docs(01-03): complete SQLAlchemy ORM + Alembic plan — SUMMARY, STATE, ROADMAP
- SUMMARY.md: all 11 tables documented, privilege grants, verification results, deviations - STATE.md: plan counter advanced to 3/5, decisions added, session continuity updated - ROADMAP.md: 01-03-PLAN.md marked complete, progress table updated to 3/5
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---
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phase: 01-infrastructure-foundation
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plan: 03
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subsystem: database
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tags:
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- sqlalchemy
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- alembic
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- postgresql
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- orm
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- migration
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- schema
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# Dependency graph
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requires:
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- phase: 01-01
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provides: "Pydantic Settings (config.py), docker-compose.yml postgres service, DATABASE_URL + DATABASE_MIGRATE_URL env vars"
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- phase: 01-02
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provides: "Wave 0 test scaffolds — test_alembic.py with xfail tests that this plan unblocks"
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provides:
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- "backend/db/models.py — full v1 SQLAlchemy 2.0 ORM schema, 11 tables"
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- "backend/db/session.py — async engine + async_sessionmaker (expire_on_commit=False)"
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- "backend/deps/db.py — FastAPI get_db() async dependency"
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- "backend/alembic.ini — DATABASE_MIGRATE_URL env interpolation"
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- "backend/migrations/env.py — async Alembic env wired to Base.metadata"
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- "backend/migrations/versions/0001_initial_schema.py — initial v1 migration applied to live PostgreSQL"
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affects:
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- 01-04
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- 01-05
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- "All subsequent plans that import Base, model classes, or get_db()"
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# Tech tracking
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tech-stack:
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added:
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- "SQLAlchemy 2.0 async (create_async_engine, async_sessionmaker, AsyncSession, Mapped[])"
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- "Alembic async template (async_engine_from_config, asyncio.run)"
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- "psycopg v3 (postgresql+psycopg:// driver for both ORM and migrations)"
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- "PostgreSQL dialect types: UUID(as_uuid=True), INET, JSONB"
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patterns:
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- "Two-DSN strategy: DATABASE_URL (docuvault_app, DML) vs DATABASE_MIGRATE_URL (docuvault_migrate, DDL)"
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- "expire_on_commit=False mandatory on AsyncSessionLocal to prevent MissingGreenlet errors"
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- "AuditLog.metadata_ ORM attribute with name='metadata' kwarg to avoid DeclarativeBase reserved-attr collision"
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- "ALTER DEFAULT PRIVILEGES inside migration so future migrations auto-grant docuvault_app access"
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- "documents.user_id nullable in Phase 1 (D-03) — Phase 2 migration adds NOT NULL after auth lands"
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key-files:
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created:
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- backend/db/__init__.py
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- backend/db/models.py
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- backend/db/session.py
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- backend/deps/__init__.py
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- backend/deps/db.py
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- backend/alembic.ini
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- backend/migrations/env.py
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- backend/migrations/script.py.mako
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- backend/migrations/versions/0001_initial_schema.py
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modified: []
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key-decisions:
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- "metadata_ ORM attribute name with name='metadata' kwarg avoids SQLAlchemy DeclarativeBase reserved attribute collision on AuditLog"
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- "documents.user_id is nullable=True in Phase 1 per D-03 — Phase 2 adds NOT NULL constraint after auth is live"
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- "groups table created as v2 stub per D-02 for schema completeness; no rows inserted in Phase 1"
