{"quest":{"id":"q-555b6bea3848","name":"Real Data Pipeline","description":"Ensure all analyses use REAL Allen Institute datasets (SEA-AD, ABC Atlas, Allen Brain Cell Atlas) — not simulated/hallucinated data. Build data ingestion pipelines that download, cache, and validate real datasets. Analyses must cite specific dataset versions and cell counts. Forge tools must be invoked during the analysis loop with real inputs, not just registered as provenance markers.","layer":"Forge","priority":92,"status":"active","created_at":"2026-04-03T22:28:49.997411+00:00","updated_at":"2026-04-11T05:44:23.589823+00:00"},"tasks":[{"id":"70b96f50834b","title":"[Forge] Integrate real Allen data into the analysis/debate pipeline","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":"open","priority":5,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 06:12:46","updated_at":"2026-04-13T10:15:59.468450+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":"docs/planning/specs/70b96f50834b_forge_integrate_real_allen_data_into_th_spec.md","provider":"any","payload_json":"{\"requirements\": {\"analysis\": 5}}"},{"id":"19c068758105","title":"[Forge] Download and cache SEA-AD transcriptomic datasets from Allen Brain Cell Atlas","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":"open","priority":5,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 06:04:41","updated_at":"2026-04-13T10:15:59.465083+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":"docs/planning/specs/19c068758105_forge_download_and_cache_sea_ad_transcr_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"a7d955b233af","title":"[Forge] Ensure Forge tools are invoked during analysis execution, not just registered","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":"open","priority":4,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 05:32:26","updated_at":"2026-04-13T10:15:59.475110+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":"docs/planning/specs/a7d955b233af_forge_ensure_forge_tools_are_invoked_du_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"},{"id":"4bd2f9deaef8","title":"[Forge] Build data validation layer — verify analyses cite real datasets","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":"open","priority":4,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 06:03:36","updated_at":"2026-04-13T10:15:59.471766+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":"docs/planning/specs/4bd2f9deaef8_forge_build_data_validation_layer_verif_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 8, \"safety\": 9}}"},{"id":"f9ba4c334c69","title":"[Forge] Add ABC Atlas (Allen Brain Cell Atlas) and MERFISH spatial datasets","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":"open","priority":3,"task_type":"one_shot","frequency":"","assigned_slot":"","started_at":null,"completed_at":"2026-04-04 06:22:01","updated_at":"2026-04-13T10:15:59.478664+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":"docs/planning/specs/f9ba4c334c69_forge_add_abc_atlas_allen_brain_cell_at_spec.md","provider":"any","payload_json":"{\"requirements\": {\"coding\": 7, \"reasoning\": 7, \"analysis\": 8}}"}],"reviews":[],"effectiveness":{},"spec_content":"---\ntitle: \"Quest: Real Data Pipeline\"\ndescription: \"Ensure all analyses use REAL Allen Institute datasets (SEA-AD, ABC Atlas, Allen Brain Cell Atlas) — not simulated/hallucinated data. Build data ingestion pipelines that download, cache, and validate r\"\ntype: quest\nlayer: Forge\npriority: 92\nstatus: active\nquest_id: q-555b6bea3848\nspec_path: docs/planning/specs/quest_real_data_pipeline_spec.md\n---\n\n# Quest: Real Data Pipeline\n\n**Layer:** Forge\n**Priority:** P92\n**Status:** active\n**Tasks:** 5 total (0 done, 5 open)\n\n## Vision\n\nEnsure all analyses use REAL Allen Institute datasets (SEA-AD, ABC Atlas, Allen Brain Cell Atlas) — not simulated/hallucinated data. Build data ingestion pipelines that download, cache, and validate real datasets. Analyses must cite specific dataset versions and cell counts. Forge tools must be invoked during the analysis loop with real inputs, not just registered as provenance markers.\n\nThis quest is not just about fetching files. It should produce analysis-ready\nevidence bundles that combine real expression data, pathway/network context,\nand literature support into mechanistic explanations that can be cited by\ndebates, notebooks, pricing, and downstream validation tasks.\n\n## Tasks\n\n- [ ] [Forge] Download and cache SEA-AD transcriptomic datasets from Allen Brain Cell Atlas (P5)\n- [ ] [Forge] Integrate real Allen data into the analysis/debate pipeline (P5)\n- [ ] [Forge] Build data validation layer — verify analyses cite real datasets (P4)\n- [ ] [Forge] Ensure Forge tools are invoked during analysis execution, not just registered (P4)\n- [ ] [Forge] Add ABC Atlas (Allen Brain Cell Atlas) and MERFISH spatial datasets (P3)\n- [ ] [Forge] Generate mechanistic evidence bundles for real-data analyses (P5)\n- [ ] [Forge] Route debate and pricing updates through fresh real-data evidence bundles (P5)\n\n## Success Criteria\n\n- [ ] All tasks completed and verified\n- [ ] Integration tested end-to-end\n- [ ] Metrics visible on Senate/Quests dashboards\n- [ ] Design supports future scaling to external compute\n- [ ] All analyses spawned by the system cite real datasets (not simulated placeholders). >95% of analysis outputs include dataset version and cell count. Forge tool invocations during analysis are logged and validated — no synthetic fallbacks.\n- [ ] Debate prompts and exchange repricing jobs can consume those bundles\n without fabricating values or falling back to synthetic placeholders\n\n## Architecture Notes\n\nThis quest is designed with a **local-first, cloud-ready** philosophy:\n- All implementations must work on the current single VM\n- All interfaces must support future migration to containers/cloud\n- Resource limits are configurable, not hardcoded\n- Executor/sandbox abstractions allow swapping implementations\n- Evidence pipelines should emit structured JSON/CSV/markdown outputs with\n provenance, so downstream consumers can compare runs and detect stale inputs\n\n## Work Log\n\n_No entries yet._\n","spec_html":"

