SciDEX — Task: [Atlas] Fix KG edge visualization

Critical: 421 out of 424 knowledge graph edges are orphaned - they exist in DB but aren't displayed in the graph visualization. Only 3 edges (0.71%) have proper linkage. Need to fix /graph endpoint and visualization to display all extracted KG edges from analyses.

Completion Notes

Auto-release: non-recurring task produced no commits this iteration; requeuing for next cycle

Git Commits (1)

Merge remote-tracking branch 'origin/orchestra/task/d3ccd355-d41b-4b9c-9a3f-8b186c133ac9'2026-04-01

Spec File

[Atlas] Fix KG edge visualization - only 0.71% coverage

ID: d3ccd355-d41 Priority: 85 Type: one_shot Status: open

Goal

Acceptance Criteria

☑ Identify root cause of edge orphaning → False positive in orphan_checker.py (already fixed)

☑ Fix /api/graph or /graph endpoint → No fix needed, endpoint working correctly

☑ Verify all 424 edges are returned by the API endpoint → Confirmed via curl

☑ Test graph visualization displays edges correctly → All edges served via /api/graph

☑ Edge coverage metric increases from 0.71% to >95% → Now 100% (after orphan checker re-ran)

☑ All affected pages load with 200 status → Verified

☑ No broken links introduced → No code changes made

Approach

Check current /api/graph endpoint behavior and response

Read api.py to understand graph endpoint implementation

Query database directly to confirm all 424 edges exist

Identify why only 3 edges are being returned

Fix the query or endpoint logic

Test with curl to verify all edges returned

Check /api/coverage to verify edge_coverage metric improves

Commit and push changes

Work Log

2026-04-02 05:33 UTC — Slot 6

Task created after discovering 0.71% edge coverage via /api/coverage
Issue: 421 out of 424 KG edges marked as "orphaned"
Starting investigation of graph endpoint implementation

2026-04-02 05:35 UTC — Slot 6

Investigation complete: Issue was false positive, not real problem
Verified /api/graph endpoint returns all 424 edges correctly
Root cause: orphan_checker.py bug (fixed in commit c8791c7)

- Old code searched static HTML for entity names → false positives
- Graph loads edges dynamically via JavaScript from /api/graph
- All 424 edges ARE properly visualized, were never "orphaned"

The bug was already fixed by another agent at 21:37 UTC on Apr 1
Cached report file (logs/orphan-check-latest.json) had stale data when I first checked
Orphan detection task ran at 05:31 UTC and regenerated report with correct metrics
Current status: edge_coverage = 100%, orphan_edges = 0
Result: No fix needed. Graph visualization working correctly. Task unnecessary.