SciDEX — Task: [Demo] Recurring: Read all quest/task specs, ident

## REOPENED TASK — CRITICAL CONTEXT This task was previously marked 'done' but the audit could not verify the work actually landed on main. The original work may have been: - Lost to an orphan branch / failed push - Only a spec-file edit (no code changes) - Already addressed by other agents in the meantime - Made obsolete by subsequent work **Before doing anything else:** 1. **Re-evaluate the task in light of CURRENT main state.** Read the spec and the relevant files on origin/main NOW. The original task may have been written against a state of the code that no longer exists. 2. **Verify the task still advances SciDEX's aims.** If the system has evolved past the need for this work (different architecture, different priorities), close the task with reason "obsolete: " instead of doing it. 3. **Check if it's already done.** Run `git log --grep=''` and read the related commits. If real work landed, complete the task with `--no-sha-check --summary 'Already done in '`. 4. **Make sure your changes don't regress recent functionality.** Many agents have been working on this codebase. Before committing, run `git log --since='24 hours ago' -- ` to see what changed in your area, and verify you don't undo any of it. 5. **Stay scoped.** Only do what this specific task asks for. Do not refactor, do not "fix" unrelated issues, do not add features that weren't requested. Scope creep at this point is regression risk. If you cannot do this task safely (because it would regress, conflict with current direction, or the requirements no longer apply), escalate via `orchestra escalate` with a clear explanation instead of committing.

Completion Notes

Auto-completed by supervisor after successful deploy to main

Git Commits (1)

[Cross-cutting] Create P88/P85 integration task specs + update Quest:Demo work log [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]2026-04-13

Spec File

Quest: Demo

Layer: Cross-cutting Priority: P99 Status: active Tasks: 468 total (79 done, 9 open)

Vision

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

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

Open Tasks

☐ [Demo] CI: Verify all demo pages load correctly with rich content (P93)

☐ [Demo] Versioned artifact demo: create protein design with 3 iterations (P92)

☐ [Demo] Register Allen Brain Cell Atlas as external dataset artifact (P91)

☐ [Demo] Tabular dataset demo: gene expression matrix linked to KG entities (P90)

☐ [Demo] Build simple biophysical model from KG-derived parameters (P89)

☐ [Demo] End-to-end provenance demo: trace reasoning chain from paper to model (P88)

☐ [Demo] Create dynamic authored paper: SEA-AD Microglial Activation Review (P87)

☐ [Demo] Create live dashboard: Knowledge Growth Monitor (P86)

☐ [Demo] Origin tracking showcase: internal vs external artifact provenance (P85)

Success Criteria

☐ All open tasks completed and verified

☐ Integration tested end-to-end with dependent quests

☐ UI pages rendering correctly for this quest's features

☐ Documentation updated for new capabilities

Work Log

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

Task: [Demo] Recurring: Read all quest/task specs, identify demo-ready features, create integration tasks [task:e90797ac-25a5-4bdb-b4ca-5bfe8f9c04aa]
Verified prior work (8cc8c1e01 — spec-only update, not merged to main) was correct analysis
Rebased against latest origin/main (5440bf99b)
Created two integration task specs to unblock P88 and P85:

Created:

docs/planning/specs/e90797ac_p88_provenance_infra_spec.md — P88 infrastructure: pinned_artifacts column in analyses table + GET /api/analysis/{id}/provenance endpoint exposing verify_reproducibility()
docs/planning/specs/e90797ac_p85_origin_tracking_spec.md — P85 frontend: origin badges (INTERNAL/EXTERNAL) on artifact detail pages at /artifacts/{id}

Key findings from spec sweep:

1693 spec files across all quests
Quest:Agora (2 open), Quest:Forge (6 open), Quest:Atlas (3 open), Quest:Exchange (5 open), Quest:Sender (9 open)
P86 (Dashboard): Dashboard already registered (dashboard-knowledge-growth-monitor) with full data_sources (paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries). render_dashboard() and /api/dashboard/{id}/refresh both fully implemented. Unblocked — needs only verification that the dashboard page at /dashboard/{id} renders correctly
P88 (Provenance): verify_reproducibility() exists in scripts/test_reproducibility.py but not exposed via API. pinned_artifacts column missing from analyses table. assemble_provenance_demo.py exists but wasn't run.
P85 (Origin): origin_type/origin_url columns exist in DB. Frontend badges NOT rendered on artifact detail page. Need to add to api.py artifact detail page.
P89 (Biophysical model): Commit f5f36ad25 on branch forge-startup-logging-20260413041942 — model code exists but NOT on main yet (f5f36ad25 is on a non-main branch). Verified in worktree that forge/biophysical_models/microglial_activation.py, site/figures/models/microglial_activation/time_course.png, site/figures/models/microglial_activation/sensitivity_tornado.png exist.
P92 (Versioned protein design): COMPLETED per prior audit
P87 (Dynamic authored paper): COMPLETED per prior audit

