{"quest":{"id":"415b277f-03b","name":"Atlas","description":"Living knowledge graph + world model — multi-representation scientific knowledge. Includes automated gap detection pipeline, gap prioritization, and continuous knowledge frontier expansion.","layer":"Atlas","priority":80,"status":"active","created_at":"2026-04-02T10:00:57.209491+00:00","updated_at":"2026-04-03 20:28:13"},"tasks":[{"id":"92bf5209-30a6-41d0-9c90-7ef0a0763190","title":"[Atlas] Fix /atlas 500 error — demo-critical layer page broken","description":"The /atlas page returns Internal Server Error (500). This is one of the five core layers and must work for demo. Investigate and fix the root cause.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"running","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"2","started_at":"2026-04-17T22:14:05.346462+00:00","completed_at":"2026-04-17T18:27:16.764446+00:00","updated_at":"2026-04-17T22:14:21.065409+00:00","summary":"","completion_notes":"In scidex-route-health.service line 9, change ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/ci_route_health.py to ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/scripts/ci_route_health.py (the replacement already exists at scripts/ci_route_health.py)\n\nChanged files:\n- .gitignore\n- .orchestra-slot.json\n- agent.py\n- api.py\n- api_shared/db.py\n- api_shared/nav.py\n- ci_route_health.py\n- ci_snapshot_prices.py\n- cli.py\n- docs/planning/specs/00739e13_fab_spec.md\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0a4a42ea_f2c_spec.md\n- docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\n- docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\n- docs/planning/specs/0d37548c_12f_spec.md\n- docs/planning/specs/0de12ae3_ba9_spec.md\n- docs/planning/specs/13d17f9d_fc6_spec.md\n- docs/planning/specs/1668104c_69f_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/19d7e4f1_87c_spec.md\n- docs/planning/specs/1a33a296_e05_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/245a4f77_da9_spec.md\n- docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\n- docs/planning/specs/2679e2c9_852_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/355a0e0b_92d_spec.md\n- docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\n- docs/planning/specs/39f47701_938_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n\nDiff stat:\n.gitignore | 2 -\n .orchestra-slot.json | 2 +-\n agent.py | 54 +-\n api.py | 3130 ++----\n api_shared/db.py | 30 +-\n api_shared/nav.py | 8 +-\n ci_route_health.py | 204 -\n ci_snapshot_prices.py | 104 -\n cli.py | 61 -\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\n docs/planning/specs/051daf58_f92_spec.md ","last_error":"Review gate REVISE attempt 4/10: scidex-route-health.service line 9 ExecStart still references /home/ubuntu/scidex/ci_route_health.py which this diff deletes, breaking the live systemd route-health job on merge — this exact blocker was flagged in all three prior reviews and remains unresolved","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/92bf5209_30a_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:25:43\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"_watchdog_repair_task_id\": \"b8520347-1c52-4f7d-9153-d1c0c3e25e39\", \"_watchdog_repair_created_at\": \"2026-04-17T13:10:04.665835+00:00\", \"_gate_retry_count\": 4, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": \"scidex-route-health.service line 9 ExecStart still references /home/ubuntu/scidex/ci_route_health.py which this diff deletes, breaking the live systemd route-health job on merge \\u2014 this exact blocker was flagged in all three prior reviews and remains unresolved\", \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_last_instructions\": \"In scidex-route-health.service line 9, change ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/ci_route_health.py to ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/scripts/ci_route_health.py (the replacement already exists at scripts/ci_route_health.py)\", \"_gate_branch\": \"orchestra/task/92bf5209-atlas-500-error-demo-critical-layer-page\", \"_gate_changed_files\": [\".gitignore\", 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\"docs/planning/specs/55888d47-5c2c-4a80-b007-2bbdc83a81ff_service_down_connection_failure_spec.md\", \"docs/planning/specs/55e3ea08_76c2_atlas_reduce_wiki_kg_link_backlog_spec.md\", \"docs/planning/specs/5a10152f_8bd_spec.md\", \"docs/planning/specs/5faca020_wiki_quality_review_spec.md\", \"docs/planning/specs/692f13b8_876_spec.md\", \"docs/planning/specs/6d5f040f-b3e2-431d-8345-d780f32e3ccb_spec.md\", \"docs/planning/specs/6db7722d_16b_spec.md\", \"docs/planning/specs/6e7d8631_63f_spec.md\", \"docs/planning/specs/7221a2c1-99dc-4f7a-aa92-56dd0a697a7e_broken_links_in_experiment_http_404_197_spec.md\", \"docs/planning/specs/77718e75-4f3d-4d2b-afdb-c5cf4152d9b9_spec.md\", \"docs/planning/specs/7c483e0e_5d1_spec.md\", \"docs/planning/specs/7ffcac76_07a_spec.md\", \"docs/planning/specs/85f207f0_aa7_spec.md\", \"docs/planning/specs/86c48eaa_senate_db_fk_integrity_spec.md\", \"docs/planning/specs/88da08c1_3d6_spec.md\", \"docs/planning/specs/8b0d3be0_0e7_spec.md\", \"docs/planning/specs/8b68a328_f55_spec.md\", \"docs/planning/specs/8ba1aa28-6d6e-42a1-810e-65dc17dee42f_spec.md\", \"docs/planning/specs/8f732eff_6f6_spec.md\", \"docs/planning/specs/93e4775f_690_spec.md\", \"docs/planning/specs/9401eb58-32bd-4a83-8823-c562758ca0eb_spec.md\", \"docs/planning/specs/9455e56c_3e3_spec.md\", \"docs/planning/specs/9b2fabdb_60f_spec.md\", \"docs/planning/specs/9b4b1e14_quality_top_hypothesis_pages_spec.md\", \"docs/planning/specs/9f0f0742_7c6_spec.md\", \"docs/planning/specs/9fcdbafb-78da_spec.md\", \"docs/planning/specs/9fef1c13_a80_spec.md\", \"docs/planning/specs/a18d6546_economics_dashboard_spec.md\", \"docs/planning/specs/a27b8c7a-1fa_economics_ci_snapshot_hypothesis_prices_spec.md\", \"docs/planning/specs/a3f12c37_8e0_spec.md\", \"docs/planning/specs/a449718f_532_spec.md\", \"docs/planning/specs/a572c16b_dd6_spec.md\", \"docs/planning/specs/a88f4944_cb09_forge_reduce_pubmed_metadata_backlog_spec.md\", \"docs/planning/specs/a9bbf4cf-0f86-4ed0-9c7b-0e951dc6393b_spec.md\", \"docs/planning/specs/aa1c8ad8_f157_senate_ci_database_integrity_check_spec.md\", \"docs/planning/specs/aa561240_161_spec.md\", \"docs/planning/specs/ab99d47b-41e1-4b96-b27e-6b087a3ce107_spec.md\", \"docs/planning/specs/b13f71fa_465_spec.md\", \"docs/planning/specs/b5053347-091e-46e8-a9d1-f4521e633a91_spec.md\", \"docs/planning/specs/b68277b4_52c_spec.md\", \"docs/planning/specs/b920b7bc_556d_static_site_generation_spec.md\", \"docs/planning/specs/bebcf954_4716_4ef3_a173_47e8c1d414b7_spec.md\", \"docs/planning/specs/c0825bd0-a0b_exchange_enrich_target_profiles_add_dru_spec.md\", \"docs/planning/specs/c0cfc918-a8f_spec.md\", \"docs/planning/specs/c0eee311_f09_spec.md\", \"docs/planning/specs/c0f32d2c-d759-47a8-8cca-04e28aa3c1d2_missing_analysis_html_spec.md\", \"docs/planning/specs/c1227e9b_0ef_spec.md\", \"docs/planning/specs/c172e5fc-48f8-42b3-9284-8e30aa787ba2_spec.md\"], \"_gate_diff_stat\": \".gitignore | 2 -\\n .orchestra-slot.json | 2 +-\\n agent.py | 54 +-\\n api.py | 3130 ++----\\n api_shared/db.py | 30 +-\\n api_shared/nav.py | 8 +-\\n ci_route_health.py | 204 -\\n ci_snapshot_prices.py | 104 -\\n cli.py | 61 -\\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\\n docs/planning/specs/051daf58_f92_spec.md | 63 -\\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\\n docs/planning/specs/0a4a42ea_f2c_spec.md | 36 -\\n ...ken_links_in_entity_http_500_9746_links_spec.md | 32 -\\n .../0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md | 26 -\\n docs/planning/specs/0d37548c_12f_spec.md | 33 -\\n docs/planning/specs/0de12ae3_ba9_spec.md | 32 -\\n docs/planning/specs/13d17f9d_fc6_spec.md | 32 -\\n docs/planning/specs/1668104c_69f_spec.md | 32 -\\n ...efcaa_cc16_static_asset_template_issues_spec.md | 15 -\\n docs/planning/specs/19d7e4f1_87c_spec.md | 32 -\\n docs/planning/specs/1a33a296_e05_spec.md | 36 -\\n .../1d21e01d-0d3_template_link_generation_spec.md | 18 +-\\n .../1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md | 68 -\\n docs/planning/specs/1f62e277_c72_spec.md | 20 -\\n .../1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md | 46 +-\\n ...bb8e888_broken_links_in_target_http_500_spec.md | 9 -\\n docs/planning/specs/2310c378_ea0_spec.md | 92 -\\n docs/planning/specs/245a4f77_da9_spec.md | 35 -\\n ...roken_links_in_entity_http_500_34_links_spec.md | 57 -\\n docs\", \"_gate_history\": [{\"ts\": \"2026-04-17 18:32:52\", \"decision\": \"REVISE\", \"reason\": \"scidex-route-health.service line 9 ExecStart still invokes /home/ubuntu/scidex/ci_route_health.py, which this diff deletes \\u2014 the live route-health systemd job breaks on merge; this is the same unresolved blocker flagged in all prior reviews.\", \"instructions\": \"Update scidex-route-health.service line 9 ExecStart from '/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/ci_route_health.py' to '/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/scripts/ci_route_health.py' (the replacement already exists at that path)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"openai:72\", \"retry_count\": 1}, {\"ts\": \"2026-04-17 18:33:44\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"sonnet-4.6:2\", \"retry_count\": 2}, {\"ts\": \"2026-04-17 18:39:50\", \"decision\": \"REVISE\", \"reason\": \"scidex-route-health.service line 9 ExecStart still references /home/ubuntu/scidex/ci_route_health.py which this diff deletes, breaking the live systemd route-health job on merge \\u2014 same blocker as Review 2, not yet fixed\", \"instructions\": \"In scidex-route-health.service line 9, change ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/ci_route_health.py to ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/scripts/ci_route_health.py\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:2\", \"retry_count\": 3}, {\"ts\": \"2026-04-17 18:45:30\", \"decision\": \"REVISE\", \"reason\": \"scidex-route-health.service line 9 ExecStart still references /home/ubuntu/scidex/ci_route_health.py which this diff deletes, breaking the live systemd route-health job on merge \\u2014 this exact blocker was flagged in all three prior reviews and remains unresolved\", \"instructions\": \"In scidex-route-health.service line 9, change ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/ci_route_health.py to ExecStart=/home/ubuntu/scidex/venv/bin/python3 /home/ubuntu/scidex/scripts/ci_route_health.py (the replacement already exists at scripts/ci_route_health.py)\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"sonnet-4.6:2\", \"retry_count\": 4}]}"},{"id":"4b8e9861-2b8f-4371-80cb-a856977f7557","title":"[Atlas] Versioned tabular datasets — overall coordination quest","description":"Coordination task for the versioned-datasets layer. Tracks the rollout of the dataset registry, the migration to Dolt, the seed dataset growth (from 3 → ~20 over time), and the integration with KG, wiki, benchmarks, squads, and economics. Picks up new sub-tasks from the quest and reprioritizes existing ones based on citation counts. See versioned_datasets_spec.md for the full design.","status":"open","priority":95,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T16:11:49.502677+00:00","updated_at":"2026-04-17T16:11:49.502677+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/versioned_datasets_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"analysis\": 7, \"reasoning\": 7}, \"completion_shas\": [\"666813384ad136b4bb22efb8d24ab30d152fc515\", \"609d90f4b5d7bf5388097a61ff6736ee6d470e5d\"], \"completion_shas_checked_at\": \"2026-04-13T00:16:17.988773+00:00\", \"completion_shas_missing\": [\"d8d68f5f2b65267ebf458777166eb1f25ca68c57\", \"92594085408808b6fd8922c9bda5db367c40674a\", \"1b27977bf66f8c15577c5e0bb9e56c43478ef0c4\"]}"},{"id":"ecf128f4-495b-4a89-8909-3f3ba5d00aff","title":"[Atlas] Squad findings bubble-up driver (driver #20)","description":"Recurring driver. Walk squad_findings rows with bubble_up_status='reviewed' and merge them into the global participation tables (agent_contributions tagged as squad_finding). The downstream v1 emit_rewards + v2 backprop_credit drivers will pay each squad member proportionally on the next cycle. Idempotent. Uses `python3 -m economics_drivers.squads.cli bubble`. See research_squads_spec.md driver #20.","status":"open","priority":94,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:24:29.644779+00:00","updated_at":"2026-04-17T17:14:49.557632+00:00","summary":"","completion_notes":"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\n\nChanged files:\n- .gitignore\n- agent.py\n- api_shared/db.py\n- api_shared/nav.py\n- check_pubmed_pipeline_status.py\n- ci_route_health.py\n- cli.py\n- docs/planning/specs/00739e13_fab_spec.md\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0a4a42ea_f2c_spec.md\n- docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\n- docs/planning/specs/0d37548c_12f_spec.md\n- docs/planning/specs/0de12ae3_ba9_spec.md\n- docs/planning/specs/13d17f9d_fc6_spec.md\n- docs/planning/specs/1668104c_69f_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/19d7e4f1_87c_spec.md\n- docs/planning/specs/1a33a296_e05_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/245a4f77_da9_spec.md\n- docs/planning/specs/2679e2c9_852_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/355a0e0b_92d_spec.md\n- docs/planning/specs/39f47701_938_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n- docs/planning/specs/3eb45ac3_complete_application_server_failure_spec.md\n- docs/planning/specs/3fea4720-77a6-4a98-999b-0b54c81cae2e_broken_links_in_analysis_http_404_10_links_spec.md\n- docs/planning/specs/42320e63_d82_spec.md\n- docs/planning/specs/43abc1dc_631_spec.md\n- docs/planning/specs/4a789ba1_bd0_spec.md\n\nDiff stat:\n.gitignore | 2 -\n agent.py | 54 +-\n api_shared/db.py | 30 +-\n api_shared/nav.py | 8 +-\n check_pubmed_pipeline_status.py | 98 -\n ci_route_health.py | 204 -\n cli.py | 61 -\n docs/planning/specs/00739e13_fab_spec.md | 22 +-\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\n docs/planning/specs/051daf58_f92_spec.md | 63 -\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\n docs/planning/specs/0850f78f_f00_spec.md | 57 -\n docs/planning/specs/0a4a42ea_f2c_spec.md | 36 -\n .../0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md | 26 -\n docs/planning/specs/0d37548c_12f_spec.md ","last_error":"Review gate REVISE: 10 blocked merge attempts; escalated via safety>=9 capability requirement","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/research_squads_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 6, \"analysis\": 6, \"safety\": 9}, \"completion_shas\": [\"f7cb6927272d6c5e9135ac34d7ca95be0ac5aa56\", \"d47a99f6e9eff8f0e6b44af26a2fce90c87f6cf6\", \"85a74200c760d239e45004790d704caf551baad0\", \"b658b96f7d55bdc7e536c36e362c3a5739a6ce4e\"], \"completion_shas_checked_at\": \"2026-04-12T23:51:28.268621+00:00\", \"completion_shas_missing\": [\"4e033bec569f7ffc8f590365b662a1ba4dbc23af\", \"4bb0893f1b8ce06a9bec87dc2832c95ed8559ce3\"], \"_gate_retry_count\": 0, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"_gate_last_instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"_gate_branch\": \"orchestra/task/ecf128f4-squad-findings-bubble-up-driver-driver-2\", \"_gate_changed_files\": [\".gitignore\", \"agent.py\", \"api_shared/db.py\", \"api_shared/nav.py\", \"check_pubmed_pipeline_status.py\", \"ci_route_health.py\", \"cli.py\", \"docs/planning/specs/00739e13_fab_spec.md\", \"docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\", \"docs/planning/specs/051daf58_f92_spec.md\", \"docs/planning/specs/05b6876b_61a_spec.md\", \"docs/planning/specs/0850f78f_f00_spec.md\", \"docs/planning/specs/0a4a42ea_f2c_spec.md\", \"docs/planning/specs/0b5285ff-c077-455e-a4d6-f0dd3b538675_spec.md\", \"docs/planning/specs/0d37548c_12f_spec.md\", \"docs/planning/specs/0de12ae3_ba9_spec.md\", \"docs/planning/specs/13d17f9d_fc6_spec.md\", \"docs/planning/specs/1668104c_69f_spec.md\", \"docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\", 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\"docs/planning/specs/5a10152f_8bd_spec.md\", \"docs/planning/specs/5faca020_wiki_quality_review_spec.md\", \"docs/planning/specs/692f13b8_876_spec.md\", \"docs/planning/specs/6d5f040f-b3e2-431d-8345-d780f32e3ccb_spec.md\", \"docs/planning/specs/6db7722d_16b_spec.md\", \"docs/planning/specs/6e7d8631_63f_spec.md\", \"docs/planning/specs/7221a2c1-99dc-4f7a-aa92-56dd0a697a7e_broken_links_in_experiment_http_404_197_spec.md\", \"docs/planning/specs/7656f1df-bdf_forge_build_automated_pubmed_update_pip_spec.md\", \"docs/planning/specs/77718e75-4f3d-4d2b-afdb-c5cf4152d9b9_spec.md\", \"docs/planning/specs/7c483e0e_5d1_spec.md\", \"docs/planning/specs/7ffcac76_07a_spec.md\", \"docs/planning/specs/85f207f0_aa7_spec.md\", \"docs/planning/specs/86c48eaa_senate_db_fk_integrity_spec.md\", \"docs/planning/specs/88da08c1_3d6_spec.md\", \"docs/planning/specs/8ad4c451_bd3_spec.md\", \"docs/planning/specs/8b0d3be0_0e7_spec.md\", \"docs/planning/specs/8b68a328_f55_spec.md\", 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docs/planning/specs/19d7e4f1_87c_spec.md | 32 -\\n docs/planning/specs/1a33a296_e05_spec.md | 36 -\\n .../1d21e01d-0d3_template_link_generation_spec.md | 18 +-\\n .../1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md | 68 -\\n docs/planning/specs/1f62e277_c72_spec.md | 20 -\\n .../1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md | 46 +-\\n ...bb8e888_broken_links_in_target_http_500_spec.md | 9 -\\n docs/planning/specs/2310c378_ea0_spec.md | 92 -\\n docs/planning/specs/245a4f77_da9_spec.md | 35 -\\n docs/planning/specs/2679e2c9_852_spec.md | 33 -\\n .../2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md | 67 -\\n docs/planning/specs/2fba3f5b_3e7_spec.md | 75 -\\n docs/planning/specs/355a0e0b_92d_spec.md | 32 -\\n docs/plann\", \"_gate_history\": [{\"ts\": \"2026-04-17 16:53:51\", \"decision\": \"REJECT\", \"reason\": \"This branch deletes the live Exchange bidding surface by removing `scidex/exchange/bidding.py` and the existing `/api/exchange/bid*` and `/exchange/bids` handlers from `api.py`, which is a concrete API contract break unrelated to driver #20.\", \"instructions\": \"Rebase or merge `origin/main` into this branch and drop the unrelated Exchange bidding deletions so the existing bidding module and routes remain intact.\\nIf bidding is being intentionally replaced, include a fully compatible replacement for `scidex/exchange/bidding.py` and preserve the current `/api/exchange/bid`, `/api/exchange/bids/*`, and `/exchange/bids` endpoints in the same change.\", \"judge_used\": \"codex:codex\", \"actor\": \"minimax:64\", \"retry_count\": 6}, {\"ts\": \"2026-04-17 16:59:16\", \"decision\": \"REVISE\", \"reason\": \"The api.py diff stat shows 3343 lines changed (mostly deletions: `++----`), which is disproportionate to the squad findings bubble-up driver described in the task spec, and the prior reviews explicitly flagged that this branch was deleting Exchange bidding code that must be preserved. The current diff excerpt only shows figure URL helpers being removed \\u2014 it doesn't confirm whether the Exchange bidding deletions flagged in reviews 1 and 2 have been resolved.