diff options
| -rw-r--r-- | README.md | 30 | ||||
| -rw-r--r-- | gn3/auth/__init__.py | 3 | ||||
| -rw-r--r-- | gn3/auth/authentication/__init__.py | 1 | ||||
| -rw-r--r-- | gn3/auth/authorisation/__init__.py | 1 | ||||
| -rw-r--r-- | gn3/migrations.py | 33 | ||||
| -rw-r--r-- | migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py | 19 | ||||
| -rw-r--r-- | mypy.ini | 3 | ||||
| -rw-r--r-- | tests/unit/auth/test_init_database.py | 29 | ||||
| -rw-r--r-- | tests/unit/conftest.py | 44 | ||||
| -rw-r--r-- | yoyo.auth.ini | 6 |
10 files changed, 169 insertions, 0 deletions
@@ -95,6 +95,36 @@ and try again. Also make sure your ~/guix-bioinformatics is up to date. See also instructions in [.guix.scm](.guix.scm). +## Migrations + +**NOTE**: Do not create migration scripts manually. Use the processes indicated below. + +### Authentication/Authorisation Migrations + +The migration scripts for the authentication and authorisation system are in the *migrations/auth* folder in the root of the repository. + +To create an new migration, do: + +```bash +$ yoyo new --config=yoyo.auth.ini -m "<description of the migration>" +``` + +That initialises an new migration script under the *migrations/auth* folder and gives it a name derived from the date, the sequence for that day, and the provided description. + +e.g. + +```bash +$ yoyo new --config=yoyo.auth.ini -m "testing a new migration" +Error: could not open editor! +Created file ./migrations/auth/20221103_02_HBzwk-testing-a-new-migration.py +``` + +Now you can open and edit the scripts to provide the appropriate SQL statements to update or rollback your schema. + +### Running the Migrations + +**TODO**: Document how to run the migrations + ## Running Tests (assuming you are in a guix container; otherwise use venv!) diff --git a/gn3/auth/__init__.py b/gn3/auth/__init__.py new file mode 100644 index 0000000..699d9e2 --- /dev/null +++ b/gn3/auth/__init__.py @@ -0,0 +1,3 @@ +"""Top-Level `Auth` module""" +from . import authorisation +from . import authentication diff --git a/gn3/auth/authentication/__init__.py b/gn3/auth/authentication/__init__.py new file mode 100644 index 0000000..8ad4cfd --- /dev/null +++ b/gn3/auth/authentication/__init__.py @@ -0,0 +1 @@ +"""The authentication module""" diff --git a/gn3/auth/authorisation/__init__.py b/gn3/auth/authorisation/__init__.py new file mode 100644 index 0000000..cc370e2 --- /dev/null +++ b/gn3/auth/authorisation/__init__.py @@ -0,0 +1 @@ +"""The authorisation module.""" diff --git a/gn3/migrations.py b/gn3/migrations.py new file mode 100644 index 0000000..7f8d694 --- /dev/null +++ b/gn3/migrations.py @@ -0,0 +1,33 @@ +"""Run the migrations in the app, rather than with yoyo CLI.""" +from pathlib import Path +from typing import Union + +from yoyo.backends import DatabaseBackend +from yoyo import read_migrations +from yoyo.migrations import Migration, MigrationList + +class MigrationNotFound(Exception): + """Raised if a migration is not found at the given path.""" + def __init__(self, migration_path: Path): + """Initialise the exception.""" + super().__init__(f"Could not find migration '{migration_path}'") + +def apply_migrations(backend: DatabaseBackend, migrations: MigrationList): + "Apply the provided migrations." + with backend.lock(): + backend.apply_migrations(backend.to_apply(migrations)) + +def rollback_migrations(backend: DatabaseBackend, migrations: MigrationList): + "Rollback the provided migrations." + with backend.lock(): + backend.rollback_migrations(backend.to_rollback(migrations)) + +def get_migration(migration_path: Union[Path, str]) -> Migration: + """Retrieve a migration at thi given `migration_path`.""" + migration_path = Path(migration_path) + if migration_path.exists(): + for migration in read_migrations(str(migration_path.parent)): + if Path(migration.path) == migration_path: + return migration + + raise MigrationNotFound(migration_path) diff --git a/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py b/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py new file mode 100644 index 0000000..d511f5d --- /dev/null +++ b/migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py @@ -0,0 +1,19 @@ +""" +Initialise the auth(entic|oris)ation database. +""" + +from yoyo import step + +__depends__ = {} # type: ignore[var-annotated] + +steps = [ + step( + """ + CREATE TABLE IF NOT EXISTS users( + user_id TEXT PRIMARY KEY NOT NULL, + email TEXT UNIQUE NOT NULL, + name TEXT + ) WITHOUT ROWID + """, + "DROP TABLE IF EXISTS users") +] @@ -48,3 +48,6 @@ ignore_missing_imports = True [mypy-xapian.