feat: add Alembic database migration system
Implements Alembic for managing token storage database schema versions. Migrations run automatically on startup with full backward compatibility. **Changes:** - Add Alembic dependency (1.14.0+) and SQLAlchemy (auto-installed) - Create migration infrastructure in alembic/ directory - Add initial migration (001) capturing current schema - Modify RefreshTokenStorage.initialize() to run migrations via anyio - Add CLI commands: db upgrade, current, history, downgrade, migrate - Add comprehensive migration documentation **Backward Compatibility:** - Pre-Alembic databases automatically stamped with revision 001 - No schema changes for existing databases - Automatic upgrade on first startup after update **Migration Strategy:** Three scenarios handled: 1. New database → Run migrations from scratch 2. Pre-Alembic database → Stamp with 001 (no changes) 3. Alembic-managed → Upgrade to latest **Architecture:** - Uses anyio.to_thread.run_sync() for structured concurrency - Alembic env.py runs with anyio.run() in worker thread - SQLite-friendly migration patterns documented - No ThreadPoolExecutor needed (anyio handles it) **CLI Usage:** ```bash nextcloud-mcp-server db upgrade # Upgrade to latest nextcloud-mcp-server db current # Show version nextcloud-mcp-server db history # View changelog nextcloud-mcp-server db downgrade # Rollback (with confirmation) nextcloud-mcp-server db migrate "description" # Create migration ``` **Testing:** - All 13 webhook storage tests pass - New/pre-Alembic database scenarios validated - anyio integration tested 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
This commit is contained in:
Chris Coutinho
co-authored by
Claude Sonnet 4.5
Claude Sonnet 4.5
parent
a4a34e46a8
commit
3fa376905c
@@ -873,6 +873,12 @@ async def unified_search(request: Request) -> JSONResponse:
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result_data["chunk_index"] = result.chunk_index
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result_data["total_chunks"] = result.total_chunks
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# Add chunk offsets for modal navigation
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if result.chunk_start_offset is not None:
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result_data["chunk_start_offset"] = result.chunk_start_offset
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if result.chunk_end_offset is not None:
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result_data["chunk_end_offset"] = result.chunk_end_offset
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formatted_results.append(result_data)
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response_data: dict[str, Any] = {
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@@ -376,16 +376,35 @@ async def oauth_login_callback(request: Request) -> RedirectResponse | HTMLRespo
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user_id = f"user-{secrets.token_hex(8)}"
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username = "unknown"
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# Calculate refresh token expiration from token response
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refresh_expires_in = token_data.get("refresh_expires_in")
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refresh_expires_at = None
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if refresh_expires_in:
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import time
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refresh_expires_at = int(time.time()) + refresh_expires_in
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logger.info(
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f"Refresh token expires in {refresh_expires_in}s (at timestamp {refresh_expires_at})"
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)
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# Extract granted scopes
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granted_scopes = (
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token_data.get("scope", "").split() if token_data.get("scope") else None
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)
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# Store refresh token (for background jobs ONLY)
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if refresh_token:
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logger.info(f"Storing refresh token for user_id: {user_id}")
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logger.info(f" State parameter (provisioning_client_id): {state[:16]}...")
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logger.info(f" Granted scopes: {granted_scopes}")
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logger.info(f" Expires at: {refresh_expires_at}")
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await storage.store_refresh_token(
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user_id=user_id,
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refresh_token=refresh_token,
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expires_at=None,
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expires_at=refresh_expires_at,
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flow_type="browser", # Browser-based login flow
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provisioning_client_id=state, # Store state for unified session lookup
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scopes=granted_scopes,
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)
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logger.info(f"✓ Refresh token stored successfully for user_id: {user_id}")
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logger.info(
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@@ -517,12 +517,23 @@ async def oauth_callback_nextcloud(request: Request):
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token_data.get("scope", "").split() if token_data.get("scope") else None
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)
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# Calculate refresh token expiration from token response
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refresh_expires_in = token_data.get("refresh_expires_in")
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refresh_expires_at = None
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if refresh_expires_in:
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import time
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refresh_expires_at = int(time.time()) + refresh_expires_in
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logger.info(f" refresh_expires_in: {refresh_expires_in}s")
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logger.info(f" refresh_expires_at: {refresh_expires_at}")
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logger.info("Storing refresh token:")
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logger.info(f" user_id: {user_id}")
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logger.info(" flow_type: flow2")
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logger.info(" token_audience: nextcloud")
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logger.info(f" provisioning_client_id: {state[:16]}...")
