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37 commits

Author SHA1 Message Date
Pier-Jean Malandrino
c878ee5f3b feat(#202): introduce Document lifecycle state machine
Adds a first-class lifecycle state to every document, distinct from
AnalysisJob.status. The lifecycle describes the document as a whole and
is the foundation for the doc-centric pivot in 0.6.0.

Domain
- DocumentLifecycleState enum (Uploaded/Parsed/Chunked/Ingested/Stale/Failed)
- Document.lifecycle_state and lifecycle_state_at fields
- Document.transition_to() validates against a transition table
  (domain/lifecycle.py) and returns a DocumentLifecycleChanged event
- InvalidLifecycleTransitionError on disallowed transitions

Persistence
- ALTER TABLE documents to add the two columns (default 'Uploaded')
- New index idx_documents_lifecycle_state for filter perf
- _COLUMN_MIGRATIONS refactored to support multiple tables
- _POST_MIGRATION_DDL list for indexes on freshly-added columns
- SqliteDocumentRepository.update_lifecycle()

Services
- AnalysisService drives transitions on parse / chunk / re-chunk / fail
  via _transition_document(); idempotent and resilient (logs WARN and
  continues if a stale state is somehow encountered)

API
- DocumentResponse exposes lifecycleState + lifecycleStateAt
  (additive — existing 'status' field kept for backwards compat)

Frontend
- Document type extended with lifecycleState and lifecycleStateAt
- DocumentLifecycleState union literal mirroring the backend enum

Tests
- 24 new tests in test_lifecycle.py covering transitions, idempotency,
  invariant preservation, and event emission
- test_repos.py: round-trip + every-enum-value check + update_lifecycle
- test_chunking.py: rechunk path now mocks document_repo correctly

Refs #202
2026-04-29 15:34:25 +02:00
Pier-Jean Malandrino
efc27932dd refactor(audit): remediate 0.5.0 audit findings — clean architecture, security, DRY, SOLID, perf
Closes the 12 MAJ raised by the release/0.5.0 audit pipeline (cf.
docs/audit/reports/release-0.5.0/summary.md → summary-reaudit.md).

Volet 1 — Reasoning architecture (audits 01/02/06/07 strengthening)
  * Domain ports: LLMProvider, ReasoningRunner, ReasoningParseError
  * Domain DTOs: LLMProviderType, ReasoningResult, ReasoningIteration
  * infra/llm/ollama_provider.py — OllamaProvider with health_check
  * infra/docling_agent_reasoning.py — runner adapter, encapsulates the
    private _rag_loop call (tracked at docling-project/docling-agent#26),
    commits OLLAMA_HOST once at boot (eliminates the per-request env race),
    translates upstream IndexError into ReasoningParseError
  * api/reasoning.py — zero coupling to docling-agent / mellea / docling-core,
    consumes app.state.reasoning_runner via the port
  * main.py — DI wires OllamaProvider + DoclingAgentReasoningRunner at boot
    when REASONING_ENABLED=true and deps are importable
  * Rename RAG_* env vars → REASONING_*, endpoint /rag → /reasoning,
    type RAGResult → ReasoningResult, frontend feature flag wiring,
    i18n strings, tests, docs (BREAKING — pre-1.0 surface, no external
    consumers in production)
  * 17 new tests: adapter unit tests with sys.modules stubs, OllamaProvider
    httpx tests, R3 concurrent-host isolation, R6 multi-iteration trace
    serialization, R13 Protocol conformance via isinstance
  * E2E Karate scenario: nav-reasoning hidden when REASONING_ENABLED=false
  * README — Live Reasoning section (env vars, archi, link to issue #26)

Bloc B — Security (audit 08, dev-only context)
  * docker-compose.yml — DEV DEFAULTS header, OpenSearch DISABLE_SECURITY_PLUGIN
    flagged as dev-only with link to OpenSearch security docs
  * main.py — boot warning if NEO4J_URI is set with the default 'changeme'
    password, so prod operators can't silently inherit it

Bloc C — DRY frontend (audit 05)
  * shared/storage/keys.ts — STORAGE_KEYS centralised (theme, locale)
  * features/settings/store.ts — dead apiUrl ref + orphan i18n keys removed
  * api/schemas.py — DOCUMENT_STATUS_UPLOADED constant

