diff --git a/src/ensembl_tui/_mysql_core_attr.py b/src/ensembl_tui/_mysql_core_attr.py index f93ea2a..22503ba 100644 --- a/src/ensembl_tui/_mysql_core_attr.py +++ b/src/ensembl_tui/_mysql_core_attr.py @@ -73,9 +73,7 @@ def load_db(db_name: pathlib.Path, table_names: set[str]) -> duckdb.DuckDBPyConn location_attrs = { - # "coord_names": "coord_system", "location": "seq_region", - # "meta": "meta", } gene_attrs = { "stableid": "gene", @@ -214,7 +212,7 @@ def start(self) -> int: def stop(self) -> int: return self.transcript_spans.max() - def to_record(self, columns: tuple[str]) -> tuple: + def to_record(self, columns: tuple[str, ...]) -> tuple: cds_blob = ( eti_storage.array_to_blob(self.cds_spans) if self.cds_spans is not None @@ -418,6 +416,3 @@ def make_gene_attr(con: duckdb.DuckDBPyConnection) -> duckdb.DuckDBPyConnection: """ con.sql(sql) return con - - -# the repeat and location related tables are left as is diff --git a/tests/test_cli.py b/tests/test_cli.py index 0798d58..bf99d84 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -102,7 +102,7 @@ def test_check_one_cds_seq(installed): "CAATTTTTGACCAAGGACTTGAAATTCCCATTGCCTCACAGAGTCCAAAAATCCACCAAG" "ACTTTCTCCTACAAGAGACCTTCCACTTTCTACTGA" ) - assert str(cds.get_slice()) == expect + assert str(seq) == expect @pytest.mark.slow