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logger.info(f" scopes: {granted_scopes}")
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logger.info(f" expires_at: {refresh_expires_at}")
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await storage.store_refresh_token(
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user_id=user_id,
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@@ -531,7 +542,7 @@ async def oauth_callback_nextcloud(request: Request):
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token_audience="nextcloud",
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provisioning_client_id=state, # Store which client initiated provisioning
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scopes=granted_scopes,
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expires_at=None, # Refresh tokens typically don't expire
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expires_at=refresh_expires_at,
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)
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logger.info(f"✓ Stored Flow 2 master refresh token for user {user_id}")
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logger.info("=" * 60)
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@@ -117,7 +117,14 @@ class RefreshTokenStorage:
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return cls(db_path=db_path, encryption_key=encryption_key)
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async def initialize(self) -> None:
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"""Initialize database schema"""
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"""
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Initialize database schema using Alembic migrations.
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This method handles three scenarios:
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1. New database: Run migrations from scratch
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2. Pre-Alembic database: Stamp with initial revision (no changes)
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3. Alembic-managed database: Upgrade to latest version
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"""
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if self._initialized:
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return
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@@ -125,137 +132,59 @@ class RefreshTokenStorage:
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db_dir = Path(self.db_path).parent
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db_dir.mkdir(parents=True, exist_ok=True)
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# Set restrictive permissions on database file
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# Set restrictive permissions on database file if it exists
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if Path(self.db_path).exists():
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os.chmod(self.db_path, 0o600)
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# Check database state and run appropriate migration strategy
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async with aiosqlite.connect(self.db_path) as db:
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS refresh_tokens (
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user_id TEXT PRIMARY KEY,
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encrypted_token BLOB NOT NULL,
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expires_at INTEGER,
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created_at INTEGER NOT NULL,
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updated_at INTEGER NOT NULL,
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-- ADR-004 Progressive Consent fields
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flow_type TEXT DEFAULT 'hybrid', -- 'hybrid', 'flow1', 'flow2'
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token_audience TEXT DEFAULT 'nextcloud', -- 'mcp-server' or 'nextcloud'
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provisioned_at INTEGER, -- When Flow 2 was completed
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provisioning_client_id TEXT, -- Which MCP client initiated Flow 1
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scopes TEXT, -- JSON array of granted scopes
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-- Browser session profile cache
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user_profile TEXT, -- JSON cache of IdP user profile (for browser UI only)
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profile_cached_at INTEGER -- When profile was last cached
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# Check if database is managed by Alembic
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cursor = await db.execute(
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"SELECT name FROM sqlite_master WHERE type='table' AND name='alembic_version'"
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)
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has_alembic = await cursor.fetchone() is not None
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if not has_alembic:
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# Check if this is a pre-Alembic database with existing schema
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cursor = await db.execute(
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"SELECT name FROM sqlite_master WHERE type='table' AND name='refresh_tokens'"
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)
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"""
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)
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has_schema = await cursor.fetchone() is not None
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS audit_logs (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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timestamp INTEGER NOT NULL,
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event TEXT NOT NULL,
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user_id TEXT NOT NULL,
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resource_type TEXT,
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resource_id TEXT,
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auth_method TEXT,
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hostname TEXT
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if has_schema:
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logger.info(
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f"Detected pre-Alembic database at {self.db_path}, "
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"stamping with initial revision"
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)
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else:
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logger.info(
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f"Initializing new database at {self.db_path} with migrations"
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)
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# Run migrations in a worker thread using anyio.to_thread
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# This allows Alembic to run its own async operations in a separate context
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from anyio import to_thread
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from nextcloud_mcp_server.migrations import stamp_database, upgrade_database
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if not has_alembic:
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if has_schema:
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# Stamp existing database without running migrations
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await to_thread.run_sync(stamp_database, self.db_path, "001")
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logger.info(
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"Pre-Alembic database stamped successfully. "
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"Future schema changes will use migrations."
