SciDEX — Task: [Demo] Add Mol* 3D protein structure viewer to top

IMPORTANT: Keep Mol* protein viewer on entity/hypothesis/challenge detail pages where it adds value. Do NOT feature it prominently on /showcase. Showcase should highlight: debate transcripts, hypothesis cards with scores, evidence tables, KG visualizations, and notebooks — the core discovery exchange features. ## 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.

Last Error

worker_exit_unclean exit_code=0

Git Commits (5)

[Verify] Mol* hypothesis viewer already resolved [task:987ffe4a-21be-4d45-bd1e-14b81a4b62b4]2026-04-23

[Verify] Mol* 3D viewer on main — orphan work-log corrected, feature verified live [task:987ffe4a-21be-4d45-bd1e-14b81a4b62b4]2026-04-23

[Verify] Mol* 3D viewer already complete; mark 987ffe4a done [task:2c0a44fe-1266-43fa-b98b-7b19084f367a]2026-04-23

[Demo] Update 987ffe4a spec: mark done, log verification [task:987ffe4a-21be-4d45-bd1e-14b81a4b62b4]2026-04-13

[Demo] Document Mol* task already complete: closes 987ffe4a-21be-4d45-bd1e-14b81a4b62b42026-04-13

Spec File

[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages

ID: 987ffe4a-21b Priority: 96 Type: one_shot Status: done

Goal

[Demo] Add Mol* 3D protein structure viewer to top hypothesis pages

Acceptance Criteria

☐ Concrete deliverables created

☐ Work log updated with timestamped entry

Work Log

2026-04-23 20:30 UTC — Slot minimax:71 watchdog (fifth verification)

Status: Already complete on main — confirmed again.
Verification: curl 'http://localhost:8000/hypothesis/h-44195347' returned HTTP 200 with 8 molstar/pdbe-molstar/PDBeMolstarPlugin references.
Root cause of 14 abandons: Workers exit cleanly (exit_code_0) because the task is already done. No code fix needed.
Result: No action required — original task 987ffe4a-21b remains done on main.

2026-04-23 16:09 UTC — Slot codex:51 watchdog

Status: Already complete on main — no code repair or reset needed.
Root cause of repeated abandons: The original task was already done, so workers exited cleanly without making substantive changes or completing the watchdog flow.
Verification: orchestra list --project SciDEX --limit 10000 shows 987ffe4a-21be-4d45-bd1e-14b81a4b62b4 status done.
Verification: curl http://localhost:8000/hypothesis/h-44195347 returned HTTP 200 with 8 molstar, 2 pdbe-molstar, and 1 PDBeMolstarPlugin references.
Verification: curl http://localhost:8000/hypothesis/h-0f025d94 returned HTTP 200 with 13 molstar, 2 pdbe-molstar, and 1 PDBeMolstarPlugin references.
Verification: curl http://localhost:8000/entity/TREM2 returned HTTP 200 with 11 molstar, 2 pdbe-molstar, and 2 PDBeMolstarPlugin references.
Verification: curl http://localhost:8000/showcase returned HTTP 200 with 0 molstar / pdbe-molstar / PDBeMolstarPlugin references, preserving the requirement to keep the viewer off showcase.
Verification: python3 -m py_compile api.py passed.
Implementation evidence: api.py contains Mol hypothesis detail integration at hypothesis_detail() (/hypothesis/{hyp_id}) with PDBe Mol lazy-loading around lines 35471-35881 in current main. Prior task-specific spec verification landed in 0b81c002f; earlier verification note landed in a8869dab3.
Result: Watchdog task c3e2da39-aded-4d67-b33e-c35aa0255b79 confirmed the original task is stale/already resolved.

2026-04-13 20:45 PT — Slot minimax:57

Status: Already complete on main — no new work needed
Verification: Tested hypothesis page h-44195347 (APOE) — Mol* 3D viewer renders correctly
Verification: Confirmed showcase (/showcase) has NO Mol* viewer content
Commits that implemented this work (under different task IDs):

- db23ef9cf [Artifacts] Add 8 PDB + 3 UniProt protein mappings for Mol* viewers [task:d271b465-bf6]
- 7fb8ef909 [Artifacts] Enrich targets with PDB/UniProt IDs + fix challenge Mol* auto-linking [task:e27b4301-b99b-41ae-ad45-d29b603468c0]
- 91ec0016e [Quality] Remove Mol* protein viewer section from /showcase page [task:b278d4d3-7b17-4069-b2a1-320a0247e3f4]

Result: Task 987ffe4a-21be-4d45-bd1e-14b81a4b62b4 closed — work addressed by commits d271b465, e27b4301, b278d4d3

2026-04-13 14:15 PT — Slot minimax:57

Status: Verified complete — task ID referenced on origin/main via a8869dab3
Verification: curl hypothesis/h-44195347 → 7 molstar references (correct)
Verification: curl showcase → 0 molstar references (correct, per requirement)
Implementation commits (from different task IDs):

- db23ef9cf [Artifacts] Add 8 PDB + 3 UniProt protein mappings for Mol* viewers
- 7fb8ef909 [Artifacts] Enrich targets with PDB/UniProt IDs + fix challenge Mol* auto-linking
- 91ec0016e [Quality] Remove Mol* protein viewer section from /showcase page

Result: Task 987ffe4a-21be-4d45-bd1e-14b81a4b62b4 verified done — already on main

Payload JSON

{
  "requirements": {
    "coding": 8
  },
  "_stall_skip_providers": [
    "minimax"
  ],
  "_stall_requeued_by": "minimax",
  "_stall_requeued_at": "2026-04-14 12:24:55",
  "_stall_skip_at": {},
  "_stall_skip_pruned_at": "2026-04-14T10:37:14.022390+00:00",
  "_watchdog_repair_task_id": "cbd94a08-a4c7-4a01-86d6-3fc7ae7a5f3d",
  "_watchdog_repair_created_at": "2026-04-23T16:15:42.090492+00:00",
  "_reset_note": "This task was reset after a database incident on 2026-04-17.\n\n**Context:** SciDEX migrated from SQLite to PostgreSQL after recurring DB\ncorruption. Some work done during Apr 16-17 may have been lost.\n\n**Before starting work:**\n1. Check if the task's goal is ALREADY satisfied (run the relevant checks)\n2. Check `git log --all --grep=task:YOUR_TASK_ID` for prior commits\n3. If complete, verify and mark done. If partial, continue. If not done, proceed.\n\n**DB change:** SciDEX now uses PostgreSQL. `get_db()` auto-detects via\nSCIDEX_DB_BACKEND=postgres env var.",
  "_reset_at": "2026-04-18T06:29:22.046013+00:00",
  "_reset_from_status": "done"
}