Bloc D — Quality (audits 02/06/07/09/10/12)
  * domain/ports.py — DocumentConverter.supports_page_batching property
    (LSP fix, replaces isinstance(ServeConverter) check)
  * domain/ports.py — VectorStore.ping() (encapsulation, replaces
    _vector_store._client.info() reach-around)
  * api/analyses.py + api/ingestion.py — path params {job_id} → {analysis_id}
    aligned with the user-facing terminology (URLs unchanged)
  * api/documents.py — Path.read_bytes() + generate_preview() wrapped in
    asyncio.to_thread, unblocks the FastAPI event loop on /preview
  * infra/docling_tree.py — PEP 604 union for isinstance (Ruff UP038)
  * src/__tests__/integration/ — cross-feature integration test relocated
    out of features/history/ so feature folders stay self-contained
  * Tightened terminal `assert X is not None` checks (isinstance(.., datetime),
    exact value comparisons)

Validation
  * 446 backend pytest, 202 frontend vitest — all green
  * ruff + ruff format + ESLint + Prettier + vue-tsc clean
  * Re-audit verdict: 0 CRIT / 0 MAJ, score ~94/100, GO

Closes #200
2026-04-29 14:00:00 +02:00
Pier-Jean Malandrino
c2550867b7 feat(neo4j): Day 3 — ChunkWriter, graph API, GraphView, README
ChunkWriter mirrors chunks into Neo4j after OpenSearch indexing, creating
HAS_CHUNK edges and DERIVED_FROM back-references to the source Elements
(via doc_items propagated from the local chunker).

Graph API: GET /api/documents/{id}/graph returns a cytoscape-shaped
payload with nodes + edges for Document / Element / Page / Chunk.
Hard cap at 200 pages returns HTTP 413 per design §8.4.

Frontend: new Graph tab in Studio results, rendered with Cytoscape.js +
dagre layout (lazy-loaded, ~175 KB gz). Legend, node styling per element
label, directional edges styled per edge type.

README gains a Neo4j section with the schema, three demo Cypher
queries, and env vars. Backend tests skip cleanly when the neo4j python
package is not installed locally.

Refs #186
2026-04-29 14:00:00 +02:00
Pier-Jean Malandrino
c1d3a687ac feat(neo4j): Day 2 — TreeWriter, TreeReader, pipeline wiring
Serialize a DoclingDocument to a Neo4j graph: Document + Page + Element
nodes with dynamic specific labels (SectionHeader, Paragraph, Table,
Figure, …), plus HAS_ROOT / PARENT_OF / NEXT / ON_PAGE edges. Replace-on-
write for idempotent re-ingestion.

The reader returns the verbatim document_json stored on the Document
node — reconstruction from graph nodes is deferred to v0.6.

Wired into AnalysisService._finalize_analysis: runs after conversion,
degrades gracefully by default, fails fast when neo4j_required is set.

Refs #186
2026-04-29 14:00:00 +02:00
Pier-Jean Malandrino
e0f8e81b63 feat: enable chunking in remote (Docling Serve) mode
Hybrid approach: reuse LocalChunker to chunk the DoclingDocument JSON
returned by Serve, so chunking works identically in both local and
remote modes without calling Serve's chunk endpoint.

Backend:
- _build_chunker() always returns LocalChunker (remove engine guard)
- Use docling-core[chunking] extra for required dependencies
- Skip client-side batching in remote mode (Serve manages its own
  resources, and batching discards document_json needed for chunking)
- Fix Serve form fields: remove generate_page_images (not a Serve
  field), use repeated form keys for to_formats and page_range
- Log Serve error response body on 4xx/5xx for diagnosis
- Fix FastAPI 204 DELETE routes missing response_model=None

Frontend:
- Update chunking feature flag to enable Prepare UI in remote mode

Closes #51
2026-04-29 14:00:00 +02:00
Pier-Jean Malandrino
efabe84d66 feat(#77): multi-step ingestion progress stepper
Visual stepper in Studio topbar: Embedding → Indexing → Done.
Each step shows pending/active/done with animated dot. Store tracks
currentStep through the pipeline. Auto-resets after 2s.
2026-04-10 22:49:20 +02:00
Pier-Jean Malandrino
995e891d9b feat: orchestrated ingestion pipeline Docling → embedding → OpenSearch
Closes #72
2026-04-10 21:12:11 +02:00
Pier-Jean Malandrino
80b0c44e8c feat(chunking): soft-delete chunk with confirmation dialog
Closes #90
2026-04-10 20:28:24 +02:00
Pier-Jean Malandrino
c74a3277b8 feat(chunking): inline chunk text editing
Closes #89
2026-04-10 19:37:29 +02:00
Pier-Jean Malandrino
3d199cb783 fix(clean-code): English mode strings, SRP extraction, rename getter
- Replace French mode strings (configurer/verifier/preparer) with English
  equivalents (configure/verify/prepare) in StudioPage.vue and tests
- Extract _build_conversion_options, _run_conversion, _finalize_analysis
  from _run_analysis_inner to respect Single Responsibility Principle
- Rename _get_default_converter to _ensure_default_converter to reflect
  its lazy-init side effect

