- Replace sequential Qdrant scroll calls with batch retrieve
(50 HTTP requests → 1 request, ~50x faster vector fetch)
- Add point_id to SearchResult to enable batch retrieval by Qdrant point ID
- Reuse query embedding from search algorithm in viz_routes
(eliminates redundant embedding call, saves ~30ms)
- Make BM25 encode() async with thread pool to avoid blocking event loop
(~4.4s was blocking, now properly async)
- Run PCA computation in thread pool to avoid blocking event loop
(~1.2s was blocking, now properly async)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Previously, pymupdf4llm.to_markdown() was called twice - once in
PyMuPDFProcessor during indexing and again in PDFHighlighter during
visualization. Different image path lengths caused different character
offsets, leading to highlighted pages not matching their chunks.
Also fixed issue where all chunks on the same page showed all highlights
instead of just their own highlight. Now restores original page contents
between chunks using xref stream caching.
Changes:
- Add PDFHighlighter class requiring pre-computed page_boundaries and
full_text from document processor (no fallback extraction)
- Pass pre-computed data from processor to highlighter
- Extract page-relative portion of chunk text for cross-page chunks
- Add bounding box highlighting using text anchor search
- Run highlight generation in parallel with embedding/BM25
- Cache and restore page contents to isolate highlights per chunk
Results: Highlighting success rate improved from 51% to 95% (121/128).
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Introduces a placeholder-based state tracking system to prevent duplicate
document processing during the gap between scanner queuing and processor
completion.
**Key Changes:**
1. **Placeholder Helper Functions** (`vector/placeholder.py`):
- `write_placeholder_point()` - Creates zero-vector placeholder when queuing
- `query_document_metadata()` - Queries for existing entry (placeholder or real)
- `delete_placeholder_point()` - Removes placeholder before writing real vectors
- `get_placeholder_filter()` - Filters placeholders from user-facing queries
2. **Scanner Updates** (`vector/scanner.py`):
- Replace `indexed_at` comparison with `modified_at` comparison
- Write placeholder before queuing each document
- Query per-document metadata instead of bulk-querying indexed_at
- Fixes bug where files were resubmitted every scan cycle
3. **Processor Updates** (`vector/processor.py`):
- Delete placeholder before upserting real vectors
- Ensures no duplicate points in Qdrant
4. **Query Filters** (all search files):
- Add `get_placeholder_filter()` to all user-facing queries
- Ensures placeholders never appear in search results or visualizations
- Applied to: bm25_hybrid.py, semantic.py, viz_routes.py, algorithms.py
**Architecture:**
- Placeholders use zero vectors with dimension from embedding service
- Payload includes `is_placeholder: True` flag for filtering
- Status field tracks: "pending", "processing", "completed", "failed"
- Deterministic UUIDs using uuid5 for consistent point IDs
**Impact:**
- Eliminates duplicate processing of same documents
- Fixes race condition where long-running documents get queued multiple times
- Prevents scanner from resubmitting files every scan cycle
- Maintains clean separation between in-flight and indexed documents
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
When vector visualization search returns zero results, the code was returning
query_coords: null, which caused JavaScript error "can't access property 0,
queryCoords is null" when the frontend tried to access the array.
Changed to return empty array [] to match expected type and prevent crash.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- algorithms.py: Revert SearchResult.id to int (all docs use int IDs now)
- semantic.py: Revert SemanticSearchResult.id to int, remove Union import
- viz_routes.py: Remove str() conversion when querying doc_id from Qdrant
- viz_routes.py: Convert doc_id from query param to int in chunk context
Fixes vector visualization which was collapsing all chunks to a single
point because Qdrant queries were failing to match doc_id (string vs int).
