def is_database_repos_default_commits(
self, database_repos: BlastDatabaseRepositories) -> bool:
"""
Checks whether the past database repos handler is linked to default commits of the database.
:param database_repos: The database repos handler.
:return: True if it's setup with default commit versions, false otherwise.
"""
return database_repos.is_at_commits(self.DEFAULT_COMMITS)
def get_database_repos(self,
force_use_git: bool = False
) -> BlastDatabaseRepositories:
"""
Gets the appropriate database repositories.
:param force_use_git: Force use of git database repos.
:return: The database repos object.
"""
if self._sub_dirs and (force_use_git
or path.exists(self._git_database_dir)):
return BlastDatabaseRepositories.create_default_repositories(
self._git_database_dir)
elif self._sub_dirs:
return BlastDatabaseRepositories.create_default_repositories(
self._git_strip_database_dir, is_dist=True)
else:
return BlastDatabaseRepositories.create_default_repositories(
self._git_database_dir)
def setup_default(self):
"""
Sets up a default database.
:return: None
"""
if path.exists(self._git_strip_database_dir):
logger.warning("Default database already exists in [%s]",
self._git_strip_database_dir)
else:
logger.info("Setting up default database in [%s]",
self._git_strip_database_dir)
database_repos = BlastDatabaseRepositories.create_default_repositories(
self._git_strip_database_dir, is_dist=True)
database_repos.build(self.DEFAULT_COMMITS)
def restore_default(self):
"""
Restores the default database.
:return: None
"""
if path.exists(self._git_database_dir):
logger.info("Removing database in [%s]", self._git_database_dir)
database_repos = BlastDatabaseRepositories.create_default_repositories(
self._git_database_dir)
database_repos.remove()
if not path.exists(self._git_strip_database_dir):
self.setup_default()
logger.info("Restored default database to [%s]",
self._git_strip_database_dir)
else:
if not path.exists(self._git_strip_database_dir):
self.setup_default()
else:
logger.info(
"Default database already in use under directory [%s]",
self._git_strip_database_dir)
def setUp(self):
self.databases_dir = tempfile.TemporaryDirectory()
self.database_repositories = BlastDatabaseRepositories.create_default_repositories(self.databases_dir.name)