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)