diff --git a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py index 8fb2acee29..b2580d4abc 100644 --- a/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py +++ b/loading_pipeline/lib/tasks/exports/write_new_variants_parquet_test.py @@ -396,6 +396,61 @@ def test_mito_write_new_variants_parquet_test( ], ) + def test_mito_write_new_variants_parquet_all_existing_test( + self, + ) -> None: + _write_existing_variants_parquet_fixture( + ['M-3-T-C', 'M-8-G-T', 'M-12-T-C', 'M-16-A-T', 'M-18-C-T'], + ReferenceGenome.GRCh38, + DatasetType.MITO, + max_key_=997, + ) + copy_project_pedigree_to_mocked_dir( + TEST_MITO_EXPORT_PEDIGREE, + ReferenceGenome.GRCh38, + DatasetType.MITO, + SampleType.WGS, + 'R0116_test_project3', + ) + worker = luigi.worker.Worker() + task = WriteNewVariantsParquetTask( + reference_genome=ReferenceGenome.GRCh38, + dataset_type=DatasetType.MITO, + sample_type=SampleType.WGS, + callset_path=TEST_MITO_CALLSET, + project_guids=[ + 'R0116_test_project3', + ], + validations_to_skip=[ALL_VALIDATIONS], + run_id=TEST_RUN_ID, + skip_expect_tdr_metrics=True, + ) + worker.add(task) + worker.run() + self.assertTrue(task.output().exists()) + self.assertTrue(task.complete()) + df = pd.read_parquet( + new_variants_parquet_path( + ReferenceGenome.GRCh38, + DatasetType.MITO, + TEST_RUN_ID, + ), + ) + self.assertEqual(len(df), 0) + self.assertEqual( + list(df.columns), + [ + 'key', + 'variantId', + 'rsid', + 'liftedOverPos', + 'commonLowHeteroplasmy', + 'haplogroupDefining', + 'mitotip', + 'sortedTranscriptConsequences', + ], + ) + @mock.patch( 'loading_pipeline.lib.tasks.write_new_variants_table.load_gencode_gene_symbol_to_gene_id', )