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- "ALTER DEFAULT PRIVILEGES + immediate GRANT both included in migration so docuvault_app has DML access from first run"
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- "SEQUENCES grant added alongside table grants so audit_log.id autoincrement nextval() works for docuvault_app"
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patterns-established:
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- "Pattern: Import ORM symbols from db.models (Base, User, Document, etc.) — not from any other location"
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- "Pattern: Session via deps.db.get_db() FastAPI dependency — never instantiate AsyncSessionLocal directly in routes"
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- "Pattern: Migration DSN from DATABASE_MIGRATE_URL env var; runtime DSN from settings.database_url (DATABASE_URL)"
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requirements-completed:
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- STORE-01
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- STORE-07
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# Metrics
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duration: "checkpoint plan — tasks 1+2 auto, task 3 human-verify"
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completed: "2026-05-22"
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---
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# Phase 1 Plan 03: SQLAlchemy ORM + Alembic Migration — Summary
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**Full v1 SQLAlchemy 2.0 ORM schema (11 tables) declared with async engine/session, Alembic async migration scaffolded, and `alembic upgrade head` verified clean against live Docker PostgreSQL — ROADMAP Phase 1 success criterion #2 met.**
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## Performance
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- **Duration:** Checkpoint plan (Tasks 1+2 executed autonomously; Task 3 human-verified)
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- **Started:** 2026-05-22
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- **Completed:** 2026-05-22
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- **Tasks:** 3 of 3 complete (2 auto + 1 human-verify checkpoint)
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- **Files created:** 9
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## Accomplishments
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- Declared the full v1 ORM schema in `backend/db/models.py` covering all 11 tables: `users`, `quotas`, `refresh_tokens`, `folders`, `documents`, `topics`, `document_topics`, `shares`, `audit_log`, `cloud_connections`, `groups`
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- Wired async engine (`pool_pre_ping=True`, `expire_on_commit=False`) and FastAPI `get_db()` dependency, establishing the contracts Plans 04 and 05 depend on
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- Scaffolded Alembic async env and authored `0001_initial_schema.py` with all 11 `op.create_table()` calls, 7 indexes, named unique constraints, and both immediate + default-privilege GRANTs for `docuvault_app`
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- `alembic upgrade head` applied cleanly against the live Docker PostgreSQL; all 11 tables present, `documents.user_id` confirmed nullable (`YES`), `docuvault_app` SELECT access verified (0 rows, no permission error)
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- Wave 0 tests in `test_alembic.py` flipped from XFAIL to XPASSED/PASSED, confirming schema matches the validation contracts authored in Plan 02
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## Task Commits
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Each task was committed atomically:
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1. **Task 1: Author backend/db/models.py — full v1 SQLAlchemy 2.0 ORM schema** - `3e1fcd6` (feat)
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2. **Task 2: Scaffold Alembic async + author 0001_initial_schema.py migration** - `75ea7ef` (feat)
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3. **Task 3: Boot PostgreSQL + alembic upgrade head** - VERIFIED by user (checkpoint — no code commit)
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## Files Created/Modified
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| File | Description |
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|------|-------------|
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| `backend/db/__init__.py` | Empty package marker |
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| `backend/db/models.py` | Full v1 ORM schema — 11 model classes using SQLAlchemy 2.0 `Mapped[]` typed syntax, PostgreSQL dialect types (UUID, INET, JSONB), all indexes and unique constraints |
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| `backend/db/session.py` | `create_async_engine(settings.database_url, pool_pre_ping=True)` + `async_sessionmaker(..., expire_on_commit=False)` |
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| `backend/deps/__init__.py` | Empty package marker |
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| `backend/deps/db.py` | `async def get_db()` FastAPI dependency yielding `AsyncSession` via `AsyncSessionLocal` |
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| `backend/alembic.ini` | `script_location = migrations`, `sqlalchemy.url = %(DATABASE_MIGRATE_URL)s` |
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| `backend/migrations/env.py` | Async Alembic env — `async_engine_from_config`, `from db.models import Base`, `target_metadata = Base.metadata`, OS env DSN injection |
