deer-flow/backend/scripts/_autogen_revision.py
AnoobFeng debb0fd161
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feat(persistence): wire alembic migrations, bootstrap schema on startup (#3706)
* 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.
2026-06-24 13:57:12 +08:00

78 lines
2.9 KiB
Python

"""Generate a new alembic revision against an ephemeral SQLite DB.
Used by ``make migrate-rev MSG="..."``. Avoids two pitfalls:
1. ``alembic.ini``'s default ``sqlalchemy.url`` (``sqlite:///./data/deerflow.db``)
points at a path that doesn't exist in a clean checkout, so a bare
``alembic revision --autogenerate`` fails with ``unable to open database file``.
2. A persistent DB might be at an unknown revision (or at no revision at all),
producing a noisy autogenerate diff that mixes "real" changes with
accidentally-detected drift.
This script builds a *fresh* temp SQLite, runs the existing alembic chain to
``head`` against it, then runs ``alembic revision --autogenerate`` against
that. The temp DB must be built from migration history -- not from
``Base.metadata.create_all`` -- so newly edited ORM fields that do not yet have
a revision remain visible to autogenerate as a real diff.
The generated file lands in
``packages/harness/deerflow/persistence/migrations/versions/`` -- exactly
where alembic puts it by default -- and the temp directory is left for the OS
to GC. Review the generated revision and switch raw ``op.add_column`` /
``op.drop_column`` calls to the idempotent helpers in ``migrations/_helpers.py``
before committing.
Run from the ``backend/`` directory:
PYTHONPATH=. uv run python scripts/_autogen_revision.py "MESSAGE"
or via Makefile:
make migrate-rev MSG="..."
"""
from __future__ import annotations
import os
import sys
import tempfile
from pathlib import Path
from alembic import command
from alembic.config import Config
import deerflow.persistence.models # noqa: F401 -- registers ORM models with Base.metadata
from deerflow.persistence.bootstrap import _escape_url_for_alembic
BACKEND_DIR = Path(__file__).resolve().parents[1]
MIGRATIONS_DIR = BACKEND_DIR / "packages/harness/deerflow/persistence/migrations"
def _alembic_config(url: str) -> Config:
cfg = Config()
cfg.set_main_option("script_location", str(MIGRATIONS_DIR))
# Shared with ``bootstrap._alembic_safe_url`` so the ConfigParser ``%``
# interpolation rule lives in one place.
cfg.set_main_option("sqlalchemy.url", _escape_url_for_alembic(url))
return cfg
def _build_temp_db_at_head() -> str:
tmpdir = tempfile.mkdtemp(prefix="deerflow-autogen-")
db_path = os.path.join(tmpdir, "autogen.db").replace(os.sep, "/")
url = f"sqlite+aiosqlite:///{db_path}"
command.upgrade(_alembic_config(url), "head")
return url
def main() -> None:
if len(sys.argv) < 2 or not sys.argv[1].strip():
print('usage: python scripts/_autogen_revision.py "describe the change"', file=sys.stderr)
sys.exit(2)
message = sys.argv[1]
url = _build_temp_db_at_head()
print(f"autogen: built temp DB at head: {url}", file=sys.stderr)
command.revision(_alembic_config(url), message=message, autogenerate=True)
if __name__ == "__main__":
main()