9 tests for generate_response_per_subquestion() and answer format validation covering multi-sub-q, empty, prompt construction, and markdown format. 8 tests for new history XML/JSON formats (sources as list-of-lists, <sub_q> wrappers in XML) and new {context_sections} prompt template.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add chunks_retrieved_per_subq_count and chunks_filtered_per_subq_count columns to query_history table with safe ALTER TABLE migration. Replace generate template {question}/{context} placeholders with {context_sections} for per-sub-question organized context sections. Update Phase 3 test assertions to match new template and schema shapes.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add SubQuestionSources, SubQuestionResult, GeneratingSubquestionEvent Pydantic models for the new per-sub-question response format. Add chunks_retrieved_per_subq_count and chunks_filtered_per_subq_count optional fields to QueryHistoryRecord and QueryHistoryDetail for per-sub-question chunk count tracking.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Restructure _query_stream() to use per-sub-question retrieval, filtering, and generation. Add generative_subquestion SSE events for progressive frontend rendering. Add format_chunks_retrieved_per_subq() and format_chunks_filtered_per_subq() with <sub_q> XML wrappers. Add empty decomposition fallback using original question as single sub-q. Update history recording for grouped sources JSON (list-of-lists format).
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add retrieve_per_subquestion() that queries ChromaDB independently per sub-question instead of joining all sub-qs into one query string. Add filter_per_subquestion() that evaluates each chunk against its own originating sub-question in a single LLM call with a redesigned grouped prompt. Add generate_response_per_subquestion() that produces markdown sections per sub-question with grouped sources and {context_sections} template support. All existing methods preserved for backward compatibility.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Root cause: PromptEditor useEffect synced localPrompts back to match prompts after every keystroke, making isDirty() always false.
- Delegate disabled control to parent via hasChanges prop (no local sync)
- Derive currentPrompts synchronously to avoid empty-textarea flash
- Add key={selectedProfile} for clean remount on profile switch
- Update PromptEditor tests for new hasChanges prop
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Convert /query endpoint from synchronous JSON to Server-Sent Events (SSE)
streaming. The frontend now receives extracted_questions as soon as the
first LLM call completes, without waiting for retrieval, filtering, and
answer generation.
Backend:
- Add StreamingQueryEvent union type (Decomposed, Retrieving, Filtering,
Generating, Completed, Error)
- Convert /query to return StreamingResponse with SSE format
- Yield events after each pipeline phase
Frontend:
- Add queryDocumentStream() using fetch + ReadableStream
- Add useQueryDocumentStream() hook with phase-aware state
- Update LTTPage to use streaming instead of mutation
- Update ResponsePanel to show phase messages (Searching documents...,
Filtering passages..., Generating answer...)
- Update ExtractedQuestionsDisplay to accept null
Tests:
- Update query_flow e2e test to mock queryDocumentStream
- 84/85 tests pass (1 pre-existing failure from removed file-input)
Chunk PDFs like 'NEC4 ACC_page_5.pdf' contain only 1 page (the extracted
page). Passing the original page number (e.g. 5) to <Page> caused
'Invalid page request' because the file only has 1 page.
- Always render pageNumber={1} for <Page> component
- Display originalPage in UI title to show source page number
- Disable prev/next navigation since chunk PDFs are single-page
- Encode filePath with encodeURIComponent to handle spaces/special chars
- Add page-level error handling in PdfViewerPage for better diagnostics
- Show PDF URL in error message to aid debugging
pdfjs-dist 5.6.205 was installed separately from react-pdf's bundled 5.4.296.
Change workerSrc from local pdfjs-dist import to unpkg CDN with dynamic version.
Uses pdfjs.version from react-pdf to ensure API/worker version match.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
react-resizable-panels v4 interprets numeric minSize/maxSize as PIXELS, not percentages.
Change minSize={15} → minSize='15%' and maxSize={60} → maxSize='60%'.
Add defaultLayout on Group for explicit 30/70 initial split.
Add min-h-0 to grid container and shrink-0 to separator.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Required for react-pdf v10 in test environment.
