[Exchange] Hypothesis detail page enrichment

[Exchange] Hypothesis detail page enrichment

Goal

Enrich hypothesis detail pages at /hypothesis/{id} with two missing features: a linked papers section showing full paper metadata, and a related hypotheses section showing other hypotheses targeting the same gene.

Acceptance Criteria

Implementation Details

Linked Papers Section (api.py lines 818-857)

PMID Extraction:

• Parses both dict format {'pmid': '12345678'} and string format 'PMID:12345678'
• Extracts PMIDs using regex pattern r'PMID:?\s*(\d{6,8})'
• Handles both evidence_for and evidence_against arrays

papers = db.execute(f"""
    SELECT pmid, title, authors, journal, year, citation_count
    FROM papers
    WHERE pmid IN ({placeholders})
    ORDER BY citation_count DESC, year DESC
""", tuple(pmids)).fetchall()

Display Format:

• Paper title as clickable PubMed link
• Authors list (or "Unknown authors")
• Journal name, year, and citation count
• Styled cards with dark background (#2a2a2a)
• Fallback messages for no PMIDs or no papers found

Related Hypotheses Section (api.py lines 858-889)

Database Query:

related = db.execute("""
    SELECT id, title, composite_score, market_price, status
    FROM hypotheses
    WHERE target_gene = ? AND id != ?
    ORDER BY composite_score DESC, market_price DESC
    LIMIT 5
""", (target_gene, hyp_id)).fetchall()

Display Format:

• Up to 5 related hypotheses
• Hypothesis title as clickable link to detail page
• Composite score (yellow), market price (green), status
• Status-based color coding: active=#81c784, other=#666
• Fallback message for no related hypotheses

HTML Template Integration (api.py lines 1044-1055)

Added two new sections between Evidence Against and Estimated Development:

<h2>Linked Papers</h2>
<div style="margin:1rem 0">
{linked_papers_html}
</div>

<h2>Related Hypotheses</h2>
<div style="margin:1rem 0">
{related_hyps_html}
</div>

Testing Results

Tested Hypothesis Pages

• h-e12109e3 (MAP6): 200 OK, 1 linked paper found, no related hypotheses
• h-76888762: 200 OK
• h-d2df6eaf: 200 OK

Example Linked Paper Display

Tau and MAP6 establish labile and stable domains on microtubules.
Kirimtay K, Huang W, Sun X, Qiang L, Wang DV, Sprouse CT, Craig EM, Baas PW
iScience (2025) · 1 citations

Database Statistics

• Papers table: 1144 records available for linking
• Hypotheses with multiple targets: APOE (5), G3BP1 (4), TARDBP (4), AQP4 (3)

Technical Notes

• File Edited: /home/ubuntu/scidex/.orchestra-worktrees/task-87eccc14-566b-4b39-ab1c-a137da61b6a1/api.py
• Database Column: Used market_price (not current_price) for hypothesis price queries
• Worktree Usage: Edited worktree version to avoid concurrent modification conflicts
• Server Testing: Verified on uvicorn port 8002 (ports 8000-8001 had conflicts)

Work Log

2026-04-01 23:45 UTC — Slot 3

• Received Exchange task: Enrich hypothesis detail pages
• Initial attempts blocked by concurrent api.py edits (23 agents active)
• Main repo file at /home/ubuntu/scidex/api.py grew from 1624→3072 lines during attempts
• Discovered worktree isolation: switched to editing worktree-specific api.py
• Added PMID extraction and papers table query (68 lines)
• Added related hypotheses query by target_gene
• Fixed schema mismatch: current_price → market_price
• Added HTML template sections for both features
• Tested 3 hypothesis pages: all return 200 OK
• Verified linked papers display with full metadata
• Verified related hypotheses display with proper fallbacks
• Result: Hypothesis detail pages successfully enriched with missing features