Add INFO log in get_settings() to print the actual model names
after merging .env and class defaults. Confirms pydantic-settings
priority: env values override class defaults as expected.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
The per-sub-question filter was all-or-nothing: if the LLM returned
9 scores for 10 chunks (common with qwen3.5-35b), every chunk was
discarded and the user got 'no relevant information found'.
Now: fewer scores → pad with 0.0; more scores → truncate. Changed
from error→warning since this is recoverable.
Also improve LTT page UI: sources collapsed by default in per-sub-q
sections, and the 'Your question' text now shows the full question
instead of being truncated.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Replace mocked DB/internal-services with real ChromaDB/SQLite via tmp_path.
Only mock truly external APIs (LLM, embedding for deterministic vectors).
13 test files rewritten (314 pass, 0 fail):
- Route tests: use TestClient + real ChromaDB, seed test data
- Service tests: use real PersistentClient/SQLite instances
- Pipeline tests: TestClient hits SSE /query endpoint, verify history
- Converted unittest.TestCase to pytest where applicable
Plus: fix metadata.py to filter None values from ChromaDB metadata
(pre-existing bug caught by real-DB ingestion tests)
Break the hardcoded per-sub-q filter prompt into 3 editable PromptService templates (filter_intro, filter_section, filter_outro) with placeholders for the for-loop iteration pattern. Refactor RelevanceFilter._build_per_subq_prompt() to compose them at runtime, falling back to built-in defaults when PromptService is unavailable.
Fix two latent bugs from Package 4:
- generate_per_subq was called by rag.py but never added to _VALID_STEPS or DB seed (would ValueError at runtime)
- _SEED_GENERATE placeholder mismatch: flat generate_response() expects {question}/{context} but Package 4 changed it to {context_sections}. Restored flat template; generate_per_subq now holds {context_sections}.
Add database backfill migration in seed_default_profiles() to INSERT OR IGNORE missing steps into existing profile rows, ensuring all 7 steps exist on restart.
Restructure System Prompts UI: remove unused flat filter/generate steps, replace with Step 2.1-2.3 (filter_intro/section/outro) and Step 3 (generate_per_subq). Update PlaceholderDocs with {context_sections}, {subq_idx}, {subq_question}.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
- Prefer integration tests (TestClient + real DB) over mocked unit tests
- Never mock database or internal services; only mock external APIs (LLM/ASR)
- Rename 'unit tests' to 'integration tests' throughout for consistency
Replace flat 3-step LLM workflow with per-sub-question architecture diagram. Document per-sub-question retrieval, filtering (single LLM call with sub-q grouping), and response generation with ## headers. Update CODE MAP to reflect completed implementation status. Add SSE event sequence with generating_subquestion events, history XML format with <sub_q> wrappers, and sources as list-of-lists JSON.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
6 stream state tests for completed, backward compat, generating_subquestion, null sources, lifecycle, and reset. 7 type tests for SubQuestionSources shape, discriminated union narrowing, and QueryResponse. 8 ResponsePanel tests for per-subq sections, source scoping, backward compat flat rendering, copy button, skeletons, and empty states. 7 citationParser tests for per-subq lookup, cross-section isolation, and processCitationsForSubq. 2 e2e tests for per-subq SSE display and progressive generation.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Redesign ResponsePanel with SubQuestionSections component that parses answer markdown on ## Sub-question N: boundaries and renders per-sub-question cards with headers, ReactMarkdown body, and collapsible sources scoped to each section. Extract FlatResponse for backward compatibility when subQuestionSources is null. Add buildCitationLookupForSubq and processCitationsForSubq for per-sub-question citation lookup scope isolation. Add anchor links in ExtractedQuestionsDisplay that smooth-scroll to matching ResponsePanel sections. Pass subQuestionSources through LTTPage.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add SubQuestionSources interface for grouped per-sub-question sources. Convert QueryStreamEvent from flat interface to discriminated union with 7 variants including generating_subquestion and completed with sub_question_sources. Add subQuestionSources to QueryStreamState. Update completed event handler to populate subQuestionSources. Make sub_question_sources optional for backward compatibility with old SSE format.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Add 6 tests for retrieve_per_subquestion and generate_response_per_subquestion to Phase 1 rag service tests. Add 4 tests for filter_per_subquestion to Phase 1 relevance filter tests. Add 2 tests for new {context_sections} generate template to Phase 3 prompt injection tests. Add TestPerSubQPipelineHistory class with 3 per-sub-q pipeline simulation tests to Phase 3 integration tests. Add generate_per_subq template seed to conftest mock_prompt_service fixture.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
5 integration tests simulating full per-sub-question pipeline with mocked services covering 2-sub-q, empty decomposition fallback, single sub-q, all-filtered, and partial retrieval. 2 acceptance tests (manual run) for real LLM verification of per-sub-question organized answers with grouped sources and ## Sub-question headers.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
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
Woody