Major improvements to vector visualization page:
- Refactor PCA to display individual chunks instead of averaged documents
- Add context expansion module for fetching surrounding text from notes and PDFs
- Update deduplication to use (doc_id, doc_type, chunk_start, chunk_end) keys
- Fix Alpine.js rendering with chunk-specific keys including offsets
- Refactor authentication helper to return NextcloudClient for better reuse
- Add async context manager support to NextcloudClient
Technical details:
- viz_routes.py: Fetch specific chunk vectors instead of averaging per document
- context.py: New module supporting both notes and PDF text extraction via PyMuPDF
- search algorithms: Extract page_number, chunk_index, total_chunks from Qdrant
- vector-viz.js/html: Use chunk positions in expansion tracking keys
This enables users to see which specific chunks match their query
and view them with surrounding context in the PCA visualization.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
This commit addresses multiple issues with async operations, PDF metadata
extraction, and type safety in document processing and search.
## Async/Await Fixes
- processor.py:259 - Added await for chunker.chunk_text(content)
- processor.py:270 - Added await for bm25_service.encode_batch(chunk_texts)
- tests/unit/test_document_chunker.py - Converted all 12 test methods to async
## PDF Metadata Enhancement
- pymupdf.py:143 - Added file_size metadata extraction
- pymupdf.py:145-206 - Refactored to extract text page-by-page
- Manually loop through pages instead of using page_chunks=True
- Generate page_boundaries metadata for precise page tracking
- Works around pymupdf.layout.activate() breaking page_chunks=True
- processor.py:32-66 - Added assign_page_numbers() helper function
- Assigns page numbers to chunks based on overlap with page boundaries
- Handles chunks spanning multiple pages
- processor.py:298-300 - Call assign_page_numbers() for PDF files
## Type Safety Fixes
- bm25_hybrid.py:184 - Removed int() conversion of doc_id
- semantic.py:131 - Removed int() conversion of doc_id
- viz_routes.py:275 - Removed int() conversion of doc_id
- Added comments documenting that doc_id can be int (notes) or str (file paths)
## Testing
- All 18 tests passing (12 unit + 6 integration)
- No type errors in modified files
- Container logs show successful processing
- Vector viz searches working correctly
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Extract CSS and JavaScript into separate static files
- Created nextcloud_mcp_server/auth/static/vector-viz.css
- Created nextcloud_mcp_server/auth/static/vector-viz.js
- Updated templates to reference external assets
- Fix vector visualization issues:
- Normalize vectors before PCA to match Qdrant's cosine distance
- Add zero-norm and NaN detection/handling for large datasets
- Enable responsive Plotly sizing (autosize + responsive config)
- Widen plot area to full viewport width with minimized margins
- Improve visualization accuracy:
- Query point now positioned correctly relative to documents
- Handles 200+ points without JSON serialization errors
- Full-width plot maximizes screen space utilization
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
This commit enhances the vector visualization interface with better score
transparency and improved UX:
**Dual-Score Display:**
- Store original algorithm scores before normalization (viz_routes.py:203)
- Display both raw and normalized scores: "Raw Score: 0.842 (89% relative)"
- Update plot hover text with dual scores (userinfo_routes.py:740)
- Fixes issue where all queries showed at least one 100% match regardless
of actual relevance (normalization artifact)
**UI Improvements:**
1. Fusion Method dropdown: Changed from x-show to :disabled
- Prevents jarring layout shift when switching algorithms
- Dropdown stays visible but grayed out when Semantic is selected
- Better UX with opacity: 0.5 and cursor: not-allowed
2. Score Threshold: Changed step from 0.1 to "any"
- Allows arbitrary float precision (0.7, 0.85, 0.123)
- Users can now fine-tune threshold values
3. Document Types: Converted multi-select to checkbox grid
- Replaced clunky Ctrl/Cmd multi-select listbox
- Checkbox grid with cleaner layout
- Positioned left of Score Threshold and Result Limit inputs
- More intuitive UX
**Technical Details:**
- Raw score ranges vary by algorithm:
- Semantic: 0.0-1.0 (cosine similarity)
- BM25 RRF: ~0.001-0.033 (Reciprocal Rank Fusion)
- BM25 DBSF: Can exceed 1.0 (Distribution-Based Score Fusion)
- Normalized scores (0-1) used for visual encoding (marker size, color)
- Original scores preserved in API response via getattr fallback
Files modified:
- nextcloud_mcp_server/auth/viz_routes.py (store original_score)
- nextcloud_mcp_server/auth/templates/vector_viz.html (UI controls)
- nextcloud_mcp_server/auth/userinfo_routes.py (plot hover text)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fix false-positive validation error where DBSF (Distribution-Based Score
Fusion) correctly produces scores > 1.0 but SearchResult validation
incorrectly rejected them.