\", \"instructions\": \"Confirm whether scidex/exchange/bidding.py exists on this branch and whether api.py still imports or references it \\u2014 if the bidding module was deleted while api.py still has /exchange/bid routes, that is a breaking import\\nIf the squad bubble-up driver legitimately removes these helpers, show that all call sites for _encode_site_url_path, _figure_url_from_filepath, _figure_url_from_prefix_and_name, _fetch_ai_portrait_url, and _fetch_hypothesis_visual_url have also been removed from the diff, otherwise removing the definitions while callers remain causes NameError at runtime\\nInspect the full api.py diff to confirm no unrelated Exchange handlers (bid, bids, bid_upgrade, etc.) were removed\", \"judge_used\": \"minimax:MiniMax-M2.7\", \"actor\": \"minimax:64\", \"retry_count\": 7}, {\"ts\": \"2026-04-17 17:02:00\", \"decision\": \"REJECT\", \"reason\": \"scidex/exchange/bidding.py is still absent on this branch (confirmed via `git show branch:scidex/exchange/bidding.py` \\u2192 fatal: not in tree), and the corresponding /api/exchange/bid, /api/exchange/bids/*, and /exchange/bids routes that import from it are deleted from api.py \\u2014 removing 7 live endpoints that exist on main is a catastrophic API contract break (regression type #6), the same issue flagged in Reviews 2 and 3 which have not been resolved.\", \"instructions\": \"Restore scidex/exchange/bidding.py from main (git checkout main -- scidex/exchange/bidding.py) and restore the /api/exchange/bid, /api/exchange/bids/{agent_id}, /api/exchange/bids/open, /api/exchange/bids/top, /api/exchange/bids/leaderboard/{artifact_id}, /api/exchange/bid/{bid_id}/cancel, /api/exchange/bid/{bid_id}/settle, and /exchange/bids route handlers in api.py \\u2014 these are the deletions that must be reverted before this branch can merge.\\nRun `git diff main...HEAD -- scidex/exchange/` to enumerate all exchange module deletions and restore any other exchange submodules that were removed alongside bidding.py.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"minimax:64\", \"retry_count\": 8}, {\"ts\": \"2026-04-17 17:09:23\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:64\", \"retry_count\": 9}, {\"ts\": \"2026-04-17 17:14:49\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:64\", \"retry_count\": 10}], \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_escalated_at\": \"2026-04-17 17:14:49\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-ecf128f4-495b-4a89-8909-3f3ba5d00aff\", \"_gate_failed_branch\": \"orchestra/task/ecf128f4-squad-findings-bubble-up-driver-driver-2\"}"},{"id":"2761f643-ff6e-4fb1-a8c5-f691511ffb4f","title":"[Atlas] Dataset PR review & merge driver (driver #27)","description":"Recurring driver. For every dataset_pull_requests row with status='open', identify a qualified reviewer (LLM judge or persona with high reputation), have them review the diff, and write the outcome back as status='merged' or 'rejected' with a reviewer_agent_id. On merge, the existing dataset commit-credit driver picks up the new commits on the next cycle. See versioned_datasets_spec.md driver #27.","status":"open","priority":92,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T19:56:07.220539+00:00","updated_at":"2026-04-17T19:56:07.220539+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/versioned_datasets_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 7, \"safety\": 7}, \"completion_shas\": [\"4535366b9485a907db6d25ef0174c8b29fc78f28\"], \"completion_shas_checked_at\": \"2026-04-13T07:39:48.899043+00:00\", \"completion_shas_missing\": [\"65def93c51706077810fd716d857a12a667dd7ae\", \"2b61a076bef4e6ce75a6d3938f38567152b4839b\", \"b4d6a7dda9c9599c169f318eea017651ce634f24\", \"464cf4dff3af4f94e6ff9cbe49a7bfdf58745135\", \"1cc76ac4f703f3e7cb6ac5390df1fd327dabb778\"]}"},{"id":"33a9825b-a0f1-4114-85f1-74412a7ba649","title":"[Atlas] Wiki mermaid LLM regen — 50 pages/run, parallel agents","description":"Repair the 1,070-diagram backlog in wiki_pages.content_md via 5 parallel agents, 50 pages per 6h run. Uses scripts/validate_mermaid.py to identify failures, regens via LLM from page prose with fabrication + regression guards. See wiki_mermaid_llm_repair_spec.md.","status":"open","priority":92,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:12:49.700530+00:00","updated_at":"2026-04-17T18:12:49.700530+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/wiki_mermaid_llm_repair_spec.md","provider":"any","payload_json":"{}"},{"id":"47c8444e-651b-4839-9128-e5ec03bfc252","title":"[Atlas] Install Dolt server + migrate first dataset (driver #26)","description":"One-shot task to install Dolt (open source 'git for tables') on the SciDEX host and mirror one canonical dataset (start with ad_genetic_risk_loci) into a Dolt database. Update the datasets table's storage_backend column from 'git_csv' to 'dolt' and populate dolt_remote. Verify the CLI still works against the migrated dataset (the Python registry currently reads CSV; add a Dolt-aware code path that connects via the MySQL wire protocol). See versioned_datasets_spec.md driver #26.","status":"open","priority":92,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:03:52.962649+00:00","updated_at":"2026-04-17T18:03:52.962649+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/versioned_datasets_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 7, \"analysis\": 7}, \"completion_shas\": [\"9774f9c11e28b9af6e860b9520aeea6aaed6c6a2\", \"cb7af848b1eef2a8e0537b997a786ada2a5a88e2\", \"39d8b13549807070358f77fb45234b8dcbfa03f2\", \"0d0bde6a75ce6994f8a6721e3d4a7f0a787e6d39\"], \"completion_shas_checked_at\": \"2026-04-13T00:39:22.680174+00:00\", \"completion_shas_missing\": [\"12654e8d24557897767cb39631711777d171d963\"]}"},{"id":"f4f09ad5-2315-46fe-a526-fa6ab92dfe23","title":"[Atlas] KG ↔ dataset cross-link driver (driver #30)","description":"Recurring driver. For every dataset row whose primary identifier matches a knowledge_graph node (e.g. ad_genetic_risk_loci.gene_symbol = kg node of type 'gene'), insert a row in node_wiki_links or knowledge_edges connecting the KG node to the dataset row. Reverse: every KG node about a gene that has tabular data should have a 'data_in' edge to the dataset row. See versioned_datasets_spec.md driver #30.","status":"open","priority":90,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T17:25:05.925820+00:00","updated_at":"2026-04-17T17:25:05.925820+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/versioned_datasets_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"analysis\": 6}, \"completion_shas\": [\"6283b71716033169e97c6dfa97fed4b177d12799\"], \"completion_shas_checked_at\": \"2026-04-13T08:29:41.471592+00:00\", \"completion_shas_missing\": [\"5b7dbe33843933fb09eaee428d9fc17985225088\", \"ca00c978ed3a2e14b2ecb2cd83349768d2c19931\", \"fdf91d736f8a76056d4543d754a6e4874f86d80f\", \"65eff9c61d2dde6acb1214055b8a9fb935be8e7d\", \"0e68f45438c452077f8ad205b6c72509a1e0e2d9\", \"2844ba85d3010e534b361b0b65bbd5ee3d492678\", 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The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would 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":"2026-04-10T12:58:45.902219+00:00","updated_at":"2026-04-13T10:12:59.452654+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"Audit reopened: ORPHAN_BRANCH — 3 commit(s) found but none on main; branch=orchestra/task/f3280e81-459b-4731-9c33-68540054db7b","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/paper_corpus_expansion_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"analysis\": 6, \"safety\": 6}, \"_gate_retry_count\": 1, \"_gate_last_decision\": \"REVISE\", \"_gate_last_reason\": \"judge timed out while reviewing a low-trust branch\", \"_gate_last_instructions\": \"Inspect `git diff origin/main..HEAD`, remove unrelated files or deletions, and retry the merge with a smaller, task-focused diff.\", \"_gate_branch\": \"orchestra/task/aaf28b6e-7054-4e15-a2cb-65e252b7c4cb\", \"_gate_changed_files\": [\"api.py\", \"docs/planning/specs/paper_corpus_expansion_spec.md\", \"tools.py\"], \"_gate_diff_stat\": \"api.py | 76 +++\\n docs/planning/specs/paper_corpus_expansion_spec.md | 116 +++++\\n tools.py | 537 ++++++++++++++++++++-\\n 3 files changed, 728 insertions(+), 1 deletion(-)\"}"},{"id":"b5d9421e-25fc-44dc-9f85-12e37bfa38c8","title":"[Atlas] Bidirectional KG-Wiki navigation system","description":"Create seamless navigation between knowledge graph nodes and wiki content:\n\n1. On /entity/{name} pages: embed wiki content inline (rendered markdown) with a link to full wiki page\n2. On /wiki/{slug} pages: show KG neighborhood — all edges where this entity is source or target\n3. On /wiki/{slug} pages: show related hypotheses mentioning this entity, sorted by score\n4. On /graph visualization: clicking a node opens a panel showing wiki summary + KG connections\n5. Auto-link: scan wiki page content for mentions of other KG entities, create hyperlinks\n6. Breadcrumb navigation: Entity Type > Entity Name > (Wiki | Graph | Hypotheses | Papers)\n7. Add wiki content snippets to hypothesis detail pages where target gene has a wiki page\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would 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":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:47:32","updated_at":"2026-04-13T10:16:03.367736+00:00","summary":"","completion_notes":"","last_error":"Audit reopened: NO_COMMITS — No commits found referencing task ID; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ad8688fe-f879-43c9-b03a-5d10e64601cc","title":"[Atlas] Add cross-reference links between wiki pages and hypotheses","description":"Many wiki entity pages discuss genes/proteins that are targets of hypotheses, but lack links to those hypotheses. Add a 'Related Hypotheses' section to wiki pages that matches entity names to hypothesis target_gene fields. This creates bidirectional navigation between Atlas and Exchange layers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would 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":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T00:15:01.857539+00:00","updated_at":"2026-04-17T00:15:01.857539+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ad8688fe_f87_spec.md","provider":"any","payload_json":"{}"},{"id":"8bbe31de-d3b8-49e4-a3ea-a1cb2be6b1ea","title":"[Atlas] CI: Database integrity and orphan analysis check","description":"Recurring check: Verify completed analyses have artifact_path/report_url set, check for broken references, validate hypothesis-analysis links, report anomalies. Helps catch orphaned content early.","status":"open","priority":85,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T21:23:47.844276+00:00","updated_at":"2026-04-16T21:23:47.844276+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/8bbe31de_d3b_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}, \"completion_shas\": [\"ac3c07364a1682da8ddda59dca3f8f549d927801\", \"de6f504a8880916fba20c367b0c01fc5891fcb4d\"], \"completion_shas_checked_at\": \"2026-04-12T23:42:07.376732+00:00\", \"completion_shas_missing\": [\"000aa035f130636990b6290d14650c4b8d22af29\", \"1d753f02a1d2aae1fd5e4323c1cc8f2cbdf14646\", \"e5910cc9aae5a4054390cb0320f3a1fd6d5601e0\", \"ce1c366d4a4863c2a8560ab64f2d8a8dea8bc805\", \"d93244ac946341cdaa0c93e3400d1e3a130a2fcf\", \"a1d5627d30b66b3924e0f7ad1d6c85ae155f3637\", \"5fc5a5375bdaa0cd90393e8aba2ec84a85caa7d5\", \"c0ba1332d12c14d46bd70015b78afd9df173b6b1\", \"4342b260ddcc5de31c21dae36c2b14f07687d986\", \"505628cb09e9285ddb6331da0cda9c9f7a345b1d\", \"829ea4d53942a8b1a0184fb75df2fc0732f5c3c8\", \"98c239519004b4ca4d90324f2d5ecbb2b59df8d3\", \"9b5f23c216b7fa11e53d02f907b135e18c919a80\", \"0c8e65f261916f4fd5d31e4d1f321fb100902553\", \"28ea75ea5f7e58c41d4a88bb87bed6577fe44c3c\", \"921c23b28a3c431c724f14c81ac7feb7288bc509\", \"d78fe7ef237186ac2fbdcd53c2e640b5010c0f7f\", \"55809a3e8e0e73ab19f9736a29e52f5952c87bcb\", \"db16b55e3fe6d364bb6a645182161c6b4a67acde\", \"a892a0dd43f71377fcbaa17163968051ec669ea3\", \"e710224452e17aeb3bdc0c07c53fe725eb281719\", \"9b2fdca71e3536d5f260e1c18fb0345730a63148\", \"da69980cf26dd12d17afa1c10b93964e87a2601d\", \"37e66a57e3c132d239076d7d9735505d6425834a\", \"290c555064377ce1511b426ceb9affa02da6ee83\", \"9690f626ff2ad7a629777e5a4d969cfb04b26e30\", \"bed4d9975dc7b403b841a3597b3eebceb140e82d\", \"67126f4e4601b09be985b261cc2aee4cb051a5e3\", \"8d650d1b3a5008ade072461bbdd495f96294bdcf\", \"0ea9452c717e3671dc7f932cbf2ca3ea69d93606\", \"cb326c6a7cb1817deee60784c6f5a22899c3e382\", \"3b24a0be81b16865d7299581afbb9870b65b1da2\", \"c830247369f98f4b7d69b61562f4b0f0a5a5d0c0\", \"4ed792cd3aa4ef7a43eea8c8956a5634070d9bc1\", \"37f2bde21a92373ccde92f448aa716e3d1a8677a\", \"a6164bcb758d78a058df7c6bb9ef7c2a7e11178a\", \"24f806ab685d539af4ab93a067d8032440cbfd1d\", \"1623a1f7021c7dbcf169e480b1e24e372eebe3d7\", \"55a9cc781f02be710db4b9b64adaf08dd85404c8\", \"c90a9efd78b2d7dbab2988294320b999160c4b66\"]}"},{"id":"55e3ea08-76c2-4974-9dc3-a304848cf1a9","title":"[Atlas] Reduce wiki-to-KG linking backlog with high-confidence crosslinks","description":"Continuously reduce the backlog of weakly linked or unlinked wiki pages using high-confidence artifact_links, node_wiki_links, and KG associations. Prioritize world-model impact and report backlog reduction each run.","status":"open","priority":82,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:10:07.402977+00:00","updated_at":"2026-04-17T18:10:07.402977+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/55e3ea08_76c2_atlas_reduce_wiki_kg_link_backlog_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"analysis\": 6, \"safety\": 6}, \"completion_shas\": [\"2393824c9a145a60b6bc4d99eaca8bae9eb4d949\"], \"completion_shas_checked_at\": \"2026-04-13T10:04:55.792546+00:00\", \"completion_shas_missing\": [\"1cc1e8c017f7fda1f55e35f3f86483e1f82d2e24\", \"580de88bc9b488262ec9ff6158f00a643b1d907a\", \"2c3c268e4116b16b61d711d8a791a4fcc217d1e3\", \"3b29e183fb2f8f055ba25c8f964bae9552e336a8\", \"52dced35847c5ab6f841ee3542305d8c36f600ec\", \"460a79e0b1a399eb2c7896cedc5b18b49ac5b705\", \"d038ee74bb8f85a5e9e7f11d6f57fef06114da4d\", \"eac104935745ebfd7c529e7a4179eba66d39b77f\", \"257d88853a5ef623306802a39b0d29262c98aaee\", \"4e47bc38dbbb2d5455c95e0b95e25e8e194c88d4\", \"75d14a3021238021fbe9dd0123aac9c60a6f4069\", \"27d2dd53502f41d58e3182d562eb907465e14494\", \"e847a04825f109c757fdbf6a5dbb1aee84b13c2f\", \"d1fff2b4bc506d4784303bae2524dc1b1135c348\", \"35f81be24516df3398c4cb6bb4eacafbfcf55cf4\", \"2dced1708e235c4b8b41aa73b8e5ef6c66514d11\", \"cafdbd8929e41c7ec6132ff7d258704081c3525d\", \"5416d373a34b742925bc2c922a1aff7676f44678\", \"6a0df564c8ca62b3e210f07ac6c765eaab26a1f3\"]}"},{"id":"c92d8c3f-9066-409a-bce5-c977a3f5a7bd","title":"[Atlas] Wiki citation enrichment — add inline citations to 15 pages","description":"Find wiki pages with refs_json but no inline [@key] citations (ORDER BY word_count DESC LIMIT 15). For each: use LLM to identify ≥3 claim↔ref matches, insert [@key] at end of relevant sentence, enrich refs_json with claim/excerpt where missing. UPDATE wiki_pages SET content_md, refs_json. Log: pages processed, citations added, refs enriched. Target ≥5 citations per pass. See wiki-citation-governance-spec.md Task 1 for full algorithm.","status":"open","priority":82,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:49:10.269554+00:00","updated_at":"2026-04-16T23:49:10.269554+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/wiki-citation-governance-spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 9}, \"completion_shas\": [\"7c8110d3ce49460a8d53f49944c3e0185fe496a8\"], \"completion_shas_checked_at\": \"2026-04-12T17:20:43.577975+00:00\", \"completion_shas_missing\": [\"57bc05f2ab151ed1201b59247cc88da841bbae80\", \"0e2ef4cb4fd21e5b10c0cf83999536c4c3473da3\", \"4b219445e73ed8f7a46ed3cd1a02a2732ff68976\", \"ceeebece2a0191df865409e57f27753dbf2fe13a\", \"06e50786e85c75105823266f779d2494fab9e131\", \"f4680fe9e47080345818355d1f211fa80656c27e\", \"63451262fad1dcb8b2161eeec07408d96df28479\", \"4ab764439bac314b67cb19783d087fbaf2e603d0\", \"ed475b3cef251fd26f299be69d4b741c93ef8450\", \"99bb59728f75826e0a475285d149f2f5c6005115\", \"8163029e879e964af29dd092d0caa5858a937625\", \"317fe8ec209e4253a63d0ab15bcb9fd793a3fded\", \"24920c6c2bf23b8801c00495a3ed1289da7f31a9\", \"3341829344c0a4f57d99549fb9351ace93c106cf\", \"8373857124d435eb262822d7deba51e8282cd9ae\", \"95f8756716cea95cf576bb10e9bfa609814ccdf0\", \"f6f091cbc6eb543ef687f1218333f72b9b7f1287\", \"bee57fb826c188492ab4b7898c2e6c52f47f2d78\", \"a61a4d6a94347ae318fdb4a2c821d2eb74baf606\", \"2a613ee58e36193fb4dec1d4f401fcf2768a2709\", \"094adea1272ab7ee335ec2d976d34ce7c161f141\", \"b20f58c567976ecbb57b98d19e700d2495eb88a9\", \"f640303068f10e5274bc181a89555e52c2f4d5e0\", \"5e6f3318932f6024ead363545534b041e8756f53\"]}"},{"id":"5eef354f-ffe4-4f26-897a-46210c6f7589","title":"[Atlas] Paper-to-wiki backlink — add missing papers to refs_json from artifact_links","description":"Find papers linked to wiki pages via artifact_links (link_type='cites', strength>0.6) but missing from refs_json. Add up to 20 gaps per pass with key={firstauthor_surname}{year} format (e.g. lai2001, fisher2020). Include authors/title/journal/year/pmid/strength. Leave claim/excerpt blank for citation-enrichment task. See wiki-citation-governance-spec.md Task 2 for full SQL query and algorithm.","status":"open","priority":80,"task_type":"recurring","frequency":"every-12h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:49:56.900344+00:00","updated_at":"2026-04-17T18:49:56.900344+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/wiki-citation-governance-spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"041d4c7c1acf49a27c2d039400f43029f3fb0bc7\", \"d71fac06fdd6661e2f7b82a9e6b35df43cb54ae9\"], \"completion_shas_checked_at\": \"2026-04-13T05:31:35.686420+00:00\", \"completion_shas_missing\": [\"e1ecd60f32a22b08971fa5fd8d386c8c89d94a57\", \"fbf11120f986c17c0eef360cf735df9bdf1ca742\", \"dd2872a44a7520fca887c5af0b4e56755c39e59e\", \"b00e6a8ea6eced4f67ff0c04dd4c2515030b6230\", \"9feab6d833aa853106609b50bf9698d505ee7b86\"]}"},{"id":"93e4775f-690c-4fd2-a2d2-6c71e9b59064","title":"[Atlas] Extract and reference figures from scientific papers","description":"Enable figure extraction from cited papers via PMC API, PDF extraction, or deep-link fallback. Figures become artifacts that agents reason about multimodally in debates. Forge tool paper_figures(pmid) for agent use. See docs/planning/specs/paper_figures_quest_spec.md","status":"open","priority":80,"task_type":"recurring","frequency":"every-2h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:48:23.698693+00:00","updated_at":"2026-04-17T18:48:23.698693+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/93e4775f_690_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"completion_shas\": [\"ea435d6fc56bcc693770c95de54450abf3d6541e\"], \"completion_shas_checked_at\": \"2026-04-13T07:42:15.417436+00:00\", \"completion_shas_missing\": [\"7d753179f1af69e284ea4435d2b5d98bbb4b69fd\", \"40accb55981d3992673f459644552df99c099363\", \"511f2e5e3ef380179f773e0a510d2508f00dd462\", \"82b3db3c43473bd5e6d6bd6e86562582113af6d4\", \"4a6213c38883c00d0212f90420a73bdbfd13573c\", 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\"407164c9184fac71c5a61247ade998e3177a710e\"]}"},{"id":"d20e0e93-fdbc-4487-b99e-0132b3e31684","title":"[Atlas] CI: Cross-link new wiki pages to KG entities","description":"Find wiki_pages without node_wiki_links entries. Match by title/content to KG entities and create links.","status":"open","priority":80,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:21:59.071684+00:00","updated_at":"2026-04-17T18:21:59.071684+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/d20e0e93-fdbc-4487-b99e-0132b3e31684_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"analysis\": 6, \"safety\": 6}, \"auto_tagged_at\": \"2026-04-03T22:29:52.509512\", \"completion_shas\": [\"0eae75275f62f86d9fe7c30c09ca127a522e6e6a\"], \"completion_shas_checked_at\": \"2026-04-13T11:07:04.444613+00:00\", \"completion_shas_missing\": [\"24b32a57363c9c7da6ec5167635d0eee72a6b880\", \"9384a6400019ad8c350484ea7e205fc82f717f98\", \"4b894f28cbdd836172db803736f54c27ad1fdc6c\", \"5f82390774d9c0baef58ede30fbdde149409bb3e\", \"6bb842ab3620e56a2cc64ee5c49d5318c60dd835\", \"361ca8e7a74cef16376fbb2bae318f0a00203ca9\", \"6429e830f65160a38c578cf5ec64f1d9a8d859fe\", \"4107afc2cd7b8ce8b6da07fdbd02732cfb73a6a0\", \"26d9368f52c539889ca9a9b66e529b2bb01c36ba\", \"71439088c612f19cdd7bcecfe316b357486cbe13\", \"e742b1fa029c8ff707b8236457401dfdf17bd4c6\", \"fdc9fa50dda4da7a1106f509717e9a2bc1eba963\", \"54d7d5c1fbadd5c1533e918f5b0470809f2b8d91\", \"b97795747c87549108d9502c50baf6c5c01f0f0b\", \"971dbbd3f9e581965bdc63e765bebd2200ce61cd\", \"c6ef139ee964ad19aacf87a4dd137fe7a4643f09\", \"fa9b3cd68146dbe4a07c240146da5e66dbb75567\", \"f1ad344481a4efeae3aaa6aca0eadc4df41f0790\", \"90a8119ec7970b03b047c254a0239bf586ef5f83\", \"9ad996edc40c4e7195d1d644286d39e5d7e4986c\", \"5326bb689e3ba7d5063085d8e6f9f9075d851ce4\"]}"},{"id":"29dc1bc3-fa9a-4010-bf53-c780a5cde6ab","title":"[Atlas] Paper processing pipeline: fetch, extract figures, read, enrich wiki","description":"Run paper_processing_pipeline.py process: fetches queued papers from PubMed, extracts figures from PMC, reads papers with LLM to extract claims, and enriches wiki pages with rich citations. See wiki quality quest spec.","status":"open","priority":75,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:20:00.785484+00:00","updated_at":"2026-04-17T19:57:48.640489+00:00","summary":"","completion_notes":"Remove the figures_fallback_middleware function and its app.middleware registration entirely from api.py.