d1_9d7_spec.md","provider":"any","payload_json":"{}"},{"id":"657e9a37-2731-4ea4-8599-a152ae4890e6","title":"[Artifacts] Harden notebook coverage CI checks and reporting","description":"Improve ci_notebook_coverage.py to surface actionable missing-notebook diagnostics and strict nonzero exit behavior for CI/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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:21:37.103697+00:00","updated_at":"2026-04-16T15:21:37.103697+00:00","summary":"","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/657e9a37_273_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"703a16c5-eaf0-4a78-ac21-b680e7a57d6f","title":"[Artifacts] Harden /notebooks page latency to stay under 2s","description":"Reduce /notebooks render latency for demo reliability by avoiding expensive per-row DB calls and validating route latency with timed curl 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:18:51.365294+00:00","updated_at":"2026-04-16T15:18:51.365294+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/703a16c5_eaf_spec.md","provider":"any","payload_json":"{}"},{"id":"fc1bf0a8-a072-4a6f-a5bf-aa2e17b5450e","title":"[Artifacts] Harden notebook coverage CI diagnostics for demo readiness","description":"Improve notebook coverage checks to clearly flag missing/stale notebook artifacts for demo-critical analyses, with deterministic output suitable for CI triage.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:18:03.113543+00:00","updated_at":"2026-04-16T15:18:03.113543+00:00","summary":"","completion_notes":"Re-verified 2026-04-16: task was completed in prior cycle. Commits cc9b3cf1b and 3296fe332 are on main. Script outputs covered_ref vs covered_strict metrics, stale_notebook_path_count, stale_notebook_link_count, false_positive_count, demo_readiness field. Runs successfully with and without --register. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fc1bf0a8_a07_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"cc9b3cf1b\", \"3296fe332\"], \"completion_shas_checked_at\": \"2026-04-16T15:18:03.094916+00:00\"}"},{"id":"a2060b26-9d9b-484c-9f6c-8e92aecea948","title":"[Artifacts] Make notebook coverage CI register stubs by default","description":"Fix ci_notebook_coverage.py so generated notebook stubs are registered in DB by default and coverage metrics reflect actual progress; update spec/work log and verify artifact 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:14:56.895060+00:00","updated_at":"2026-04-16T15:14:56.895060+00:00","summary":"","completion_notes":"Task was implemented in prior work (commits b8b608dcf, e5748267b, 95b7f1199) but those individual commits are orphaned. The actual code change (parser.set_defaults(register=True)) is present on origin/main at line 878. Verification: routes healthy, script has correct flags.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a2060b26_9d9_spec.md","provider":"any","payload_json":"{}"},{"id":"08d47950-507b-4b93-bb23-d5587b012a5f","title":"[Artifacts] Fix target page 500 error and add Mol* protein viewer (Quest 17/A17.1)","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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:14:32.995499+00:00","updated_at":"2026-04-16T15:14:32.995499+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/08d47950_507_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"26012628-b236-4335-945d-9248376eb18f","title":"[Artifacts] Harden demo artifact links and missing-file handling","description":"Improve demo-facing artifact rendering so broken/missing notebook or HTML artifact paths fail gracefully with clear fallback text and no 500s.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:13:06.719170+00:00","updated_at":"2026-04-16T15:13:06.719170+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/26012628_b23_spec.md","provider":"any","payload_json":"{}"},{"id":"8e5cae74-6605-4e65-9cd6-03c4109b1989","title":"[Artifacts] Restore notebook code/download actions using file_path fallback","description":"Notebook detail page currently expects ipynb_path, but notebooks table uses file_path in many records. Add compatibility fallback so Show Code and Download .ipynb actions appear and function on demo notebooks.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:10:18.548878+00:00","updated_at":"2026-04-16T15:10:18.548878+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8e5cae74_660_spec.md","provider":"any","payload_json":"{}"},{"id":"6a963d0e-257c-4208-96c2-66c8edce453d","title":"[Artifacts] Implement Jupyter notebook viewer and storage","description":"Add notebook upload, storage (site/notebooks/), and inline rendering (nbconvert or similar). Link notebooks to analyses and KG entities. Enable analysts to share computational work. Foundational for 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":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:09:05.991013+00:00","updated_at":"2026-04-16T15:09:05.991013+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6a963d0e_257_spec.md","provider":"any","payload_json":"{}"},{"id":"d47d76d4-b36c-4f50-824f-756a2ecb90c4","title":"[Artifacts] Dashboard artifact type: living web views that auto-update from data sources","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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:07:50.647304+00:00","updated_at":"2026-04-16T15:07:50.647304+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d47d76d4_b36_spec.md","provider":"any","payload_json":"{}"},{"id":"1d1de7bf-8df1-4526-9b08-1931f82a3e47","title":"[Artifacts] Fix /notebooks page 500 error - add missing schema columns","description":"The /notebooks page returns 500 because the notebooks table is missing is_spotlight and tags columns that api.py expects. Need to run a migration to add these columns and verify the page renders.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:05:55.624635+00:00","updated_at":"2026-04-16T15:05:55.624635+00:00","summary":"","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/1d1de7bf_8df_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"5f999c9d-063b-4555-9629-7f4447c5a259","title":"[Artifacts] Make hypothesis evidence cards keyboard-accessible","description":"Improve demoability by making hypothesis evidence cards and action links fully keyboard-accessible with clear focus states and semantic controls across hypothesis detail surfaces.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:05:21.020015+00:00","updated_at":"2026-04-16T15:05:21.020015+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5f999c9d_063_spec.md","provider":"any","payload_json":"{}"},{"id":"11289662-ef97-4658-896e-b3eb5d14e443","title":"[Artifacts] Backfill gene_expression_context for remaining 21 hypotheses","description":"21 hypotheses are still missing gene_expression_context. Backfill with structured markdown covering Allen Brain Atlas expression patterns, cell-type specificity, SEA-AD data, and disease associations for each target gene.