def test_schema_is_sane(self):
dropdb()
createdb()
self.assertFalse(schema_is_sane())
createtable(tables[0][0])
self.assertFalse(schema_is_sane())
for tablename, _ in tables[1:]:
createtable(tablename)
self.assertTrue(schema_is_sane())
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())
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):
# data are the same, no change
sys.exit(0)
do_biom_update(cur)
do_fq_update(cur)
update_biom_sha(cur)