def test_getdatabase_postgres_nohostname_noport_setdefault(self):
"""Check get_database set default hostname and port for MySQL"""
try:
db = AccessionID(dbname='taxadb', dbtype='postgres',
password="******",
username="******")
self.assertEqual(int(db.get('port')), 5432)
self.assertEqual(db.get('hostname'), 'localhost')
except SystemExit as err:
unittest.skip("Can't test function: %s" % str(err))
def test_getdatabase_postgres_nohostname_noport_setdefault(self):
"""Check get_database set default hostname and port for MySQL"""
try:
db = AccessionID(dbname='taxadb', dbtype='postgres',
password="******",
username="******")
self.assertEqual(int(db.get('port')), 5432)
self.assertEqual(db.get('hostname'), 'localhost')
except SystemExit as err:
unittest.skip("Can't test function: %s" % str(err))
def main():
"""
Main program function
"""
# Get arguments
args = get_arguments()
# Step 1
print("STEP 1: Extracting Genbank IDS from BLAST output...")
accession = extract_genbank_id(args.blast_output_file)
chunks = [accession[i:i + 999] for i in range(0, len(accession), 999)]
print("Found {0} ids !".format(len(accession)))
#print(accession)
# Step 3
print("STEP 2: Writing results to file '{0}'...".format(
args.taxonomy_file))
accession_db = AccessionID(dbtype='sqlite', dbname=args.taxadb_file)
tax_db = TaxID(dbtype='sqlite', dbname=args.taxadb_file)
taxids = accession_db.taxid(accession)
#taxids = [accession_db.taxid(acc) for acc in accession]
#print(taxids)
write_results(chunks, accession_db, tax_db, args.taxonomy_file)
print("DONE !")
def test_setconfig_nodbname_raises(self):
"""Check method raises SystemExit when no dbname set"""
with self.assertRaises(SystemExit):
AccessionID(dbtype='sqlite')
def test_set_config_option_unset_section(self):
"""Check set throws AttributeError as required section for settings
option is not defined yet"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
with self.assertRaises(AttributeError):
db.set('newoption', 'newvalue', section="UNSET_SECCTION")
def test_getdatabase_nouser_or_nopasswd(self):
"""Check get_database throws SystemExit when no user or no password
is set"""
with self.assertRaises(SystemExit):
AccessionID(dbname='taxadb', dbtype='mysql')
def test_get_config_nooption(self):
"""Check get method returns None when an option is not found in the
configuration file"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
self.assertIsNone(db.get('unknown'))
def test_get_config_returnsNone(self):
"""Check get method returns None when an option has no value in
configuration file"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
db.set('foobar', None)
self.assertIsNone(db.get('foobar'))
def test_set_args(self):
"""Check we can set config from dict as args"""
db = AccessionID(dbtype='sqlite',
dbname=os.path.join(self.testdir, 'test_db.sqlite'))
self.assertEqual(db.get('dbtype'), 'sqlite')
self.assertEqual(os.path.basename(db.get('dbname')), 'test_db.sqlite')
def test_set_config_with_wrong_section(self):
"""Check we catch exception by using config file with wrong section"""
with self.assertRaises(SystemExit):
AccessionID(config=os.path.join(self.testdir,
'taxadb-nosection.cfg'))
def test_getdatabase_sqlite_throws(self):
"""Check get_database throws SystemExit when wrong or inaccessible
db"""
with self.assertRaises(SystemExit):
db = AccessionID(dbname='/unaccessible', dbtype='sqlite')
def test_setconfig_from_configfile(self):
"""Check passing a configuration file is ok"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
self.assertEqual(db.get('dbname'), 'taxadb/test/test_db.sqlite')
self.assertEqual(db.get('dbtype'), 'sqlite')
def test_setconfig_from_envvar(self):
"""Check using configuration from environment variable is ok"""
self._set_config_from_envvar()
db = AccessionID()
self.assertEqual(db.get('dbname'), 'taxadb/test/test_db.sqlite')
self.assertEqual(db.get('dbtype'), 'sqlite')
def test_set_args(self):
"""Check we can set config from dict as args"""
db = AccessionID(dbtype='sqlite',
dbname=os.path.join(self.testdir, 'test_db.sqlite'))
self.assertEqual(db.get('dbtype'), 'sqlite')
self.assertEqual(os.path.basename(db.get('dbname')), 'test_db.sqlite')
def test_set_config_option_unset_section(self):
"""Check set throws AttributeError as required section for settings
option is not defined yet"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
with self.assertRaises(AttributeError):
db.set('newoption', 'newvalue', section="UNSET_SECCTION")
def test_get_config_returnsNone(self):
"""Check get method returns None when an option has no value in
configuration file"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
db.set('foobar', None)
self.assertIsNone(db.get('foobar'))
def test_get_config_nooption(self):
"""Check get method returns None when an option is not found in the
configuration file"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
self.assertIsNone(db.get('unknown'))
def test_setconfig_from_configfile(self):
"""Check passing a configuration file is ok"""
db = AccessionID(config=os.path.join(self.testdir, 'taxadb.cfg'))
self.assertEqual(db.get('dbname'), 'taxadb/test/test_db.sqlite')
self.assertEqual(db.get('dbtype'), 'sqlite')
def test_setconfig_from_envvar(self):
"""Check using configuration from environment variable is ok"""
self._set_config_from_envvar()
db = AccessionID()
self.assertEqual(db.get('dbname'), 'taxadb/test/test_db.sqlite')
self.assertEqual(db.get('dbtype'), 'sqlite')