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:34:56.778744+00:00","updated_at":"2026-04-16T14:34:56.778744+00:00","summary":"","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/11289662_ef9_spec.md","provider":"any","payload_json":"{}"},{"id":"893367f9-549c-4b7d-a20e-c74f0bf46936","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:31:25.787849+00:00","updated_at":"2026-04-16T14:31:25.787849+00:00","summary":"","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/893367f9-549_artifacts_create_jupyter_notebooks_for_spec.md","provider":"any","payload_json":"{}"},{"id":"a17-25-AVUI0001","title":"[Artifacts] Artifact version browser UI: timeline, diff view, provenance graph","description":"Build UI components for browsing artifact versions. Version timeline sidebar showing all versions with tags and timestamps. Diff view highlighting metadata changes between versions. Provenance graph visualization showing how artifacts derive from each other (reuse subgraph_widget_html pattern). Add to artifact detail pages and analysis detail pages. Depends on: a17-20-VAPI0001, a17-24-REPR0001.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T11:32:14.688583+00:00","updated_at":"2026-04-16T11:32:14.688583+00:00","summary":"","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/a17-25-AVUI0001_version_browser_ui_spec.md","provider":"any","payload_json":"{}"},{"id":"b4decce3-0038-42d8-baf3-6371401a7b1c","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:06:39","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a5e3dc05-420f-4f91-bae1-871c5b38ada1","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:07:53","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"af18d401-16fe-4178-ac53-eb1119220580","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:58:35","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"add4959c-f14f-4fbc-9d20-437f6bd9117b","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:12:17","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"7b09cfd7-dc74-4b91-ab5b-2aabc0841b94","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:15:36","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"14c46dca-72a7-4372-898a-00631903d97b","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:29:33","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"80d0f802-266c-4937-88cc-bd13374c7379","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:22:02","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"822b9ab8-e1fb-4994-be62-7a14fe3a1165","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:24:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"8dd10b8c-6e6b-4854-9e22-58ff723aed4d","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:22:41","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"877e8326-48cc-4aaa-af9b-cbc45e0c8766","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:25:04","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b50485e9-a193-4ddb-bfd2-f1f82643df0e","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:58:50","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c80cfeca-c519-4416-aa51-3644cac89fe8","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:15:06","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"197485b6-8700-48fe-945e-76da1777ad89","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. 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Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 08:05:07","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"0606c3d1-a525-45d3-890f-3798b01478bb","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. 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Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:55:38","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"80695148-1b06-4629-8118-79abe6a9edf7","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:55:17","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b7726b67-ee24-4ad6-aac1-899e790d6633","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:55:01","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"2844c0f7-79ac-4095-97ae-0af9eb69f1de","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:58:41","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ef95105e-dce2-4b57-8d30-e39a5c8f77c8","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"77eecefe-9276-49d5-997f-48206710b1e9","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:51","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"debcde79-f0a9-4f87-bfab-c87b49cdbb71","title":"[Artifacts] Create Jupyter notebooks for top 5 analyses","description":"Generate rendered Jupyter notebooks demonstrating data analysis for the top 5 analyses. Include gene expression plots, pathway enrichment, and statistical tests.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a17-03-116C8FD8","title":"[Artifacts] Build rich notebook viewer page","description":"Improve /notebook/{id} to render Jupyter notebooks with full fidelity: code cells with syntax highlighting, markdown cells, output images/plots, execution metadata. Use nbconvert or client-side rendering. Show table of contents, cell navigation.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:58:13","updated_at":"2026-04-02 09:43:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a17-28-DASH0001","title":"[Artifacts] Dashboard artifact type: living web views that auto-update from data sources","description":"Add dashboard as a new artifact type. Dashboards are HTML templates bound to data sources (SQL queries, artifact references, API endpoints, KG queries). They auto-refresh on a configurable interval and re-render when underlying data changes. Dashboards can be embedded in authored papers or displayed standalone at /dashboard/{id}. They are versioned like any artifact.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:29:10","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-28-DASH0001_dashboard_artifact_type_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"a17-23-MODL0001","title":"[Artifacts] Model artifact type: biophysical, deep learning, statistical models","description":"Define model artifact metadata schema supporting multiple model families: biophysical (equations, parameters, species, reactions), deep_learning (architecture, framework, layer_config, training_metrics, checkpoint_path), statistical (model_type, features, coefficients, fit_metrics). Models link to datasets (trained_on), hypotheses (tests/supports), analyses (produced_by), and other models (fine_tuned_from). Register via register_model(model_family, title, metadata, trained_on_dataset_id). Models are versioned -- each training run or parameter update creates a new version. Depends on: a17-18-VERS0001, a17-19-TYPE0001.","status":"done","priority":89,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:53:32","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-23-MODL0001_model_artifact_type_spec.md","provider":"any","payload_json":"{}"},{"id":"218a4d85-6022-407b-a659-562a10ca3d41","title":"[Artifacts] CI: Register generated notebook stubs in DB coverage","description":"Update scripts/artifacts_notebook_coverage_ci.py so generated notebook stubs are linked in notebooks table, improving measurable coverage for Quest 17.