Merge pull request #14329 from jdavcs/release_22.05_dbinit_error (57645b10) · Commits · NDIP / Galaxy

lib/galaxy/model/migrations/scripts.py

+66 −3

Original line number	Diff line number	Diff line
		@@ -14,7 +14,10 @@ from alembic.script import ScriptDirectory
		from sqlalchemy import create_engine
		from sqlalchemy.engine import Engine

		from galaxy.model.database_utils import is_one_database
		from galaxy.model.database_utils import (
		database_exists,
		is_one_database,
		)
		from galaxy.model.migrations import (
		AlembicManager,
		DatabaseConfig,
		@@ -38,6 +41,51 @@ GXY_CONFIG_PREFIX = "GALAXY_CONFIG_"
		TSI_CONFIG_PREFIX = "GALAXY_INSTALL_CONFIG_"


		class DatabaseDoesNotExistError(Exception):
		def __init__(self, db_url: str) -> None:
		super().__init__(
		f"""The database at {db_url} does not exist. You must
		create and initialize the database before running this script. You
		can do so by (a) running `create_db.sh`; or by (b) starting Galaxy,
		in which case Galaxy will create and initialize the database
		automatically."""
		)


		class DatabaseNotInitializedError(Exception):
		def __init__(self, db_url: str) -> None:
		super().__init__(
		f"""The database at {db_url} is empty. You must
		initialize the database before running this script. You can do so by
		(a) running `create_db.sh`; or by (b) starting Galaxy, in which case
		Galaxy will initialize the database automatically."""
		)


		def verify_database_is_initialized(db_url: str) -> None:
		"""
		Intended for use by scripts that run database migrations (manage_db.sh,
		run_alembic.sh). Those scripts are meant to run on a database that has been
		initialized with the appropriate metadata (e.g. galaxy or install model).

		This function will raise an error if the database does not exist or has not
		been initialized*.

		*NOTE: this function cannot determine whether a database has been properly
		initialized; it can only tell when a database has not been initialized.
		"""
		if not database_exists(db_url):
		raise DatabaseDoesNotExistError(db_url)

		engine = create_engine(db_url)
		try:
		db_state = DatabaseStateCache(engine=engine)
		if db_state.is_database_empty() or db_state.contains_only_kombu_tables():
		raise DatabaseNotInitializedError(db_url)
		finally:
		engine.dispose()


		def get_configuration(argv: List[str], cwd: str) -> Tuple[DatabaseConfig, DatabaseConfig, bool]:
		"""
		Return a 3-item-tuple with configuration values used for managing databases.
		@@ -120,7 +168,15 @@ class LegacyScripts:
		def __init__(self, argv: List[str], cwd: Optional[str] = None) -> None:
		self.argv = argv
		self.cwd = cwd or os.getcwd()
		self.database = self.DEFAULT_DB_ARG
		self._database: Optional[str] = None # Do not assign default value: `None` means we don't know yet.

		@property
		def database(self):
		if self._database is None:
		raise LegacyScriptsException(
		"Attempt to access identifier of database before processing the script arguments"
		)
		return self._database

		def run(self) -> None:
		"""
		@@ -147,8 +203,9 @@ class LegacyScripts:
		If last argument is a valid database name, pop and assign it; otherwise assign default.
		"""
		arg = self.argv[-1]
		self._database = self.DEFAULT_DB_ARG
		if arg in ["galaxy", "install"]:
		self.database = self.argv.pop()
		self._database = self.argv.pop()

		def rename_config_argument(self) -> None:
		"""
		@@ -196,6 +253,12 @@ class LegacyScripts:
		elif self.database == "install":
		self.argv.append("tsi@head")

		def get_db_url(self):
		if self.database in ["galaxy", self.DEFAULT_DB_ARG]:
		return self.gxy_url
		elif self.database == "install":
		return self.tsi_url

		def _rename_arg(self, old_name, new_name) -> None:
		pos = self.argv.index(old_name)
		self.argv[pos] = new_name

scripts/manage_db_adapter.py

+3 −0

Original line number	Diff line number	Diff line
		@@ -25,12 +25,15 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
		from galaxy.model.migrations.scripts import (
		invoke_alembic,
		LegacyScripts,
		verify_database_is_initialized,
		)


		def run():
		ls = LegacyScripts(sys.argv, os.getcwd())
		ls.run()
		db_url = ls.get_db_url()
		verify_database_is_initialized(db_url)
		invoke_alembic()

test/unit/data/model/migrations/test_scripts.py

+27 −0

Original line number	Diff line number	Diff line
		import random

		import pytest

		from galaxy.model.migrations.scripts import (
		DatabaseDoesNotExistError,
		DatabaseNotInitializedError,
		LegacyScripts,
		LegacyScriptsException,
		verify_database_is_initialized,
		)


		@@ -145,3 +150,25 @@ class TestLegacyScripts:
		argv = ["caller", "--alembic-config", "path-to-alembic", "downgrade"]
		with pytest.raises(LegacyScriptsException):
		LegacyScripts(argv).convert_args()

		def test_access_database_id(self):
		db = "galaxy"
		argv = ["caller", "--alembic-config", "path-to-alembic", "upgrade", db]
		ls = LegacyScripts(argv)
		ls.run()
		assert ls.database == db

		def test_access_database_id_before_processing_script_args_raises_error(self):
		argv = ["caller", "--alembic-config", "path-to-alembic", "upgrade"]
		with pytest.raises(LegacyScriptsException):
		LegacyScripts(argv).database

		def test_verify_database_is_init_raises_error_if_no_database(self):
		nonexistant_path = str(random.random())[2:]
		db_url = f"sqlite:////{nonexistant_path}"
		with pytest.raises(DatabaseDoesNotExistError):
		verify_database_is_initialized(db_url)

		def test_verify_database_is_init_raises_error_if_database_not_initialized(self, sqlite_memory_url):
		with pytest.raises(DatabaseNotInitializedError):
		verify_database_is_initialized(sqlite_memory_url)