class AMRDatabasesManagerIT(unittest.TestCase):
RESFINDER_DEFAULT_COMMIT = 'e8f1eb2585cd9610c4034a54ce7fc4f93aa95535'
POINTFINDER_DEFAULT_COMMIT = '8706a6363bb29e47e0e398c53043b037c24b99a7'
PLASMIDFINDER_DEFAULT_COMMIT = '81919954cbedaff39056610ab584ab4c06011ed8'
def setUp(self):
self.databases_dir = tempfile.TemporaryDirectory()
self.databases_manager = AMRDatabasesManager(
database_dir=self.databases_dir.name, sub_dirs=True)
def tearDown(self):
self.databases_dir.cleanup()
def testSetupDefault(self):
blast_database_repos = self.databases_manager.get_database_repos()
# Verify that databases don't exist beforehand
self.assertFalse(
path.exists(blast_database_repos.get_repo_dir('resfinder')),
'resfinder path exists before creation of database')
self.assertFalse(
path.exists(blast_database_repos.get_repo_dir('pointfinder')),
'pointfinder path exists before creation of database')
self.assertFalse(
path.exists(blast_database_repos.get_repo_dir('plasmidfinder')),
'plasmidfinder path exists before creation of database')
# Setup default database
self.databases_manager.setup_default()
# Verify that resfinder/pointfinder paths exist
self.assertTrue(
path.exists(blast_database_repos.get_repo_dir('resfinder')),
'resfinder path does not exist')
self.assertTrue(
path.exists(blast_database_repos.get_repo_dir('pointfinder')),
'pointfinder path does not exist')
self.assertTrue(
path.exists(blast_database_repos.get_repo_dir('plasmidfinder')),
'plasmidfinder path does not exist')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_database_dir(),
'resfinder-info.ini')),
'resfinder info file does not exist')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_database_dir(),
'pointfinder-info.ini')),
'pointfinder info file does not exist')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_database_dir(),
'plasmidfinder-info.ini')),
'plasmidfinder info file does not exist')
# Verify we've removed the .git directories
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('resfinder'),
'.git')), 'resfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('pointfinder'),
'.git')),
'pointfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('plasmidfinder'),
'.git')),
'plasmidfinder .git directory was not removed')
config = configparser.ConfigParser()
# Verify that the info.ini file has correct git commits for default database
config.read(
path.join(blast_database_repos.get_database_dir(),
'resfinder-info.ini'))
self.assertEqual(config['GitInfo']['resfinder_db_commit'],
self.RESFINDER_DEFAULT_COMMIT,
'invalid resfinder commit')
config.read(
path.join(blast_database_repos.get_database_dir(),
'pointfinder-info.ini'))
self.assertEqual(config['GitInfo']['pointfinder_db_commit'],
self.POINTFINDER_DEFAULT_COMMIT,
'invalid pointfinder commit')
config.read(
path.join(blast_database_repos.get_database_dir(),
'plasmidfinder-info.ini'))
self.assertEqual(config['GitInfo']['plasmidfinder_db_commit'],
self.PLASMIDFINDER_DEFAULT_COMMIT,
'invalid plasmidfinder commit')
def testRestoreDefault(self):
# Build initial default database
self.databases_manager.setup_default()
# Build updated database
blast_database_repos_git = self.databases_manager.get_database_repos(
force_use_git=True)
blast_database_repos_git.build({
'resfinder':
self.RESFINDER_DEFAULT_COMMIT,
'pointfinder':
self.POINTFINDER_DEFAULT_COMMIT,
'plasmidfinder':
self.PLASMIDFINDER_DEFAULT_COMMIT
})
# Verify that updated database is the one that gets returned by get_database_handler()
blast_database_repos = self.databases_manager.get_database_repos()
self.assertFalse(blast_database_repos.is_dist(), 'Invalid is_dist')
self.assertEqual(blast_database_repos.get_database_dir(),
path.join(self.databases_dir.name, 'update'),
'Invalid database directory')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_repo_dir('resfinder'),
'.git')),
'Not using git version (updated version) of resfinder database')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_repo_dir('pointfinder'),
'.git')),
'Not using git version (updated version) of pointfinder database')
self.assertTrue(
path.exists(
path.join(blast_database_repos.get_repo_dir('plasmidfinder'),
'.git')),
'Not using git version (updated version) of plasmidfinder database'
)
# Restore default database
self.databases_manager.restore_default()
# Verify that default database (git stripped version) is the one that gets returned by get_database_handler()
blast_database_repos = self.databases_manager.get_database_repos()
self.assertTrue(blast_database_repos.is_dist(), 'Invalid is_dist')
self.assertEqual(blast_database_repos.get_database_dir(),
path.join(self.databases_dir.name, 'dist'),
'Invalid database directory')
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('resfinder'),
'.git')), 'resfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('pointfinder'),
'.git')),
'pointfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(blast_database_repos.get_repo_dir('plasmidfinder'),
'.git')),
'plasmidfinder .git directory was not removed')
def testIsHandlerDefaultCommitsTrue(self):