\nIf stale figure URLs are the underlying problem, update stored figure references to point to real existing URLs, or emit a truthful 404/redirect instead of a synthetic 200 placeholder.\n\nChanged files:\n- .orchestra-slot.json\n- agent.py\n- api.py\n- api_shared/db.py\n- api_shared/nav.py\n- ci_route_health.py\n- ci_snapshot_prices.py\n- cli.py\n- docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\n- docs/planning/specs/051daf58_f92_spec.md\n- docs/planning/specs/05b6876b_61a_spec.md\n- docs/planning/specs/0850f78f_f00_spec.md\n- docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\n- docs/planning/specs/113c18f2-broken-links-in-mission-http-0-1155-link_spec.md\n- docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\n- docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\n- docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\n- docs/planning/specs/1f62e277_c72_spec.md\n- docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\n- docs/planning/specs/220f930a-3bc3-4804-9618-15906ee1dcb1_broken_links_in_analysis_http_404_16619_spec.md\n- docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\n- docs/planning/specs/2310c378_ea0_spec.md\n- docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\n- docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\n- docs/planning/specs/2fba3f5b_3e7_spec.md\n- docs/planning/specs/39d76f99-75b5-4451-83d0-01e462b9aca5_broken_links_in_entity_http_404_10_links_spec.md\n- docs/planning/specs/3d5cb5ea-broken-links-in-image-http-0-141-links_spec.md\n- docs/planning/specs/3df7390a_4cd6_spec.md\n- docs/planning/specs/3eb45ac3_complete_application_server_failure_spec.md\n- docs/planning/specs/3fea4720-77a6-4a98-999b-0b54c81cae2e_broken_links_in_analysis_http_404_10_links_spec.md\n- docs/planning/specs/4e5c9924_11bc_4268_spec.md\n- docs/planning/specs/4e76d954-e253-441a-af7b-b28d18059f59_spec.md\n- docs/planning/specs/4ea61e17-0b95-445c-aa1b-961696f16126_broken_links_in_figures_http_0_1252_spec.md\n- docs/planning/specs/50fd9c87-f086-4576-9d61-fa249719cb44_spec.md\n- docs/planning/specs/51bbc267-83b1-41e6-bef4-ff90a3a91e0e_spec.md\n- docs/planning/specs/53b098aba384_exchange_design_capital_allocation_mode_spec.md\n- docs/planning/specs/53c618dd_a199_4fcb_9356_d43fbc922f59_spec.md\n- docs/planning/specs/55888d47-5c2c-4a80-b007-2bbdc83a81ff_service_down_connection_failure_spec.md\n- docs/planning/specs/55e3ea08_76c2_atlas_reduce_wiki_kg_link_backlog_spec.md\n- docs/planning/specs/5faca020_wiki_quality_review_spec.md\n\nDiff stat:\n.orchestra-slot.json | 2 +-\n agent.py | 54 +-\n api.py | 2745 ++---\n api_shared/db.py ","last_error":"Review gate REJECT: 10 blocked merge attempts; escalated via safety>=9 capability requirement","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/quest_wiki_quality_improvement_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"coding\": 5, \"safety\": 9}, \"_gate_retry_count\": 0, \"_gate_last_decision\": \"REJECT\", \"_gate_last_reason\": \"figures_fallback_middleware (api.py:910-933) still converts missing /figures/*.svg 404s into HTTP 200 placeholder responses, hiding real missing-figure breakage \\u2014 this was explicitly rejected in Reviews 1 and 3 and has not been removed.\", \"_gate_last_instructions\": \"Remove the figures_fallback_middleware function and its app.middleware registration entirely from api.py.\\nIf stale figure URLs are the underlying problem, update stored figure references to point to real existing URLs, or emit a truthful 404/redirect instead of a synthetic 200 placeholder.\", \"_gate_branch\": \"orchestra/task/29dc1bc3-paper-processing-pipeline-fetch-extract\", \"_gate_changed_files\": [\".orchestra-slot.json\", \"agent.py\", \"api.py\", \"api_shared/db.py\", \"api_shared/nav.py\", \"ci_route_health.py\", \"ci_snapshot_prices.py\", \"cli.py\", \"docs/planning/specs/0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md\", \"docs/planning/specs/051daf58_f92_spec.md\", \"docs/planning/specs/05b6876b_61a_spec.md\", \"docs/planning/specs/0850f78f_f00_spec.md\", \"docs/planning/specs/0afd971e-686d-400b-98a4-f71293db1351_broken_links_in_entity_http_500_9746_links_spec.md\", \"docs/planning/specs/113c18f2-broken-links-in-mission-http-0-1155-link_spec.md\", \"docs/planning/specs/197efcaa_cc16_static_asset_template_issues_spec.md\", \"docs/planning/specs/1d21e01d-0d3_template_link_generation_spec.md\", \"docs/planning/specs/1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md\", \"docs/planning/specs/1f62e277_c72_spec.md\", \"docs/planning/specs/1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md\", \"docs/planning/specs/220f930a-3bc3-4804-9618-15906ee1dcb1_broken_links_in_analysis_http_404_16619_spec.md\", \"docs/planning/specs/22ef73fa-7c9e-4b0c-9bdc-187bdbb8e888_broken_links_in_target_http_500_spec.md\", \"docs/planning/specs/2310c378_ea0_spec.md\", \"docs/planning/specs/25dc2ab9-6d9e-4e1d-a415-eb8af9628b2c_broken_links_in_entity_http_500_34_links_spec.md\", \"docs/planning/specs/2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md\", \"docs/planning/specs/2fba3f5b_3e7_spec.md\", 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\"docs/planning/specs/8ba1aa28-6d6e-42a1-810e-65dc17dee42f_spec.md\", \"docs/planning/specs/8f4afe64-1b76_broken_links_in_figures_http_404_10_links_spec.md\", \"docs/planning/specs/90c11837_broken_links_in_api_http_0_19_links_spec.md\", \"docs/planning/specs/93e4775f_690_spec.md\", \"docs/planning/specs/9401eb58-32bd-4a83-8823-c562758ca0eb_spec.md\", \"docs/planning/specs/9fcdbafb-78da_spec.md\", \"docs/planning/specs/a27b8c7a-1fa_economics_ci_snapshot_hypothesis_prices_spec.md\", \"docs/planning/specs/a3f12c37_8e0_spec.md\", \"docs/planning/specs/a453a671-3a25_broken_links_in_figures_http_404_28_links_spec.md\", \"docs/planning/specs/a88f4944_cb09_forge_reduce_pubmed_metadata_backlog_spec.md\", \"docs/planning/specs/a9bbf4cf-0f86-4ed0-9c7b-0e951dc6393b_spec.md\", \"docs/planning/specs/ab99d47b-41e1-4b96-b27e-6b087a3ce107_spec.md\", \"docs/planning/specs/ada9e2bb-493_broken_links_in_entity_http_500_661_link_spec.md\", 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\"docs/planning/specs/ed11ca4e_870_spec.md\", \"docs/planning/specs/efd97ee8_311_spec.md\", \"docs/planning/specs/f118e1e4_cf1_spec.md\", \"docs/planning/specs/f16d52db-3450-4d3d-b2cb-4c46831aa06b_spec.md\", \"docs/planning/specs/f6ca89b0_server_infrastructure_fix.md\", \"docs/planning/specs/f9253512-8561-4916-9405-ea42a6f54d45_spec.md\", \"docs/planning/specs/fe44e35f_broken_notebook_links_spec.md\", \"docs/planning/specs/ffb59345_708_spec.md\", \"docs/planning/specs/linkcheck-853068682d39.md\"], \"_gate_diff_stat\": \".orchestra-slot.json | 2 +-\\n agent.py | 54 +-\\n api.py | 2745 ++---\\n api_shared/db.py | 30 +-\\n api_shared/nav.py | 8 +-\\n ci_route_health.py | 204 -\\n ci_snapshot_prices.py | 104 -\\n cli.py | 61 -\\n .../0514eb5b_fe0e_46f0_af49_cdeef6d6eaf5_spec.md | 24 -\\n docs/planning/specs/051daf58_f92_spec.md | 31 -\\n docs/planning/specs/05b6876b_61a_spec.md | 11 -\\n docs/planning/specs/0850f78f_f00_spec.md | 29 +-\\n ...ken_links_in_entity_http_500_9746_links_spec.md | 32 -\\n ...roken-links-in-mission-http-0-1155-link_spec.md | 70 -\\n ...efcaa_cc16_static_asset_template_issues_spec.md | 15 -\\n .../1d21e01d-0d3_template_link_generation_spec.md | 18 +-\\n .../1e337153-1ae0-4a95-a573-bc5f1cdddc58_spec.md | 68 -\\n docs/planning/specs/1f62e277_c72_spec.md | 20 -\\n .../1fe0f02e-fcc9-4d27-b836-84d337b8acec_spec.md | 46 +-\\n ...broken_links_in_analysis_http_404_16619_spec.md | 46 -\\n ...bb8e888_broken_links_in_target_http_500_spec.md | 9 -\\n docs/planning/specs/2310c378_ea0_spec.md | 92 -\\n ...roken_links_in_entity_http_500_34_links_spec.md | 57 -\\n .../2f33adfc-814c-42cc-838a-e1d8f080e4e8_spec.md | 67 -\\n docs/planning/specs/2fba3f5b_3e7_spec.md | 43 -\\n ...roken_links_in_entity_http_404_10_links_spec.md | 30 -\\n ...-broken-links-in-image-http-0-141-links_spec.md | 73 -\\n docs/planning/specs/3df7390a_4cd6_spec.md | 47 -\\n ...ac3_complete_application_server_failure_spec.md | 18 -\\n ...ken_links_in_analysis_http_404_10_links_spec.md | 55 -\\n docs/planning/specs/4e5c9924_11bc_4268_spec.md | 68 -\\n .../4e76d954-e253-441a-af7b-b28d18059f59_spec.md | 41 -\\n ...12\", \"_gate_history\": [{\"ts\": \"2026-04-17 19:15:49\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:60\", \"retry_count\": 6}, {\"ts\": \"2026-04-17 19:35:38\", \"decision\": \"REJECT\", \"reason\": \"`api.py` adds `figures_fallback_middleware` that turns any missing `/figures/*.svg` asset into HTTP 200 with a generic placeholder SVG, which hides real missing-figure breakage instead of fixing it.\", \"instructions\": \"Remove the 200-placeholder fallback for missing `/figures/*.svg` files and preserve a truthful missing-asset response (or a targeted redirect to a real replacement figure).\\nIf the goal is to resolve stale figure URLs, update the callers or stored figure references to stable existing URLs, or document and escalate missing generated figures instead of masking them with a synthetic success response.\", \"judge_used\": \"codex:codex\", \"actor\": \"minimax:60\", \"retry_count\": 7}, {\"ts\": \"2026-04-17 19:45:24\", \"decision\": \"REVISE\", \"reason\": \"Auto-deploy blocked: Merge failed (conflicts?):\", \"instructions\": \"Inspect `git diff origin/main..HEAD`, rebase or merge origin/main into the task branch, and resolve only task-relevant conflicts before retrying.\", \"judge_used\": \"\", \"actor\": \"minimax:60\", \"retry_count\": 8}, {\"ts\": \"2026-04-17 19:49:29\", \"decision\": \"REJECT\", \"reason\": \"figures_fallback_middleware (lines 906-930) was rejected in a prior review and remains unaddressed \\u2014 it converts 404s on missing /figures/*.svg assets to HTTP 200 placeholder responses, hiding real missing-figure breakage instead of fixing it\", \"instructions\": \"Remove figures_fallback_middleware entirely. If stale figure URLs are the problem, update the stored figure references or caller code to point to stable existing URLs instead of masking the 404 at the middleware layer.\\nIf figure URLs legitimately change on regeneration, implement a redirect to the new URL rather than a 200 placeholder, so clients and link checkers get truthful information about the asset's location.\", \"judge_used\": \"minimax:MiniMax-M2.7\", \"actor\": \"minimax:60\", \"retry_count\": 9}, {\"ts\": \"2026-04-17 19:57:48\", \"decision\": \"REJECT\", \"reason\": \"figures_fallback_middleware (api.py:910-933) still converts missing /figures/*.svg 404s into HTTP 200 placeholder responses, hiding real missing-figure breakage \\u2014 this was explicitly rejected in Reviews 1 and 3 and has not been removed.\", \"instructions\": \"Remove the figures_fallback_middleware function and its app.middleware registration entirely from api.py.\\nIf stale figure URLs are the underlying problem, update stored figure references to point to real existing URLs, or emit a truthful 404/redirect instead of a synthetic 200 placeholder.\", \"judge_used\": \"max:claude-sonnet-4-6\", \"actor\": \"minimax:60\", \"retry_count\": 10}], \"_gate_judge_used\": \"max:claude-sonnet-4-6\", \"_gate_escalated_at\": \"2026-04-17 19:57:48\", \"_gate_escalated_to\": \"safety>=9\", \"_gate_failed_workspace_path\": \"/home/ubuntu/scidex/.orchestra-worktrees/task-29dc1bc3-fa9a-4010-bf53-c780a5cde6ab\", \"_gate_failed_branch\": \"orchestra/task/29dc1bc3-paper-processing-pipeline-fetch-extract\"}"},{"id":"b399cd3e-8b24-4c13-9c7b-a58254ba5bdb","title":"[Atlas] Wiki quality pipeline: score pages and process improvement queues","description":"Run wiki_quality_pipeline.py: (1) score 200 random pages, queue low-quality ones, (2) process up to 5 items from each of the 4 queues (citation_enrichment, prose_improvement, figure_enrichment, kg_enrichment). Uses LLM for citation and prose work, DB-only for figure and KG linking. See docs/planning/wiki-quality-guidelines.md for standards.","status":"open","priority":75,"task_type":"recurring","frequency":"every-6h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T18:38:12.350001+00:00","updated_at":"2026-04-17T18:38:12.350001+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/quest_wiki_quality_improvement_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5, \"coding\": 5}, \"completion_shas\": [\"c4f4f5413ad77a0c7f800c9773692e875f9d5dc9\"], \"completion_shas_checked_at\": \"2026-04-13T06:12:33.158305+00:00\", \"completion_shas_missing\": [\"c76d419ddde97d9b3cbf4c21e9d2d3521a43e487\"]}"},{"id":"6b77122a-719d-4f88-b50d-5848157eba31","title":"[Atlas] Wiki citation coverage report — daily metrics snapshot","description":"Compute and store daily citation coverage metrics: total wiki pages, pages with refs_json (%), pages with inline citations (%), pages with linked papers (%), refs with claim/excerpt/figure_ref fields. Print report matching format in spec. Store snapshot in wiki_citation_metrics table or as analysis artifact. Flag top 20 uncited pages (have refs_json, no [@key] markers) sorted by word_count DESC. See wiki-citation-governance-spec.md Task 3.","status":"open","priority":72,"task_type":"recurring","frequency":"every-24h","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:20:01.314608+00:00","updated_at":"2026-04-17T11:20:01.314608+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/wiki-citation-governance-spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5, \"reasoning\": 5, \"safety\": 6}, \"completion_shas\": [\"761ba91a8c7af4bd559b342293b9338c96d40f17\"], \"completion_shas_checked_at\": \"2026-04-12T20:07:27.465852+00:00\", \"completion_shas_missing\": [\"ac308cd7285ed71f48b2e944d13534d61ed6b9dc\", \"99c5ce1b5701049f657e394ac2aeeb8e5f0e563a\", \"17b760b257a6d4f28df63ccb54a3f568addef5d7\", \"3a04f0a5a93beaba7191acb5ea1c9fc8fa5fa5bf\", \"a7846c21f43043a17cd08c3fee9f26a5047ec91c\", \"b2b05723fc44878ef73f4537a143699607d6db4a\", \"b627652c5b14ae363fd7dce0ff669c906e3ae376\", \"9070250c1544e7053fdb38690401a6ca329de5de\", \"5267e010c877a2a06e2c3a9c00b368a8de94e07f\", \"85d0e86413043974ea1b1e8e8efbfe2ccd892b3b\", \"0c22abb57d001296d6936a35dbf8b599c9d442dd\", \"628111811d06128aede292d137135a5821b47b02\", \"69b5c1a0065ce6a4192d39043187108dd51fcca0\", \"eff16ad9044dfab361566ee37c64a74eba545a65\", \"35ebbc5015e7c65d45dd4041a3b7af146f25fc8e\", \"664955c39922557e95f776c100c7aaa59972949a\", \"f08dd736f9277f24e54463933b286062d08e4404\", \"65103c0900693d2c6d4d6c31b0e412d12e8593ee\", \"fefc96722975dd2efe7cf7ae276ba26ade54c88c\", \"0e854bac4ece9737898ee6e25782cb5ec7d61bcb\", \"c8a37f0197b35a77f2bb8f3b2fbcdd0e6c384ec9\", \"2e6b13d4f4c96312f38528c80a67ade85ac960cf\", \"20e1c0f218c651ca2f3a70556e9e7b7abe322104\", \"3d3801bff5d78c1b80e78c0b2a018afffa7daf03\", \"2fed1657e860dc38f0b3e92ba6c1f5383f2b44b0\", \"f5ac59cfa8c44ed8dc13bb9ace74ba9a1aa26b49\", \"1a21c3a201e69c0dafa314d1c4e4cdc58e8aff91\", \"ec635098087e3c94b49cbcc1e632936ac42e3d71\", \"1cf6bdb2efdec0a605b62cf38245b873050948a6\", \"a24d3c821fc69cbf2634355d87ca052e8ca968dd\", \"b35435fd3c8040f5a837083b9836a846c0f8e6e3\", \"9b3236e1eb64bd0ba4e4377ef2e7558aed3f32fd\", \"724c565f8a34821f373dbe38271c854abcd6df30\", \"556d201eff45e4de2dfb239f30e6caaf3de47f24\", \"3bbf827fbf5ff5e62938da7adc440aa6816fdc21\", \"c68c6447a957744b8db765b89e8d3a051c0d10f8\", \"01e56d551de158d94221bc71f927bab17e98a8b5\", \"3e4548024af446fde5e39be4bfd5588c1076e4a6\", \"215131eaeb24b21ac923287bfb51e97cf8603388\", \"c234d6344b2ef7c1139662784fcd1a1a9f28c51a\", \"cc33f11e282a588659e2e14d621a56889deadd79\", \"9a92a8049ee6f792a2223f389b0381919f2a5997\", \"9889b9d9baeb16e78938f034f6c1e40b233d70e4\", \"6181e2b3617239dc511f2184eb17bdcc0aa2b928\", \"e146bf1710acc4112390f533386f4b96586a29c4\", \"cedd77cddcd0822e5f45be9359fb09a67801793a\", \"aa4c7bf670940ba6b9f91e66559e2f51f7f997b9\", \"dc7bee9184a473edc164b946e9d422a95b59f3fe\", \"7c0effaf1f8625baee0aa2e3632444b3984bbc6a\", \"ec6c744a4a8a08f0b58d545ebc5f39e4d8dc946b\", \"194e0db2b367d25e00553118823aab8fa145cb67\", \"262e38b9e21bcfe5ed36f116707b89166c8c6be1\", \"c85ce285e08df1af517deb52a15aa33694d6afc5\", \"da1085c7cf3bd4260ed6cd11f47f0643988367b3\", \"161221456886eb22c57aa0d6dcf1bf172eb4ed6c\", \"b797d4a2bb0e77e290ac6298b320c24c62f79711\", \"b953a920d8b4d6260b1c511e6f420e913e7beb77\", \"e73961244bcbfdd2c10594378091626feb22d0cc\", \"62e716c7133d3061c3bd0ef329cb9e30770482cb\", \"13df6dd1222114502e6856186120cf7a3a044b72\", \"b90ac582384516980bdc094b36148c744cb7b821\", \"5609b4a905eb40379330f9a0bd352b7fa0729413\", \"b3f6a2f3db4ee8a7302ff8a6a2de75582278442a\"]}"},{"id":"46666cb6-08c6-4db8-89d3-f11f7717e8cd","title":"[Atlas] Wiki quality: disease pages Wikipedia parity audit (top 20)","description":"For the top 20 disease wiki pages by word count, compare against Wikipedia using wiki_wikipedia_parity.py or manual LLM review. Identify sections present in Wikipedia but missing/thin in SciDEX. Schedule follow-up improvement tasks for the 5 biggest gaps. Create tasks in Orchestra for identified gaps. Reference: docs/planning/specs/q-wiki-quality_spec.md heuristic H5.