Quest: Real Data Pipeline

Layer: Forge\nPriority: P92\nStatus: active\nTasks: 5 total (0 done, 5 open)

Vision

Ensure all analyses use REAL Allen Institute datasets (SEA-AD, ABC Atlas, Allen Brain Cell Atlas) — not simulated/hallucinated data. Build data ingestion pipelines that download, cache, and validate real datasets. Analyses must cite specific dataset versions and cell counts. Forge tools must be invoked during the analysis loop with real inputs, not just registered as provenance markers.

This quest is not just about fetching files. It should produce analysis-ready
evidence bundles that combine real expression data, pathway/network context,
and literature support into mechanistic explanations that can be cited by
debates, notebooks, pricing, and downstream validation tasks.

Tasks

☐ [Forge] Download and cache SEA-AD transcriptomic datasets from Allen Brain Cell Atlas (P5)
\n
☐ [Forge] Integrate real Allen data into the analysis/debate pipeline (P5)
\n
☐ [Forge] Build data validation layer — verify analyses cite real datasets (P4)
\n
☐ [Forge] Ensure Forge tools are invoked during analysis execution, not just registered (P4)
\n
☐ [Forge] Add ABC Atlas (Allen Brain Cell Atlas) and MERFISH spatial datasets (P3)
\n
☐ [Forge] Generate mechanistic evidence bundles for real-data analyses (P5)
\n
☐ [Forge] Route debate and pricing updates through fresh real-data evidence bundles (P5)

Success Criteria

☐ All tasks completed and verified
\n
☐ Integration tested end-to-end
\n
☐ Metrics visible on Senate/Quests dashboards
\n
☐ Design supports future scaling to external compute
\n
☐ All analyses spawned by the system cite real datasets (not simulated placeholders). >95% of analysis outputs include dataset version and cell count. Forge tool invocations during analysis are logged and validated — no synthetic fallbacks.
\n
☐ Debate prompts and exchange repricing jobs can consume those bundles
\n without fabricating values or falling back to synthetic placeholders

Architecture Notes

This quest is designed with a local-first, cloud-ready philosophy:\n

  • All implementations must work on the current single VM
    • \n
  • All interfaces must support future migration to containers/cloud
    • \n
  • Resource limits are configurable, not hardcoded
    • \n
  • Executor/sandbox abstractions allow swapping implementations
    • \n
  • Evidence pipelines should emit structured JSON/CSV/markdown outputs with
    • \n
provenance, so downstream consumers can compare runs and detect stale inputs

Work Log

_No entries yet._

","spec_file":"quest_real_data_pipeline_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":"Agent Ecosystem","layer":"Forge","priority":96,"status":"active","description":"Background agent fleet management — agent registry, health monitoring, task routing, and auto-scaling. Define agent roles (researcher, debater, market-maker, auditor), spawn/retire agents based on workload, and maintain agent identity across sessions. Goal: a self-managing ecosystem of specialized agents.","task_count":8,"done_count":0},{"name":"Analysis Sandboxing","layer":"Forge","priority":90,"status":"active","description":"Run all analyses in isolated environments (containers, cgroups, or sandboxed subprocesses) so a runaway analysis cannot corrupt the database, filesystem, or other running services. Each analysis gets its own temp directory, restricted filesystem access, and resource budget. Design for future migration to external container runtimes (Docker, AWS Batch, K8s) while running locally today.","task_count":5,"done_count":1},{"name":"Tool Playground","layer":"Forge","priority":88,"status":"paused","description":"Interactive tool interfaces with live API calls, structured results, external links","task_count":1,"done_count":0},{"name":"Forge","layer":"Forge","priority":80,"status":"active","description":"Scientific execution engine — tool registry, background agent orchestration, agent spawning, and tool-augmented analysis. Manages the ecosystem of background agents that perform research tasks.","task_count":425,"done_count":45},{"name":"AI Tools Landscape","layer":"Forge","priority":64,"status":"paused","description":"Living catalog of AI-for-science tools, platforms, agents, and benchmarks. Uses wiki entity_type='ai_tool' with structured frontmatter (category, specializations, pricing, benchmarks, open-source status). Browsing page at /forge/landscape with filters by category, specialization, pricing. Seeded with 23 entries from inspirations page. Kept current via agent scanning + staleness badges. Spec: docs/planning/specs/q-ai-tools-landscape_spec.md","task_count":5,"done_count":0},{"name":"Visual Artifacts","layer":"Forge","priority":55,"status":"active","description":"AI-generated visual artifacts — infographics, hypothesis cards, entity portraits, protocol illustrations. Uses MiniMax image-01 and GLM CogView-4 with quality evaluation via vision models.","task_count":5,"done_count":5}]}