[Atlas] NeuroWiki entity linking done

[Atlas] NeuroWiki entity linking

Goal

For every knowledge graph node matching a NeuroWiki page, add neurowiki_url. Use the NeuroWiki URL pattern (neurowiki.xyz/wiki/ENTITY). Display links on graph visualization and hypothesis detail pages.

Acceptance Criteria

Approach

Read AGENTS.md and relevant source files

Understand existing code patterns before modifying

Implement changes following existing conventions (f-string HTML, SQLite, Bedrock Claude)

Test: curl affected pages, verify rendering, run scidex status

Commit atomically with descriptive message

Work Log

2026-04-01 20:00 PT — Slot 14

• Started task: Add NeuroWiki entity linking to KG nodes
• Read api.py, graph.html, and database schema
• Implemented neurowiki_url() helper function in api.py
• Updated /api/graph and /api/graph/{analysis_id} endpoints to include neurowiki_url for each node
• Updated graph.html: nodes now clickable, tooltip shows NeuroWiki link
• Updated hypothesis_detail: entity names in knowledge edges now link to NeuroWiki
• Tested: All pages load (200), NeuroWiki links working
• Committed changes: 40b8e37
• Result: Done ✓ — Graph nodes and hypothesis entities now have clickable NeuroWiki links

2026-04-25 18:00 PT — Slot 77

• Verified task: graph nodes already have wiki_url via node_wiki_links + wiki_entities join
• Found gap: subgraph_widget_html() used for inline KG edge tiles on analysis/hypothesis

pages did NOT lookup NeuroWiki URLs — entity names linked only to internal /entity/ pages

• Fix: Added wiki_url_map lookup in subgraph_widget_html(), updated _render_kg_edge_tile()

to prefer NeuroWiki URL (with external link + target=_blank) when available,
fall back to internal entity/hypothesis page otherwise

• Syntax check passed, import verified
• Committed: 3ac5868b3
• Result: Done ✓ — subgraph_widget_html KG edge tiles now link to NeuroWiki when available