Replace full_text responses with character-level deltas computed from
DashScope's monotonically-growing 'text' field. Stash-only events (empty
text) are skipped; trailing stash chars sent alongside deltas and
appended on pause to complete final sentences.
Backend:
- Delta = text[len(prev_text):] — simple suffix diff, no merge logic
- Track item_id for utterance boundaries, prepend space separator
- Send stash alongside delta for frontend pause handler
Frontend:
- Accumulate deltas locally (transcriptRef += msg.delta)
- Store lastStashRef from each message
- On pause: append stash to text, fire onFinalTranscript
Plan: .plans/phase2_enhancement_delta_sse.md updated to Complete
DashScope stashes are ~7-char rolling windows, not cumulative. Each partial
event replaces the previous. Completed events rarely sent. This caused text to
jump/replace during streaming and disappear on pause.
Backend:
- Add _merge_stash() — finds overlapping suffix between successive stashes
and appends only new characters, reconstructing full utterance from partials
- format_transcription_event returns raw stash for read_events to merge
- read_events maintains partial_buffer via _merge_stash, clears on completed
- Guard against empty/whitespace-only stashes
Frontend:
- transcriptRef + onFinalTranscriptRef avoid stale closures in pause handler
- stopStreaming fires onFinalTranscript(currentText) before clearing partial
- Removed blind setPartialTranscript('') that erased text on pause
Tests: 16/16 ws_protocol tests pass, frontend tests unchanged
Plan: Updated phase2_implementation_plan.md to Complete with 11-bug log
- Add DashScope ASR and video upload config fields to Settings
- Create Pydantic models (video.py, asr.py)
- Create VideoService with validation, save, serve, delete
- Create ASR client stub with float32_to_s16le utility
- Implement POST /api/v1/video/upload with streaming validation
- Implement GET /api/v1/video/{video_id} with FileResponse
- Create WebSocket ASR endpoint stub
- Register new routers in main.py
- Update .env.example and requirements.txt
- Add reference examples for DashScope integration
- 8 tests passing (3 config + 5 video upload)
Follows Deepseek JSON Output guide: the prompt now includes the word 'json' and a format example derived from the Pydantic model schema. Added _pydantic_to_json_instruction() helper that builds a human-readable schema description with EXAMPLE JSON OUTPUT.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Added complete_structured() to mock classes, split response lists between LLMClientDP (decompose) and LLMClient (filter+generate), and patched both clients in all integration tests.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
Uses Deepseek's json_object response_format (not json_schema, which Deepseek does not support). Always disables thinking mode. Includes unit tests (12) and acceptance tests (5).
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
- POST /api/v1/v2/highlights/batch: compute and cache highlights for cited chunks
- GET /api/v1/v2/highlights: serve cached highlighted HTML pages
- chunks.py router registered in main.py
- Dynamic DB path computation (prompts.db -> highlights.db), no Settings changes
- 7 endpoint tests: POST 200/422, GET 200/404, mock service verification
- ChunkHighlightService.compute_highlights_batch(): single LLM call across
all cited chunks, grouped by sub-question, with structured output
- render_highlight_html(): self-contained HTML page with yellow-highlighted
relevant sentences, LLM reason annotations, and View Original PDF footer
- Per-target error isolation, ChromaDB miss handling, graceful degradation
- 14 tests: 7 batch service + 7 HTML rendering
DOCX and TXT ingestion now produces chunk_file_path + per-chunk PDF files matching the PDF ingestion flow. Uses reportlab to render chunk text as simple PDFs with automatic text wrapping.
- Add reportlab==4.2.5 to requirements.txt
- New utils/text_to_pdf.py: generate_text_pdf() renders chunk text as PDF
- Ingest router DOCX/TXT branches: generate chunk_N.pdf per chunk, store in chunk_file_paths
- Graceful degradation: chunk_file_path stays None if PDF generation fails
- Update test_phase1_ingest_page_aware.py assertions: DOCX chunks now HAVE chunk_file_path
- New test_phase5_docx_pdf_generation.py: 5 tests (DOCX PDF gen, TXT PDF gen, PDF regression, file count, graceful degradation)
- 361 backend tests pass (4 pre-existing embedding failures unrelated)
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>
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>
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>
- 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
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>
Add 4 REST endpoints for RAG database management: GET /documents, GET /documents/{id}/chunks, DELETE /documents/{id}, DELETE /chunks/{id}. Register documents router in main.py. 8 unit tests covering all CRUD operations.
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus <clio-agent@sisyphuslabs.ai>
The LLM (Qwen3.5 via OpenRouter) returns JSON wrapped in markdown code blocks:
```json
["project manager", "limits", ...]
```
But the code was trying to parse this directly with json.loads(), causing:
- QueryDecomposer to return empty keywords
- RelevanceFilter to fail with "Expecting value: line 1 column 1"
Changes:
- Added _extract_json_from_markdown() helper function to both modules
- Strips markdown code block markers (```json and ```) before JSON parsing
- Added unit tests for markdown code block handling
Ultraworked with [Sisyphus](https://github.com/code-yeongyu/oh-my-openagent)
Co-authored-by: Sisyphus \u003cclio-agent@sisyphuslabs.ai\u003e
Woody