**Root Cause**: SearchResult.__post_init__() enforced scores in [0.0, 1.0]
range, but DBSF sums normalized scores from multiple retrieval systems
(dense semantic + sparse BM25), resulting in scores like 1.55 when both
systems strongly agree a document is relevant.
**Changes**:
- Relaxed validation to allow any score ≥ 0.0 (algorithms.py:147-157)
- Updated SearchResult and SemanticSearchResult documentation to explain
score ranges for RRF ([0.0, 1.0]) vs DBSF (unbounded)
- Added comprehensive test coverage for both fusion methods
- Added DBSF fusion option to vector visualization UI
- Updated viz routes and vizApp() to support fusion parameter selection
**Testing**: All 157 unit tests pass, type checking passes, ruff passes
Fixes error: "Configuration error: Score must be between 0.0 and 1.0, got 1.1528953"
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- viz_routes.py: Extract "dense" vector from named vector dict
- semantic.py: Specify using="dense" for BM25 hybrid collections
- Fixes "X must be 2D array" error in hybrid search
- Fixes "Dense vector is not found" error in semantic search
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Remove obsolete search algorithm imports (Fuzzy, Keyword, Hybrid)
- Update UI to only show Semantic and BM25 Hybrid algorithms
- Replace manual weight controls with RRF fusion info message
- Update default algorithm from "hybrid" to "bm25_hybrid"
- Remove weight parameters (semantic_weight, keyword_weight, fuzzy_weight)
- Update score_threshold default from 0.7 to 0.0 for RRF scoring
- Document ty type checker in CLAUDE.md
Fixes unresolved-import type errors after BM25 refactor.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
This commit addresses critical performance issues with vector visualization
search (reducing time from 40s to ~2s) and improves result visualization
through better visual encoding.
## Performance Fixes
### 1. Fix blocking sleep in retry decorator (base.py:51)
- Changed `time.sleep(5)` to `await anyio.sleep(5)` in @retry_on_429
- Prevents entire event loop from freezing during rate limit retries
- Impact: Reduced search time from 22s to 16s initially
### 2. Add concurrency limiting for verification (verification.py:77-93)
- Added `anyio.Semaphore(20)` to limit concurrent HTTP requests
- Prevents connection pool exhaustion (RequestError) from 90+ simultaneous requests
- Fixes false filtering (was filtering 77/90 results incorrectly)
- Note: Semaphore still in code but verification removed from viz endpoint
### 3. Remove unnecessary verification from viz endpoint (viz_routes.py:483-486)
- Visualization only needs Qdrant metadata (title, excerpt), not full content
- Verification only required for sampling (LLM needs full note content)
- Impact: Reduced search time from 43.7s to ~2s (final fix)
### 4. Restore streaming scanner pattern (scanner.py)
- Process notes one-at-a-time using async generator
- Avoids loading all notes into memory
## Visualization Improvements
### 5. Result-relative score normalization (viz_routes.py:489-504)
- Normalize scores within result set: best=1.0, worst=0.0
- Removes arbitrary RRF normalization (theoretical max didn't make sense)
- Makes visual encoding meaningful regardless of algorithm scores
### 6. Power scaling for marker sizes (userinfo_routes.py:743)
- Changed from linear `8 + (score * 12)` to power `6 + (score² * 14)`
- Creates dramatic visual contrast: 0.0→6px, 0.5→9.5px, 1.0→20px
- Combined with opacity (0.2-1.0) for clear visual hierarchy
### 7. Multi-channel visual encoding (userinfo_routes.py:740-745)
- Size: Exponentially scaled with score²
- Opacity: Linear 0.2-1.0 (keeps all points visible)
- Color: Viridis gradient (blue→yellow)
- Effect: Top results are large/bright/opaque, context results small/dim/transparent
## Result
- Search time: 40s → ~2s (20x faster)
- Visual contrast: Subtle → dramatic (clear result hierarchy)
- No arbitrary cutoffs: All results visible, best naturally highlighted
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Move access verification from individual search algorithms to final output
stage, eliminating redundant API calls and improving performance.
