fix: move Alembic to package submodule for Docker compatibility
- Move alembic/ directory to nextcloud_mcp_server/alembic/ subpackage - Update migrations.py to use package location instead of alembic.ini - Update env.py to set script_location dynamically - Update alembic.ini for development CLI usage - Fix Dockerfile typo: .vnev -> .venv This fixes FileNotFoundError when running in Docker with non-editable install. The alembic package is now installed with the main package, making it work in both development and production environments. Resolves: Docker startup error 'alembic.ini not found at /app/.venv/lib/python3.12/site-packages/alembic.ini' 🤖 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
c4b3df04a0
commit
54b69f0d68
@@ -0,0 +1,133 @@
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"""Alembic environment configuration for nextcloud-mcp-server.
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This module configures how Alembic runs database migrations for the
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token storage database. It supports both online and offline migration modes.
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Uses anyio for async operations, consistent with the project's async patterns.
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"""
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import logging
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from pathlib import Path
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import anyio
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from sqlalchemy import pool
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from sqlalchemy.engine import Connection
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from sqlalchemy.ext.asyncio import async_engine_from_config
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from alembic import context
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# Configure logging
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logger = logging.getLogger("alembic.env")
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# This is the Alembic Config object, which provides
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# access to the values within the .ini file in use.
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config = context.config
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# Update script location to point to package location
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# This allows alembic to find migrations when installed in site-packages
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script_location = Path(__file__).parent
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config.set_main_option("script_location", str(script_location))
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# We don't use SQLAlchemy models, so target_metadata is None
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# Migrations will be written manually using op.execute() for raw SQL
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target_metadata = None
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def get_database_url() -> str:
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"""
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Get the database URL from Alembic config or environment.
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The URL can be set in alembic.ini or passed via -x database_url=...
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when running Alembic commands.
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Returns:
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Database URL (SQLite URL format)
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"""
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# Check if URL is passed via -x database_url=...
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url = context.get_x_argument(as_dictionary=True).get("database_url")
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if not url:
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# Fall back to alembic.ini configuration
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url = config.get_main_option("sqlalchemy.url")
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if not url:
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# Default to /app/data/tokens.db for Docker deployments
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db_path = Path("/app/data/tokens.db")
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url = f"sqlite+aiosqlite:///{db_path}"
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logger.warning(
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f"No database URL configured, using default: {url}. "
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"Set sqlalchemy.url in alembic.ini or pass -x database_url=..."
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)
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return url
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def run_migrations_offline() -> None:
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"""Run migrations in 'offline' mode.
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This configures the context with just a URL and not an Engine,
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though an Engine is acceptable here as well. By skipping the
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Engine creation we don't even need a DBAPI to be available.
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Calls to context.execute() here emit the given string to the
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script output.
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This mode is useful for generating SQL scripts without database access.
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"""
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url = get_database_url()
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context.configure(
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url=url,
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target_metadata=target_metadata,
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literal_binds=True,
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dialect_opts={"paramstyle": "named"},
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)
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with context.begin_transaction():
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context.run_migrations()
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def do_run_migrations(connection: Connection) -> None:
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"""Execute migrations within a database connection."""
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context.configure(connection=connection, target_metadata=target_metadata)
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with context.begin_transaction():
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context.run_migrations()
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async def run_async_migrations() -> None:
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"""Run migrations in 'online' mode with async support.
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In this scenario we create an async Engine and associate
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a connection with the context.
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"""
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# Get database URL and update config
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url = get_database_url()
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config.set_main_option("sqlalchemy.url", url)
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# Create async engine
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connectable = async_engine_from_config(
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config.get_section(config.config_ini_section, {}),
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prefix="sqlalchemy.",
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poolclass=pool.NullPool, # Don't pool connections for migrations
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)
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async with connectable.connect() as connection:
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await connection.run_sync(do_run_migrations)
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await connectable.dispose()
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def run_migrations_online() -> None:
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"""Run migrations in 'online' mode.
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This function is called from storage.py's initialize() method via
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anyio.to_thread.run_sync(), so it always runs in a worker thread
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with its own event loop. We can safely use anyio.run() here.
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"""
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anyio.run(run_async_migrations)
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if context.is_offline_mode():
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run_migrations_offline()
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else:
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run_migrations_online()
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@@ -0,0 +1,185 @@
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"""Initial schema for token storage database
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This migration creates the initial database schema including:
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- refresh_tokens: OAuth refresh tokens and user profiles
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- audit_logs: Audit trail for security events
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- oauth_clients: OAuth client credentials (DCR)
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- oauth_sessions: OAuth flow session state (ADR-004 Progressive Consent)
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- registered_webhooks: Webhook registration tracking (both OAuth and BasicAuth)
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- schema_version: Legacy schema version tracking (deprecated, use alembic_version)
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Revision ID: 001
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Revises:
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Create Date: 2025-12-17 22:00:00.000000
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"""
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from alembic import op
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# revision identifiers, used by Alembic.
