* feat(persistence): wire alembic migrations + bootstrap schema on startup
Closes#3682. Pre-#3658 DBs lack the `runs.token_usage_by_model` column
because alembic was never wired up — startup only ran `create_all`,
which never ALTERs existing tables.
Adds a hybrid bootstrap in FastAPI lifespan (replaces bare `create_all`):
- empty DB → create_all + stamp head
- legacy DB → stamp 0001_baseline + upgrade head
- versioned DB → upgrade head
Concurrency: Postgres `pg_advisory_lock` (cross-process); SQLite
per-engine `asyncio.Lock` + 30s `PRAGMA busy_timeout` on both prod and
alembic engines. Column revisions use `safe_add_column` /
`safe_drop_column` idempotent helpers as fallback.
Other bits:
- 0001 baseline (chain root) + 0002 add `runs.token_usage_by_model`
- `include_object` filter so alembic ignores LangGraph checkpointer tables
- `make migrate-rev MSG="..."` for authoring new revisions
(no migrate/stamp targets — startup is the only execution path)
- Tests: three-branch decision, concurrency, #3682 regression, env
filter, blocking-IO gate anchor
- CLAUDE.md: new "Schema migrations" section
* fix(style): fix lint error
* perf(persistence): address review feedback on alembic bootstrap
Behavioural fixes
- _SQLITE_LOCKS now keyed via WeakKeyDictionary so id-reuse after GC
cannot return a stale, loop-bound lock and the cache cannot leak one
entry per disposed engine.
- safe_add_column compares nullable / server_default against the desired
column when the name already exists and emits a warning on drift,
surfacing manual-ALTER workarounds instead of silently no-op'ing.
- _postgres_lock issues SET LOCAL idle_in_transaction_session_timeout=0
before pg_advisory_lock, so managed Postgres cannot kill the idle
lock-holding session mid-upgrade and silently release the advisory
lock.
- legacy branch now backfills missing baseline tables via a restricted
create_all (Base.metadata.create_all scoped to _BASELINE_TABLE_NAMES).
Restores pre-#1930 upgraders whose channel_* tables were never
provisioned, without pre-empting future create_table revisions for
newly-added models.
Schema parity
- runs.token_usage_by_model gains server_default=text("'{}'") in both
the ORM model and the 0001_baseline create_table, matching what 0002
adds via ALTER. create_all and alembic-upgrade paths now produce
identical column definitions.
- New parity test compares Base.metadata.create_all output against a
pure alembic upgrade base->head, asserting column-set, nullable, and
server_default agree across all tables (normalized through the same
helper safe_add_column's drift check uses).
Guards
- test_baseline_table_names_constant_matches_0001 pins
_BASELINE_TABLE_NAMES to 0001_baseline.upgrade()'s actual output --
the constant cannot drift silently when someone edits 0001.
- test_legacy_backfill_skips_non_baseline_tables verifies the restricted
backfill does not create a phantom table on Base.metadata, modelling
a future revision that would otherwise collide on op.create_table.
Doc residuals
- Three-branch decision table is now consistent across bootstrap.py
top docstring, engine.py comment, test module docstring, and
CLAUDE.md.
- Stale test anchor in blocking_io/test_persistence_engine_sqlite.py
docstring now points at the real file.
* fix(style): fix lint error
* fix(persistence): close drift detection holes
- _check_column_drift compares column type via a family equivalence
allowlist ({JSON, JSONB}). Catches the wrong-type workaround
`TEXT NOT NULL DEFAULT '{}'` that previously slipped through silently,
while keeping Postgres JSON/JSONB dialect reflection quiet. Reflected
and desired type are also echoed in every drift warning's payload for
operator triage.
- Extract _escape_url_for_alembic so bootstrap._alembic_safe_url and
scripts/_autogen_revision share the ConfigParser % escape rule
instead of duplicating it.
- backend/README.md: add `make migrate-rev MSG=...` to Commands and a
Schema Migrations section per the repo's README/CLAUDE.md sync policy.
- test_base_to_dict.py: scope the test ORM class to an isolated MetaData
so the create_all-vs-alembic parity test (added in the previous
commit) is not polluted by the phantom table on the full pytest
session.
