Quest: Demo

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

Success Criteria

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

Tasks using this spec (1)

[Demo] Recurring: Read all quest/task specs, identify demo-r

File: quest_demo_spec.md

Modified: 2026-04-25 22:00

Size: 8.7 KB