Closes #136, closes #137, closes #138
2026-04-10 13:45:13 +02:00
Pier-Jean Malandrino
9907b7f040 fix(arch): inject repositories and extract domain logic
- Add DocumentRepository and AnalysisRepository protocols in domain/ports.py (#128)
- Refactor persistence repos from module functions to SqliteDocumentRepository
  and SqliteAnalysisRepository classes
- Inject repos into AnalysisService and new DocumentService class via
  constructor, removing direct imports of persistence and infra.settings (#129)
- Move _merge_results, _classify_error, _extract_html_body to domain/services.py (#130)
- Update main.py composition root to build and wire all dependencies
- Switch api/documents.py to Depends pattern matching api/analyses.py
- Update all tests to use injected mocks instead of module-level patches

Closes #128, closes #129, closes #130
2026-04-10 11:44:33 +02:00
Pier-Jean Malandrino
d810fda333 fix: preserve batch progress on analysis completion
Re-read the job from DB before mark_completed so that
progress_current/progress_total written during batched conversion
are not overwritten by the stale in-memory object.

Add regression unit test and e2e assertion on final progress values.
2026-04-09 15:51:36 +02:00
Pier-Jean Malandrino
704ba550d4 feat: make document max size configurable via MAX_FILE_SIZE_MB env var
Replace hardcoded 5 MB upload limit with a configurable setting.
Backend exposes the value via /api/health, frontend reads it
dynamically for validation and UI messages.

Closes #48
2026-04-08 10:27:38 +02:00
Pier-Jean Malandrino
fc866ce229 feat: batch large documents with page_range and progress reporting
Use Docling's native page_range parameter to split large PDFs into
sequential batches, preventing memory exhaustion and timeouts.
Progress is reported via existing polling mechanism.

Closes #56
2026-04-07 17:54:40 +02:00
Pier-Jean Malandrino
af10c200f0 fix: cancel running conversion when analysis job is deleted (#64)
Track background tasks per job ID. On delete, cancel the task to release
the converter lock instead of letting phantom jobs run to completion.
2026-04-07 17:07:55 +02:00
Pier-Jean Malandrino
302b24cc4c fix: route _on_task_done errors through _classify_error (#63)
Unhandled task exceptions now produce user-friendly messages instead of
raw Python tracebacks in the error_message field.
2026-04-07 17:06:16 +02:00
Pier-Jean Malandrino
c281b6c551 fix: classify pipeline errors into user-friendly messages (M1)
Raw PyTorch/Docling stack traces are no longer shown to the user.
Common failures (missing compiler, OOM, lock contention, corrupted
document) are mapped to actionable messages. Unknown errors are
truncated to 200 chars.

Ref #57 (M1)
2026-04-07 15:32:38 +02:00
Pier-Jean Malandrino
f58b563a13 fix: make default table_mode configurable via DEFAULT_TABLE_MODE (H1)
TableFormerMode.ACCURATE is very expensive on CPU (~3-5x slower).
The default can now be set to "fast" on resource-constrained
environments (HF Spaces) via the DEFAULT_TABLE_MODE env var.

User-specified table_mode in the request still takes precedence.