* Fix stale AIO sandbox cache reuse
* Address AIO sandbox review feedback
* Distinguish sandbox health check failures
* Keep local discovery recoverable when the runtime check fails
LocalContainerBackend.discover() shares _is_container_running, which now
raises on transient daemon errors instead of returning False. Discovery has
no exception handling in _discover_or_create_with_lock(_async), so a brief
Docker hiccup turned a recoverable "could not verify, create instead" into a
hard acquire failure. Catch the check failure inside discover() and return
None so an unverifiable container is simply not adopted, restoring the
pre-change fall-through while keeping raise-on-unknown semantics protecting
the destroy path.
Reported by fancy-agent on PR #3494.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* Narrow the not-found match in container inspect error handling
A bare "not found" substring also matches transient failures like "command
not found" or "context not found", which would misclassify a check error as
"container definitely gone" and bypass the raise-on-unknown contract. Keep
Docker's specific "No such object"/"No such container" phrases, and only
trust a generic "not found" (Apple Container) when the message names the
inspected container or refers to a container/object.
Reported by WillemJiang on PR #3494.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
* feat(detectors): add static blocking IO inventory
* refactor(detectors): drop superseded runtime probe; clarify static report path
- Remove the #2924 custom runtime blocking IO probe entirely:
backend/tests/support/detectors/blocking_io.py,
backend/tests/test_blocking_io_detector.py,
backend/tests/test_blocking_io_probe_integration.py, and the
pytest_addoption / pytest_runtest_call / pytest_runtest_teardown /
pytest_sessionfinish / pytest_terminal_summary hooks plus the
blocking_io_detector fixture from backend/tests/conftest.py.
Its narrow DEFAULT_BLOCKING_CALL_SPECS (time.sleep, requests, httpx,
os.walk, Path.resolve, Path.read_text, Path.write_text) cannot serve
as a CI gate; a Blockbuster-backed runtime detector will land in a
separate follow-up PR. Leaving the half-coverage probe alongside
the static inventory in this PR added a redundant detect path with
no production value.
- Address Copilot review comments on backend/README.md and
backend/CLAUDE.md by stating explicitly that the JSON report writes
to .deer-flow/blocking-io-findings.json at the repository root,
whether the target is invoked from the repo root or from backend/.
Verified: pytest tests/test_detect_blocking_io_static.py (18 passed),
ruff check + format on touched files (passed), make detect-blocking-io
from both repo root and backend/ produce the same 105-finding report
at <repo-root>/.deer-flow/blocking-io-findings.json.
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix(nginx): defer cors to gateway allowlist
Remove proxy-level wildcard CORS handling so browser origins are controlled by the Gateway allowlist and stay aligned with CSRF origin checks.
* docs: document gateway cors allowlist
Clarify that same-origin nginx access needs no CORS headers while split-origin or port-forwarded browser clients must opt in with GATEWAY_CORS_ORIGINS.
* docs(gateway): record cors source of truth
Document that Gateway CORSMiddleware and CSRFMiddleware share GATEWAY_CORS_ORIGINS as the split-origin source of truth.
* fix(gateway): align cors origin normalization
* docs: clarify gateway langgraph routing
* docs(gateway): update runtime routing note
* fix: make tool argument behavior discoverable
The write_file tool already supported append=false by default with append=true for end-of-file writes, but the parsed docstring did not describe append in the model-facing schema. This records the overwrite default and append path in the tool description, adds resilient schema regression coverage, and keeps backend sandbox docs aligned.
The regression now also checks that every public parameter in the existing tool schema test matrix has a description. Enabling docstring parsing on setup_agent and update_agent fills the two existing gaps with their existing Args docs instead of duplicating descriptions elsewhere.
