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* 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.
122 lines
4.8 KiB
Python
122 lines
4.8 KiB
Python
"""Regression test for GitHub issue #3682.
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End-to-end shape:
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1. Hand-build a SQLite DB that mirrors a real pre-#3658 deployment -- the
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``runs`` table is missing the ``token_usage_by_model`` column, mirroring
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what every existing user's DB looked like after the upgrade that triggered
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the issue.
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2. Run ``init_engine`` (the entry point used by the FastAPI Gateway
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lifespan), which now routes through ``bootstrap_schema``.
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3. Confirm a real ``SELECT`` against the column succeeds, demonstrating the
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500 from the original issue is gone.
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The pre-fix codepath would have raised
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``sqlalchemy.exc.OperationalError: no such column: runs.token_usage_by_model``
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on step 3.
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"""
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from __future__ import annotations
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import sqlite3
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from pathlib import Path
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from uuid import uuid4
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import pytest
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import sqlalchemy as sa
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import deerflow.persistence.models # noqa: F401 -- registers ORM models
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from deerflow.persistence.base import Base
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from deerflow.persistence.engine import close_engine, get_session_factory, init_engine
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from deerflow.persistence.run import RunRepository
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pytestmark = pytest.mark.asyncio
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def _seed_pre_3658_database(db_path: Path) -> None:
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"""Build a DB that looks like a pre-PR-#3658 deployment.
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Uses the synchronous ``sqlite3`` driver so the seed is independent of the
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async engine under test.
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"""
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db_path.parent.mkdir(parents=True, exist_ok=True)
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# Easiest way to get the legacy shape exactly right: create_all then
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# ALTER away the new column.
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sync_url = f"sqlite:///{db_path.as_posix()}"
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sync_engine = sa.create_engine(sync_url)
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try:
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Base.metadata.create_all(sync_engine)
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with sync_engine.begin() as conn:
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conn.execute(sa.text("ALTER TABLE runs DROP COLUMN token_usage_by_model"))
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finally:
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sync_engine.dispose()
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async def test_legacy_database_recovers_token_usage_column(tmp_path: Path) -> None:
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db_path = tmp_path / "legacy.db"
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_seed_pre_3658_database(db_path)
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# Sanity: confirm we did indeed land in the buggy pre-fix shape before
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# init_engine touches the file.
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with sqlite3.connect(db_path) as raw:
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cols = {row[1] for row in raw.execute("PRAGMA table_info(runs)").fetchall()}
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assert "run_id" in cols
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assert "token_usage_by_model" not in cols
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version_table_count = raw.execute("SELECT count(*) FROM sqlite_master WHERE type='table' AND name='alembic_version'").fetchone()[0]
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assert version_table_count == 0
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# Run the same init_engine path FastAPI lifespan uses on startup.
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url = f"sqlite+aiosqlite:///{db_path.as_posix()}"
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await init_engine(backend="sqlite", url=url, sqlite_dir=str(tmp_path))
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try:
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# The column must now be present.
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with sqlite3.connect(db_path) as raw:
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cols = {row[1] for row in raw.execute("PRAGMA table_info(runs)").fetchall()}
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assert "token_usage_by_model" in cols
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version_row = raw.execute("SELECT version_num FROM alembic_version").fetchone()
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assert version_row[0] == "0002_runs_token_usage"
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# And the read path that originally 500'd must now succeed.
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sf = get_session_factory()
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assert sf is not None
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repo = RunRepository(sf)
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# No rows yet -- the point is just that the SELECT does not raise
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# ``no such column: runs.token_usage_by_model``.
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result = await repo.aggregate_tokens_by_thread(thread_id=str(uuid4()))
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assert result["total_tokens"] == 0
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assert result["by_model"] == {}
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finally:
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await close_engine()
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async def test_legacy_database_with_manual_alter_still_bootstraps(tmp_path: Path) -> None:
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"""User-side workaround scenario: someone already applied the manual
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``ALTER TABLE runs ADD COLUMN token_usage_by_model JSON`` from the issue
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write-up. The hybrid bootstrap must just stamp head, not double-add the
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column, and not error.
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"""
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db_path = tmp_path / "manual_altered.db"
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db_path.parent.mkdir(parents=True, exist_ok=True)
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sync_engine = sa.create_engine(f"sqlite:///{db_path.as_posix()}")
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try:
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Base.metadata.create_all(sync_engine)
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# Don't strip the column -- this is the "user already ran the
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# workaround" case where create_all already produced it.
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finally:
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sync_engine.dispose()
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url = f"sqlite+aiosqlite:///{db_path.as_posix()}"
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await init_engine(backend="sqlite", url=url, sqlite_dir=str(tmp_path))
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try:
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with sqlite3.connect(db_path) as raw:
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cols = [row[1] for row in raw.execute("PRAGMA table_info(runs)").fetchall()]
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# No duplicate column -- list, not set, to catch dupes.
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assert cols.count("token_usage_by_model") == 1
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version_row = raw.execute("SELECT version_num FROM alembic_version").fetchone()
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assert version_row[0] == "0002_runs_token_usage"
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finally:
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await close_engine()
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