def test_create_database(self):
dropdb()
create_database()
self.assertTrue(database_connectivity())
self.assertTrue(database_exists())
self.assertTrue(schema_is_sane())
self.assertFalse(schema_has_data())
continue
else:
fq_url = "ftp://%s" % parts[1]
try:
filename = fq_to_sample_id.search(fq_url).group(0)
except:
continue
sample_id = filename.rstrip('.fastq.gz').strip('seqs_')
insert_fastq_sample(cur, sample_id, fq_url)
if __name__ == '__main__':
import sys
if not database_connectivity():
sys.stderr.write("Cannot connect to the database\n")
sys.exit(1)
if not database_exists():
sys.stderr.write('Database does not exist\n')
sys.exit(1)
if not schema_is_sane():
sys.stderr.write('Schema does not appear to be sane\n')
sys.exit(1)
c = connect(user=agr.admin_db_user, host=agr.db_host,
password=agr.admin_db_password, dbname=agr.db_name)
c.set_isolation_level(ISOLATION_LEVEL_AUTOCOMMIT)
cur = c.cursor()
if biom_unchanged(cur):
def test_database_connectivity(self):
# assumes we actually can connect with the provided credentials
self.assertTrue(database_connectivity())
self.assertFalse(database_connectivity(user='******'))
