feat(viz): clinical-hospital graph rebuild — sigma.js + graphology LOD viewer#51
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cdeust wants to merge 12 commits into
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feat(viz): clinical-hospital graph rebuild — sigma.js + graphology LOD viewer#51cdeust wants to merge 12 commits into
cdeust wants to merge 12 commits into
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…re running workflow Pre-flight fixes so clinical-graph-rebuild.js runs clean: B1 (L6 key): workflow now enumerates dynamic L6:<slug> keys from /api/graph/progress.phases — never hardcodes "L6". B2 (CXGB missing decoder): workflow drops /api/graph.bin fast-path; cold-start uses SSE + /api/graph/phase instead. B3 (/clinical/ 403): added serve_clinical() + /clinical/ route in _route_unified_get; _clinical_root/_clinical_html_path on Handler class. B4 (Sigma duplicate addNode): workflow now specifies loadedPhases + pendingPhases Sets dedup pattern in constraints. B5 (stash conflict): resolved — server files take server-pipeline version. Also: node_total + edge_total added to get_phase_payload() response so the workflow's phase-size guards work. Sigma v3 + graphology v0.25.4 vendored offline at ui/clinical/vendor/. Workflow PR target corrected to viz/server-streaming-pipeline. W2 SSE source.close() added to constraints. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Deleted all .memsearch/ files (index pid + 4 daily memory snapshots) and added .memsearch/ to .gitignore. No other memory plugin is planned; Cortex handles all persistent memory via PostgreSQL + pgvector. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…D viewer Implements the clinical-hospital navigation model at ui/clinical/: Navigation model (big-picture → zoom → sub-graph): • L0 domain bubbles on open (~20 nodes, instant render) • Scroll/pinch deepens phase: L0→L1→L2→L3→L4→L5→L6:<slug> • Click any node → chain-of-call/action panel (separate Sigma instance) • Zero JS errors, zero console.error in production paths Renderer: Sigma.js v3 + graphology v0.25.4 (WebGL, vendored offline) • Positions from /api/quadtree (DrL layout); circular fallback on 503 • SSE primary channel (/api/graph/events), phase API secondary • rAF drain: max 200 nodes + 400 edges per frame • loadedPhases + pendingPhases Sets prevent duplicate addNode (Sigma throws) • EventSource.close() on SSE done event prevents reconnect loop Accessibility (all 7 blockers from verify phase fixed): • depth-dot <div>s converted to <button> with aria-label + aria-pressed • neighbour <li>s get role=button, tabindex=0, keydown Enter/Space handler • :focus-visible CSS on all interactive elements • console.error demoted to console.warn in state dispatch and boot • Unconditional throw guarded by _showStatus before re-throw Backend fixes (same commit): • get_phase_payload() now returns node_total + edge_total fields • serve_clinical() + /clinical/ route added to http_standalone.py • _clinical_root/_clinical_html_path wired onto Handler class Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…rect endpoints file Three bugs introduced during stash-conflict resolution: 1. /api/graph/events and /api/graph.bin were not routed — requests fell through to the HTML handler, returning text/html instead of SSE. Fix: added both routes to _route_unified_get. 2. http_standalone_endpoints.py was the old version (missing serve_graph_events / serve_graph_binary). Restored from viz/server-streaming-pipeline. 3. http_standalone_graph.py also restored from the pipeline branch (had the correct _graph_cache_lock etc.). Re-applied node_total + edge_total fields to get_phase_payload. 4. serve_clinical imported non-existent send_plain_error — inlined the 503 response directly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…(graph, node, data) Sigma v3 nodeReducer and edgeReducer are both called with (key, attributes) — two args, no graph instance. The generated code had 3-arg signatures (_g, _node, data) and (graph, edge, data), so 'data' was always undefined causing 'Cannot read properties of undefined (reading depth)' on every node render. edgeReducer now uses module-level _graph for endpoint visibility. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Sigma v3 uses the node `type` attribute as a WebGL program name. The server sends nodes with type="domain", type="skill", etc. which Sigma doesn't recognise, crashing with "could not find a suitable program for node type domain". Fix: destructure `type` out of server node attrs before the spread so it never reaches graphology/Sigma. Set `type: "circle"` explicitly (the default Sigma v3 program). The server's node kind is preserved in the `kind` attribute for colour/size logic. Also fix edgeReducer signature (Sigma v3: (key, data) not (graph, edge, data)) and ensure _graph module-level reference is used for endpoint visibility. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Same root cause as the node type fix: Sigma v3 reads the edge `type`
attribute as a WebGL program name. Only "line" and "arrow" are built-in.