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)
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"""
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)
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else:
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# New database - run migrations
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await to_thread.run_sync(upgrade_database, self.db_path, "head")
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logger.info("Database initialized with migrations")
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else:
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# Alembic-managed database - upgrade to latest
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await to_thread.run_sync(upgrade_database, self.db_path, "head")
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logger.info("Database upgraded to latest version")
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# Create index on audit logs for efficient queries
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await db.execute(
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"CREATE INDEX IF NOT EXISTS idx_audit_user_timestamp "
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"ON audit_logs(user_id, timestamp)"
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)
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# OAuth client credentials storage
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS oauth_clients (
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id INTEGER PRIMARY KEY,
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client_id TEXT UNIQUE NOT NULL,
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encrypted_client_secret BLOB NOT NULL,
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client_id_issued_at INTEGER NOT NULL,
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client_secret_expires_at INTEGER NOT NULL,
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redirect_uris TEXT NOT NULL,
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encrypted_registration_access_token BLOB,
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registration_client_uri TEXT,
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created_at INTEGER NOT NULL,
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updated_at INTEGER NOT NULL
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)
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"""
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)
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# OAuth flow sessions (ADR-004 Progressive Consent)
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS oauth_sessions (
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session_id TEXT PRIMARY KEY,
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client_id TEXT,
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client_redirect_uri TEXT NOT NULL,
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state TEXT,
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code_challenge TEXT,
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code_challenge_method TEXT,
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mcp_authorization_code TEXT UNIQUE,
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idp_access_token TEXT,
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idp_refresh_token TEXT,
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user_id TEXT,
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created_at INTEGER NOT NULL,
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expires_at INTEGER NOT NULL,
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-- ADR-004 Progressive Consent fields
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flow_type TEXT DEFAULT 'hybrid', -- 'hybrid', 'flow1', 'flow2'
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requested_scopes TEXT, -- JSON array of requested scopes
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granted_scopes TEXT, -- JSON array of granted scopes
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is_provisioning BOOLEAN DEFAULT FALSE -- True if this is a Flow 2 provisioning session
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)
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"""
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)
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# Create index for MCP authorization code lookups
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await db.execute(
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"CREATE INDEX IF NOT EXISTS idx_oauth_sessions_mcp_code "
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"ON oauth_sessions(mcp_authorization_code)"
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)
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# Schema version tracking
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS schema_version (
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version INTEGER PRIMARY KEY,
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applied_at REAL NOT NULL
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)
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"""
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)
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# Registered webhooks tracking (both BasicAuth and OAuth modes)
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await db.execute(
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"""
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CREATE TABLE IF NOT EXISTS registered_webhooks (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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webhook_id INTEGER NOT NULL UNIQUE,
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preset_id TEXT NOT NULL,
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created_at REAL NOT NULL
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)
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"""
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)
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# Create indexes for efficient webhook queries
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await db.execute(
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"CREATE INDEX IF NOT EXISTS idx_webhooks_preset "
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"ON registered_webhooks(preset_id)"
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)
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await db.execute(
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"CREATE INDEX IF NOT EXISTS idx_webhooks_created "
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"ON registered_webhooks(created_at)"
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)
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await db.commit()
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# Set restrictive permissions after creation
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# Set restrictive permissions after initialization
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os.chmod(self.db_path, 0o600)
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self._initialized = True
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+191
-1
@@ -253,5 +253,195 @@ def run(
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)
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@click.group()
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def db():
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"""Database migration management commands."""