## Changes
**New:**
- `search/verification.py`: Centralized verification using anyio task groups
- Deduplicates results by (doc_id, doc_type) before verification
- Verifies all unique documents in parallel using structured concurrency
- Filters out inaccessible documents in single pass
**Modified Search Algorithms:**
- `search/semantic.py`: Removed _deduplicate_and_verify() and _verify_document_access()
- `search/keyword.py`: Removed _verify_access() and parallel verification
- `search/fuzzy.py`: Removed _verify_access() and parallel verification
- `search/hybrid.py`: Removed nextcloud_client parameter passing
All algorithms now return unverified results from Qdrant payload.
**Modified Output Stages:**
- `server/semantic.py`: Added verify_search_results() call after search
- `auth/viz_routes.py`: Added verify_search_results() call after search
Both endpoints now verify access once at final stage with deduplication.
## Performance Impact
**Before:**
- Hybrid mode (limit=10): 30 API calls (10 per algorithm × 3 algorithms)
- Single algorithm: 10-20 API calls (with verification buffer)
**After:**
- Hybrid mode (limit=10): 10 API calls (deduplicated verification)
- Single algorithm: 10 API calls (deduplicated verification)
**Performance Gain:** 3x reduction in API calls for hybrid search
## Architecture Benefits
- **Separation of concerns**: Algorithms handle scoring, output stage handles security
- **Deduplication**: Each document verified exactly once
- **Parallel execution**: All verifications run concurrently via anyio task groups
- **Consistency**: Same verification logic across MCP tools and viz endpoints
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Vector Visualization Improvements:
- Add interactive vector viz tab with Alpine.js and Plotly.js to user info page
- Refactor viz route CSS for better scoping and maintainability
- Remove unused nextcloud_host variable
Performance Optimizations:
- Parallelize access verification in fuzzy and keyword search algorithms
- Use asyncio.gather() to verify multiple documents concurrently
- Add exception handling with return_exceptions=True for resilience
Dependencies:
- Update third_party/oidc submodule to include RFC 9728 resource_url support
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Skip tracing for /app/vector-sync/status to reduce noise from HTMX polling.
Metrics collection continues for this endpoint.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Move Webhooks tab to the right (User Info | Vector Sync | Vector Viz | Webhooks)
- Use request.user.display_name instead of session for viz routes
- Fixes session middleware error when accessing via iframe
- Add /app/vector-viz endpoint for interactive search testing
- Implement server-side PCA dimensionality reduction (768-dim → 2D)
- Support multi-select document type filter for cross-app search
- Support all search algorithms: semantic, keyword, fuzzy, hybrid
- Display 2D scatter plot of vector embeddings using Plotly
- Show search results with scores and document types
- Register viz routes in app.py
- Add custom PCA implementation using numpy eigendecomposition
- Replace sklearn.decomposition.PCA with custom implementation
- Maintains same API (fit, transform, fit_transform)
- Supports explained_variance_ratio_ for variance analysis
- Removes scikit-learn dependency from project
- Add type hints and assertion for type safety
Chris Coutinho