*] ignore_missing_imports = True + +[mypy-yoyo.*] +ignore_missing_imports = True diff --git a/tests/unit/auth/test_init_database.py b/tests/unit/auth/test_init_database.py new file mode 100644 index 0000000..bf1ed1d --- /dev/null +++ b/tests/unit/auth/test_init_database.py @@ -0,0 +1,29 @@ +"""Test the auth database initialisation migration.""" +from contextlib import closing + +import pytest +import sqlite3 + +from gn3.migrations import get_migration, apply_migrations, rollback_migrations +from tests.unit.conftest import ( + apply_single_migration, rollback_single_migration) + +migration_path = "migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py" + +@pytest.mark.unit_test +def test_initialise_the_database(auth_testdb): + with closing(sqlite3.connect(auth_testdb)) as conn, closing(conn.cursor()) as cursor: + cursor.execute("SELECT name FROM sqlite_schema WHERE type='table'") + result = cursor.fetchall() + assert "users" not in [row[0] for row in cursor.fetchall()] + apply_single_migration(auth_testdb, get_migration(migration_path)) + cursor.execute("SELECT name FROM sqlite_schema WHERE type='table'") + assert "users" in [row[0] for row in cursor.fetchall()] + +@pytest.mark.unit_test +def test_rollback_initialise_the_database(auth_testdb): + with closing(sqlite3.connect(auth_testdb)) as conn, closing(conn.cursor()) as cursor: + apply_single_migration(auth_testdb, get_migration(migration_path)) + rollback_single_migration(auth_testdb, get_migration(migration_path)) + cursor.execute("SELECT name FROM sqlite_schema WHERE type='table'") + assert "users" not in [row[0] for row in cursor.fetchall()] diff --git a/tests/unit/conftest.py b/tests/unit/conftest.py new file mode 100644 index 0000000..bc974d9 --- /dev/null +++ b/tests/unit/conftest.py @@ -0,0 +1,44 @@ +"""Fixtures for unit tests.""" +from typing import Union +from pathlib import Path +from datetime import datetime +from tempfile import TemporaryDirectory + +import pytest +from yoyo import get_backend +from yoyo.migrations import Migration, MigrationList + +from gn3.app import create_app +from gn3.migrations import apply_migrations, rollback_migrations + +@pytest.fixture(scope="session") +def client(): + """Create a test client fixture for tests""" + # Do some setup + with TemporaryDirectory() as testdir: + testdb = Path(testdir).joinpath( + f'testdb_{datetime.now().strftime("%Y%m%dT%H%M%S")}') + app = create_app({"AUTH_DB": testdb}) + app.config.update({"TESTING": True}) + app.testing = True + yield app.test_client() + # Clean up after ourselves + testdb.unlink(missing_ok=True) + +@pytest.fixture() +def test_app_config(client): # pylint: disable=redefined-outer-name + """Return the test application's configuration object""" + return client.application.config + +@pytest.fixture() +def auth_testdb(test_app_config): # pylint: disable=redefined-outer-name + """Get the test application's auth database file""" + return test_app_config["AUTH_DB"] + +def apply_single_migration(db_uri: Union[Path, str], migration: Migration): + """Utility to apply a single migration""" + apply_migrations(get_backend(f"sqlite:///{db_uri}"), MigrationList([migration])) + +def rollback_single_migration(db_uri: Union[Path, str], migration: Migration): + """Utility to rollback a single migration""" + rollback_migrations(get_backend(f"sqlite:///{db_uri}"), MigrationList([migration])) diff --git a/yoyo.auth.ini b/yoyo.auth.ini new file mode 100644 index 0000000..097c17b --- /dev/null +++ b/yoyo.auth.ini @@ -0,0 +1,6 @@ +[DEFAULT] +sources = ./migrations/auth/ +migration_table = _yoyo_migration +batch_mode = off +verbosity = 0 + |