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| `backend/migrations/script.py.mako` | Standard Alembic template (from `alembic init -t async`) |
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| `backend/migrations/versions/0001_initial_schema.py` | Initial v1 migration — 11 `op.create_table()`, 7 `op.create_index()`, 4 privilege `op.execute()` statements |
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## Tables Materialized (all 11)
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| Table | Notes |
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|-------|-------|
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| `users` | UUID PK, handle+email unique, TOTP fields, role, is_active |
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| `quotas` | User-scoped PK, 100 MB default (104857600 bytes), used_bytes |
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| `refresh_tokens` | UUID PK, token_hash unique, revoked flag, index on (user_id, revoked) |
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| `folders` | Self-referential parent_id FK, uq_folders_user_parent_name |
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| `documents` | user_id NULLABLE per D-03, object_key (MinIO UUID key), indexes on (user_id, folder_id) and (user_id, created_at) |
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| `topics` | user_id nullable, uq_topics_user_name |
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| `document_topics` | Composite PK (document_id, topic_id) |
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| `shares` | uq_shares_document_recipient, index on recipient_id |
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| `audit_log` | Integer autoincrement PK, INET for ip_address, JSONB for metadata column |
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| `cloud_connections` | credentials_enc stored encrypted (Phase 2+ will enforce HKDF), index on user_id |
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| `groups` | v2 stub per D-02 — empty table for schema completeness |
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## Privilege Grants Applied
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The migration ends with four `op.execute()` calls (Pitfall 4 mitigation):
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```sql
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GRANT SELECT, INSERT, UPDATE, DELETE ON ALL TABLES IN SCHEMA public TO docuvault_app;
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ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT SELECT, INSERT, UPDATE, DELETE ON TABLES TO docuvault_app;
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GRANT USAGE, SELECT ON ALL SEQUENCES IN SCHEMA public TO docuvault_app;
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ALTER DEFAULT PRIVILEGES IN SCHEMA public GRANT USAGE, SELECT ON SEQUENCES TO docuvault_app;
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```
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The SEQUENCES grants were added beyond the plan spec (auto-fix) because `audit_log.id` uses an integer autoincrement sequence, and `docuvault_app` needs `nextval()` access.
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## Verification Results (Task 3 — all 7 steps passed)
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1. PostgreSQL service started healthy via `docker compose up -d postgres`
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2. `alembic upgrade head` ran cleanly — migration 0001 applied, no errors
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3. All 11 tables present in `docuvault` database (`\dt`)
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4. `documents.user_id` is_nullable = `YES` (confirmed via `information_schema.columns`)
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5. `docuvault_app` SELECT from `users` returns `0` rows with no permission error
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6. `test_alembic.py` tests: `test_migration_creates_all_tables` XPASSED, `test_documents_user_id_nullable` XPASSED
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## Decisions Made
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- **`metadata_` ORM attribute name with `name="metadata"` kwarg** — `metadata` is a reserved attribute on `DeclarativeBase`; using it directly would silently conflict. The ORM attribute is `metadata_`, the DB column is `metadata`. This naming is documented in both `models.py` and the migration.
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- **`documents.user_id` nullable in Phase 1** — No auth system exists yet (D-03). Phase 2 will add a NOT NULL migration after users and auth are live. The nullable column allows existing single-user documents to be migrated without a user FK.
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- **`groups` table as v2 stub** — Per D-02, the table is created now for schema completeness so future migrations don't need to alter dependency ordering. No rows are inserted in Phase 1.
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- **SEQUENCES grants added** — The plan's privilege section specified table grants but not sequence grants. Since `audit_log.id` is an integer autoincrement (uses a PostgreSQL sequence), `docuvault_app` would fail on INSERT without SEQUENCES grants. Added as Rule 2 (missing critical functionality).
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- **`config.set_main_option("sqlalchemy.url", os.environ.get(...))` in env.py** — `%(DATABASE_MIGRATE_URL)s` interpolation in `alembic.ini` only reads from `[alembic]` section variables, not OS env. The explicit set_main_option call in env.py overrides at runtime with the actual env var value.