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would 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":68,"task_type":"one_shot","frequency":"weekly","assigned_slot":"","started_at":null,"completed_at":"2026-04-10 11:31:27","updated_at":"2026-04-13T10:12:59.491567+00:00","summary":"","completion_notes":"Auto-completed by supervisor after successful deploy to main","last_error":"Audit reopened: ORPHAN_BRANCH — 2 commit(s) found but none on main; branch=?","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/q-wiki-quality_spec.md","provider":"any","payload_json":"{\"_gate_retry_count\": 1, \"_gate_last_decision\": \"REJECT\", \"_gate_last_reason\": \"The commit removes 335 lines of resource dashboard code from api.py (efficiency rankings, wasted resources, utilization timeline) which is unrelated to the Wikipedia parity task scope. This appears to be scope creep - the task spec doesn't mention dashboard removal, and this is functionality removal that should be a separate task.\"}"},{"id":"61065e83-6983-443f-b947-285ef943b798","title":"[Atlas] PubMed evidence update pipeline","description":"Fetch new PubMed abstracts and update evidence links","status":"open","priority":50,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T02:27:38.002931+00:00","updated_at":"2026-04-17T02:27:38.002931+00:00","summary":"","completion_notes":"script-mode, 0.2s","last_error":"","time_estimate_hours":0.0,"completion_count":6,"spec_path":"docs/planning/specs/61065e83_698_spec.md","provider":"any","payload_json":"{\"command\": \"python3 pubmed_update_pipeline.py --limit 149\", \"timeout\": 600, \"working_dir\": \"/home/ubuntu/scidex\", \"success_exit_codes\": [0], \"completion_shas\": [\"43e3a2f981474bcd40b5cc5aa7845d25217d15d4\", \"e40e5c7f320d93cd0830f56de2e171a5b892cbc8\"], \"completion_shas_checked_at\": \"2026-04-12T00:05:47.220859+00:00\"}"},{"id":"4fd68907-8c2a-45c3-8f25-d4a7c2489b16","title":"[Atlas] Fix _cache_page NameError on /atlas page (HTTP 500)","description":"The /atlas page returns 500 because atlas_page() calls _cache_page() which doesn't exist. Should be _set_cached_page() + return HTMLResponse(page). Production confirmed error via journalctl.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"archived","priority":98,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T02:25:05.438495+00:00","updated_at":"2026-04-17T07:03:06.777992+00:00","summary":"","completion_notes":"Released by agent on cross-binding detection.","last_error":"zombie_sweeper: dead_slot_stale_heartbeat=2026-04-17T03:45:15.180651+00:00","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/4fd68907_8c2_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 11:21:29\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"00535ea0-4f75-414b-ba25-68ed28df5d7c","title":"[Atlas] Fix /atlas 500 error — _cache_page NameError","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":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"1","started_at":"2026-04-17T07:00:50.002304+00:00","completed_at":"2026-04-17T07:00:49.802442+00:00","updated_at":"2026-04-17T07:03:06.442337+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/00535ea0_4f7_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [\"minimax\"], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-14 12:21:56\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"93f1ec58-bf37-4eaf-9640-a21296958330","title":"[Atlas] World model curation — artifacts as knowledge, promotion through debate + economics","description":"The world model is NOT just the knowledge graph or the wiki. It is ALL artifacts collectively: hypotheses, analyses, datasets, papers, debates, notebooks, KG edges, gaps, squad findings. The KG and wiki are VIEWS into the world model, not the model itself.\n\nWORLD MODEL = the totality of SciDEX's curated knowledge artifacts + their relationships + their quality assessments + their provenance chains.\n\nCURATION IS THE CORE ACTIVITY — more important than generation:\n1. PROMOTION: A hypothesis that survives rigorous debate, accumulates evidence, and crosses quality thresholds gets promoted to high-confidence status. Its causal claims become trusted background knowledge.\n2. DEMOTION: A hypothesis contradicted by new evidence gets demoted. Its claims are flagged in future debates.\n3. MERGING: Duplicate or convergent artifacts are consolidated. The surviving artifact is richer.\n4. ARCHIVAL: Low-quality, stale, or superseded artifacts are archived. The active world model stays clean.\n5. ENRICHMENT: Artifacts gain evidence, citations, data links, debate history over time. Quality rises.\n\nPRIORITIZATION VIA ECONOMICS:\n- Gap bounties direct attention to the world model's weakest regions (thin landscapes)\n- Hypothesis market prices reflect collective confidence — high prices attract scrutiny, low prices attract investigation\n- Challenge prizes reward VALIDATED improvements to the world model (not just proposals)\n- Token rewards scale with quality: a promoted hypothesis earns 10x an archived one\n\nPRIORITIZATION VIA DEBATE:\n- Debates are the QUALITY MECHANISM — they test claims, surface contradictions, and force evidence\n- The world model improves when debate resolves a genuine scientific question\n- Collective intelligence emerges from the interaction of multiple agents with different perspectives (Theorist proposes, Skeptic challenges, Expert contextualizes, Synthesizer integrates)\n- The promotion pipeline IS the collective intelligence loop\n\nDELIVERABLES:\n1. Define promotion criteria: composite_score >= 0.8, quality_verified=1, debate_count >= 3, unique_evidence_citations >= 5\n2. Implement promotion pipeline in post_process.py: after scoring, check promotion criteria, create high-confidence KG edges for promoted hypotheses\n3. Inject promoted claims as background context in future debate prompts (the Theorist knows what the world model says)\n4. Implement demotion: when new debate evidence contradicts a promoted claim, flag for review\n5. Track world model health metrics: promoted_count, demoted_count, active_hypothesis_quality_distribution, evidence_coverage_by_domain\n6. Wire economics: token rewards proportional to world-model-improvement (promotion events), not just task completion\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T12:55:20.202582+00:00","updated_at":"2026-04-14T12:55:20.202582+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/93f1ec58_bf3_spec.md","provider":"any","payload_json":"{\"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-12 08:14:25\", \"completion_shas\": [\"54de768ddd6ae4f25da6e676e274e3d622365173\", \"49d7515958f3665dd0b5debd67edf9ecb1bd3e41\", \"c99b7df72b73b8200838797a6640a3979717c35e\", \"3ea89897e0aaa1d47c5ffafbcb28202f15c6cd46\"], \"completion_shas_checked_at\": \"2026-04-14T12:55:20.183555+00:00\", \"completion_shas_missing\": [\"8867598db13ccf53cd8cf7277ceda3599968dbd7\", \"03427797bc4c76af491aede48ab8cb477ae0ba50\", \"d1f6375f839242116bca23d1eecc37f96722dcc0\", \"49d7515958f3665dd0b5debd67edf9ecb1bd3e41\", \"c99b7df72b73b8200838797a6640a3979717c35e\", \"3ea89897e0aaa1d47c5ffafbcb28202f15c6cd46\", \"1a06f8e6c0e4057af71e3c2644978376a66bb64d\", \"edb6446ed695275625ed13aa986768b531c8652b\", \"24c47e8b3070aec3640870614dab711852b05b7b\", \"6601d5f6336296aede08010d0ce54b7cef3a310a\", \"5aaae786fa939c6a2bacbb4d7c04563dd930f762\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"0c47f958-e5da-4239-9172-e7a0e070319b","title":"[Atlas] Fix /atlas 500 error: undefined _cache_page and dict iteration bug","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-13T21:06:05.102378+00:00","updated_at":"2026-04-13T21:06:05.102378+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/0c47f958_e5d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"bebb458ae26aba91ff7494b15ebf49bce79ef360\", \"f9a8e8ead3292e1a4a089d899719eac70ee69668\"], \"completion_shas_checked_at\": \"2026-04-13T21:06:05.083328+00:00\"}"},{"id":"6c2a7034-69a0-45c1-9c00-130545496e0b","title":"[Atlas] Fix /atlas page returning 500 Internal Server Error","description":"","status":"archived","priority":96,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 01:00:06","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6c2a7034_69a_spec.md","provider":"any","payload_json":"{}"},{"id":"fcd03e81-ef26-4674-8dca-501653582930","title":"[Atlas] Escalate: Database corruption blocks mermaid task ef972520","description":"Task ef972520 (Add mermaid pathway diagrams to 10 entity pages) was incorrectly marked complete but is actually blocked.\n\n**Blocker**: Database corruption at `/home/ubuntu/scidex/scidex.db` (4GB, \"database disk image is malformed\")\n\n**Impact**: All database operations fail, including:\n- Running mermaid generation scripts (mermaid/add_mermaid_top50_entities.py, etc.)\n- API endpoints that depend on the database\n\n**Evidence**:\n1. `sqlite3 /home/ubuntu/scidex/scidex.db \"PRAGMA integrity_check;\"` returns \"Error: database disk image is malformed\"\n2. The worktree's scidex.db is empty (0 bytes)\n3. Git history shows mermaid work was verified complete in commit f8904f28e (13,639/13,640 entities have diagrams)\n\n**Recommended action**: \n1. Restore database from backup or repair corrupted DB\n2. Re-verify mermaid diagram coverage\n3. If coverage is sufficient, close task ef972520 as \"already done\"","status":"done","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:27:37.910532+00:00","updated_at":"2026-04-17T08:27:37.910532+00:00","summary":"","completion_notes":"Task fcd03e81-escalate-database-corruption-blocks-merm confirmed:\n- DB corruption present but not blocking mermaid work — database remains fully functional for all queries\n- Mermaid coverage: 14,039/14,040 wiki entities (99.99%+) \n- Task ef972520 (mermaid diagrams) is genuinely complete — 1 missing entity is a blank placeholder, not a real entity\n- API healthy: /api/status returns 200 with analyses=388, hypotheses=677\n- Entity page /api/wiki/genes-akt1 confirmed to contain embedded mermaid flowchart\n- No code changes needed — investigation only","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"68a89bcf-b396-420f-bf73-b907abf52d58","title":"[Atlas] Fix /atlas page returning HTTP 500","description":"The /atlas page returns HTTP 500. This is a key demo page showing the knowledge graph. Need to investigate the error and fix it.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-15T23:07:06.545657+00:00","updated_at":"2026-04-15T23:07:06.545657+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/68a89bcf_b39_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:37:35\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\", \"completion_shas\": [\"38b5ba3d881baff28ab893a5983c5224c575a91b\", \"2138e78f222e3a683bf00455148e31b164e88245\", \"c3bdc352becdd0539d66559ec46656abbc82e95a\", \"4e521d7aef67e69f64bc78acea855a4faa71f2d5\"], \"completion_shas_checked_at\": \"2026-04-15T23:07:06.527850+00:00\"}"},{"id":"6380c395-86dd-4451-9484-1416fc4cb56c","title":"[Atlas] Fix /atlas 500 error — _cache_page is not defined","description":"The /atlas page returns 500 because atlas_page() calls _cache_page() which doesn't exist. Fix: replace with direct return of page HTML string.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-15T21:36:42.768750+00:00","updated_at":"2026-04-15T21:36:42.768750+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/6380c395_86d_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-13 23:39:14\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"3e902ee5-ae1c-478e-aa2a-66bff8f2de3d","title":"[Atlas] Fix wiki_entities compat view: entity pages 500 error","description":"The wiki_entities table was renamed to wiki_pages with a new schema, but api.py still has 31 references to wiki_entities (SELECT * FROM wiki_entities, etc). This causes all /entity/ pages to 500 error. Fix by: 1) Creating a compat VIEW wiki_entities that maps wiki_pages columns to old column names (title->entity_name, content_md->summary, etc), 2) Removing the broken trigger creation in init_db that tries to create AFTER trigger on what is now a view, 3) Fixing FTS search to use wiki_pages instead of wiki_entities_fts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-14T01:02:31.008293+00:00","updated_at":"2026-04-14T01:02:31.008293+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/3e902ee5_ae1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"38156d900fb168a1a868ef94ffd97eec3aafbf3a\", \"78acdc1940963b7e1ad7e4aabc256696a31b4683\", \"f77aabba2551de8dba3bbc0b56feec149ab889db\"], \"completion_shas_checked_at\": \"2026-04-14T01:02:30.993620+00:00\", \"completion_shas_missing\": [\"c29656a899551004d3cb91c19b16912506657b40\"]}"},{"id":"22eb3b44-2093-496b-99fc-b88182f181f1","title":"[Atlas] Fix wiki_entities→wiki_pages migration in api.py (entity pages broken)","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":"2026-04-14T00:56:19.989122+00:00","updated_at":"2026-04-14T00:56:19.989122+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/22eb3b44_209_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"132af7ed181e387818d05988754ddb2edd1f1fdf\", \"64a228dfd974e71606aca7015efbd709835f9ef9\", \"5f4e99c5513a353167d69eb59d9e155e03dc0f84\"], \"completion_shas_checked_at\": \"2026-04-14T00:56:19.969876+00:00\"}"},{"id":"af95478d-af4e-4bb8-84df-049da114d3df","title":"[Atlas] Fix /atlas page 500 error","description":"The /atlas page returns a 500 error. This is a critical demo page for the Knowledge Graph layer. Need to diagnose and fix.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-14T00:04:27.055097+00:00","updated_at":"2026-04-14T00:04:27.055097+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/af95478d_af4_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"3bae03068b3a513bac634fc2825c14e7fcb86b60\"], \"completion_shas_checked_at\": \"2026-04-14T00:04:27.039142+00:00\"}"},{"id":"a7751a08-37ca-4a5d-bf12-12b2f6a72ba5","title":"[Atlas] Fix /atlas page returning 500 Internal Server Error","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":"2026-04-13T23:47:24.676901+00:00","updated_at":"2026-04-13T23:47:24.676901+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/a7751a08_37c_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}, \"completion_shas\": [\"7031198ab14830072444a4b7de0aa18ae0c746b6\", \"1453cd24eb54cd18cf8aacbb64b290413c41c954\"], \"completion_shas_checked_at\": \"2026-04-13T23:47:24.657284+00:00\", \"completion_shas_missing\": [\"4ef656c49d5a95b57636bae6588f665b2f007523\"]}"},{"id":"c52b3591-9466-40fb-88dc-8b6f5e26eba1","title":"[Atlas] Fix /atlas page 500 error","description":"The /atlas page returns HTTP 500 Internal Server Error. Needs investigation and fix.","status":"archived","priority":95,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 23:44:55","updated_at":"2026-04-03 15:54:29","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c52b3591_946_spec.md","provider":"any","payload_json":"{}"},{"id":"547d8a08-4377-4a91-ab0f-5878d11a7755","title":"[Atlas] Model artifacts WS1: model_versions schema + migration","description":"Add model_versions table per quest_model_artifacts_spec. DDL ready in spec. Includes external vs internal badge, code_repo_url, code_commit_sha, training_params, eval_metrics, promotion_state lifecycle.","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:28:10.173888+00:00","updated_at":"2026-04-16T22:28:10.173888+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/task-id-pending_model_artifacts_ws1_schema_spec.md","provider":"any","payload_json":"{}"},{"id":"6391cf49-0d28-4222-9648-16c13d208676","title":"[Atlas] Import NeuroWiki content into SciDEX wiki subsystem","description":"Create a wiki content subsystem for SciDEX by importing NeuroWiki's 17,315 pages.\n\n1. Create wiki_pages table: id, slug, title, content_md, entity_type (gene/protein/mechanism/therapeutic/etc), \n frontmatter_json (preserve all metadata), refs_json (structured references with PMIDs/DOIs),\n neurowiki_commit (git commit hash for update tracking), source_repo, \n word_count, last_synced, created_at, updated_at\n2. Write import_neurowiki.py that:\n - Reads all .md files from /home/ubuntu/NeuroWiki/content/\n - Parses YAML frontmatter (title, tags, refs, dates)\n - Stores markdown body and structured metadata\n - Records source commit: d5f005552f8dae962eb90814161cb953a2a7d985\n - Maps NeuroWiki directory structure to entity_type (content/genes/ -> gene, content/proteins/ -> protein)\n3. Create /wiki/{slug} endpoint to render wiki pages with SciDEX styling\n4. Cross-link: for each wiki page, find matching KG nodes and hypotheses by entity name\n5. Track neurowiki_commit so we can pull updates: git -C /home/ubuntu/NeuroWiki log --oneline -1\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":93,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-14T03:03:58.825581+00:00","updated_at":"2026-04-14T03:03:58.825581+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":"{\"completion_shas\": [\"ae3bbb11c31a74dd740cc5b6c4b3d8814bcb9e5c\"], \"completion_shas_checked_at\": \"2026-04-14T03:03:58.806678+00:00\"}"},{"id":"3facef4e-f094-4661-a77d-dc064e6869c4","title":"[Atlas] Model artifacts WS5: feedback loop into world model","description":"Promoted model outputs (annotations, predictions) flow back as KG edges with attribution + confidence propagation.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:49:14.547067+00:00","updated_at":"2026-04-16T23:49:14.547067+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/task-id-pending_model_artifacts_ws5_feedback_loop_spec.md","provider":"any","payload_json":"{}"},{"id":"5d28a0c1-b64a-47df-93be-9edf36afe281","title":"[Atlas] Fix wiki_entities table missing — entity pages all error","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":"2026-04-16T09:28:12.293034+00:00","updated_at":"2026-04-16T09:28:12.293034+00:00","summary":"","completion_notes":"Task reopened by audit (ORPHAN_BRANCH flag) but work is verified complete on main:\n\nVERIFIED: \n- wiki_entities table exists in scidex.db with 13640 rows\n- /entity/APOE returns HTTP 200 with rich content (4776 KG edges, 14 hypotheses, infobox, 3D PDB structure)\n- /entity/TREM2 returns HTTP 200 with rich content \n- Table has full schema: entity_name PK, entity_type, neurowiki_url, summary, extracted_relations, page_exists, last_synced, created_at, mermaid_diagram, infobox_data\n- 3 FTS triggers + history trigger all present\n- Work landed via squash merges visible in HEAD history (81eddfc97, bce11e477, 79e10de7b)\n\nThe original 2 commits were already merged into main via prior squash merges — the audit flag was stale.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5d28a0c1_b64_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}, \"completion_shas\": [\"9a3b0cb53\", \"7410645d2\"], \"completion_shas_checked_at\": \"2026-04-16T09:28:12.121496+00:00\"}"},{"id":"ea9c4b21-bcbc-4652-9a3e-ffacb8e21d57","title":"[Atlas] Fix 500 error on /atlas page — _cache_page NameError","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":"2026-04-16T08:12:31.731130+00:00","updated_at":"2026-04-16T08:12:31.731130+00:00","summary":"","completion_notes":"Verified: commit 50f38aa71 contains the fix (replacing undefined `_cache_page` with `_set_cached_page` + `return page`). /atlas endpoint returns HTTP 200. Task was reopened only because prior worker exited without calling orchestra complete.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ea9c4b21_bcb_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"5047ea9c-5ccd-451c-bbce-a4ea40d25551","title":"[Atlas] Add KG statistics and top entity browser to /atlas page","description":"The /atlas page is currently a static 27KB page with minimal interactivity. Add: 1) KG stats dashboard (total edges, edge types, top connected entities), 2) Top 50 entities by connection count with links to /entity/, 3) Recent KG edges list. This makes /atlas the gateway to exploring the knowledge graph.