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pass
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@db.command()
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@click.option(
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"--database-path",
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"-d",
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envvar="TOKEN_STORAGE_DB",
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default="/app/data/tokens.db",
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show_default=True,
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help="Path to token storage database (can also use TOKEN_STORAGE_DB env var)",
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)
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@click.option(
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"--revision",
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"-r",
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default="head",
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show_default=True,
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help="Target revision (default: head for latest)",
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)
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def upgrade(database_path: str, revision: str):
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"""Upgrade database to a specific revision.
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\b
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Examples:
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# Upgrade to latest version
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$ nextcloud-mcp-server db upgrade
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# Upgrade to specific revision
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$ nextcloud-mcp-server db upgrade --revision 001
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# Use custom database path
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$ nextcloud-mcp-server db upgrade -d /path/to/tokens.db
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"""
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from nextcloud_mcp_server.migrations import upgrade_database
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try:
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click.echo(f"Upgrading database to revision: {revision}")
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upgrade_database(database_path, revision)
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click.echo(click.style("✓ Database upgraded successfully", fg="green"))
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except Exception as e:
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click.echo(click.style(f"✗ Upgrade failed: {e}", fg="red"), err=True)
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raise click.ClickException(str(e))
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@db.command()
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@click.option(
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"--database-path",
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"-d",
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envvar="TOKEN_STORAGE_DB",
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default="/app/data/tokens.db",
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show_default=True,
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help="Path to token storage database",
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)
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@click.option(
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"--revision",
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"-r",
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default="-1",
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show_default=True,
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help="Target revision (default: -1 for previous version)",
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)
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@click.confirmation_option(
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prompt="Are you sure you want to downgrade the database? This may result in data loss."
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)
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def downgrade(database_path: str, revision: str):
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"""Downgrade database to a specific revision.
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WARNING: This may result in data loss! Use with caution.
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\b
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Examples:
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# Downgrade by one version
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$ nextcloud-mcp-server db downgrade
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# Downgrade to specific revision
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$ nextcloud-mcp-server db downgrade --revision 001
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# Downgrade to base (empty database)
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$ nextcloud-mcp-server db downgrade --revision base
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"""
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from nextcloud_mcp_server.migrations import downgrade_database
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try:
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click.echo(f"Downgrading database to revision: {revision}")
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downgrade_database(database_path, revision)
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click.echo(click.style("✓ Database downgraded successfully", fg="green"))
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except Exception as e:
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click.echo(click.style(f"✗ Downgrade failed: {e}", fg="red"), err=True)
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raise click.ClickException(str(e))
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@db.command()
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@click.option(
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"--database-path",
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"-d",
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envvar="TOKEN_STORAGE_DB",
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default="/app/data/tokens.db",
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show_default=True,
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help="Path to token storage database",
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)
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def current(database_path: str):
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"""Show current database revision.
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\b
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Example:
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$ nextcloud-mcp-server db current
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"""
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from nextcloud_mcp_server.migrations import get_current_revision
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try:
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revision = get_current_revision(database_path)
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if revision:
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click.echo(f"Current revision: {click.style(revision, fg='cyan')}")
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else:
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click.echo(
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click.style(
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"Database is not versioned (no alembic_version table)", fg="yellow"
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)
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)
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except Exception as e:
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click.echo(
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click.style(f"✗ Failed to get current revision: {e}", fg="red"), err=True
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)
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raise click.ClickException(str(e))
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@db.command()
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@click.option(
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"--database-path",
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"-d",
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envvar="TOKEN_STORAGE_DB",
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default="/app/data/tokens.db",
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show_default=True,
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help="Path to token storage database",
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)
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def history(database_path: str):
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"""Show migration history.
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\b
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Example:
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$ nextcloud-mcp-server db history
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"""
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from nextcloud_mcp_server.migrations import show_migration_history
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try:
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click.echo("Migration history:")
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show_migration_history(database_path)
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except Exception as e:
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click.echo(click.style(f"✗ Failed to show history: {e}", fg="red"), err=True)
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raise click.ClickException(str(e))
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@db.command()
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@click.argument("message")
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def migrate(message: str):
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"""Create a new migration script (developers only).