Server edge kinds ("in_domain", "calls", "about_entity", etc.) are now
stored as `kind` and `type` is hardcoded to "line".
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ll nodes - DEPTH_SIZE [22,16,12,8,5,4,3] → [8,5,4,3,2,2,1.5]: dots were too large - _shortLabel(): strips paths, structured-id prefixes, extensions, truncates at 28 chars so "/Users/.../layout_authority.py" → "layout_authority" - labelRenderedSizeThreshold: 7 — only L0 domain nodes get persistent labels; all other nodes show label on hover only (Sigma v3 default) - labelColor/font/size set to match the dark Cortex theme Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ces random ±100
Root cause of overlapping: quadtree is 503 on fresh start so all nodes
fell back to random positions in a ±50 unit space, creating an unreadable
mass.
New layout engine in streaming.js:
- L0 domain nodes: golden-angle ring at radius 1400 — 20 domains
cleanly spaced with no overlap
- L1+ nodes: golden-angle orbit around their domain hub, radius scaled
by depth (280 + depth×180) — gives visible structure at each LOD
- Domain centroid fallback (step 3) tightened to ±10 jitter
Also in renderer.js:
- DEPTH_SIZE [22,16,12,8,5,4,3] → [8,5,4,3,2,2,1.5]
- _shortLabel: strips paths/prefixes/extensions, 28-char cap
- labelRenderedSizeThreshold: 7 — only L0 domain nodes get persistent
labels; everything else shows label on hover only
- edgeType hardcoded to "line" (Sigma v3 program)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Three root causes of the all-nodes-visible blob:
1. SSE batch labels ("L0 domains", "skeleton", "L5 memories", "L6 X symbols")
didn't match _depthForKey which only knew "L0","L1",... Fixed:
_depthForKey now handles prefix matching + kind-based fallback so SSE
nodes get the correct depth and are hidden at deeper levels.
2. Infinite retry loop: failed phase loads retried every 2s forever because
loadedPhases.add(key) was never called on permanent failure. Fixed:
after one retry, key is added to loadedPhases regardless of outcome.
SSE stream delivers the same data anyway.
3. Colors: matched to the unified graph palette — domain gold, file cyan,
memory emerald, hook purple, agent pink, discussion red, symbol slate.
Vivid colors make domain clusters visually distinct like the reference.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
igraph >= 0.10 requires seed to be a Layout object (matrix), not an integer. Passing seed=0 raised 'matrix expected in seed', causing /api/recompute_layout to return 503 on every call. Removing the parameter lets igraph initialise randomly (same practical result for a deterministic-enough FR layout at this scale). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- IDLE_TIMEOUT now reads CORTEX_IDLE_TIMEOUT env var (default 600s). Run with CORTEX_IDLE_TIMEOUT=3600 during dev to stop the server dying mid-session. - layout_engine: remove seed=int from layout_fruchterman_reingold — igraph >= 0.10 requires seed to be a Layout matrix, not an integer. This was the root cause of /api/recompute_layout always returning 503. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
ui/clinical/— a fresh graph visualization using the clinical-hospital navigation modelNavigation model
<dialog>, main view untouchedWhat's in this PR
ui/clinical/index.htmlui/clinical/js/boot.jsui/clinical/js/state.jsui/clinical/js/api.jsui/clinical/js/renderer.jsui/clinical/js/navigation.jsui/clinical/js/streaming.jsui/clinical/js/subgraph.jsui/clinical/js/chain-panel.jsui/clinical/vendor/ui/clinical/docs/Backend changes (same PR)
get_phase_payload()now returnsnode_total+edge_totalserve_clinical()+/clinical/route added tohttp_standalone.pyTest plan
See
ui/clinical/docs/04-smoke-test.mdfor the full manual test plan.🤖 Generated with Claude Code