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:03:34.416470+00:00","updated_at":"2026-04-17T05:03:34.416470+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/218a4d85_602_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5}}"},{"id":"a7a07b25-9642-4689-b40f-13a5ff116689","title":"[Artifacts] Heal stale notebook refs in coverage CI","description":"Detect and repair stale notebook_path and notebook link references when notebook files are missing, and emit explicit remediation summary.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:20:53.802444+00:00","updated_at":"2026-04-16T17:20:53.802444+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a7a07b25_964_spec.md","provider":"any","payload_json":"{}"},{"id":"3b0c93d0-552b-4454-97b6-2bb7d660ab2a","title":"[Artifacts] Generate recent analysis summaries in notebook coverage CI","description":"Extend ci_notebook_coverage.py to emit machine-readable and human-readable summaries for recent completed analyses while preserving coverage/stub behavior for Quest 17 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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:20:10.175996+00:00","updated_at":"2026-04-16T17:20:10.175996+00:00","summary":"","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/3b0c93d0_552_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"3e32e658-1198-4b23-bac0-dc6e3ac9cb99","title":"[Artifacts] Enrich 15+ more targets with PDB/UniProt IDs for Mol* viewers","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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:17:27.699061+00:00","updated_at":"2026-04-16T17:17:27.699061+00:00","summary":"","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/3e32e658_119_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"6483159a-ae48-4602-b07f-443fe701b45b","title":"[Artifacts] Evidence balance matrix: visual for/against balance bar on hypothesis pages","description":"Add a visual evidence balance bar to the Evidence tab on hypothesis pages (Quest 17 A17.6). Shows ratio of supporting vs opposing evidence with strength breakdown (high/medium/low). Sort evidence items by strength. Makes hypothesis pages more compelling for demo.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:11:31.186696+00:00","updated_at":"2026-04-16T17:11:31.186696+00:00","summary":"","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/6483159a_ae4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"5942d9a9-09e5-4607-ad14-c3e18c4f1670","title":"[Artifacts] Resolve migration version collisions for deterministic schema upgrades","description":"Fix duplicate migration number collisions (002/040/041/042) by renumbering conflicting migration files and updating migration metadata strings so migration_runner can execute all migrations deterministically.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:11:06.605274+00:00","updated_at":"2026-04-16T17:11:06.605274+00:00","summary":"","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/5942d9a9_09e_spec.md","provider":"any","payload_json":"{}"},{"id":"f3f89c06-7ffd-4472-8b73-9ef9196ae0a7","title":"[Artifacts] Populate structural_data (PDB/UniProt/AlphaFold) for top 15 demo targets to activate Mol* viewer","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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:10:06.453208+00:00","updated_at":"2026-04-16T17:10:06.453208+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/f3f89c06_7ff_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"5012ddb4-d9f2-403c-951d-718dec624ded","title":"[Artifacts] Harden notebook stub filename and HTML escaping","description":"Improve ci_notebook_coverage.py to sanitize notebook stub filenames for unsafe analysis IDs and escape rendered HTML fields to avoid malformed pages/XSS in generated 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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:06:34.899477+00:00","updated_at":"2026-04-16T17:06:34.899477+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5012ddb4_d9f_spec.md","provider":"any","payload_json":"{}"},{"id":"fc23fb55-8d86-4425-9189-cfd9873b7842","title":"[Artifacts] Link generated notebook stubs into artifacts registry","description":"Update notebook coverage CI flow so newly generated notebook stubs are registered in artifacts tables and reflected in DB-linked coverage metrics.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:04:26.154515+00:00","updated_at":"2026-04-16T17:04:26.154515+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/fc23fb55_8d8_spec.md","provider":"any","payload_json":"{}"},{"id":"87de622d-5608-4717-b583-0c36c93a44bb","title":"[Artifacts] Canonicalize malformed /artifacts/// links","description":"Fix malformed duplicate-slash artifact URLs (e.g., /artifacts///) causing link-check failures by normalizing link generation and adding guard logic/tests where appropriate.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:02:42.252968+00:00","updated_at":"2026-04-16T17:02:42.252968+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/87de622d_560_spec.md","provider":"any","payload_json":"{}"},{"id":"ff90b5cf-54bf-45f6-a31d-36ad5bc87135","title":"[Artifacts] Harden Mol* fallback gene escaping and URL encoding","description":"Improve /hypothesis Mol* dynamic fallback by JS-safe gene literal handling and URL encoding for manual RCSB/AlphaFold search links to keep 3D artifact panel reliable for unusual target gene symbols.\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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:01:43.430919+00:00","updated_at":"2026-04-16T17:01:43.430919+00:00","summary":"","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/ff90b5cf_54b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"5c9770d2-c54e-4b7e-ab10-5f97c1aa4775","title":"[Artifacts] Repair broken internal links on /artifacts and /agent-performance","description":"Investigate HTTP 0 link failures reported by CI for /artifacts and /agent-performance; patch route/link generation and verify via targeted 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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:59:00.423935+00:00","updated_at":"2026-04-16T16:59:00.423935+00:00","summary":"","completion_notes":"Verified: commit 1ac5d3254 (Is-ancestor of current main HEAD 18536b033) contains the link checker fix. All endpoints return 200/3xx. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5c9770d2_c54_spec.md","provider":"any","payload_json":"{}"},{"id":"6110182f-0cfb-4a6d-8b6f-ba18acefea89","title":"[Artifacts] Integrate 3D protein structure viewer (Mol* or NGL)","description":"Embed Mol* or NGL Viewer for protein structures. Fetch from PDB/AlphaFold. Display on entity pages for proteins. Add to analysis artifacts. Show predicted vs. experimental structures side-by-side. Quest 17.\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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:58:14.712417+00:00","updated_at":"2026-04-16T16:58:14.712417+00:00","summary":"","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/6110182f_0cf_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8}}"},{"id":"11d9d78b-9f47-43e5-aa8d-fecb2ce1fb6f","title":"[Artifacts] Seed notebooks DB from existing site/notebooks/ files","description":"The notebooks table is empty despite 100+ notebook files in site/notebooks/. Seed the DB by scanning the directory, extracting metadata from .ipynb files, and inserting records to make /notebooks non-empty for Quest 17.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:46:05.805178+00:00","updated_at":"2026-04-16T16:46:05.805178+00:00","summary":"","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/11d9d78b_9f4_spec.md","provider":"any","payload_json":"{}"},{"id":"b1802f3a-ff6e-4920-b723-b474c5631b29","title":"[Artifacts] Register existing notebooks in database","description":"98 Jupyter notebook HTML files exist in site/notebooks/ but notebooks table has 0 entries. Register all existing notebooks in the DB by mapping filenames to analysis IDs so they appear on analysis/hypothesis pages (Linked Notebooks section).\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:39:17.402351+00:00","updated_at":"2026-04-16T16:39:17.402351+00:00","summary":"","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/b1802f3a_ff6_spec.md","provider":"any","payload_json":"{}"},{"id":"96e927b5-46cd-49e8-813d-6c3d5a7b4913","title":"[Artifacts] Add Mol* 3D protein viewers to hypothesis pages with target genes","description":"Hypotheses referencing specific proteins/genes should embed interactive Mol* viewers. Check which already have them, add to those missing.\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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:34:10.590731+00:00","updated_at":"2026-04-16T16:34:10.590731+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/96e927b5_mol_protein_viewer_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"a17-04-8AF4EBD9","title":"[Artifacts] Gene expression analysis notebook - SEA-AD","description":"Create real Jupyter notebook analyzing SEA-AD data: fetch cell-type expression from Allen API, compute differential expression (microglia vs neurons for AD genes), generate heatmap and volcano plot, pathway enrichment via Enrichr, summary findings. Register in DB.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:47:15","updated_at":"2026-04-02 09:43:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"a17-29-EMBD0001","title":"[Artifacts] Artifact embed rendering: resolve {{artifact:ID}} markers in documents","description":"Build a rendering engine that resolves {{artifact:ID}} embed markers in authored papers and dashboards. When rendering, look up the referenced artifact and produce inline HTML: figures render as images with captions, datasets render as summary tables, models render as metric cards, hypotheses render as scored cards with evidence, dashboards render as live iframes. Support {{artifact:ID:view}} where view can be summary, full, chart, or table.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 04:59:43","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-29-EMBD0001_artifact_embed_rendering_spec.md","provider":"any","payload_json":"{}"},{"id":"a17-24-REPR0001","title":"[Artifacts] Reproducible analysis chains: pin artifact versions in analysis specs","description":"Extend analysis specifications to include a pinned_artifacts field: list of (artifact_id, version_number) tuples that fix the exact inputs used. When an analysis runs, auto-snapshot all input artifact versions into the analysis provenance_chain. Add verify_reproducibility(analysis_id) that checks whether pinned versions still exist and match content_hash. Add /api/analysis/{id}/provenance endpoint showing full input/output artifact DAG with versions. This ensures any reasoning chain can be replayed with identical inputs. Depends on: a17-20-VAPI0001.","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:01:39","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-24-REPR0001_reproducible_analysis_chains_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"631c0248-c30b-41d0-90d1-c894b71a5a29","title":"[Artifacts] Build figure gallery and citation system","description":"Create /figures page and per-hypothesis figure galleries. Display figures extracted via paper_figures() tool. Add citation links, PMC deep links, alt text. Enable agents to reference specific figures in debates. Quest 17.\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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:26:38.812661+00:00","updated_at":"2026-04-16T20:26:38.812661+00:00","summary":"","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/631c0248_c30_spec.md","provider":"any","payload_json":"{}"},{"id":"a17-30-DREF0001","title":"[Artifacts] Dashboard data source refresh engine","description":"Build the engine that evaluates dashboard data sources and re-renders dashboard HTML. Supports: sql_query (run against scidex.db), artifact_ref (fetch latest version of an artifact), kg_query (query knowledge graph), api_endpoint (fetch from internal API). Results injected into template_html at {{data:KEY}} placeholders. Track last_rendered_at and cache rendered HTML. Trigger re-render on interval or when source artifacts are updated.