# Setup default database
self.databases_manager.setup_default()
blast_database_repos = self.databases_manager.get_database_repos()
self.assertTrue(
AMRDatabasesManager.is_database_repos_default_commits(
blast_database_repos), "Database is not default")
def testIsHandlerDefaultCommitsFalse(self):
# Setup database
blast_database_repos = self.databases_manager.get_database_repos(
force_use_git=True)
blast_database_repos.update(
{'resfinder': 'dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2'})
self.assertFalse(
AMRDatabasesManager.is_database_repos_default_commits(
blast_database_repos), "Database is default")
class AMRDatabasesManagerIT(unittest.TestCase):
RESFINDER_DEFAULT_COMMIT = 'e8f1eb2585cd9610c4034a54ce7fc4f93aa95535'
POINTFINDER_DEFAULT_COMMIT = '8706a6363bb29e47e0e398c53043b037c24b99a7'
def setUp(self):
self.databases_dir = tempfile.TemporaryDirectory()
self.databases_manager = AMRDatabasesManager(
database_dir=self.databases_dir.name, sub_dirs=True)
def tearDown(self):
self.databases_dir.cleanup()
def testGetHandlerGitStripDir(self):
self.assertIsInstance(self.databases_manager.get_database_handler(),
AMRDatabaseHandlerStripGitDir,
'Invalid instance returned')
def testGetHandlerGit(self):
self.assertIsInstance(
self.databases_manager.get_database_handler(force_use_git=True),
AMRDatabaseHandler, 'Invalid instance returned')
def testSetupDefault(self):
database_handler = self.databases_manager.get_database_handler()
# Verify that databases don't exist beforehand
self.assertFalse(path.exists(database_handler.get_resfinder_dir()),
'resfinder path exists before creation of database')
self.assertFalse(
path.exists(database_handler.get_pointfinder_dir()),
'pointfinder path exists before creation of database')
# Setup default database
self.databases_manager.setup_default()
# Verify that resfinder/pointfinder paths exist
self.assertTrue(path.exists(database_handler.get_resfinder_dir()),
'resfinder path does not exist')
self.assertTrue(path.exists(database_handler.get_resfinder_dir()),
'pointfinder path does not exist')
self.assertTrue(
path.exists(
path.join(database_handler.get_database_dir(), 'info.ini')),
'info file does not exist')
# Verify we've removed the .git directories
self.assertFalse(
path.exists(path.join(database_handler.get_resfinder_dir(),
'.git')),
'resfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(database_handler.get_pointfinder_dir(), '.git')),
'pointfinder .git directory was not removed')
config = configparser.ConfigParser()
config.read(path.join(database_handler.get_database_dir(), 'info.ini'))
# Verify that the info.ini file has correct git commits for default database
self.assertEqual(config['GitInfo']['resfinder_db_commit'],
self.RESFINDER_DEFAULT_COMMIT,
'invalid resfinder commit')
self.assertEqual(config['GitInfo']['pointfinder_db_commit'],
self.POINTFINDER_DEFAULT_COMMIT,
'invalid pointfinder commit')
def testRestoreDefault(self):
# Build initial default database
self.databases_manager.setup_default()
# Build updated database
database_handler_git = self.databases_manager.get_database_handler(
force_use_git=True)
database_handler_git.build(
resfinder_commit=self.RESFINDER_DEFAULT_COMMIT,
pointfinder_commit=self.POINTFINDER_DEFAULT_COMMIT)
# Verify that updated database is the one that gets returned by get_database_handler()
database_handler = self.databases_manager.get_database_handler()
self.assertIsInstance(database_handler, AMRDatabaseHandler,
'Invalid instance returned')
self.assertTrue(
path.exists(path.join(database_handler.get_resfinder_dir(),
'.git')),
'Not using git version (updated version) of resfinder database')
self.assertTrue(
path.exists(
path.join(database_handler.get_pointfinder_dir(), '.git')),
'Not using git version (updated version) of pointfinder database')
# Restore default database
self.databases_manager.restore_default()
# Verify that default database (git stripped version) is the one that gets returned by get_database_handler()
database_handler = self.databases_manager.get_database_handler()
self.assertIsInstance(database_handler, AMRDatabaseHandlerStripGitDir,
'Invalid instance returned')
self.assertFalse(
path.exists(path.join(database_handler.get_resfinder_dir(),
'.git')),
'resfinder .git directory was not removed')
self.assertFalse(
path.exists(
path.join(database_handler.get_pointfinder_dir(), '.git')),
'pointfinder .git directory was not removed')
def testIsHandlerDefaultCommitsTrue(self):
# Setup default database
self.databases_manager.setup_default()
database_handler = self.databases_manager.get_database_handler()
self.assertTrue(
AMRDatabasesManager.is_handler_default_commits(database_handler),
"Database is not default")
def testIsHandlerDefaultCommitsFalse(self):
# Setup database
database_handler = self.databases_manager.get_database_handler(
force_use_git=True)
database_handler.update(
resfinder_commit='dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2')
self.assertFalse(
AMRDatabasesManager.is_handler_default_commits(database_handler),
"Database is default")