chore(dev): update submodule to mark completed tasks as Done

GRAPHRAG_QUICK_START.md

@@ -0,0 +1,199 @@
+# GraphRAG Quick Start Guide
+
+## Enable GraphRAG in SciDK
+
+### 1. Set Environment Variable
+```bash
+export SCIDK_GRAPHRAG_ENABLED=1
+```
+
+### 2. Optional: Add Anthropic API Key (Better Entity Extraction)
+```bash
+export SCIDK_ANTHROPIC_API_KEY=sk-ant-your-key-here
+```
+
+### 3. Start SciDK
+```bash
+python3 -m scidk
+```
+
+### 4. Navigate to Chat
+Open browser: `http://localhost:5000/chat`
+
+---
+
+## Example Queries
+
+### Schema-Agnostic Examples (Works with ANY Neo4j Database)
+
+```
+How many nodes are in the database?
+
+Find all File nodes
+
+Show me recent scans
+
+List all folders
+
+What types of nodes exist?
+
+Find files with name=test.txt
+
+Count all relationships
+```
+
+### For File-Based Graphs (SciDK Default Schema)
+```
+Find all files in my project
+
+Show recent file scans
+
+How many Python files are there?
+
+List all folders containing CSV files
+
+Find files modified this week
+```
+
+---
+
+## UI Features
+
+### Basic Mode (Default)
+- Type natural language queries
+- Get conversational responses
+- Chat history saved automatically
+
+### Verbose Mode (Toggle Checkbox)
+- See extracted entities (IDs, labels, properties)
+- View execution time
+- See result counts
+- Colored entity badges
+
+### Actions
+- **Send:** Submit query (or press Enter)
+- **Clear History:** Delete all messages
+- **Verbose Toggle:** Show/hide technical details
+
+---
+
+## API Usage
+
+### Query Endpoint
+```bash
+curl -X POST http://localhost:5000/api/chat/graphrag \
+  -H "Content-Type: application/json" \
+  -d '{"message": "How many files are there?"}'
+```
+
+### Response Format
+```json
+{
+  "status": "ok",
+  "reply": "Found 42 files in the database.",
+  "metadata": {
+    "entities": {
+      "identifiers": [],
+      "labels": ["File"],
+      "properties": {},
+      "intent": "count"
+    },
+    "execution_time_ms": 1234,
+    "result_count": 1
+  }
+}
+```
+
+---
+
+## Configuration Reference
+
+### Required
+```bash
+SCIDK_GRAPHRAG_ENABLED=1          # Turn on GraphRAG
+```
+
+### Optional
+```bash
+SCIDK_ANTHROPIC_API_KEY=...       # Better entity extraction
+SCIDK_GRAPHRAG_VERBOSE=true       # Always show metadata
+SCIDK_GRAPHRAG_SCHEMA_CACHE_TTL_SEC=300  # Schema cache duration
+```
+
+### Privacy Controls
+```bash
+SCIDK_GRAPHRAG_ALLOW_LABELS=File,Folder  # Only query these labels
+SCIDK_GRAPHRAG_DENY_LABELS=User,Secret   # Never query these labels
+```
+
+---
+
+## Troubleshooting
+
+### "GraphRAG disabled"
+**Solution:** Set `SCIDK_GRAPHRAG_ENABLED=1`
+
+### "Neo4j is not configured"
+**Solution:** Set Neo4j connection:
+```bash
+export NEO4J_URI=neo4j://localhost:7687
+export NEO4J_USERNAME=neo4j
+export NEO4J_PASSWORD=your_password
+```
+
+### "neo4j-graphrag not installed"
+**Solution:** Install dependency:
+```bash
+pip install neo4j-graphrag>=0.3.0
+```
+
+### Queries return "No results"
+**Possible causes:**
+1. Empty database → Run a scan first
+2. Wrong node labels → Check schema with "What types of nodes exist?"
+3. Query too specific → Try broader query
+
+---
+
+## Testing
+
+### Run Pytest
+```bash
+python3 -m pytest tests/test_graphrag_*_simple.py -v
+```
+
+### Run E2E Tests
+```bash
+npm run e2e -- chat-graphrag.spec.ts
+```
+
+---
+
+## Architecture
+
+```
+User Query
+    ↓
+Entity Extractor (extract IDs, labels, properties, intent)
+    ↓
+Neo4j Schema Discovery (CALL db.labels(), db.relationshipTypes())
+    ↓
+neo4j-graphrag Text2CypherRetriever (generate Cypher)
+    ↓
+Neo4j Execution
+    ↓
+Result Formatting
+    ↓
+Response to User
+```
+
+**Key Feature:** Schema-agnostic - works with ANY Neo4j database!
+
+---
+
+## Learn More
+
+- **Implementation:** `scidk/services/graphrag/`
+- **Tests:** `tests/test_graphrag_*_simple.py`
+- **E2E Tests:** `e2e/chat-graphrag.spec.ts`
+- **Session Summary:** `dev/sessions/2026-02-07-graphrag-integration-summary.md`

e2e/browse.spec.ts

@@ -18,8 +18,8 @@ test('files page loads and shows stable hooks', async ({ page, baseURL }) => {
   await expect(page.getByTestId('files-title')).toBeVisible();
   await expect(page.getByTestId('files-root')).toBeVisible();
 
-  // Let network settle and ensure no console errors
-  await page.waitForLoadState('networkidle');
+  // Wait briefly for any delayed errors (skip networkidle due to polling on datasets page)
+  await page.waitForTimeout(1000);
   const errors = consoleMessages.filter((m) => m.type === 'error');
   expect(errors.length).toBe(0);
 });