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:26:36","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a17-30-DREF0001_dashboard_refresh_engine_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6}}"},{"id":"6b8a1f3c-789f-40d3-a453-3c5390a91b1b","title":"[Artifacts] Score 20 unscored artifacts for quality","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\n500 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:07:20.206295+00:00","updated_at":"2026-04-17T05:07:20.206295+00:00","summary":"","completion_notes":"Verified: commit 3ff898d63 is on origin/main (IS ancestor of HEAD 3adfc59a1). The scoring script was previously fixed to use `quality_score IS NULL` and cross-reference the papers table. Ran the script and scored 20 more paper artifacts (avg quality 0.900). No additional code changes needed — the task was already addressed in the prior run. [task:6b8a1f3c-789f-40d3-a453-3c5390a91b1b]","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"038fdcec-ba13-4929-af22-c96b139dbea6","title":"[Artifacts] Score 20 unscored artifacts for quality","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\n400 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:42:50.156607+00:00","updated_at":"2026-04-16T22:42:50.156607+00:00","summary":"","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}}"},{"id":"9d76b427-9a2f-4921-862f-cab47b91ea9a","title":"[Artifacts] Score 20 unscored artifacts for quality","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\n500 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:42:59.337459+00:00","updated_at":"2026-04-16T21:42:59.337459+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"0cb88d39-1b95-4fcb-9c73-0b89aca7cbe1","title":"[Artifacts] Score 20 unscored artifacts for quality","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\n500 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:38:48.134364+00:00","updated_at":"2026-04-16T21:38:48.134364+00:00","summary":"","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}}"},{"id":"4a10b553-254c-4566-918b-de50dbd2e5e7","title":"[Artifacts] Score 20 unscored artifacts for quality","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\n500 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:31:41.830952+00:00","updated_at":"2026-04-16T21:31:41.830952+00:00","summary":"","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}}"},{"id":"9ffdbdeb-a309-4c03-b1f4-6a5091fbb6f3","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create the /artifacts page showing all artifacts with filtering by type, search, and links to detail pages. Key demo surface for Quest 17.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:10:04.840983+00:00","updated_at":"2026-04-16T21:10:04.840983+00:00","summary":"","completion_notes":"Verification evidence: /artifacts page exists and returns 200, has filtering by artifact_type, search via q param, and links to detail pages. All acceptance criteria met.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5b6097a8-f06_artifacts_build_artifact_gallery_page_a_spec.md","provider":"any","payload_json":"{}"},{"id":"f3c9fb95-4eb3-4ab7-8ab6-bf9f3ae6facd","title":"[Artifacts] Score 20 unscored artifacts for quality","description":"520 artifacts lack quality scores. Evaluate each for completeness, accuracy, and presentation.\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,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:08:15.905642+00:00","updated_at":"2026-04-16T21:08:15.905642+00:00","summary":"","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/f3c9fb95_artifact_scoring_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"fe72b392-1da0-408f-8659-552fc8c7d21b","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:55:07.282964","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"78d97e78-8dd6-4ba0-b67f-c2978d4e152e","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:37:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5a5907bd-08d2-4ede-92d1-7066b2456ec5","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:03:20","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d805db90-9970-40bb-9349-0aac53b756ed","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:00:46","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"1cb80090-2ce6-4cfb-bead-f307eb3c6d58","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:11:12","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"62200c0a-fb95-458a-9b5e-9265f367cd8e","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:16:29","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c4a61f49-d2b6-4704-9e7f-f81142f6822f","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:28:13","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"bbb695b8-8234-4629-b763-8e0b1038128b","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:22:11","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e77e1f28-68aa-47d0-aef5-27bbb917ef83","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:27:20","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"6317be66-d837-4c29-aee3-38086a3047ea","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:27:20","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"83194e45-d010-40ff-9f74-a3cd254106a6","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:55:20","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"f642d540-feb4-45e4-9b6c-ab9345ebc6b8","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:56:57","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"666a70b3-9531-4236-acdf-819434ae2c09","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:04:47","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"98fe550b-6a48-4e51-9e06-5dd166fac6e3","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:36:56","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"5f2520e9-cd4f-43a3-8654-6d0a8917bec5","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:27:22","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"d825ae56-b5a5-4758-9c58-65e550927fc0","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. 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Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:59:26","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"dafb0ad3-8177-449a-a720-e940bc660133","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:41:00","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"86012349-4c9d-4ca9-ae92-2fad79ddbd73","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:40","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"b9807f4f-89b8-446c-95bb-bb879b5863e5","title":"[Artifacts] Build artifact gallery page at /artifacts","description":"Create a browsable gallery of all artifacts (figures, notebooks, code blocks) with filtering by type and search. Link to parent analyses and hypotheses.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:51:15","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"a17-05-D7D1D5F8","title":"[Artifacts] Evidence matrix on hypothesis pages","description":"Add structured evidence table on hypothesis detail pages. For each citation: PMID, title, year, relevance score (0-1), evidence type (supports/contradicts/neutral), key finding excerpt. Sortable by relevance. Color-coded rows. Pull from hypothesis evidence_for/evidence_against fields.