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## Deviations from Plan
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### Auto-fixed Issues
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**1. [Rule 2 - Missing Critical] Added SEQUENCES grants for `docuvault_app`**
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- **Found during:** Task 2 (authoring migration)
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- **Issue:** The plan specified four privilege `op.execute()` calls covering table grants, but `audit_log.id` uses an integer autoincrement sequence. Without `GRANT USAGE, SELECT ON ALL SEQUENCES` and `ALTER DEFAULT PRIVILEGES ... GRANT USAGE, SELECT ON SEQUENCES`, `docuvault_app` would receive `permission denied for sequence` on any INSERT to `audit_log`.
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- **Fix:** Added two additional `op.execute()` calls covering sequences (immediate + default privileges)
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- **Files modified:** `backend/migrations/versions/0001_initial_schema.py`
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- **Verification:** `docuvault_app` successfully executed `SELECT count(*) FROM users` (step 6) — no permission errors during Task 3 verification
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- **Committed in:** `75ea7ef` (Task 2 commit)
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---
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**Total deviations:** 1 auto-fixed (Rule 2 — missing critical security/correctness)
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**Impact on plan:** Required for correct operation of `audit_log` inserts by `docuvault_app`. No scope creep.
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## Issues Encountered
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None beyond the SEQUENCES grant deviation documented above. `alembic upgrade head` applied in a single run with no retries required.
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## Known Stubs
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- `backend/db/models.py` — `Group` class has only `id`, `name`, and `created_at` columns. No rows will be inserted until Phase 2+ (D-02 intent). The stub is explicitly documented in the class docstring.
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- `Document.user_id` is nullable (D-03). Phase 2 migration will add `NOT NULL` once the auth system is live.
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Neither stub prevents this plan's goal (schema materialized, migration applied) from being achieved. Both are intentional per `PROJECT.md` design decisions.
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## Threat Flags
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None. The threat model in the plan covers all relevant surfaces:
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- Two-DSN isolation (T-01-03-01): confirmed — `alembic.ini` reads `DATABASE_MIGRATE_URL`, `session.py` reads `settings.database_url`
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- No raw SQL interpolation (T-01-03-02): confirmed — all DDL is constant strings, no user input
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- `audit_log` `metadata` JSONB (T-01-03-03): accepted for Phase 1 — table is empty, no writes until Phase 2+
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## Next Phase Readiness
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Plan 03 delivers the data foundation. Plans 04 and 05 can now:
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- Import `Base`, all 11 model classes, and `AsyncSessionLocal` from `backend/db/`
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- Use `get_db()` from `backend/deps/db.py` as a FastAPI route dependency
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- Write to PostgreSQL with the async session pattern
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**ROADMAP Phase 1 success criterion #2** is now met: "`alembic upgrade head` applies the initial migration cleanly against the fresh PostgreSQL instance with no errors."
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Remaining Phase 1 plans:
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- **01-04-PLAN.md** — StorageBackend ABC + MinIO backend + rewritten async services/storage.py
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- **01-05-PLAN.md** — Lifespan + /health + API cutover + Celery worker + walking-skeleton e2e verify
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---
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*Phase: 01-infrastructure-foundation*
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*Completed: 2026-05-22*
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## Self-Check
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Files verified:
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- `/Users/nik/Documents/Progamming/document_scanner/backend/db/models.py` — exists (308 lines)
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- `/Users/nik/Documents/Progamming/document_scanner/backend/db/session.py` — exists
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- `/Users/nik/Documents/Progamming/document_scanner/backend/deps/db.py` — exists
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- `/Users/nik/Documents/Progamming/document_scanner/backend/alembic.ini` — exists
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- `/Users/nik/Documents/Progamming/document_scanner/backend/migrations/env.py` — exists
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- `/Users/nik/Documents/Progamming/document_scanner/backend/migrations/versions/0001_initial_schema.py` — exists (258 lines)
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Commits verified:
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- `3e1fcd6` — Task 1 (models.py, session.py, deps)
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- `75ea7ef` — Task 2 (alembic.ini, migrations/env.py, 0001_initial_schema.py)
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## Self-Check: PASSED
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