Constraint: Issue #2831 asks for a small docstring/schema discoverability fix without changing runtime file-writing behavior
Rejected: Changing write_file defaults | would alter existing overwrite semantics and broaden the fix beyond schema discoverability
Rejected: Exact phrase assertions | too brittle for future docstring rewording while testing the same behavior
Confidence: high
Scope-risk: narrow
Directive: Keep model-facing tool parameters documented through parsed docstrings or equivalent schema descriptions
Tested: cd backend && uv run pytest tests/test_setup_agent_tool.py tests/test_update_agent_tool.py tests/test_tool_args_schema_no_pydantic_warning.py tests/test_sandbox_tools_security.py::test_str_replace_and_append_on_same_path_should_preserve_both_updates -q
Tested: cd backend && uv run ruff check packages/harness/deerflow/sandbox/tools.py packages/harness/deerflow/tools/builtins/setup_agent_tool.py packages/harness/deerflow/tools/builtins/update_agent_tool.py tests/test_tool_args_schema_no_pydantic_warning.py
Not-tested: Full backend test suite
Co-authored-by: OmX <omx@oh-my-codex.dev>
* Fix the lint error
---------
Co-authored-by: OmX <omx@oh-my-codex.dev>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix: prevent concurrent subagent file write conflicts
Serialize same-path str_replace operations in sandbox tools
Guard AioSandbox write_file/update_file with the existing sandbox lock
Add regression tests for concurrent str_replace and append races
Verify with backend full tests and ruff lint checks
* fix(sandbox): Fix the concurrency issue of file operations on the same path in isolated sandboxes.
Ensure that different sandbox instances use independent locks for file operations on the same virtual path to avoid concurrency conflicts. Change the lock key from a single path to a composite key of (sandbox.id, path), and add tests to verify the concurrent safety of isolated sandboxes.
* feat(sandbox): Extract file operation lock logic to standalone module and fix concurrency issues
Extract file operation lock related logic from tools.py into a separate file_operation_lock.py module.
Fix data race issues during concurrent str_replace and write_file operations.
* fix(security): disable host bash by default in local sandbox
* fix(security): address review feedback for local bash hardening
* fix(ci): sort live test imports for lint
* style: apply backend formatter
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Add LangSmith tracing setup instructions across the project:
- .env.example: add LANGSMITH_* env vars (commented out)
- README.md + translations (zh/ja/fr/ru): add LangSmith Tracing section
under Advanced with setup steps and env var reference
- backend/README.md: add detailed LangSmith Tracing section with setup,
env var table, how-it-works explanation, and Docker notes
- docker-compose.yaml: update LANGCHAIN_TRACING_V2 to LANGSMITH_TRACING
for naming consistency with the rest of the project
Made-with: Cursor
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* fix(threads): clean up local thread data after thread deletion
Delete DeerFlow-managed thread directories after the web UI removes a LangGraph thread.
This keeps local thread data in sync with conversation deletion and adds regression coverage for the cleanup flow.
* fix(threads): address thread cleanup review feedback
Encode thread cleanup URLs in the web client, keep cache updates explicit when no thread search data is cached, and return a generic 500 response from the cleanup endpoint while documenting the sanitized error behavior.
---------
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
* feat(feishu): stream updates on a single card
* fix(feishu): ensure final message on stream error and warn on missing card ID
- Wrap streaming loop in try/except/finally so a is_final=True outbound
message is always published, even when the LangGraph stream breaks
mid-way. This prevents _running_card_ids memory leaks and ensures the
Feishu card shows a DONE reaction instead of hanging on "Working on it".
- Log a warning when _ensure_running_card gets no message_id back from
the Feishu reply API, making silent fallback to new-card behavior
visible in logs.
- Add test_handle_feishu_stream_error_still_sends_final to cover the
error path.
- Reformat service.py dict comprehension (ruff format, no logic change).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
* Avoid blocking inbound on Feishu card creation
---------
Co-authored-by: songyaolun <songyaolun@bytedance.com>
Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
add oauth schema to MCP server config (extensions_config.json)
support client_credentials and refresh_token grants
implement token manager with caching and pre-expiry refresh
inject OAuth Authorization header for MCP tool discovery and tool calls
extend MCP gateway config models to read/write OAuth settings
update docs and examples for OAuth configuration
add unit tests for token fetch/cache and header injection
Updated documentation to accurately cover all backend subsystems including
subagents, memory, middleware chain, sandbox, MCP, skills, and gateway API.
Fixed broken MCP_SETUP.md link in root README.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add README.md with project overview, quick start, and API reference
- Add CONTRIBUTING.md with development setup and contribution guidelines
- Add docs/ARCHITECTURE.md with detailed system architecture diagrams
- Add docs/API.md with complete API reference for LangGraph and Gateway
- Add docs/README.md as documentation index
- Update CLAUDE.md with improved structure and new features
- Update docs/TODO.md to reflect current status
- Update pyproject.toml description
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