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T05:09:54.355684+00:00","updated_at":"2026-04-16T05:09:54.355684+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/5047ea9c_5cc_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"27fc92bf65725f2fa217aab62c947859b892768c\"], \"completion_shas_checked_at\": \"2026-04-16T05:09:54.335543+00:00\"}"},{"id":"8771989e-86f4-4d93-90eb-04cb0ffc38b3","title":"[Atlas] Add mermaid pathway diagrams to top 5 wiki entity pages","description":"Quest 16 D16.8: Enrich the top 5 demo-critical wiki pages (TREM2, APOE, LRP1, microglia, tau) with mermaid pathway diagrams showing disease mechanism cascades. These diagrams should illustrate how the entity connects to Alzheimer's disease pathology. Add the diagrams as mermaid code blocks in the wiki content.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T04:40:41.569871+00:00","updated_at":"2026-04-16T04:40:41.569871+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8771989e_86f_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"b74bbc08-0587-459c-acd4-f90d6e45d3ce","title":"[Atlas] Populate papers table from hypothesis PubMed citations","description":"Extract all PMIDs referenced in hypotheses evidence_for/evidence_against fields. For each PMID, fetch metadata from PubMed API and insert into papers table. Link papers to analyses via cited_in_analysis_ids. papers table currently has 0 rows but 118 hypotheses reference PubMed papers.","status":"done","priority":92,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:13:30","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"0e5fef1b-99e2-41f1-ac6c-c6ababe4ba27","title":"[Atlas] Fix /atlas 500 error - undefined _cache_page function","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":91,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T10:49:12.794352+00:00","updated_at":"2026-04-16T10:49:12.794352+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/0e5fef1b_99e_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 8}}"},{"id":"645fd0bd-08f4-4507-aa04-4cd9a261523c","title":"[Atlas] Enrich top demo entities with cross-links and rich content","description":"Ensure TREM2, APOE, LRP1, PARP1, microglia, tau, amyloid-beta entity pages have all cross-links: related hypotheses, KG edges, wiki pages, pathway diagrams, and target drug data. D16.8 + Quest 4 D-PRIORITY.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T10:38:44.708416+00:00","updated_at":"2026-04-16T10:38:44.708416+00:00","summary":"","completion_notes":"Verified all 7 target entities (TREM2, APOE, LRP1, PARP1, MICROGLIA, TAU, AMYLOID-BETA) have: page_exists=1 in wiki_entities, mermaid diagrams populated, KG edges (25,031 total in DB), drug data in targets table (TREM2/MAPT/APOE/LRP1/PARP1), and API returns 200 with all cross-links. The prior orphan commit (a97b8e553) added scripts that were never merged, but the data they would have created already exists in the DB via other means.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/645fd0bd_08f_spec.md","provider":"any","payload_json":"{}"},{"id":"15aba113-6c49-471d-a8f5-93a462caeca0","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T07:52:03.412275+00:00","updated_at":"2026-04-17T07:52:03.412275+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{}"},{"id":"b0a06309-1763-4424-b9c2-55ac18d82533","title":"[Atlas] Fix /entity/ links that emit wiki slugs + add slug fallback in entity_detail","description":"User reported /entity/genes-foxp3 404. Data is intact (wiki_pages has slug, knowledge_edges has 515 FOXP3 edges, canonical_entities has 15 matches) but 3 sites in api.py emit /entity/ hrefs pointing at wiki slugs where the route expects entity symbols: (1) line 31795 target-page 'Wiki:' link, (2) line 12833 FTS search entity-type callback that aliases slug AS entity_name then emits the slug as /entity/ link — this is how the user found the bug via search for 'foxp'. Fix: redirect both href emitters to /wiki/ since the underlying data is a wiki page. Add defensive slug-to-symbol redirect in entity_detail so existing bookmarks and any remaining bad emitters auto-correct to the canonical URL.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T15:52:22.566116+00:00","updated_at":"2026-04-16T15:52:22.566116+00:00","summary":"","completion_notes":"VERIFIED COMPLETE on main (fa99b3314). All acceptance criteria pass. Local spec commit e4ece2d1e staged (push blocked by no git creds, supervisor will pick it up on next sync).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"completion_shas\": [\"e4ece2d1e\"], \"completion_shas_checked_at\": \"2026-04-16T15:52:22.512558+00:00\"}"},{"id":"ac64eac9-3d36-487d-8b01-fcaee3d14911","title":"[Atlas] Extract knowledge edges from existing synthesizer outputs into KG","description":"The synthesizer generates knowledge_edges JSON in its output (verified 14 edges in first analysis), but post_process.py is never called retroactively for existing sessions. Write a migration script to parse all 17 synthesizer rounds, extract knowledge_edges, link via session→analysis, and insert into knowledge_edges table. This will populate the Atlas layer knowledge graph from zero to ~100+ edges.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T15:03:14.183548+00:00","updated_at":"2026-04-16T15:03:14.183548+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ac64eac9_3d3_spec.md","provider":"any","payload_json":"{}"},{"id":"3b4f5b13-7579-4f67-9e1d-6e40a2663d25","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T14:20:31.599333+00:00","updated_at":"2026-04-16T14:20:31.599333+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3b4f5b13-757_atlas_expand_knowledge_graph_add_edges_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"c082be9d-2fcf-470a-bc67-0031f55e5829","title":"[Atlas] Upgrade /atlas to dynamic dashboard with KG stats, top entities, and recent edges","description":"The /atlas page serves a 154-line static HTML file. Replace it with a dynamic page showing: KG stats (edges, entities, types), top entities by edge count, recent edges, entity type distribution, and links to the interactive graph. This is a demo-critical layer that needs to showcase the knowledge graph.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T14:04:20.181328+00:00","updated_at":"2026-04-16T14:04:20.181328+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c082be9d_2fc_spec.md","provider":"any","payload_json":"{}"},{"id":"20951642-5f0b-4ec7-916a-c08038db4a3d","title":"[Atlas] Enrich entity pages — add linked hypotheses, papers, and experiments sections","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":"2026-04-16T13:36:25.188195+00:00","updated_at":"2026-04-16T13:36:25.188195+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/20951642_5f0_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"2f85b14b-a137-4515-a0eb-9dac6a5d4dba","title":"[Atlas] Add mermaid pathway diagrams to top wiki pages without them","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":"2026-04-16T13:23:21.007623+00:00","updated_at":"2026-04-16T13:23:21.007623+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/2f85b14b_a13_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"41ee5870-ec2a-4988-93ea-23662483f3d9","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:46:25.613068","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"61fa12c3-df56-43ce-870c-9243943d3778","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:10:17","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":"6eb21c9a-df53-4037-be15-0e0721e3dc19","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:11:41","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":"bebf31e5-a1b2-4524-8142-6bf90cff15ca","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:04:12","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":"0931ce65-8a37-47e8-9f29-bbc8f0b24683","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:18:20","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":"b6b1b567-81d9-4101-855d-4ea50eceaa5b","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:23:56","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":"2e1761f6-a5d0-49a8-9920-8c78f8182b8a","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:01:11","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":"f764f06b-e245-425b-8658-2fee6a39f4cf","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:24:29","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":"5012a44f-ab50-4523-9c98-b475ad154c34","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:23:57","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":"7d7e8a51-fa67-4657-aeba-37d9d718c632","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:25:14","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":"9a4ac8a4-cfd7-4678-92b1-a2ebe12e46c3","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:59:30","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":"faa8f308-3d89-4b9d-afba-6590640ada00","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. 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Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"2","started_at":null,"completed_at":"2026-04-03 07:31:20","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":"ef9b2f76-0cf9-458b-bfed-b1809ee82dc1","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:07:52","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":"10130688-34f1-4acd-87ea-e0c4195b7208","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:04:16","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":"fb9a3e0a-a19c-4335-8739-330b2a16dbb2","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:06:47","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":"b50f587e-bc6b-4c6a-92b0-450f76d0b923","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:57:44","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":"160862fb-921c-4894-ae08-61fd6ff41913","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:19:44","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":"7e170cf5-0295-43ec-bf98-a9eb6eb755af","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:22:24","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":"6c5d46e2-af7a-4c96-a411-bd029bbf1481","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:58:14","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":"5077c041-700d-49a2-96cc-56435a7ffaf0","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:43:32","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":"ad926265-c29f-447b-8575-9be5811ba1d4","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 07:58:18","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":"78dba023-8cc0-4a68-bf96-d6b66e0b2e0f","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:27:20","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":"8504d096-5f2a-4652-a2c8-0ae7d3a28ba9","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:54:01","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":"ee4cf66c-8b59-47ca-a332-f49b2050e65c","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 09:46:30","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":"43452d4f-6fd5-4d23-89c6-5a9f2b06e71d","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:41","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":"ed2d94eb-9f47-4379-be9c-bfef07130ac5","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:39:46","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":"46bcae1a-31fc-4aaa-9cf8-86113183d6f3","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 10:06:53","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":"1e1ff2d8-43b7-4bec-a3bc-60f7a6e51162","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","status":"archived","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 11:40:07","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":"894415a3-8ebb-4fad-be6a-c6df4eb4ca5f","title":"[Atlas] Expand knowledge graph — add edges from PubMed abstracts for top entities","description":"Use NLP/LLM extraction to add KG edges from paper abstracts. Focus on top 50 entities by connection count. Target: 2000+ new edges with evidence.","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":"08e05e95-ff0d-4581-a007-f7210779487e","title":"[Atlas] Design world model multi-representation framework","description":"Design the architecture for SciDEX world models — multiple interconnected representations of scientific knowledge:\n\nCreate docs/planning/specs/world_model_framework_spec.md defining:\n\n1. **Representation types** and their strengths:\n - Knowledge Graph (Neo4j): structured relationships, inference, path finding\n - Wiki Pages (markdown): natural language depth, context, narrative\n - Papers (PubMed): primary evidence, citations, temporal provenance\n - Hypotheses (scored): actionable predictions, testable claims\n - Causal Models: directed causal edges with confidence, interventional reasoning\n - Notebooks (Jupyter): computational artifacts, reproducible analysis\n - Ontologies: canonical type hierarchies (gene > protein > pathway > disease)\n\n2. **Unification layer**: Every artifact has a canonical entity_id. A single entity (e.g. APOE) links to:\n - Its wiki page (/wiki/apoe)\n - Its KG neighborhood (/entity/APOE) \n - All hypotheses mentioning it\n - All papers studying it\n - All causal edges involving it\n - All analyses that generated knowledge about it\n\n3. **World model score**: Composite metric for how well-understood an entity is:\n wiki_depth + kg_connectivity + hypothesis_coverage + evidence_count + causal_clarity\n\n4. **Gap detection**: Identify entities that are wiki-rich but KG-poor (or vice versa) to prioritize research\n\n5. **Artifact registry table**: id, artifact_type, entity_ids (JSON), content_hash, created_by, quality_score","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:14:23","updated_at":"2026-04-02T06:25:55.835588+00:00","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":"a592b68f-1688-4977-b1b7-ba8434ed96cf","title":"[Atlas] Create papers table and literature corpus tracking","description":"The Atlas world model vision requires tracking every PubMed paper cited across SciDEX. Create a 'papers' table with schema: id, pmid, title, authors, journal, year, abstract, cited_in_analysis_ids, first_cited_at. Backfill from existing analyses' PubMed citations. Add /api/papers endpoint.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:21:29","updated_at":"2026-04-02T04:18:37.233315+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/a592b68f_168_spec.md","provider":"any","payload_json":"{}"},{"id":"q04-a1-0A9E71A3","title":"[Atlas] Enrich entity pages for demo targets","description":"Ensure entity pages for TREM2, APOE, LRP1, PARP1, microglia, tau, amyloid-beta, SMPD1, CYP46A1 are rich with: KG neighborhood visualization, linked hypotheses, linked wiki pages, related papers, gene expression summary. Fix any 500 errors on entity pages.","status":"done","priority":90,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 09:48:56","updated_at":"2026-04-02 09:43:32","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"353da173-093c-46eb-a78d-882e1cc29a55","title":"[Atlas] Cross-link hypotheses to wiki pages via target genes","description":"Create artifact_links between hypotheses and wiki pages for their target genes. This enables the 'Wiki Pages' section on hypothesis detail pages. Currently hypothesis pages show 'No linked wiki pages' even when relevant wiki content exists.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:21:08.091377+00:00","updated_at":"2026-04-16T21:21:08.091377+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/353da173_093_spec.md","provider":"any","payload_json":"{}"},{"id":"466d13f2-ec31-44b6-8230-20eb239b6b3a","title":"[Atlas] Add infoboxes to top 20 most-connected wiki entities","description":"536 wiki entities lack infobox_data. Add structured infoboxes (JSON with type, description, key properties) to the 20 most-connected entities that don't have one yet.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:07:00.691843+00:00","updated_at":"2026-04-16T21:07:00.691843+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/466d13f2_ec3_spec.md","provider":"any","payload_json":"{}"},{"id":"2486a7ca-0a36-40ab-9523-4b0fd0c8f5c3","title":"[Atlas] Enrich top entities: TREM2, APOE, LRP1, PARP1 — ensure rich wiki pages with cross-links","description":"These are the most-referenced entities across hypotheses. Each should have: a wiki page with mermaid diagrams, links to hypotheses that reference them, KG neighborhood view, and PubMed references.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T17:54:01.059212+00:00","updated_at":"2026-04-16T17:54:01.059212+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":"{}"},{"id":"3ac441ed-e3fc-494e-96b9-c0df1f415881","title":"[Atlas] Export reproducibility capsules as RO-Crate bundles with archival identifiers","description":"Export SciDEX reproducibility capsules as RO-Crate-compatible bundles with archival source identifiers and checksums.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T17:41:51.189282+00:00","updated_at":"2026-04-16T17:41:51.189282+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/rocrate_swh_export_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 6, \"safety\": 9}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"max_outlook\", \"_stall_requeued_at\": \"2026-04-12 09:26:52\", \"completion_shas\": [\"dcc329a3619cbb3f4a15c4354b62d084b3c8a434\"], \"completion_shas_checked_at\": \"2026-04-12T12:46:15.903742+00:00\", \"completion_shas_missing\": [\"e60d639963b60f539c811feab7604f4dec822ba8\", \"73fecc5698271deacd5c54400c5c0005a2a406a3\", \"c760419723d17a64356340cf805ecdc2c344ef79\", \"6bf61507d5d050c328dd5b136944419cdf5c475e\", \"f2a439c0addd927345d0a7dcff844b8561b0131d\"], \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"6d3bfa16-9273-4d70-9ddd-3b304bfea663","title":"[Atlas] Rich hover popover for wiki citations — claim + excerpt + figure_ref","description":"Replace thin citation tooltip in api.py with rich hover popover. Popover shows: author/year/journal header, paper title, green claim box (↳ Claim:), italic excerpt with figure_ref, PubMed link. Add data-ref-key attribute to elements. 150ms show debounce, 300ms hide delay, pointer-events:auto so PubMed link is clickable. See wiki-citation-popover-spec.md for complete JS implementation.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T17:40:40.535020+00:00","updated_at":"2026-04-16T17:40:40.535020+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/wiki-citation-popover-spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 6, \"safety\": 6}}"},{"id":"4f715110-8d67-4ad2-8bbb-6215950f6c39","title":"[Atlas] Backfill KG edges for zero-edge hypotheses from gene/disease/pathway data","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T17:30:54.415748+00:00","updated_at":"2026-04-16T17:30:54.415748+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/4f715110_8d6_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"c4689ba8-a3c7-4736-a983-58db8945701c","title":"[Atlas] Add KG stats API endpoint and Atlas entity search API","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T16:14:46.438544+00:00","updated_at":"2026-04-16T16:14:46.438544+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c4689ba8_a3c_spec.md","provider":"any","payload_json":"{}"},{"id":"3ab06ea6-c38a-4016-aff0-73df9ac035ba","title":"[Atlas] Add entity detail pages with KG neighborhood, evidence, and wiki cross-links","description":"Create rich entity detail pages at /entity/ showing: 1) Entity info (type, description), 2) KG neighborhood (top connected entities with edge types), 3) Linked hypotheses, 4) Linked papers, 5) Wiki page content if available. Entities should be accessible from /atlas and from KG visualizations. This is D-PRIORITY work for Quest 4 (Atlas) and Quest 16 (Demo). Focus on top demo entities: TREM2, APOE, LRP1, microglia, tau, amyloid-beta.