Refactor polyfills to use named variables to avoid TS class name conflicts.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
ResponsePanel now calls processCitations() on answer text before rendering.
Custom ReactMarkdown 'a' component adds target="_blank" to all citation links.
Adds tests for citation link rendering and unmatched citation fallback.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Replace numeric [1] labels with [filename, page N] format in context chunks.
Update LLM prompt to instruct inline citation using bracket labels.
Enables traceable source references in generated answers.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
ResponsePanel and ChunkList View PDF links now open /pdf-viewer page instead of raw PDF download.
Update ChunkList test mock from getChunkPdfUrl to getPdfViewerUrl.
Add DOMMatrix polyfill to test setup for react-pdf/jsdom compatibility.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Replace fixed CSS Grid with react-resizable-panels v4 (Group/Panel/Separator).
Upper panel (video + query) defaults to 30%, lower panel (response) to 70%.
Draggable divider with hover/active state via data-separator attributes.
Add ResizeObserver and DOMRect polyfills to test setup for jsdom compatibility.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Replace KeywordsDisplay test with ExtractedQuestionsDisplay test. Update e2e mock data for extracted_questions. Fix QueryInput to show submitted question inline with submit button.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Delete KeywordsDisplay (blue pills) and create ExtractedQuestionsDisplay (numbered list). Rename keywords to extracted_questions in types and LTTPage.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Update prompt assertion in decomposer test and field assertions in query endpoint tests to match extracted_questions rename.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Change QueryDecomposer prompt to generate 2-5 sub-questions instead of keywords. Rename API field from keywords to extracted_questions across models, service, and router.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Mark sub-phases 2.1 (Remove Upload) and 2.2 (Question Display) as done.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Show submitted question as italic text below the input area after clicking submit. Clears when user starts typing a new question.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
- Add page_number and chunk_file_path to SourceMetadata model and query router
- Add GET /chunks/{file_path}/pdf endpoint with path traversal protection
- Add View PDF links in ResponsePanel source cards and ChunkList component
- Update TypeScript types and API helper for chunk PDF URLs
- Add backend tests (5) and frontend ChunkList tests (7)
- Update enhancement plan: all 3 features complete
Delete document endpoint now removes associated chunk PDF files from document_chunk/ before ChromaDB deletion. Delete chunk endpoint removes individual chunk PDF. Missing files logged as warnings, not errors.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
PDF uploads now use parse_pdf_by_page() -> chunk_pages() -> extract page PDFs -> enhanced metadata with page_number, chunk_file_path, and document_id. Same-filename replacement deletes old chunks and PDFs before re-ingest. DOCX/TXT keep original flat flow with document_id added. RAGService.ingest_document() accepts optional document_id parameter.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
New pdf_extractor.py with extract_page_as_pdf() and extract_pages_as_pdf() for extracting individual PDF pages as separate files. Adds document_chunk_path setting to config and document_chunk/ to .gitignore.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Enhance extract_metadata() with three new optional fields for page-aware chunking support. Validates list length mismatches. Fully backward compatible — existing callers unaffected.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add chunk_pages() to TokenChunkingStrategy: one chunk per page with 200-token overlap from adjacent pages. Uses original page text for main content, decoded tokens for overlap. Never splits a page regardless of size.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add parse_pdf_by_page() that returns List[Tuple[int, str]] with 1-indexed page numbers. Pages with no extractable text are skipped. Follows same error handling as existing parse_pdf().
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
ChromaDB 1.5.8 calls embed_query() during collection.query(), but the wrapper only implemented __call__ (used by collection.add()). Added embed_query() as alias and refactored to shared _embed() method.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
When uploading files, the backend passes them through NamedTemporaryFile, causing os.path.basename to return temp names like 'tmp90i7xqa8.pdf'. Added original_filename parameter to extract_metadata() so the actual upload filename is stored.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Sub-phase 1.5.3: Full RAG Database page with document listing, expandable chunk viewer, delete with confirmation, and document upload. Adds TypeScript types, API functions, TanStack Query hooks (useQuery + useMutation with cache invalidation), and three new components (DocumentList, ChunkList, DocumentUpload).
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Woody