This commit fixes two critical issues with PDF processing:
1. **Text extraction mismatch (context expansion bug)**:
- Indexing used pymupdf4llm.to_markdown() producing markdown text
- Context expansion used page.get_text() producing plain text
- Different text formats caused character offset misalignment
- Search would find correct chunk, but expansion showed wrong section
- Fixed by making context.py use pymupdf4llm.to_markdown() consistently
2. **Diagnostic logging for page number assignment**:
- Added logging to verify page_boundaries exist in metadata
- Added logging to verify assign_page_numbers() assigns values
- Helps diagnose why page numbers show as null in search results
3. **mime_type storage bug**:
- Fixed incorrect field reference in processor.py:405
- Was using file_metadata.get("content_type", "")
- Should use content_type from WebDAV response
Changes:
- nextcloud_mcp_server/search/context.py: Use pymupdf4llm.to_markdown()
for PDF text extraction to match indexing method
- nextcloud_mcp_server/vector/processor.py: Add diagnostic logging for
page boundaries and assignment, fix mime_type storage
- tests/unit/client/test_webdav.py: Fix import sorting
🤖 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).
- scanner.py: Use file_info['id'] as doc_id instead of file_path
- scanner.py: Pass file_path in DocumentTask for content retrieval
- processor.py: Store file_path in Qdrant payload for later lookup
- context.py: Add _get_file_path_from_qdrant() to resolve file_id → file_path
- context.py: Update get_chunk_with_context() to handle file ID resolution
This makes the system resilient to file renames since file IDs are stable
identifiers in Nextcloud, while file paths can change.
Notes are indexed as "{title}\n\n{content}" in processor.py but were
being retrieved as just content during chunk expansion, causing
chunk_start_offset and chunk_end_offset to be misaligned.
This fix reconstructs the full content structure when fetching notes
for chunk expansion, ensuring the displayed chunks match the excerpts
shown in search results.
Fixes chunk/excerpt mismatch reported in vector visualization.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
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>
- Get container dimensions before creating Plotly layout to render at correct size immediately
- Add init() method with window resize listener for responsive plot sizing
- Remove post-render resize call (no longer needed with explicit dimensions)
- Improve colorbar positioning and scene domain configuration
This eliminates the visual "jump" during initial render and ensures the plot resizes smoothly when the browser window changes size.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Two fixes for the vector visualization page:
1. **CSS Loading Fix**: Moved CSS <link> from vector_viz.html fragment
to user_info.html <head> block. HTMX fragments don't process <link>
tags in <head>, causing unstyled page. Now CSS loads correctly.
2. **Camera Preservation**: Modified renderPlot() to preserve camera
position when toggling query point visibility. Previously, toggling
the "Show Query Point" checkbox would reset zoom/rotation to default.
Now reads existing camera settings from plot before updating.
Related: nextcloud_mcp_server/auth/static/vector-viz.js:123-130
Related: nextcloud_mcp_server/auth/templates/user_info.html:12
🤖 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 updates the web interface to better align with Nextcloud's
design system and improve the Vector Viz layout.
Changes:
- Replace emoji icons with Material Design SVG icons for better
consistency with Nextcloud apps
- Simplify navigation styling with minimal padding and subtle active
states (250px width)
- Update CSS variables to match Nextcloud design system
- Restructure Vector Viz from two-column to single-column vertical
layout for better plot visibility
- Move search controls to compact horizontal grid at top
- Make navigation toggle always visible (not just on mobile)
- Fix plot container sizing with overflow:visible to prevent colorbar
clipping
- Remove heavy shadows and custom card styling for cleaner aesthetic
- Add error and success page templates with consistent styling
Technical details:
- Preserve Alpine.js for reactive functionality
- Use CSS Grid for responsive horizontal controls layout
- Add smooth transitions for navigation collapse/expand
- Maintain HTMX for dynamic content loading
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Migrates from custom word-based chunking to LangChain's MarkdownTextSplitter
for better semantic search quality. This implements the chunking portion of
ADR-011.
Changes:
- Replace custom regex word chunker with MarkdownTextSplitter
- Optimized for Markdown content (headers, code blocks, lists)
- Convert from word-based (512 words) to character-based (2048 chars) chunking
- Maintain backward-compatible ChunkWithPosition interface
- Update configuration defaults and validation
- Update all unit tests (12/12 passing)
Benefits:
- Respects markdown structure boundaries
- Never breaks code blocks or headers mid-chunk
- Preserves semantic coherence within chunks
- Expected 20-30% improvement in recall quality
- Industry-standard approach (used by production RAG systems)
Note: Full reindex required to apply new chunking to existing documents.
Current vector database still contains old word-based chunks.
Related: ADR-011 (Improving Semantic Search Quality)
🤖 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>
Chris Coutinho