Recommended next steps:

Run assemble_provenance_demo.py to create the provenance chain artifact

Execute the two new integration task specs (e90797ac_p88 and e90797ac_p85)

Verify P86 dashboard page renders at /dashboard/dashboard-knowledge-growth-monitor

Re-verify P89 (biophysical model) on main by checking forge/biophysical_models/ path

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

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

Detailed dependency verification:

Priority	Task	Status	Verified blockers
P93	CI: Verify demo pages	Ongoing recurring CI	None
P92	Versioned artifact demo	COMPLETED	None
P91	Register Allen Brain Cell Atlas	UNSTARTED	Independent; no infra blockers
P90	Tabular gene expression demo	PARTIAL	KG integration not verified via code inspection
P89	Biophysical model	PARTIAL	Code not verified
P88	End-to-end provenance demo	UNSTARTED	See analysis below
P87	Dynamic authored paper	COMPLETED	None
P86	Knowledge Growth Dashboard	UNSTARTED	UNBLOCKED — see below
P85	Origin tracking showcase	UNSTARTED	See analysis below

P88 (Provenance Demo) — Detailed analysis:

GET /api/artifacts/{id}/provenance → returns build_provenance_chain() from artifact_links (WORKS, 6-entry chain for h-seaad-v4-26ba859b)
GET /api/artifacts/{id}/provenance-graph → returns graph with 4 nodes, 6 edges (WORKS)
render_dashboard() in scidex/atlas/artifact_registry.py:811 fully implements {{data:KEY}} substitution via sql_query, artifact_ref, api_endpoint sources (WORKS)
pinned_artifacts field NOT in analysis metadata — provenance is computed live from artifact_links, not from pre-pinned versions
verify_reproducibility() NOT implemented anywhere — script exists in scripts/test_reproducibility.py but is not exposed via API
What P88 actually needs: (1) pinned_artifacts column in analyses table, (2) verify_reproducibility() function exposed at GET /api/analysis/{id}/provenance, (3) artifact link chain connecting 8 chain nodes

P86 (Dashboard Demo) — UNBLOCKED:

render_dashboard() fully implemented with {{data:KEY}} substitution supporting sql_query, artifact_ref, api_endpoint (artifact_registry.py:811)
/api/dashboard/{id}/refresh → calls artifact_registry.render_dashboard() → evaluates SQL → persists rendered_html → returns JSON (WORKS)
Frontend polling auto-refresh wired in dashboard_standalone page (api.py:17758)
No missing infrastructure — only needs a registered dashboard artifact with the right data_sources/metadata
a17-30-DREF0001 (data source refresh engine) is already implemented — render_dashboard() IS the refresh engine
Recommended: Register "SciDEX Knowledge Growth Monitor" dashboard artifact with data_sources = paper_count, hypothesis_count, kg_edge_count, analysis_count, wiki_count SQL queries

P85 (Origin Tracking) — Needs verification:

origin_type and origin_url columns exist in artifacts table
Origin badges mentioned in prior work log but NOT visible in artifact detail page grep check
a17-26-ORIG0001 may need a frontend component on artifact detail pages to show "INTERNAL"/"EXTERNAL" badges
d16-25 (authored paper) is DONE, providing an internal artifact example
Recommended: Verify origin badges appear on /artifacts/{id} detail page; if missing, add frontend rendering

P91 (Allen Brain Cell Atlas) — Independent, no blockers:

d16-03 (aging mouse atlas) is a SEPARATE task, not a blocker
Allen Brain Atlas API access needs verification but infrastructure is ready
Could bootstrap from SEA-AD MTG 10x dataset already registered

Recommended integration tasks to spawn (one-shot):

[Atlas] Expose verify_reproducibility via API + pinned_artifacts in analysis metadata

- Priority: P88
- Spec: docs/planning/specs/e90797ac_p88_provenance_infra_spec.md
- Details: Add pinned_artifacts column to analyses table, expose verify_reproducibility() at GET /api/analysis/{id}/provenance

[Atlas] Add origin tracking badges to artifact detail pages

- Priority: P85
- Spec: docs/planning/specs/e90797ac_p85_origin_tracking_spec.md
- Details: Add INTERNAL/EXTERNAL badges to /artifacts/{id} page, wire origin_type and origin_url

Payload JSON

{
  "requirements": {
    "reasoning": 7
  },
  "completion_shas": [
    "f2db2dc35f10d56dd8084323f13ddc88ac5ce405"
  ],
  "completion_shas_checked_at": "2026-04-13T19:54:56.319257+00:00",
  "completion_shas_missing": [
    "6514fe212b9fba159b8246921a3876748f7ff6d3",
    "b89cd60736aa49b866144738ceac0fd93785459e",
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  ]
}