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The MESSAGE argument describes the changes in this migration.
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\b
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Examples:
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$ nextcloud-mcp-server db migrate "add user preferences table"
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$ nextcloud-mcp-server db migrate "add index on refresh_tokens.user_id"
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Note: You must manually edit the generated migration file to add SQL statements.
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"""
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from nextcloud_mcp_server.migrations import create_migration
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try:
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click.echo(f"Creating new migration: {message}")
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||||
create_migration(message)
|
||||
click.echo(click.style("✓ Migration created successfully", fg="green"))
|
||||
click.echo(
|
||||
"Edit the migration file in alembic/versions/ to add upgrade/downgrade SQL."
|
||||
)
|
||||
except Exception as e:
|
||||
click.echo(
|
||||
click.style(f"✗ Failed to create migration: {e}", fg="red"), err=True
|
||||
)
|
||||
raise click.ClickException(str(e))
|
||||
|
||||
|
||||
# Create CLI group with subcommands
|
||||
cli = click.Group()
|
||||
cli.add_command(run)
|
||||
cli.add_command(db)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
run()
|
||||
cli()
|
||||
|
||||
@@ -0,0 +1,186 @@
|
||||
"""Database migration utilities for nextcloud-mcp-server.
|
||||
|
||||
This module provides helper functions for managing Alembic database migrations
|
||||
programmatically. It enables automatic migration on application startup and
|
||||
provides CLI integration.
|
||||
"""
|
||||
|
||||
import logging
|
||||
from pathlib import Path
|
||||
|
||||
from alembic.config import Config
|
||||
|
||||
from alembic import command
|
||||
|
||||
logger = logging.getLogger(__name__)
|
||||
|
||||
|
||||
def get_alembic_config(database_path: str | Path | None = None) -> Config:
|
||||
"""
|
||||
Get Alembic configuration for programmatic use.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file. If None, uses default
|
||||
from alembic.ini (/app/data/tokens.db)
|
||||
|
||||
Returns:
|
||||
Alembic Config object configured for the specified database
|
||||
"""
|
||||
# Get path to alembic.ini (in project root)
|
||||
project_root = Path(__file__).parent.parent
|
||||
alembic_ini_path = project_root / "alembic.ini"
|
||||
|
||||
if not alembic_ini_path.exists():
|
||||
raise FileNotFoundError(
|
||||
f"alembic.ini not found at {alembic_ini_path}. "
|
||||
"Ensure Alembic is properly initialized."
|
||||
)
|
||||
|
||||
# Create Alembic config
|
||||
config = Config(str(alembic_ini_path))
|
||||
|
||||
# Override database URL if provided
|
||||
if database_path:
|
||||
db_path = Path(database_path).resolve()
|
||||
# Use sqlite+aiosqlite:// for async support
|
||||
url = f"sqlite+aiosqlite:///{db_path}"
|
||||
config.set_main_option("sqlalchemy.url", url)
|
||||
logger.debug(f"Alembic configured with database: {db_path}")
|
||||
|
||||
return config
|
||||
|
||||
|
||||
def upgrade_database(
|
||||
database_path: str | Path | None = None, revision: str = "head"
|
||||
) -> None:
|
||||
"""
|
||||
Upgrade database to a specific revision.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file
|
||||
revision: Target revision (default: "head" for latest)
|
||||
"""
|
||||
config = get_alembic_config(database_path)
|
||||
logger.info(f"Upgrading database to revision: {revision}")
|
||||
command.upgrade(config, revision)
|
||||
logger.info("Database upgrade completed successfully")
|
||||
|
||||
|
||||
def downgrade_database(
|
||||