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T16:02:25.329294+00:00","updated_at":"2026-04-16T16:02:25.329294+00:00","summary":"","completion_notes":"Entity detail pages already implemented on main. Live verification at http://localhost:8000/entity/TREM2, /entity/APOE, /entity/LRP1 confirms: 1) Entity info with infobox, 2) KG neighborhood (top connected entities with edge types), 3) Linked hypotheses, 4) Linked papers, 5) Wiki cross-links, 6) Experiments section. Branch is clean with only .orchestra-slot.json modified.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/3ab06ea6_c38_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"975332ad-863e-48c4-adab-1f1a83144918","title":"[Atlas] Migrate knowledge graph to Neo4j","description":"Migration script reads all edges from knowledge_edges SQLite and imports into Neo4j as typed nodes/relationships. Maintain SQLite as write-through cache. /api/graph reads from Neo4j with fallback. Acceptance: all edges in Neo4j; migration idempotent; API response <200ms.","status":"done","priority":88,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:15:22","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/975332ad-863_atlas_migrate_knowledge_g_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"8f814a23-d026-4bee-a3b8-70a9b96a3b62","title":"[Atlas] Expand wiki_entities from NeuroWiki corpus","description":"Only 11 wiki_entities exist, but NeuroWiki has 16K+ pages. Implement bulk ingestion: fetch top gene/protein/disease/drug pages from neurowiki.xyz API or scrape index, insert into wiki_entities table, link to KG entities. Goal: 1000+ entities.","status":"done","priority":87,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:22:25","updated_at":"2026-04-02T04:18:37.669965+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8f814a23_d02_spec.md","provider":"any","payload_json":"{}"},{"id":"0b5285ff-c077-455e-a4d6-f0dd3b538675","title":"[Atlas] Clean and deduplicate knowledge graph entities","description":"Many KG entities appear under different names or cases. Implement entity deduplication: normalize entity names to canonical form, merge duplicate edges, update all references. Use fuzzy matching (APOE vs ApoE vs apolipoprotein E). Create canonical_entities table if not exists.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T11:10:38.236287+00:00","updated_at":"2026-04-17T11:10:38.236287+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\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"17ccd1cd-4f6e-4138-9855-96d5b2af5bb1","title":"[Atlas] FOXP1 wiki page — rewrite with ≥8 inline citations, speech/language featured","description":"Rewrite genes-foxp1 wiki page: (1) Fetch PubMed metadata for PMIDs 21572417, 20380929, 28264148, (2) Enrich all refs_json entries with claim/excerpt/figure_ref/strength, (3) Rewrite content_md with ≥8 [@key] inline citations spread across sections, (4) Add FOXP1 Syndrome section and FOXP2 paralog relationship section, (5) Remove boilerplate filler. Speech/language disorder must be prominently featured — FOXP1's role is under-appreciated vs FOXP2. UPDATE wiki_pages SET content_md=?, refs_json=? WHERE slug='genes-foxp1'.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:49:28.470551+00:00","updated_at":"2026-04-16T20:49:28.470551+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/wiki-foxp1-inline-citations-spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}, \"_stall_skip_providers\": [], \"_stall_requeued_by\": \"minimax\", \"_stall_requeued_at\": \"2026-04-11 04:56:25\", \"_stall_skip_at\": {}, \"_stall_skip_pruned_at\": \"2026-04-14T10:37:14.022390+00:00\"}"},{"id":"1f3a73e2-1cad-4c07-bc84-745555a92029","title":"[Atlas] Extract KG edges from hypothesis descriptions for richer graph","description":"Hypothesis descriptions (avg 13K chars) contain rich mechanistic information but are not yet mined for KG edges. Extract gene-gene, gene-process, and gene-disease relationships from the 149 hypothesis descriptions to dramatically expand the knowledge graph. Use NLP pattern matching similar to extract_more_edges.py.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:48:53.347670+00:00","updated_at":"2026-04-16T18:48:53.347670+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1f3a73e2_1ca_spec.md","provider":"any","payload_json":"{}"},{"id":"d043d92e-5781-41da-a9ee-351a89548d52","title":"[Atlas] Add summaries to key demo entities missing them","description":"Top demo entities (APOE, APP, BDNF, ASTROCYTE, NEURON, GSK3B, BIN1, PSEN2, BACE1, CDK5, ADAM10, CLU, MAPT, IL-6) have empty or very short summaries. Add curated scientific summaries.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T18:45:10.332180+00:00","updated_at":"2026-04-16T18:45:10.332180+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d043d92e_578_spec.md","provider":"any","payload_json":"{}"},{"id":"8033d9d1-70e0-440c-b84d-55658686c162","title":"[Atlas] Add /api/entity/{name} JSON endpoint for KG entity details","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":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T18:36:51.851326+00:00","updated_at":"2026-04-16T18:36:51.851326+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8033d9d1_70e_spec.md","provider":"any","payload_json":"{}"},{"id":"428bc015-c37b-42ce-9048-e05ba260c1d4","title":"[Atlas] Generate Jupyter notebooks for completed analyses","description":"notebooks table has 0 entries. For each completed analysis, generate a Jupyter notebook with: debate transcript summary, hypotheses ranked table, KG visualization, key citations. Store in site/notebooks/, link to analysis_id in DB, add download links to analysis pages.","status":"done","priority":86,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:25:05","updated_at":"2026-04-02T04:18:37.870698+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/428bc015_c37_spec.md","provider":"any","payload_json":"{}"},{"id":"d0bf8206-1774-4caf-aa98-f2574d42be18","title":"[Atlas] Expand KG edge density (currently 1.0 edges/entity, target 5+)","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\n1836 edges across 1800 entities. Extract new edges from paper abstracts and hypothesis descriptions.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T22:29:20.077596+00:00","updated_at":"2026-04-16T22:29:20.077596+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":"d3bbc304-8104-478c-bf2e-353c7195257c","title":"[Atlas] FOXP2 wiki page — rewrite with ≥8 inline citations, fix duplicate H1 and key names","description":"Rewrite genes-foxp2 wiki page: (1) Fetch PubMed metadata for PMIDs 11564484, 19836308, 18455009, 32024995, 11944110, 17641220, 15802617, 34258912, 28731452, (2) Build new refs_json replacing bad key names (foxp, foxpa, foxpb) with descriptive ones (lai2001, fisher2020, etc), (3) Remove duplicate # FOXP2 Gene H1 heading, (4) Rewrite content_md per spec structure with ≥8 [@key] inline citations, (5) Feature lai2001 discovery and enard2002 evolution prominently. UPDATE wiki_pages SET content_md=?, refs_json=? WHERE slug='genes-foxp2'.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T22:17:36.806905+00:00","updated_at":"2026-04-16T22:17:36.806905+00:00","summary":"","completion_notes":"Verified via live DB query. Confirmed all acceptance criteria met: ≥8 inline citations (has 22), rich refs_json with all fields, descriptive keys, no duplicate H1, seminal papers featured, disease associations cited. The page was updated in a prior session via scripts/update_foxp_wiki_pages.py. This session: merged task branch, resolved conflict, verified DB content, added final work log entry.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/wiki-foxp2-inline-citations-spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"reasoning\": 6, \"safety\": 6}}"},{"id":"b2d68f22-1249-46c9-a488-a834cbaf2017","title":"[Atlas] Link April 1-2 orphaned analyses to HTML reports","description":"32 completed analyses (31 from Apr 1, 1 from Apr 2) have empty artifact_path/report_url. Check if HTML files exist and link them, similar to April 3 fix.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:35:33.972310+00:00","updated_at":"2026-04-16T21:35:33.972310+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/b2d68f22_124_spec.md","provider":"any","payload_json":"{}"},{"id":"e1ef6351-5980-4dac-9135-b08df8a2169a","title":"[Atlas] Link April 3 analyses to their generated HTML reports","description":"6 April 3 analyses have HTML files in site/analyses/ but empty artifact_path/report_url in DB. Update DB to link analyses to their reports so they're visible on the site.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:26:47.696573+00:00","updated_at":"2026-04-16T21:26:47.696573+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/e1ef6351_598_spec.md","provider":"any","payload_json":"{}"},{"id":"901f9b7a-521d-47ff-9458-25270f59bbcc","title":"[Atlas] Backfill KG edges for 56 zero-edge analyses from hypothesis gene/disease data","description":"56 of 80 analyses have 0 KG edges in the knowledge_edges table. Use target_gene, disease, and hypothesis titles to derive basic entity relationships (gene-disease, gene-pathway associations) and insert as KG edges with speculative epistemic_status. This expands the world model from 382 to ~1000+ edges and connects all analyses to the KG.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T21:19:33.800138+00:00","updated_at":"2026-04-16T21:19:33.800138+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/901f9b7a_521_spec.md","provider":"any","payload_json":"{}"},{"id":"e27b0be3-4a30-44d6-9f91-7cf4482afaa0","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:59:22.536600+00:00","updated_at":"2026-04-16T20:59:22.536600+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/e27b0be3-4a3_atlas_cross_link_wiki_pages_with_hypoth_spec.md","provider":"any","payload_json":"{}"},{"id":"3367b1d6-0e6b-40d3-9071-417b2fbae4fe","title":"[Atlas] Backfill target_gene_canonical_id with UniProt IDs for all 199 hypotheses","description":"The target_gene_canonical_id column is empty for all 199 hypotheses. Map target_gene to UniProt accession IDs using the existing uniprot_mapping in api.py. This enables linking to external databases (UniProt, AlphaFold, STRING).\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:59:10.860639+00:00","updated_at":"2026-04-16T20:59:10.860639+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/3367b1d6_0e6_spec.md","provider":"any","payload_json":"{}"},{"id":"259c7624-0e4f-48f9-981f-094b0f4667b3","title":"[Atlas] Add infoboxes to top 50 wiki entities missing them","description":"\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:57:26.831421+00:00","updated_at":"2026-04-16T20:57:26.831421+00:00","summary":"","completion_notes":"Task is already complete — audit of wiki_entities table shows 13640 total, 0 missing infobox_data. Prior task 0d37548c (commit 4e3098835) resolved the infobox gap for all entities. Branch pushed with spec file documenting the verification. No code changes needed.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/259c7624_0e4_spec.md","provider":"any","payload_json":"{}"},{"id":"a93a2d13-e233-4817-a3d2-176f2056012c","title":"[Atlas] Add /api/entities and /api/atlas/stats JSON endpoints","description":"Add JSON API endpoints for KG entity browsing: 1) /api/entities — paginated list of entities with connection counts, filterable by type, 2) /api/atlas/stats — KG statistics (total edges, edge types, relation types, growth over time). These endpoints support the new dynamic /atlas page and future integrations.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:53:59.458291+00:00","updated_at":"2026-04-16T20:53:59.458291+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/a93a2d13_e23_spec.md","provider":"any","payload_json":"{}"},{"id":"76d59251-e440-427b-a7d5-c48ee54b4626","title":"[Atlas] Fix KG edge links: route hypotheses to /hypothesis/ and analyses to /analysis/","description":"KG edge links in entity pages, subgraph widgets, and atlas recent edges all link to /entity/ regardless of type. Hypothesis IDs (h-*) should link to /hypothesis/ and analysis IDs (SDA-*) should link to /analysis/ for proper 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":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:47:34.968164+00:00","updated_at":"2026-04-16T20:47:34.968164+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/76d59251_e44_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7}}"},{"id":"c93d110d-3b17-411d-a476-e47053ac484f","title":"[Atlas] Generate mermaid diagrams for next 100 top-connected entities","description":"817 entities with 30+ KG edges still lack mermaid pathway diagrams. Generate diagrams for the next 100 most-connected entities to increase wiki visual richness. D16.8 from QUESTS.md.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:37:36.844421+00:00","updated_at":"2026-04-16T20:37:36.844421+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/c93d110d_3b1_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"b3796dbe-9491-4e99-a495-2f925ca0d1fd","title":"[Atlas] Add infoboxes to APOE, APP, astrocyte, and neuron entity pages","description":"Key demo entities APOE, APP, astrocyte, and neuron are missing structured infoboxes. Generate JSON infobox data for these entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:34:48.245079+00:00","updated_at":"2026-04-16T20:34:48.245079+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/b3796dbe_949_spec.md","provider":"any","payload_json":"{}"},{"id":"30d7214d-fe8f-4ca3-b938-2cfe9d1ec05a","title":"[Atlas] Generate infobox data for top 50 most-connected wiki entities","description":"660 wiki entities lack infobox_data. Generate structured infobox JSON for the 50 most-connected entities without infoboxes to improve entity page quality.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T20:27:14.711007+00:00","updated_at":"2026-04-16T20:27:14.711007+00:00","summary":"","completion_notes":"Task is obsolete. Database query confirms all 13,640 wiki_entities have infobox_data populated. Task d6a62b0c already achieved 100% infobox coverage. No remaining work to do.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/30d7214d_fe8_spec.md","provider":"any","payload_json":"{}"},{"id":"70d09bd3-4271-4e2f-8610-7aafa2f0bd3f","title":"[Atlas] Build /papers page — browse 2374 scientific papers with search and filtering","description":"Build /papers listing page for 2374 papers in DB. Show title, authors, year, journal, citation count, linked hypotheses. Support search and filtering.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-16T20:25:17.261872+00:00","updated_at":"2026-04-16T20:25:17.261872+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/70d09bd3_427_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"ae601ae711c529364b1c29280c529238c64eb0c3\"], \"completion_shas_checked_at\": \"2026-04-16T20:25:17.235259+00:00\"}"},{"id":"ff35c45e-ec24-4296-b4ab-19dcbeebed04","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T11:43:06.814259","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"af823ce6-0584-4a25-988b-fe7b09dc113f","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"","updated_at":"2026-04-03T05:28:08.772468","summary":"","completion_notes":null,"last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"3dcdb410-66f6-4899-ba84-39b4745e9d24","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 13:44:01","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":"1447405d-628d-4b74-aab2-ec6578d9749b","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 14:02:43","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":"166ff557-a637-4609-8f21-3c2eb7b91248","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:13:14","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":"4817d351-80c7-4698-81c9-bde2b1486465","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:17:03","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":"1f73ffcc-487c-4d55-8144-cb379be76437","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:24:10","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":"0a6ac1f8-4699-479b-9aed-ea5842f1cde0","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 15:31:51","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":"c42344b2-2c85-453f-8cac-1b8e7c3c5f02","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:20:49","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":"6d32250a-bfbd-4edd-8be9-1f56d12ed9d8","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-03 05:24:11","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":"a4cf9cb4-96c2-4fc9-afb2-9bac1cec3e3c","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:23:06","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":"6f9179e8-9e98-4e25-9ee5-67350f4be14c","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. 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Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 16:56:20","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":"41d33f28-381d-497b-b7ce-270f1bc05b44","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:19:44","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":"2fa668e3-4409-417d-950e-b0759e165e51","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. Create artifact_links connecting wiki pages to related hypotheses, analyses, and experiments.","status":"archived","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 17:34:50","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":"73b9f418-9dbd-4c97-9c90-f25ddfd175dd","title":"[Atlas] Cross-link wiki pages with hypotheses and analyses","description":"Many wiki pages mention entities that appear in hypotheses but lack explicit links. 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Need to fix /graph endpoint and visualization to display all extracted KG edges from analyses.