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:51:43","updated_at":"2026-04-02 09:43:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"9f0f0742-7c6a-40c6-b4b6-f3e81ee139d8","title":"[Forge] Register AI-generated image artifact subtype in artifact registry","description":"Ensure artifact_registry handles AI-generated images: figure type with generation_method=ai metadata. Add 'ai_image' to canonical subtypes if needed. Verify deduplication works for regenerated images.\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":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:11:49.456916+00:00","updated_at":"2026-04-17T11:11:49.456916+00:00","summary":"","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/9f0f0742_7c6_spec.md","provider":"any","payload_json":"{}"}],"reviews":[{"task_count":3,"total_tokens":150000,"total_cost":0.45000000000000007,"output_score":1376.2,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374745+00:00"}],"effectiveness":{"task_count":3,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":904,"total_kg_edges":36432,"total_papers":1695,"total_tokens":150000,"total_duration":2152403.892382,"avg_impact":68810.0,"avg_effectiveness":1376.2},"spec_content":"---\ntitle: \"Quest: Artifacts\"\ndescription: \"Rich, debatable artifacts with full provenance — experiments, models, datasets, notebooks, dynamic documents — each with lineage, evidence profiles, and governed schemas\"\ntype: quest\nlayer: Cross-cutting\npriority: 90\nstatus: active\nquest_id: 8db4834c-51e\nspec_path: docs/planning/specs/quest_artifacts_spec.md\n---\n\n# Quest: Artifacts\n\n**Layer:** Cross-cutting\n**Priority:** P90\n**Status:** active\n\n## Vision\n\nEvery piece of knowledge in SciDEX is an **artifact** — a versioned, provenanced, debatable\nunit of scientific evidence. Artifacts range from raw data (papers, datasets, experiments)\nthrough derived knowledge (hypotheses, KG edges, models) to composed outputs (authored papers,\ndashboards, analyses).\n\nEvery artifact tracks:\n- **Origin** — where it came from (internal/external), with canonical URL\n- **Lineage** — full chain of parent artifacts and processing steps that produced it\n- **Evidence profile** — accumulated debates, citations, usage signals, quality trajectory\n- **Schema compliance** — validated metadata per governed schema\n- **Versions** — immutable snapshots with diffs and provenance per version\n\nArtifacts are **debatable** — any artifact can be the subject of structured multi-agent debate\n(see q-artifact-debates). Evidence accumulates through usage, citation, replication, and debate,\ncreating a self-correcting quality signal. Highly-valued artifacts rise; poorly-supported ones\nare flagged for review.\n\nArtifact schemas **evolve through governance** (see q-schema-governance) — agents propose new\nfields and types through the Senate, ensuring integrity while adapting to new scientific needs.\n\n## Related Quests\n\n| Quest | Relationship |\n|-------|-------------|\n| **Experiment Extraction** (q-experiment-extraction) | Extracts structured experiments from papers as rich artifacts |\n| **Artifact Debates** (q-artifact-debates) | Makes any artifact debatable; evidence accumulation |\n| **Schema Governance** (q-schema-governance) | Governs how artifact schemas evolve |\n| **Epistemic Rigor** (q-epistemic-rigor) | Falsifiability, evidence chains, trust propagation |\n| **Evidence Chains** (b5298ea7) | Normalized evidence entries with provenance |\n| **Knowledge Units** (08c73de3) | Atomic, composable evidence blocks |\n\n## Open Tasks\n\n### Foundation\n- [ ] [Artifacts] Add version tracking schema to artifacts table (P95) — a17-18-VERS0001\n- [ ] [Artifacts] Extend artifact_type to include figure, code, model, protein_design, dataset (P94) — a17-19-TYPE0001\n- [ ] [Artifacts] General-purpose artifact origin tracking (origin_type, origin_url) (P93) — a17-26-ORIG0001\n- [ ] [Artifacts] Version-aware artifact registry API: create_version, get_history, diff (P93) — a17-20-VAPI0001\n\n### Artifact Types\n- [ ] [Artifacts] External dataset references: track datasets like we track papers (P92) — a17-21-EXTD0001\n- [ ] [Artifacts] Tabular dataset support: schema tracking, column metadata, linkage to KG (P91) — a17-22-TABL0001\n- [ ] [Artifacts] Authored paper artifact type: dynamic documents that embed other artifacts (P91) — a17-27-APAP0001\n- [ ] [Artifacts] Dashboard artifact type: living web views that auto-update from data sources (P90) — a17-28-DASH0001\n- [ ] [Artifacts] Model artifact type: biophysical, deep learning, statistical models (P89) — a17-23-MODL0001\n\n### Rendering & Reproducibility\n- [ ] [Artifacts] Artifact embed rendering: resolve {{artifact:ID}} markers in documents (P88) — a17-29-EMBD0001\n- [ ] [Artifacts] Reproducible analysis chains: pin artifact versions in analysis specs (P87) — a17-24-REPR0001\n- [ ] [Artifacts] Dashboard data source refresh engine (P86) — a17-30-DREF0001\n\n### UI\n- [ ] [Artifacts] Build artifact gallery page at /artifacts (P85)\n- [ ] [Artifacts] Artifact version browser UI: timeline, diff view, provenance graph (P85) — a17-25-AVUI0001\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- [ ] >80% of artifacts have non-null structured metadata\n- [ ] Evidence profiles visible on all artifact detail pages\n- [ ] Processing step lineage captured for derived artifacts\n- [ ] Schema validation active for all artifact types\n\n## Work Log\n\n_No entries yet._\n\n## Notebook Quality Initiative (2026-04-07)\n\n### Problem\nOf 358 registered notebooks:\n- 273 are rich (>200KB, real Jupyter output with code cells + figures)\n- 67 are stubs (<10KB, empty HTML shells ~800 bytes)\n- 18 are thin summaries (10-50KB, no jp-Notebook class)\n- 85 total are not real Jupyter output\n\nStubs show as broken/empty when users click notebook links from analyses.\n\n### Goals\n1. Zero stub notebooks (<10KB) — regenerate from analysis data or archive\n2. All 18 spotlight notebooks must have >50KB with executed code cells\n3. Every notebook link from /analyses/ pages leads to real content\n4. Notebook quality score visible on /notebooks page\n\n### Approach\n- Use `scripts/generate_nb_sea_ad_001.py` as template for regeneration\n- Pull hypotheses + debate transcripts from the linked analysis\n- Call real Forge tools (PubMed, STRING, Reactome, Enrichr) for data\n- Execute via nbconvert ExecutePreprocessor\n- Update DB rendered_html_path + file_path\n\n### Tasks\n- P94: Ensure all 18 spotlight notebooks have rich content\n- P92: Audit and regenerate 67 stub notebooks\n- P90: Review notebook links from analysis pages\n","spec_html":"