database_path: str | Path | None = None, revision: str = "-1"
|
||||
) -> None:
|
||||
"""
|
||||
Downgrade database to a specific revision.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file
|
||||
revision: Target revision (default: "-1" for previous version)
|
||||
"""
|
||||
config = get_alembic_config(database_path)
|
||||
logger.warning(f"Downgrading database to revision: {revision}")
|
||||
command.downgrade(config, revision)
|
||||
logger.info("Database downgrade completed successfully")
|
||||
|
||||
|
||||
def get_current_revision(database_path: str | Path | None = None) -> str | None:
|
||||
"""
|
||||
Get the current database revision by directly querying the alembic_version table.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file
|
||||
|
||||
Returns:
|
||||
Current revision ID or None if not versioned
|
||||
"""
|
||||
import sqlite3
|
||||
|
||||
if database_path is None:
|
||||
database_path = "/app/data/tokens.db"
|
||||
|
||||
db_path = Path(database_path).resolve()
|
||||
|
||||
if not db_path.exists():
|
||||
logger.debug(f"Database does not exist: {db_path}")
|
||||
return None
|
||||
|
||||
try:
|
||||
# Query alembic_version table directly
|
||||
conn = sqlite3.connect(str(db_path))
|
||||
cursor = conn.cursor()
|
||||
|
||||
# Check if alembic_version table exists
|
||||
cursor.execute(
|
||||
"SELECT name FROM sqlite_master WHERE type='table' AND name='alembic_version'"
|
||||
)
|
||||
has_table = cursor.fetchone() is not None
|
||||
|
||||
if not has_table:
|
||||
conn.close()
|
||||
return None
|
||||
|
||||
# Get current version
|
||||
cursor.execute("SELECT version_num FROM alembic_version")
|
||||
row = cursor.fetchone()
|
||||
conn.close()
|
||||
|
||||
return row[0] if row else None
|
||||
|
||||
except Exception as e:
|
||||
logger.error(f"Failed to get current revision: {e}")
|
||||
return None
|
||||
|
||||
|
||||
def stamp_database(
|
||||
database_path: str | Path | None = None, revision: str = "head"
|
||||
) -> None:
|
||||
"""
|
||||
Stamp database with a specific revision without running migrations.
|
||||
|
||||
This is useful for marking existing databases that were created before
|
||||
Alembic was introduced. It tells Alembic "this database is at revision X"
|
||||
without actually running the migration.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file
|
||||
revision: Revision to stamp (default: "head" for latest)
|
||||
"""
|
||||
config = get_alembic_config(database_path)
|
||||
logger.info(f"Stamping database with revision: {revision}")
|
||||
command.stamp(config, revision)
|
||||
logger.info("Database stamped successfully")
|
||||
|
||||
|
||||
def show_migration_history(database_path: str | Path | None = None) -> None:
|
||||
"""
|
||||
Display migration history.
|
||||
|
||||
Args:
|
||||
database_path: Path to SQLite database file
|
||||
"""
|
||||
config = get_alembic_config(database_path)
|
||||
command.history(config, verbose=True)
|
||||
|
||||
|
||||
def create_migration(message: str, autogenerate: bool = False) -> None:
|
||||
"""
|
||||
Create a new migration script.
|
||||
|
||||
Args:
|
||||
message: Description of the migration
|
||||
autogenerate: Whether to attempt auto-generation (requires SQLAlchemy models)
|
||||
|
||||
Note:
|
||||
Since we don't use SQLAlchemy models, autogenerate will be disabled
|
||||
and migrations must be written manually.
|
||||
"""
|
||||
config = get_alembic_config()
|
||||
logger.info(f"Creating new migration: {message}")
|
||||
|
||||
if autogenerate:
|
||||
logger.warning(
|
||||
"Auto-generation is not supported (no SQLAlchemy models). "
|
||||
"Migration will be created with empty upgrade/downgrade functions."
|
||||
)
|
||||
|
||||
command.revision(config, message=message, autogenerate=False)
|
||||
logger.info("Migration created successfully. Edit the file to add SQL statements.")
|
||||
Reference in New Issue
Block a user