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revision = "001"
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down_revision = None
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branch_labels = None
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depends_on = None
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def upgrade() -> None:
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"""Create initial database schema."""
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# Refresh tokens table (OAuth mode only, for background jobs)
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op.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',
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token_audience TEXT DEFAULT 'nextcloud',
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provisioned_at INTEGER,
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provisioning_client_id TEXT,
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scopes TEXT,
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-- Browser session profile cache
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user_profile TEXT,
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profile_cached_at INTEGER
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)
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"""
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)
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# Audit logs table (both OAuth and BasicAuth modes)
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op.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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)
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"""
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)
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# Index on audit logs for efficient queries
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op.execute(
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"""
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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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)
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# OAuth client credentials storage (OAuth mode only)
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op.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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op.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',
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requested_scopes TEXT,
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granted_scopes TEXT,
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is_provisioning BOOLEAN DEFAULT FALSE
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)
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"""
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)
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# Index for MCP authorization code lookups
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op.execute(
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"""
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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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)
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# Legacy schema version tracking table
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# NOTE: This is deprecated in favor of Alembic's alembic_version table
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# Kept for backward compatibility with pre-Alembic databases
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op.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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op.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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# Indexes for efficient webhook queries
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op.execute(
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"""
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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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)
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op.execute(
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"""
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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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)
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def downgrade() -> None:
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"""Drop all tables and indexes.
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WARNING: This will destroy all data in the database!
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Use with extreme caution.
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"""
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# Drop indexes first
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op.execute("DROP INDEX IF EXISTS idx_webhooks_created")
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op.execute("DROP INDEX IF EXISTS idx_webhooks_preset")
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op.execute("DROP INDEX IF EXISTS idx_oauth_sessions_mcp_code")
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op.execute("DROP INDEX IF EXISTS idx_audit_user_timestamp")
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# Drop tables
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op.execute("DROP TABLE IF EXISTS registered_webhooks")
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op.execute("DROP TABLE IF EXISTS schema_version")
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op.execute("DROP TABLE IF EXISTS oauth_sessions")
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op.execute("DROP TABLE IF EXISTS oauth_clients")
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op.execute("DROP TABLE IF EXISTS audit_logs")
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op.execute("DROP TABLE IF EXISTS refresh_tokens")
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@@ -19,33 +19,39 @@ def get_alembic_config(database_path: str | Path | None = None) -> Config:
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"""
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Get Alembic configuration for programmatic use.
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Works in both development and installed (Docker) modes by using
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package location instead of alembic.ini file.
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Args:
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database_path: Path to SQLite database file. If None, uses default
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from alembic.ini (/app/data/tokens.db)
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(/app/data/tokens.db for Docker)
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Returns:
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Alembic Config object configured for the specified database
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"""
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# Get path to alembic.ini (in project root)
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project_root = Path(__file__).parent.parent
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alembic_ini_path = project_root / "alembic.ini"
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from nextcloud_mcp_server import alembic as alembic_package
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if not alembic_ini_path.exists():
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raise FileNotFoundError(
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f"alembic.ini not found at {alembic_ini_path}. "
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"Ensure Alembic is properly initialized."
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)
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# Use package location (works in both editable and installed modes)
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if alembic_package.__file__ is None:
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raise RuntimeError("alembic package __file__ is None")
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script_location = Path(alembic_package.__file__).parent
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# Create Alembic config
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config = Config(str(alembic_ini_path))
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# Create config programmatically (no alembic.ini needed at runtime)
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config = Config()
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config.set_main_option("script_location", str(script_location))
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config.set_main_option("path_separator", "os") # Suppress deprecation warning
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# Override database URL if provided
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# Set database URL
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if database_path:
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db_path = Path(database_path).resolve()
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# Use sqlite+aiosqlite:// for async support
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url = f"sqlite+aiosqlite:///{db_path}"
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config.set_main_option("sqlalchemy.url", url)
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logger.debug(f"Alembic configured with database: {db_path}")
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else:
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db_path = Path("/app/data/tokens.db") # Default for Docker
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url = f"sqlite+aiosqlite:///{db_path}"
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config.set_main_option("sqlalchemy.url", url)
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logger.debug(f"Alembic script location: {script_location}")
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logger.debug(f"Database: {db_path}")
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return config
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