SciDEX — Task: [Exchange] Enrich top 3 hypotheses with deep descr

## 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 (2)

Squash merge: orchestra/task/992a786c-enrich-top-3-hypotheses-with-deep-descri (2 commits)2026-04-13

[Exchange] Enrich top 3 hypotheses with PubMed abstracts and improve evidence rendering [task:992a786c-5fa3-4bc0-9b63-7fe40d01391d]2026-04-02

Spec File

[Exchange] Enrich top 3 hypotheses with deep descriptions and evidence chains

ID: 992a786c-5fa3-4bc0-9b63-7fe40d01391d Priority: 99 Type: one_shot

Goal

Enrich the top 3 hypotheses by composite score with PubMed abstracts in their evidence citations, and improve the evidence rendering on hypothesis detail pages to show abstracts, strength badges, and better formatting.

Acceptance Criteria

☑ Fetch PubMed abstracts for all evidence citations (for/against) of top 3 hypotheses

☑ Store abstracts in the evidence_for/evidence_against JSON fields

☑ Update hypothesis detail page rendering to show abstracts, strength badges

☑ Verify syntax compiles

Top 3 Hypotheses (by composite_score)

h-856feb98 — Hippocampal CA3-CA1 circuit rescue (0.725)

h-58e4635a — SASP-Mediated Complement Cascade (0.707)

h-bdbd2120 — Gamma entrainment therapy (0.705)

Work Log

2026-04-02 11:15 PT — Slot 18

Identified top 3 hypotheses by composite_score
Found all 3 already had rich descriptions (9-13K chars), pathway diagrams, clinical trials, gene expression context
Missing: PubMed abstracts in evidence citations (0/124 citations had abstracts)
Wrote script to fetch abstracts via NCBI E-utilities API
Enriched: h-856feb98 (51 abstracts), h-58e4635a (27 abstracts), h-bdbd2120 (41 abstracts)
Updated evidence rendering in api.py to show abstracts, strength badges, better spacing
Total: 119 citations now have PubMed abstracts

2026-04-13 18:56 PT — Slot 50 (remediation)

Audit found prior commit (3520762bd) was on orphan branch, never merged to main
Abstract data existed in DB but rendering was incomplete: _ev_card() received no abstract parameter
Fixed: Added abstract parameter to _ev_card(), extract ev.get('abstract','') at each call site, render abstract_html in card body
Pushed fix to orchestra/task/992a786c-enrich-top-3-hypotheses-with-deep-descri
Syntax verified: python3 -m py_compile api.py ✓

Payload JSON

{
  "requirements": {
    "analysis": 7,
    "reasoning": 6
  },
  "completion_shas": [
    "3520762bd3b8ac1c9d017e3676a1808faa1ab85a"
  ],
  "completion_shas_checked_at": "2026-04-13T19:00:25.479198+00:00",
  "completion_shas_missing": [
    "c6e8e08af16a417dc7e3f8e453bb893ca3a883c4",
    "bc8a157c3fa87ac83ff6aadbce872ecff4d6ad58"
  ]
}