Ref #57 (H1)
2026-04-07 15:32:38 +02:00
Pier-Jean Malandrino
09145206d2 fix: limit upload to 5 MB / 20 pages max and increase conversion timeout
Prevents PyTorch/Docling pipeline crashes on HF Spaces CPU by:
- Reducing max file size from 50 MB to 5 MB
- Adding configurable MAX_PAGE_COUNT setting (env var, default unlimited)
- Increasing conversion timeout from 600s to 900s
- Adding frontend upload validation with explicit error messages
- Exposing maxPageCount via /api/health for dynamic UI hints
2026-04-07 10:56:16 +02:00
Pier-Jean Malandrino
c82fd66ffc Add docstrings to all public methods
Domain model state transitions, repository CRUD operations, and service
methods now have descriptive docstrings to lower the contribution
barrier for an open-source project.
2026-04-03 13:54:52 +02:00
Pier-Jean Malandrino
360ea7ea8f Stream upload reads in 64 KB chunks
Read uploaded files in fixed-size chunks instead of a single file.read()
to reduce peak memory pressure. Also enforces the size limit during
streaming so oversized payloads are rejected before fully buffered.
2026-04-03 13:52:32 +02:00
Pier-Jean Malandrino
c2e91262c6 Limit concurrent analyses with asyncio.Semaphore
Unbounded asyncio.create_task calls could exhaust CPU and memory on
modest hardware. Add a configurable semaphore (MAX_CONCURRENT_ANALYSES,
default 3) so excess jobs queue instead of running all at once.
2026-04-03 13:51:53 +02:00
Pier-Jean Malandrino
69ce1df5a1 Narrow exception handlers for better diagnostics
Replace broad `except Exception` with specific types (FileNotFoundError,
PermissionError, OSError) so errors are properly categorized in logs.
Users reporting bugs will get actionable messages instead of generic ones.
2026-04-03 13:48:33 +02:00
Pier-Jean Malandrino
c50106c185 Centralize config through Settings singleton
UPLOAD_DIR and DB_PATH were read directly from os.environ, bypassing
the Settings dataclass. This caused an inconsistency where overriding
Settings had no effect on these values. Now all modules import from
infra.settings.settings.
2026-04-03 13:47:53 +02:00
Pier-Jean Malandrino
8856daf3c9 Force .pdf extension on uploaded files regardless of user input
The file content is already validated as PDF, so the user-supplied
extension should not be trusted or written to disk.
2026-04-03 13:03:21 +02:00
Pier-Jean Malandrino
4af6b5b231 Add chunk-to-bbox hover highlighting in Prepare mode
Extract bounding boxes from chunk doc_items provenance in the chunker,
propagate through domain/service/API layers, and render highlighted
bboxes on canvas when hovering a chunk card. Reset highlights on
mode and page changes to prevent stale visual state.
2026-04-02 14:47:31 +02:00
Pier-Jean Malandrino
a9517d38eb Add chunking service orchestration, API endpoints, and wiring
AnalysisService gains rechunk() and inline chunking during conversion.
ChunkingOptionsRequest/ChunkResponse schemas, POST rechunk endpoint,
and conditional chunker injection in main.py (local engine only).
2026-04-02 12:33:07 +02:00
Pier-Jean Malandrino
2b991108f7 Rebase sync 2026-03-31 16:55:17 +02:00
Pier-Jean Malandrino
001cf6807c Fix audit findings: security, robustness, and dead code
- Remove dead get_analysis_service() function in main.py
- Scope file deletion to UPLOAD_DIR to prevent path traversal
- Parse datetime strings back to datetime objects in repos
- Add 10-minute polling timeout in frontend analysis store
- Accept .pdf extension (not just MIME type) on drag-and-drop
- Guard localStorage access for private browsing compatibility

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-03-31 16:52:36 +02:00
Pier-Jean Malandrino
0af3b81b8f Fix zombie jobs and unprotected JSON parse
Bug #1: _on_task_done now receives job_id via functools.partial and
calls _mark_failed when the background task raises or is cancelled,
preventing jobs from being stuck in RUNNING state forever.

Bug #5: _parse_response wraps json.loads in try/except JSONDecodeError
so malformed json_content strings fall back gracefully instead of crashing.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-03-31 16:52:36 +02:00
Pier-Jean Malandrino
a63af61b73 Fix lint ans test errors 2026-03-31 16:35:48 +02:00
Pier-Jean Malandrino
3743ed4ca8 Refactor backend to hexagonal architecture for converter extensibility
Extract domain value objects and ports from parsing.py, move Docling-specific
code to infra/local_converter.py, and convert analysis_service to a class
with injected DocumentConverter. This prepares the codebase for plugging in
alternative conversion backends (e.g. Docling Serve) via the Protocol pattern.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
2026-03-31 10:34:07 +02:00
pjmalandrino
577225d10e Add qualityt check and contributing doc 2026-03-21 15:34:54 +01:00
pjmalandrino
2db251182f Refacto and add cp paste btn 2026-03-21 15:03:10 +01:00
pjmalandrino
ad1f1a81d3 Mke some fixes and refacto 2026-03-20 12:36:26 +01:00
pjmalandrino
e69ff90650 Connect options with model configuration 2026-03-20 08:59:20 +01:00
pjmalandrino
5fff141045 Radical architecture change, migration to a more lightweight 2026-03-17 16:06:27 +01:00