Quest: Artifacts

Layer: Cross-cutting\nPriority: P90\nStatus: active

Vision

Every piece of knowledge in SciDEX is an artifact — a versioned, provenanced, debatable
unit of scientific evidence. Artifacts range from raw data (papers, datasets, experiments)
through derived knowledge (hypotheses, KG edges, models) to composed outputs (authored papers,
dashboards, analyses).

Every artifact tracks:\n

  • Origin — where it came from (internal/external), with canonical URL
    • \n
  • Lineage — full chain of parent artifacts and processing steps that produced it
    • \n
  • Evidence profile — accumulated debates, citations, usage signals, quality trajectory
    • \n
  • Schema compliance — validated metadata per governed schema
    • \n
  • Versions — immutable snapshots with diffs and provenance per version
    • \n

Artifacts are debatable — any artifact can be the subject of structured multi-agent debate
(see q-artifact-debates). Evidence accumulates through usage, citation, replication, and debate,
creating a self-correcting quality signal. Highly-valued artifacts rise; poorly-supported ones
are flagged for review.

Artifact schemas evolve through governance (see q-schema-governance) — agents propose new
fields and types through the Senate, ensuring integrity while adapting to new scientific needs.

Related Quests

QuestRelationship
Experiment Extraction (q-experiment-extraction)Extracts structured experiments from papers as rich artifacts
Artifact Debates (q-artifact-debates)Makes any artifact debatable; evidence accumulation
Schema Governance (q-schema-governance)Governs how artifact schemas evolve
Epistemic Rigor (q-epistemic-rigor)Falsifiability, evidence chains, trust propagation
Evidence Chains (b5298ea7)Normalized evidence entries with provenance
Knowledge Units (08c73de3)Atomic, composable evidence blocks
\n

Open Tasks

Foundation

\n
☐ [Artifacts] Add version tracking schema to artifacts table (P95) — a17-18-VERS0001
\n
☐ [Artifacts] Extend artifact_type to include figure, code, model, protein_design, dataset (P94) — a17-19-TYPE0001
\n
☐ [Artifacts] General-purpose artifact origin tracking (origin_type, origin_url) (P93) — a17-26-ORIG0001
\n
☐ [Artifacts] Version-aware artifact registry API: create_version, get_history, diff (P93) — a17-20-VAPI0001

Artifact Types

\n
☐ [Artifacts] External dataset references: track datasets like we track papers (P92) — a17-21-EXTD0001
\n
☐ [Artifacts] Tabular dataset support: schema tracking, column metadata, linkage to KG (P91) — a17-22-TABL0001
\n
☐ [Artifacts] Authored paper artifact type: dynamic documents that embed other artifacts (P91) — a17-27-APAP0001
\n
☐ [Artifacts] Dashboard artifact type: living web views that auto-update from data sources (P90) — a17-28-DASH0001
\n
☐ [Artifacts] Model artifact type: biophysical, deep learning, statistical models (P89) — a17-23-MODL0001

Rendering & Reproducibility

\n
☐ [Artifacts] Artifact embed rendering: resolve {{artifact:ID}} markers in documents (P88) — a17-29-EMBD0001
\n
☐ [Artifacts] Reproducible analysis chains: pin artifact versions in analysis specs (P87) — a17-24-REPR0001
\n
☐ [Artifacts] Dashboard data source refresh engine (P86) — a17-30-DREF0001

UI

\n
☐ [Artifacts] Build artifact gallery page at /artifacts (P85)
\n
☐ [Artifacts] Artifact version browser UI: timeline, diff view, provenance graph (P85) — a17-25-AVUI0001

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
\n
☐ >80% of artifacts have non-null structured metadata
\n
☐ Evidence profiles visible on all artifact detail pages
\n
☐ Processing step lineage captured for derived artifacts
\n
☐ Schema validation active for all artifact types

Work Log

_No entries yet._

Notebook Quality Initiative (2026-04-07)

Problem

\nOf 358 registered notebooks:\n
  • 273 are rich (>200KB, real Jupyter output with code cells + figures)
    • \n
  • 67 are stubs (<10KB, empty HTML shells ~800 bytes)
    • \n
  • 18 are thin summaries (10-50KB, no jp-Notebook class)
    • \n
  • 85 total are not real Jupyter output
    • \n

Stubs show as broken/empty when users click notebook links from analyses.

Goals

\n
  • Zero stub notebooks (<10KB) — regenerate from analysis data or archive
    • \n
  • All 18 spotlight notebooks must have >50KB with executed code cells
    • \n
  • Every notebook link from /analyses/ pages leads to real content
    • \n
  • Notebook quality score visible on /notebooks page

    • Approach

    \n
    • Use scripts/generate_nb_sea_ad_001.py as template for regeneration
      • \n
    • Pull hypotheses + debate transcripts from the linked analysis
      • \n
    • Call real Forge tools (PubMed, STRING, Reactome, Enrichr) for data
      • \n
    • Execute via nbconvert ExecutePreprocessor
      • \n
    • Update DB rendered_html_path + file_path
      • \n
    \n

    Tasks

    \n
    • P94: Ensure all 18 spotlight notebooks have rich content
      • \n
    • P92: Audit and regenerate 67 stub notebooks
      • \n
    • P90: Review notebook links from analysis pages
      • \n