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:34:39","updated_at":"2026-04-02T05:31:39.630282+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d3ccd355_d41_spec.md","provider":"any","payload_json":"{}"},{"id":"d2464435-fe00-4457-9315-f9a6d07f57b9","title":"[Atlas] Extract directed causal edges from debate transcripts","description":"Enhance knowledge_edges table to include edge_type field (causal, correlation, inhibits, activates, etc.). Parse debate_rounds content with LLM to extract causal claims (e.g., 'TREM2 activates C3', 'APOE4 inhibits Aβ clearance'). Add directionality and evidence_strength to edges.","status":"done","priority":85,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 04:27:20","updated_at":"2026-04-02T04:18:38.095124+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/d2464435_fe0_spec.md","provider":"any","payload_json":"{}"},{"id":"e543e406-4cca-45d0-a062-2fabc24dc2d3","title":"[Atlas] Papers enrichment from PubMed API","description":"For all PMIDs referenced in hypotheses evidence_for/evidence_against, fetch full metadata from NCBI PubMed E-utilities API (title, authors, journal, year, abstract, DOI). Populate the papers table. Currently 0 rows.","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:34:20","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"atl-ds-02-XREF","title":"[Atlas] Cross-reference tabular datasets with KG: bidirectional entity linking","description":"When a tabular dataset is registered, automatically identify columns that map to existing KG entities (genes, proteins, diseases, brain regions, etc.) and create artifact_links. When browsing a KG entity, show linked datasets that mention it. When browsing a dataset, show KG context for each column. This creates a bridge between the graph world model and structured tabular observations. Depends on: atl-ds-01-GROW.","status":"done","priority":83,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:06:13","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/atl-ds-02-XREF_dataset_kg_crossref_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"740cbad0-3e42-4b57-9acb-8c09447c58e6","title":"[Atlas] Link 10 wiki pages to knowledge graph (17257/17399 unlinked)","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\n17257 wiki pages have no KG edges. Create edges linking them to hypotheses, targets, and analyses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:33:29.930314+00:00","updated_at":"2026-04-16T23:33:29.930314+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":"5f217892-0cc7-4f03-bb82-81090458db1f","title":"[Atlas] Link 10 wiki pages to knowledge graph (17191/17333 unlinked)","description":"17191 wiki pages have no KG edges. Create edges linking them to hypotheses, targets, and analyses.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:21:02.340134+00:00","updated_at":"2026-04-16T23:21:02.340134+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/5f217892_wiki_kg_links_spec.md","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}}"},{"id":"e8b9010e-f1d8-4cbc-892c-3219a9cca325","title":"[Atlas] Extract KG edges from 800+ unmined paper abstracts","description":"About 850 papers have abstracts that haven't been processed for KG edge extraction. Run NLP pattern matching on these to discover new gene-disease-pathway relationships. Target: 1000+ new edges.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:20:26.105273+00:00","updated_at":"2026-04-16T23:20:26.105273+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/e8b9010e_f1d_spec.md","provider":"any","payload_json":"{}"},{"id":"e1eec0a1-9ba2-4030-94e1-a1c6372efba8","title":"[Atlas] Build entity explorer — /entity/{name} with cross-linked content","description":"Create entity detail pages that aggregate: wiki content, KG edges (in/out), related hypotheses, papers mentioning the entity, debates referencing it. Enable discovery through the knowledge graph.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T22:59:30.987928+00:00","updated_at":"2026-04-16T22:59:30.987928+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"e38ee040-850d-4795-acb1-d9c3fa7ecc6c","title":"[Atlas] Extract causal models from debate transcripts and wiki content","description":"Build directed causal models from SciDEX content:\n\n1. Create causal_edges table: id, source_entity, target_entity, direction (causes/prevents/modulates), \n confidence, mechanism_description, evidence_pmids, source_type (debate/wiki/paper), source_id\n2. Extract causal claims from debate transcripts (Theorist/Expert rounds contain causal reasoning)\n3. Extract causal claims from wiki pages (look for patterns: \"X causes Y\", \"X leads to Y\", \"X inhibits Y\")\n4. Deduplicate and merge: same causal edge from multiple sources increases confidence\n5. Visualize causal DAGs on entity pages: show upstream causes and downstream effects\n6. Identify causal contradictions: where debate Skeptic disagrees with established wiki causal claims","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:02:07","updated_at":"2026-04-02T06:25:55.835588+00:00","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":"daaa57b2-25b2-4fc8-a249-95ba4d1b12ec","title":"[Atlas] Link wiki_entities to knowledge graph nodes","description":"wiki_entities table has 991 rows, knowledge_edges has 665 edges. Cross-reference wiki entity names with KG node names and create linkages. Update the /graph visualization to show wiki-linked nodes differently. The link_neurowiki.py script exists as a starting point.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:13:50","updated_at":"2026-04-02T06:05:12.235648","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"835063c6-8fa1-426e-9113-76b7aaed8fdb","title":"[Atlas] Entity detail pages — /entity/{name} route","description":"Create /entity/{name} endpoint in api.py showing all SciDEX knowledge about an entity: hypotheses mentioning it, analyses involving it, KG neighbors, NeuroWiki link, papers. Acceptance: /entity/TREM2 shows connected hypotheses, KG neighbors, papers.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:39:47","updated_at":"2026-04-02T05:33:43.702690+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"ed421469-317a-46da-b33f-d440a705cd9f","title":"[Atlas] Entity canonicalization and ontology alignment","description":"Build kg_normalize.py: (a) map relation types to controlled vocabulary of ~20 canonical relations, (b) merge duplicate entities, (c) align entity types to fixed ontology (gene, protein, pathway, disease, drug, phenotype, cell_type, brain_region). Runs in post_process.py pipeline. Acceptance: relations <=25 types; no duplicates.","status":"done","priority":82,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:25:56","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ed421469-317_atlas_entity_canonicaliza_spec.md","provider":"any","payload_json":"{}"},{"id":"19a3814d-ffc8-4e9f-a477-1386a5024def","title":"[Atlas] Backfill kg_edges_generated counts for hypotheses","description":"50 hypotheses have kg_edges_generated = NULL or 0. Count actual KG edges per hypothesis from knowledge_edges table and update the counts.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:52:36.402391+00:00","updated_at":"2026-04-17T09:52:36.402391+00:00","summary":"","completion_notes":"Backfill completed — 681 hypotheses processed: 513 with accurate kg_edges_generated > 0, 168 confirmed edge-free. DB has WAL-level corruption (PRAGMA integrity_check shows hundreds of errors) but updates succeeded via DEFERRED isolation with BEGIN IMMEDIATE transactions. Prior orphan commits (b4c46257, 61da3c4c0) only touched spec file; actual DB work done this session and pushed as 4ca4efe0f.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/19a3814d_ffc_spec.md","provider":"any","payload_json":"{}"},{"id":"c70f2a1d-cc4b-4594-91da-95d14b00ae21","title":"[Atlas] Add mermaid pathway diagrams to 10 entity pages (7641 have them)","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\n5999 wiki entities lack pathway diagrams. Create mermaid diagrams for the most-connected entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:48:40.724595+00:00","updated_at":"2026-04-17T09:48:40.724595+00:00","summary":"","completion_notes":"Work verified on origin/main as 96fcf5bd3. wiki_entities: 14,039/14,040 have mermaid diagrams (99.99%+ coverage). Task description cited 5999 missing when created; bulk mermaid work since then has covered nearly all entities.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"claude","payload_json":"{\"requirements\": {\"coding\": 8, \"reasoning\": 8, \"analysis\": 8}, \"completion_shas\": [\"96fcf5bd37b9774737ba81d2b2534acc9807e6b4\"], \"completion_shas_checked_at\": \"2026-04-17T09:48:40.702393+00:00\"}"},{"id":"2f9e1663-0d21-4e3b-b703-b150536bc22b","title":"[Atlas] Fetch full metadata for backfilled papers from PubMed","description":"1,228 papers were backfilled from hypothesis JSON evidence. They have PMID, claim-as-title, journal, year but no full abstract or author data. Fetch full metadata from PubMed E-utilities API to enrich the papers table: abstract, full title, authors, mesh_terms, doi. Use batch fetching with efetch (500 PMIDs at a time). Update papers table with fetched data. This improves the Atlas world model and paper detail pages.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T09:45:50.055597+00:00","updated_at":"2026-04-17T09:45:50.055597+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/2f9e1663_0d2_spec.md","provider":"any","payload_json":"{}"},{"id":"ef972520-4095-44a1-8ba8-009635d971b6","title":"[Atlas] Add mermaid pathway diagrams to 10 entity pages (7600 have them)","description":"6040 wiki entities lack pathway diagrams. Create mermaid diagrams for the most-connected entities.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T08:23:15.002907+00:00","updated_at":"2026-04-17T08:23:15.002907+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":"131994cb-552f-45c1-9507-2d712e3433aa","title":"[Atlas] Link 17 targets to their wiki pages and back-fill missing entity references","description":"17 targets are missing wiki_page_id references. Many have matching wiki pages that should be linked. Fix by querying wiki_pages for matching gene symbols and updating targets table.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T06:00:27.642024+00:00","updated_at":"2026-04-17T06:00:27.642024+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/131994cb_552_spec.md","provider":"any","payload_json":"{}"},{"id":"4fc6de25-8157-4220-88ac-281a0d0a69fd","title":"[Atlas] Bulk mermaid diagrams batch 2: 200 more entities","description":"Generate mermaid diagrams for the next 200 entities with 30+ KG edges. Targeting 800+ total entities with diagrams.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T05:31:39.880987+00:00","updated_at":"2026-04-17T05:31:39.880987+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/4fc6de25_815_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 5, \"analysis\": 5}}"},{"id":"be470b6c-915e-43e8-939e-cc89ce67a097","title":"[Atlas] Build entity detail pages with cross-linked content from all representations","description":"For each entity in wiki_entities, build a rich /entity/{name} page showing: wiki content, related hypotheses, KG edges, papers mentioning it, debates referencing it.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-16T23:41:41.248326+00:00","updated_at":"2026-04-16T23:41:41.248326+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":"{}"},{"id":"5a40b801-0e05-4802-864b-af0b77133c46","title":"[Atlas] CI: Verify and repair KG edge consistency","description":"Check for orphan edges (referencing nonexistent entities), duplicate edges, and edges with NULL evidence_strength. Fix or remove.","status":"closed","priority":80,"task_type":"recurring","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 23:30:36","updated_at":"2026-04-04T12:52:01.010298+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/5a40b801_kg_edge_consistency_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}, \"auto_tagged_at\": \"2026-04-03T22:29:52.503714\"}"},{"id":"274e6ea5-38ff-4e85-aae3-e3916af3da55","title":"[Atlas] Neo4j graph sync from SQLite knowledge_edges","description":"Sync all 665+ knowledge_edges from SQLite to the running Neo4j instance. Create nodes for each unique entity, create relationships with proper types. Neo4j is running as scidex-neo4j service. This enables more powerful graph queries than SQLite.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:15:01","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c85062ae-21ae-45b8-9e3f-9fb42da99dc4","title":"[Atlas] Fix KG edge extraction + deduplication","description":"AT4.1: Fix source/source_id key mapping in post_process.py edge extraction. Add edge deduplication — same source/target/relation across analyses should merge with increased evidence_strength, not create duplicates.\n\nAcceptance: Edge extraction handles both key formats. Duplicates merged.","status":"done","priority":80,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:47:11","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c85062ae_21a_fix_kg_edge_extracti_spec.md","provider":"any","payload_json":"{}"},{"id":"22be72fe-e0db-41f4-aebb-9ea69303be89","title":"[Atlas] Enrich hypotheses with structured PubMed citations","description":"For all 132 hypotheses, verify PMID references in evidence_for/evidence_against fields. Cross-reference against papers table. Add missing citation metadata. Flag hypotheses with invalid or missing PMIDs.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":79,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:30:12.119835+00:00","updated_at":"2026-04-17T10:30:12.119835+00:00","summary":"","completion_notes":"Verification run 2026-04-17: Papers table has 17,443 PMIDs (up from 1,153 on 2026-04-01). Analyzed 682 hypotheses with 10,740 evidence entries. 665 invalid PMIDs are intentional placeholders (N/A, computational, synthetic_*, etc.) not actual errors. 17 missing PMIDs are valid but for very old papers not in PubMed. 106 hypotheses have no evidence. Work confirmed on main at commit 7dc71021e (enrich_hyp_papers.py).","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"85f3ccfa-539d-4c45-bee2-690f36715fa6","title":"[Atlas] Wiki content generation for entities without NeuroWiki pages","description":"For KG entities that dont have NeuroWiki pages, auto-generate wiki-quality content:\n\n1. Identify entities in knowledge_edges that have no matching wiki page\n2. For each, use Claude to generate a structured wiki page:\n - Title, description, biological function\n - Key relationships (from KG edges)\n - Relevant hypotheses (from SciDEX)\n - Literature references (from papers table)\n - Disease associations\n3. Store as generated wiki pages (marked as auto-generated vs imported)\n4. Quality threshold: only publish if > 3 KG edges AND > 1 paper reference\n5. This extends SciDEX beyond neuroscience as new analyses explore other domains","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:16:34","updated_at":"2026-04-02T06:25:55.835588+00:00","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":"daf4f3d4-1811-4378-af38-c118d7eec65b","title":"[Atlas] NeuroWiki content ingestion pipeline","description":"Fetch NeuroWiki pages for KG entities, extract structured facts. New wiki_entities table (entity_name, neurowiki_url, summary, extracted_relations, last_synced). /api/atlas/entity/{name} returns merged KG+wiki data. Acceptance: populated for all KG nodes with wiki pages; entity pages linked from graph viz.","status":"done","priority":78,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:13:48","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/daf4f3d4-181_atlas_neurowiki_content_i_spec.md","provider":"any","payload_json":"{}"},{"id":"81759c6c-1dee-4e9a-a16d-a37b71fd7b02","title":"[Atlas] Score wiki quality on 20 pages (daily heuristics)","description":"Sample 20 wiki pages, score on 6 heuristics (intro quality, prose ratio, depth, crosslinks, completeness) via LLM. Store in wiki_quality_scores. Run: python3 /home/ubuntu/scidex/scripts/wiki_quality_scorer.py --n 20. Then check /senate/wiki-quality dashboard.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:48:24.375185+00:00","updated_at":"2026-04-17T10:48:24.375185+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/q-wiki-quality_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 6, \"safety\": 6}, \"completion_shas\": [\"ddefca09759cb60f401e18c9907c2db9fce0b4d0\", \"caa88af4d88e4effc30cd4dedc047a568759ccf0\"], \"completion_shas_checked_at\": \"2026-04-17T10:48:24.357137+00:00\"}"},{"id":"a32ea90d-00e1-406f-83fe-57e4a7d33003","title":"[Atlas] Auto-generate wiki pages for KG entities without NeuroWiki content","description":"For entities in knowledge_edges that lack wiki_pages entries, generate stub pages with: entity type, known relationships, related hypotheses, and linked papers.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:35:37.802534+00:00","updated_at":"2026-04-17T10:35:37.802534+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":"{}"},{"id":"1e853871-fac2-4ca4-b7ea-54a1474b98ae","title":"[Atlas] Backfill wiki_entities page_exists for entities with wiki pages","description":"Many wiki_entities have page_exists=0 even when matching wiki_pages exist. Scan all wiki_entities and update page_exists based on fuzzy slug matching to wiki_pages table.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:21:01.097317+00:00","updated_at":"2026-04-17T10:21:01.097317+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/1e853871_fac_spec.md","provider":"any","payload_json":"{}"},{"id":"76873c15-3f31-4d84-932d-ab99b60ccfd5","title":"[Atlas] Automated KG enrichment from hypothesis evidence citations","description":"Parse PMID citations from hypothesis evidence_for/against. Extract entities and relationships. Add as new KG edges with provenance.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T10:16:17.400946+00:00","updated_at":"2026-04-17T10:16:17.400946+00:00","summary":"","completion_notes":"Task re-evaluated for orphan branch audit. Real work (enrich_hyp_kg.py + spec) already landed on main in 78fb9251c. This slot added: (1) stdout buffering fix for test mode compatibility, (2) 9 unit tests in tests/test_enrich_hyp_kg.py covering VALID_RELATIONS/VALID_ENTITY_TYPES, PMID parsing from evidence JSON, LLM extraction filtering, already_enriched check. All tests pass. Spec acceptance criteria updated to all checked.","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 7, \"reasoning\": 6}}"},{"id":"196b0234-7231-4fa1-9ab5-aaebb1457d12","title":"[Atlas] Artifact interconnection and provenance tracking","description":"Create the artifact registry that connects all knowledge representations:\n\n1. Create artifacts table: id, artifact_type (wiki_page/hypothesis/analysis/paper/kg_edge/notebook/causal_edge),\n entity_ids (JSON), title, quality_score, created_by, provenance_chain (JSON: what produced this),\n content_hash, created_at\n2. Create artifact_links table: source_artifact_id, target_artifact_id, link_type (supports/contradicts/extends/cites)\n3. When a debate generates a hypothesis that cites a paper that discusses an entity with a wiki page — \n trace the full provenance chain\n4. Visualization: on any artifact page, show the provenance graph (what led to this knowledge)\n5. Quality propagation: high-quality upstream artifacts boost downstream artifact scores","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 07:11:52","updated_at":"2026-04-02T06:25:55.835588+00:00","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":"a7e9909f-de74-4295-853b-34a4b91fcf2d","title":"[Atlas] Link KG nodes to NeuroWiki pages","description":"For each entity in the knowledge graph, check if a NeuroWiki page exists at neurowiki.xyz/{entity_name}. Store the mapping in wiki_entities table. Show NeuroWiki links on graph visualization. Acceptance: >50% of KG entities linked to wiki pages.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 05:39:32","updated_at":"2026-04-02T05:33:43.702726+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"22c4c017-8b86-4047-9d08-cf55f16da817","title":"[Atlas] NeuroWiki entity linking","description":"AT4.2: For every knowledge graph node matching a NeuroWiki page, add neurowiki_url. Use the NeuroWiki URL pattern (neurowiki.xyz/wiki/ENTITY). Display links on graph visualization and hypothesis detail pages.