    ","spec_file":"quest_artifacts_spec.md","commits":[{"hash":"abc8d0179","message":"[Exchange] Verify /challenge broken links are false positives: all 36 pages return 200 [task:e5a1490f-9ab6-4275-a96b-bd34ceb84fcf]","date":"2026-04-17"},{"hash":"440d6072c","message":"[Senate] Final work log update: document branch push to remote [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"8eefea2c0","message":"[Atlas] Add redirects in api.py for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"bdf2e04e8","message":"[Atlas] Document /mission HTTP 0 fix: already addressed in c5d7a696 [task:e50f7fed-ccde-4104-b98a-205bb500e792]","date":"2026-04-17"},{"hash":"f39b5d3b0","message":"[Atlas] Fix broken /entity links: clean corrupted data + add cleanup script [task:326c7abd-3ad2-4ae5-9a0e-e9981d611890]","date":"2026-04-17"},{"hash":"a4954541c","message":"Squash merge: orchestra/task/09b3a393-broken-links-in-api-http-0-30-links (1 commits)","date":"2026-04-17"},{"hash":"40b62c4b8","message":"[Atlas] Verify /api broken links: all 10 endpoints HTTP 200, no code changes needed [task:09b3a393-777f-4379-85c6-2bf55f6e69c0]","date":"2026-04-17"},{"hash":"6e54e1ccc","message":"On orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: stash unrelated changes","date":"2026-04-17"},{"hash":"53f087f8e","message":"index on orchestra/task/326c7abd-broken-links-in-entity-http-400-64-links: f3b466710 [Atlas] Add /mission→/missions redirect in api.py; confirm /mission broken links are false positives [task:c0d66faa-91be-41e3-909d-d6359c5b936e]","date":"2026-04-17"},{"hash":"58b5eb786","message":"[Atlas] Verify /analysis broken links: all 10 pages HTTP 200, false positive [task:a7c6d6d2-17bb-4e1c-b131-10677c65e9d0]","date":"2026-04-17"},{"hash":"0be6ce64a","message":"[Senate] Update spec work log: service verified operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"53c7da02f","message":"Squash merge: orchestra/task/c13f680a-broken-links-in-site-http-404-198-links (1 commits)","date":"2026-04-17"},{"hash":"20a14e537","message":"[Atlas] Fix /site/notebooks/ 404 in api.py: add redirect to /notebooks/ route [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"},{"hash":"52e043bda","message":"Squash merge: orchestra/task/c5d7a696-broken-links-in-target-http-0-765-links (3 commits)","date":"2026-04-17"},{"hash":"aead3c46d","message":"[Atlas] Restore nb-top5- prefix-stripping fallback removed in prior commit [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"1786c8cc4","message":"[Atlas] Wire up suppress_transient_http0_noise() in link checker to prevent false-positive tasks [task:c5d7a696-2296-468a-83a2-2d3cabc6901e]","date":"2026-04-17"},{"hash":"13c833f16","message":"[Atlas] Add redirects for /site/notebooks/ and root-level .ipynb URLs to /notebooks/ path [task:f92194bf-f23c-4bf3-97d4-676c02f5fb42]","date":"2026-04-17"},{"hash":"25d912117","message":"[Senate] Update spec work log: document MERGE GATE rebase fix [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"06151c073","message":"[Senate] Update spec: verify service operational, no code changes needed [task:c2780f51-4c91-4cae-a1ff-4edaf6375c59]","date":"2026-04-17"},{"hash":"dc15730ae","message":"[Atlas] Fix /notebook top5-SDA-* broken links: add prefix-stripping fallback in notebook_detail [task:c13f680a-60bf-49f3-aa42-a05602d77405]","date":"2026-04-17"}],"related_quests":[{"name":"Epistemic Rigor","layer":"Cross-cutting","priority":95,"status":"active","description":"Evolve SciDEX toward rigorous scientific epistemology: 6-tier epistemic classification (T0 axiom → T5 contested) with asymmetric promotion/demotion (Gödel Machine principle), adversarial Falsifier persona as 5th debate round, proof-gated KG updates with contradiction checking against established knowledge, GFlowNet-inspired diverse hypothesis portfolio maintenance (anti-monoculture rules), pre-registration of predictions before analysis, replication status tracking (unreplicated/replicated/failed_replication), and calibration-adjusted believability weights. Every claim must be traceable to ground truth.","task_count":14,"done_count":14},{"name":"Search","layer":"Cross-cutting","priority":95,"status":"active","description":"Universal search across all SciDEX content with autocomplete","task_count":200,"done_count":13},{"name":"Economics","layer":"Cross-cutting","priority":94,"status":"active","description":"Resource economics — token/cost tracking, belief evolution, impact scoring. Extends to quadratic staking (agents stake reputation quadratically for high-confidence assertions), calibration tracking (per-persona hit rate on predictions vs outcomes), GFlowNet-inspired diversity bonuses (reward-proportional resource allocation preserving competing hypotheses), and contested claim prediction markets.","task_count":196,"done_count":9},{"name":"Evolutionary Arenas","layer":"Cross-cutting","priority":73,"status":"active","description":"Elo tournaments × LMSR markets × evolutionary operators for scientific artifacts. Pairwise LLM-judged matches produce quality signals that fuse with market prices; top-ranked artifacts spawn mutate/crossover/refine variants; adaptive loops dig deeper on winners. Bridges Bradley-Terry ≡ Elo ≡ LMSR via shared functional form. Spec: docs/planning/specs/q-evolutionary-arenas_spec.md","task_count":8,"done_count":7},{"name":"Resources","layer":"Cross-cutting","priority":70,"status":"active","description":"Resource tracking — Bedrock costs, API call logging, budget monitoring","task_count":1,"done_count":1},{"name":"UI","layer":"Cross-cutting","priority":66,"status":"active","description":"UI/Infrastructure — consistent styling, responsive design, loading states","task_count":933,"done_count":173}]}