\n\nAcceptance: Graph nodes have clickable NeuroWiki links where they exist.","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:05:19","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/22c4c017_8b8_neurowiki_entity_lin_spec.md","provider":"any","payload_json":"{}"},{"id":"atl-ds-01-GROW","title":"[Atlas] Dataset-driven knowledge growth: extract KG edges from tabular datasets","description":"Build a pipeline that takes registered tabular datasets and extracts KG edges from them. For example, a gene expression dataset with columns (gene, tissue, expression_level) can generate edges like (gene)-[expressed_in]->(tissue) with expression_level as edge weight. Define extraction templates per dataset schema pattern. Each extraction run creates versioned KG edge artifacts linked to the source dataset. This lets us grow the knowledge graph from structured data, not just papers. Depends on: a17-22-TABL0001 (Artifacts quest).","status":"done","priority":75,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:28:48","updated_at":null,"summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/atl-ds-01-GROW_dataset_driven_kg_growth_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"36c43703-d777-442c-9b42-a02b1aa91bdf","title":"[Atlas] Improve prose on 5 lowest-scoring wiki pages","description":"Run wiki_prose_improver.py --batch 5 to rewrite intros and convert bullet-heavy sections to prose on the 5 pages with lowest quality scores. Verify word count increased. Run: python3 /home/ubuntu/scidex/scripts/wiki_prose_improver.py --batch 5. Target: H1 score improves by >=2 points on each page improved.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"daily","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:33:21.375118+00:00","updated_at":"2026-04-17T11:33:21.375118+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/q-wiki-quality_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"58e8a867c8961aedfc68743abcef0563d8d38c34\", \"0a9e94e66312f26e28f1206a63853f1f3aa5ee56\", \"58da0f8aa47f411a9e95466857188c0e86bcfb74\"], \"completion_shas_checked_at\": \"2026-04-17T11:33:21.358852+00:00\"}"},{"id":"49a8441d-0739-4937-bceb-9f159f2c7b29","title":"[Atlas] NeuroWiki continuous sync mechanism","description":"Set up ongoing sync between NeuroWiki and SciDEX wiki subsystem. Store the git commit hash used for last import. Create sync script that diffs against stored commit, imports new/changed pages. Track sync stats.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\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":"2026-04-17T11:27:47.385659+00:00","updated_at":"2026-04-17T11:27:47.385659+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":"{}"},{"id":"5c39b522-1ca2-4ac7-9300-7a1879a2f090","title":"[Atlas] NeuroWiki continuous sync mechanism","description":"Set up ongoing sync between NeuroWiki and SciDEX wiki subsystem:\n\n1. Store the NeuroWiki git commit hash used for last import\n2. Create sync_neurowiki.py that: git -C /home/ubuntu/NeuroWiki pull, then diff against stored commit\n3. For changed/new files: re-import into wiki_pages table, update refs and metadata\n4. For SciDEX-generated content that NeuroWiki doesnt have: track separately (source=scidex)\n5. Merge strategy: NeuroWiki content is authoritative for existing pages, SciDEX extends beyond\n6. Run as periodic job (daily or on-demand)\n7. Track sync stats: pages imported, pages updated, new entities discovered","status":"archived","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:33:03","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":"f97afbe3-d6f7-41ed-a398-95bc5b11c41c","title":"[Atlas] Gap-driven analysis pipeline","description":"Create a mechanism to automatically trigger new analyses from knowledge_gaps. For each open gap, generate a debate question and queue it for the orchestrator. 22 gaps exist but only 1 is open.","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:47:44","updated_at":"2026-04-02T06:09:46.402005+00:00","summary":"","completion_notes":"","last_error":"Worker lease expired (30m); requeued","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"cd3efac3-5b1e-48e2-b751-6f64b89ed51d","title":"[Atlas] Entity page cross-linking with analyses and hypotheses","description":"Entity pages at /entity/{name} should show all analyses and hypotheses that mention the entity. Query analyses.question and hypotheses.title/description for entity name mentions. Add a Related Research section to entity pages.","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 06:43:06","updated_at":"2026-04-02T06:05:12.235648","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":"ab42bc64-183c-4769-be86-eaf226ed1ab3","title":"[Atlas] Causal discovery from debate transcripts","description":"Extend post_process.py to extract causal claims from debates: cause/effect entities, mechanism, directionality, confidence, source PMID. New edge_type column on knowledge_edges. Acceptance: new analyses produce causal edges; 21 existing backfilled; /api/graph filters by edge_type; directed arrows on graph.","status":"done","priority":72,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:37:11","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/ab42bc64-183_atlas_causal_discovery_fr_spec.md","provider":"any","payload_json":"{}"},{"id":"c1227e9b-0efb-4197-b443-7a2d2beb5a90","title":"[Atlas] Build /atlas explorer with search, filter by entity type, and graph neighborhood view","description":"Replace static atlas.html with dynamic explorer. Search entities, filter by type, show local KG neighborhood for selected entity.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T11:58:07.499279+00:00","updated_at":"2026-04-17T11:58:07.499279+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"","provider":"any","payload_json":"{}"},{"id":"c102d632-c859-41ab-a90a-f80ed6b4fed7","title":"[Atlas] Dynamic Atlas explorer page","description":"AT4.3: Replace static atlas.html with dynamic /atlas route in api.py. Show: search box for genes/proteins/diseases, entity detail with all knowledge_edges, related hypotheses, NeuroWiki link, neighborhood subgraph.\n\nAcceptance: /atlas lets user search 'TREM2' and see all connections, hypotheses, NeuroWiki content.","status":"done","priority":70,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:00:04","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c102d632_c85_dynamic_atlas_explor_spec.md","provider":"any","payload_json":"{}"},{"id":"2382f69a-c3ff-4875-822a-325192a8946d","title":"[Atlas] Analysis-to-KG impact scoring","description":"Compute world model impact per analysis: new edges contributed, new entities introduced, centrality change, gaps resolved. Store as kg_impact_score on analyses table. Acceptance: all analyses scored; recalculated on KG changes; visible and sortable on /analyses/.","status":"done","priority":68,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:27:40","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/2382f69a-c3f_atlas_analysis-to-kg_impa_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"abccce36-5377-4096-8494-fc41ecdeebe4","title":"[Atlas] Literature corpus management","description":"Create papers table (pmid, title, abstract, journal, year, cited_by_analyses, cited_by_hypotheses, kg_edges_sourced). Build literature_manager.py extracting PMIDs from all analyses/hypotheses, fetching metadata via NCBI. /api/atlas/papers endpoint. Acceptance: populated; citation network stats page accessible from nav.","status":"done","priority":65,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:27:58","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/abccce36-537_atlas_literature_corpus_m_spec.md","provider":"any","payload_json":"{}"},{"id":"24a2737e-928c-41a5-a271-85c5a67a960f","title":"[Atlas] Add /datasets page — route returns 404","description":"The /datasets route returns 404. A datasets registry exists (economics_drivers/datasets/, 3 seed AD datasets in datasets/ dir, database tables: datasets/dataset_versions/dataset_citations) but there is no web page to browse it. Add a FastAPI route at /datasets that lists registered datasets from the database with links to view each one. The datasets CLI shows the data: python3 -m economics_drivers.datasets.cli list. Follow existing patterns from /notebooks, /artifacts, /wiki pages in api.py.\n\n\n## REOPENED TASK — CRITICAL CONTEXT\n\nThis task was previously marked 'done' but the audit could not verify\nthe work actually landed on main. The original work may have been:\n- Lost to an orphan branch / failed push\n- Only a spec-file edit (no code changes)\n- Already addressed by other agents in the meantime\n- Made obsolete by subsequent work\n\n**Before doing anything else:**\n\n1. **Re-evaluate the task in light of CURRENT main state.** Read the\n spec and the relevant files on origin/main NOW. The original task\n may have been written against a state of the code that no longer\n exists.\n\n2. **Verify the task still advances SciDEX's aims.** If the system\n has evolved past the need for this work (different architecture,\n different priorities), close the task with reason \"obsolete: \"\n instead of doing it.\n\n3. **Check if it's already done.** Run `git log --grep=''`\n and read the related commits. If real work landed, complete the\n task with `--no-sha-check --summary 'Already done in '`.\n\n4. **Make sure your changes don't regress recent functionality.** Many\n agents have been working on this codebase. Before committing, run\n `git log --since='24 hours ago' -- ` to see what\n changed in your area, and verify you don't undo any of it.\n\n5. **Stay scoped.** Only do what this specific task asks for. Do not\n refactor, do not \"fix\" unrelated issues, do not add features that\n weren't requested. Scope creep at this point is regression risk.\n\nIf you cannot do this task safely (because it would regress, conflict\nwith current direction, or the requirements no longer apply), escalate\nvia `orchestra escalate` with a clear explanation instead of committing.\n","status":"done","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-17T15:24:19.486776+00:00","updated_at":"2026-04-17T15:24:19.486776+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/24a2737e_928_spec.md","provider":"any","payload_json":"{\"completion_shas\": [\"91c799ace\", \"fca366435\"], \"completion_shas_checked_at\": \"2026-04-17T15:24:19.467894+00:00\", \"completion_shas_missing\": [\"7b35de848e72b7849979ae41a734e356e1bce1f0\", \"66192a444dfa761b1cf18ae02a3ac4f990b60256\", \"26587d8dc77c05cf84b5c91d0d62720af1fb8dbc\", \"307eb757d4f2644c63d310717ade98b88d8a02dc\", \"8f540bbbeefdc2613f82ceb5111b6ade10012b8d\", \"af127e89d0010f50019b63ec3c6c5b914c212732\", \"0fe3effc1c954967358c06894f7c9486828f77ef\", \"d9b46f50d81824d7cf08ae97717f77c39f14fe37\", \"4880d6338f89d95ba23dcd871575081335ebf65b\", \"58b3df0c039789a01453482d5a7d6bb3d97342c1\", \"6252db719707f2ad38070464c80460fddf4cf808\", \"eb9b7c8a911cd8200cb3d1cea0b89ac990e93a07\", \"a6aaf3a2b6c2a88d0b43b877f216d1ff7dff7e43\", \"d17c2f2c45c73fad0d60d780f5086488805deee6\", \"3ee258e865ede3e7fca329d3257d6b3f78b4521a\", \"9696a0c661fb97a37e888088f578fcd6670435c1\", \"2f94cbdd79b78ce2b8d1463f5a1b3cea4ce29ac0\", \"de04cbfd893727c2e996365c8cfac5959253846d\", \"918dd51b19dd0d74b3448beb54b5a824ea4463af\", \"85864a8dcd608ea11a1f078657bec411ece65db9\", \"e2776b789381f920d733b0ea5837d53a05b21180\", \"de7c35fa202ff6cd9b8535c4c73c3d6ef43a5db5\", \"00c3873ceff176773695da936bb044f2a0c8fa98\", \"eac8c083a3a6e85b10f1a11986ab7b352c453f87\", \"b8a1eadbed4fc63acef4b3dc54450a49e73d3028\", \"d2951d81f77b75527c1141d85bedd84ec9286987\", \"caaa84d840647f405762dfb5bc1844cd9405db6b\", \"aee6c994a9d819c894730596084e16b123113f6a\", \"46c88f25a2e76077cbf7f276e204db55795a3585\", \"4395614d4bfc4b41f5c80a6555dfae3c7e1ddef7\", \"65cf43fc84905972c85688a8d70f26e28cba314c\", \"f1fab0c60cd0a44811bd187a550f8eace2498fea\", \"149c24b34b75b5da2ceea7f279b3b3579395306e\", \"2d6e106a804bab60de98b971a020212e7c58502f\", \"728748f1f84327cd17c75478cd3334f99c1d991d\", \"f50e3f7d7e65f1f0e67809e5c93f12591c846269\", \"629028d6492a6e79ceeffe72600b79577911e516\", \"d24d112e521e2f57ad00a2c069c2da9bcb969575\"], \"requirements\": {\"coding\": 7, \"analysis\": 6}}"},{"id":"76beb6c8-7ccd-4f79-9cf9-f6567a5cc067","title":"[Atlas] Jupyter notebook artifact registry","description":"Create notebooks table and /notebooks page. Track computational artifacts: title, description, associated_analysis_id, associated_entities, file_path, rendered_html_path. Render .ipynb to static HTML. Acceptance: registry API; rendered notebooks accessible; linked to analyses and KG entities.","status":"done","priority":60,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:26:50","updated_at":"2026-04-02T03:05:17.609939+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/76beb6c8-7cc_atlas_jupyter_notebook_ar_spec.md","provider":"any","payload_json":"{}"},{"id":"8fcdf0bb-9434-4dbc-a695-bd650212688d","title":"[Atlas] Auto-generate gaps from graph structure","description":"AT4.4: After each analysis, scan the knowledge graph for thin areas (entities with few edges, pathways with no drug connections, disease nodes with no gene associations). Generate new knowledge_gap rows.\n\nAcceptance: After running an analysis, 1-3 new gaps are created from graph topology.","status":"done","priority":55,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 02:59:42","updated_at":"2026-04-02T01:31:39.888633+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/8fcdf0bb_943_auto_generate_gaps_f_spec.md","provider":"any","payload_json":"{}"},{"id":"c0ca1165-b555-4816-8173-c7ef3670bda5","title":"[Atlas] Dynamic how.html with live stats","description":"AT4.5: Convert how.html from static to dynamic route in api.py. Replace hardcoded stats (595+ papers, 16 hypotheses) with live DB queries.\n\nAcceptance: /how page shows current counts matching dashboard.","status":"done","priority":50,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-02 03:05:47","updated_at":"2026-04-02T02:17:38.974483+00:00","summary":"","completion_notes":"","last_error":"","time_estimate_hours":0.0,"completion_count":0,"spec_path":"docs/planning/specs/c0ca1165_b55_dynamic_how_html_wit_spec.md","provider":"any","payload_json":"{}"}],"reviews":[{"task_count":9,"total_tokens":450000,"total_cost":1.35,"output_score":8150.2824,"efficiency_rating":"normal","reviewed_at":"2026-04-17T11:29:14.374703+00:00"}],"effectiveness":{"task_count":9,"total_lines_added":0,"total_lines_removed":0,"total_files_modified":0,"total_hypotheses":2358,"total_kg_edges":715279,"total_papers":18166,"total_tokens":450000,"total_duration":5028692.218719,"avg_impact":407514.1222222222,"avg_effectiveness":8150.282444444445},"spec_content":"---\ntitle: \"Quest: Atlas\"\ndescription: \"Living knowledge graph + world model — multi-representation scientific knowledge. Includes automated gap detection pipeline, gap prioritization, and continuous knowledge frontier expansion.\"\ntype: quest\nlayer: Atlas\npriority: 80\nstatus: active\nquest_id: 415b277f-03b\nspec_path: docs/planning/specs/quest_atlas_spec.md\n---\n\n# Quest: Atlas\n\n**Layer:** Atlas \n**Priority:** P80 \n**Status:** active \n**Tasks:** 460 total (83 done, 3 open)\n\n## Vision\n\nLiving knowledge graph + world model — multi-representation scientific knowledge. Includes automated gap detection pipeline, gap prioritization, and continuous knowledge frontier expansion.\n\n## Open Tasks\n\n- [ ] [Atlas] Cross-link wiki pages with hypotheses and analyses (P85)\n- [ ] [Atlas] Dataset-driven knowledge growth: extract KG edges from tabular datasets (P85)\n- [ ] [Atlas] Cross-reference tabular datasets with KG: bidirectional entity linking (P83)\n\n\n## Success Criteria\n\n- [ ] All open tasks completed and verified\n- [ ] Integration tested end-to-end with dependent quests\n- [ ] UI pages rendering correctly for this quest's features\n- [ ] Documentation updated for new capabilities\n\n## Work Log\n\n_No entries yet._\n","spec_html":"

Quest: Atlas

Layer: Atlas \nPriority: P80 \nStatus: active \nTasks: 460 total (83 done, 3 open)

Vision

Living knowledge graph + world model — multi-representation scientific knowledge. Includes automated gap detection pipeline, gap prioritization, and continuous knowledge frontier expansion.

Open Tasks

☐ [Atlas] Cross-link wiki pages with hypotheses and analyses (P85)
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☐ [Atlas] Dataset-driven knowledge growth: extract KG edges from tabular datasets (P85)
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☐ [Atlas] Cross-reference tabular datasets with KG: bidirectional entity linking (P83)

Success Criteria

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

Work Log

_No entries yet._

","spec_file":"quest_atlas_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":"Experiment Extraction","layer":"Atlas","priority":93,"status":"active","description":"Extract structured experimental findings from papers with full lineage — methods, results, statistics, context","task_count":9,"done_count":8},{"name":"Multi-Source Literature Search","layer":"Atlas","priority":90,"status":"active","description":"Expand SciDEX's literature search from PubMed-centric to multi-source, covering Paperclip MCP (8M+ biomedical papers across arXiv/bioRxiv/PMC/OpenAlex/OSF), Semantic Scholar (citation networks + influence metrics), OpenAlex (already partial), and CrossRef (already partial). SciDEX already has a PaperCorpus abstraction layer with adapter classes — this quest extends it with new adapters, strengthens the citation/reference model beyond PMID as primary key, refactors legacy PubMed-only pipelines to use the generic layer, and integrates Paperclip MCP for agent-native deep-dive capabilities (search, grep, map, ask-image, sql). Goal: any SciDEX component that searches literature or cites papers goes through a unified multi-source interface.","task_count":0,"done_count":0},{"name":"Gap Factory","layer":"Atlas","priority":85,"status":"active","description":"Automated knowledge gap generation, decomposition, and value-scoring pipeline.\n\nCore principles:\n- Gaps are almost never \"resolved\" — they represent open questions that require extraordinary convergent evidence (5+ analyses, 2+ debates, composite score ≥0.85) to close.\n- Gaps have VALUE proportional to: importance × log(1 + dependent_hypotheses) × tractability.\n- Gaps decompose into subproblems (gap_subproblems table) and form dependency networks (gap_dependencies: blocks / informs / subsumes / requires / contradicts).\n- New gaps are identified by: debate transcript analysis, KG contradiction detection, paper frontier scanning, hypothesis-gap mismatch analysis.\n\nStatus model (graduated evidence thresholds):\n open → investigating → partially_addressed → substantially_addressed → resolved\n\nInfrastructure delivered (2026-04-06):\n- Migration 054: gap_dependencies, gap_subproblems, value_if_resolved column, resolution_criteria\n- update_gap_statuses() with graduated thresholds\n- Dashboard shows \"Active Gaps\" (non-resolved) instead of \"Open Gaps\"\n\nOpen workstreams:\n1. Gap identification: scan new papers/debates for unresolved questions\n2. Gap decomposition: LLM-driven subproblem extraction from gap descriptions\n3. Gap dependency mapping: connect gaps to hypotheses and other gaps\n4. Gap value scoring: count downstream impact on hypothesis portfolios\n5. Gap tournaments: Elo-rank gaps by \"most important to solve\" via LLM judge\n6. Gap-hypothesis matching: surface which hypotheses address which gaps","task_count":9,"done_count":6},{"name":"Wiki","layer":"Atlas","priority":75,"status":"active","description":"NeuroWiki world model integration — rich wiki pages with mermaid, infoboxes, cross-links","task_count":384,"done_count":10}]}