diff --git a/v03_pipeline/lib/reference_data/compare_globals.py b/v03_pipeline/lib/reference_data/compare_globals.py index 0b5c2993d..1feb0ac12 100644 --- a/v03_pipeline/lib/reference_data/compare_globals.py +++ b/v03_pipeline/lib/reference_data/compare_globals.py @@ -21,7 +21,7 @@ class Globals: paths: dict[str, str] versions: dict[str, str] enums: dict[str, dict[str, list[str]]] - selects: dict[str, set[str]] + selects: dict[str, dict[str, hl.dtype]] def __getitem__(self, name: str): return getattr(self, name) @@ -50,7 +50,11 @@ def from_dataset_configs( dataset_ht = dataset_ht.transmute( **get_enum_select_fields(dataset_ht, dataset_config), ) - selects[dataset] = set(dataset_ht.row) - set(dataset_ht.key) + selects[dataset] = { + k: v.dtype + for k, v in dict(dataset_ht.row).items() + if k not in set(dataset_ht.key) + } return cls(paths, versions, enums, selects) @classmethod @@ -69,32 +73,52 @@ def from_ht( if dataset in ht.row: # NB: handle an edge case (mito high constraint) where we annotate a bool from the reference dataset collection selects[dataset] = ( - set(ht[dataset]) + {k: v.dtype for k, v in dict(ht[dataset]).items()} if isinstance(ht[dataset], hl.StructExpression) - else set() + else {} ) return cls(paths, versions, enums, selects) +def validate_selects_types( + ht1_globals: Globals, + ht2_globals: Globals, + dataset: str, +) -> None: + # Assert that all shared annotations have identical types + shared_selects = ( + ht1_globals['selects'][dataset].keys() + & ht2_globals['selects'].get(dataset).keys() + ) + mismatched_select_types = [ + (select, ht2_globals['selects'][dataset][select]) + for select in shared_selects + if ( + ht1_globals['selects'][dataset][select] + != ht2_globals['selects'][dataset][select] + ) + ] + if mismatched_select_types: + msg = f'Unexpected field types detected in {dataset}: {mismatched_select_types}' + raise ValueError(msg) + + def get_datasets_to_update( ht1_globals: Globals, ht2_globals: Globals, validate_selects: bool = True, ) -> list[str]: datasets_to_update = set() - for field in dataclasses.fields(Globals): if field.name == 'selects' and not validate_selects: continue - datasets_to_update.update( ht1_globals[field.name].keys() ^ ht2_globals[field.name].keys(), ) for dataset in ht1_globals[field.name].keys() & ht2_globals[field.name].keys(): - if ht1_globals[field.name].get(dataset) != ht2_globals[field.name].get( - dataset, - ): + if field.name == 'selects': + validate_selects_types(ht1_globals, ht2_globals, dataset) + if ht1_globals[field.name][dataset] != ht2_globals[field.name][dataset]: logger.info(f'{field.name} mismatch for {dataset}') datasets_to_update.add(dataset) - return sorted(datasets_to_update) diff --git a/v03_pipeline/lib/reference_data/compare_globals_test.py b/v03_pipeline/lib/reference_data/compare_globals_test.py index 0d290489b..786964fcb 100644 --- a/v03_pipeline/lib/reference_data/compare_globals_test.py +++ b/v03_pipeline/lib/reference_data/compare_globals_test.py @@ -103,8 +103,15 @@ def test_create_globals_from_dataset_configs( self.assertTrue( dataset_config_globals.selects == { - 'a': {'test_select', 'test_enum_id'}, - 'b': {'test_select', 'field2', 'test_enum_id'}, + 'a': { + 'test_select': hl.tint32, + 'test_enum_id': hl.tint32, + }, + 'b': { + 'test_select': hl.tint32, + 'field2': hl.tint32, + 'test_enum_id': hl.tint32, + }, }, ) @@ -134,7 +141,11 @@ def test_create_globals_from_dataset_configs_single_dataset(self, mock_read_tabl self.assertTrue( dataset_config_globals.selects == { - 'b': {'test_select', 'field2', 'test_enum_id'}, + 'b': { + 'test_select': hl.tint32, + 'field2': hl.tint32, + 'test_enum_id': hl.tint32, + }, }, ) @@ -186,8 +197,8 @@ def test_from_rdc_or_annotations_ht(self): self.assertTrue( rdc_globals.selects == { - 'gnomad_non_coding_constraint': {'z_score'}, - 'screen': {'region_type_ids'}, + 'gnomad_non_coding_constraint': {'z_score': hl.tfloat32}, + 'screen': {'region_type_ids': hl.tarray(hl.tint32)}, }, ) @@ -198,13 +209,13 @@ def test_get_datasets_to_update_version_different(self): # 'a' has a different version, 'c' is missing version in ht2_globals versions={'a': 'v2', 'b': 'v2', 'c': 'v1'}, enums={'a': {}, 'b': {}, 'c': {}}, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ht2_globals=Globals( paths={'a': 'a_path', 'b': 'b_path'}, versions={'a': 'v1', 'b': 'v2'}, enums={'a': {}, 'b': {}}, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ) self.assertTrue(result == ['a', 'c']) @@ -216,13 +227,13 @@ def test_get_datasets_to_update_path_different(self): paths={'a': 'a_path', 'b': 'old_b_path', 'c': 'extra_c_path'}, versions={'a': 'v1', 'b': 'v2'}, enums={'a': {}, 'b': {}}, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ht2_globals=Globals( paths={'a': 'a_path', 'b': 'b_path'}, versions={'a': 'v1', 'b': 'v2'}, enums={'a': {}, 'b': {}}, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ) self.assertTrue(result == ['b', 'c']) @@ -238,13 +249,13 @@ def test_get_datasets_to_update_enum_different(self): 'b': {'enum_key_1': []}, 'c': {}, }, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ht2_globals=Globals( paths={'a': 'a_path', 'b': 'b_path'}, versions={'a': 'v1', 'b': 'v2'}, enums={'a': {'test_enum': ['C', 'D']}, 'b': {'enum_key_2': []}}, - selects={'a': set(), 'b': set()}, + selects={'a': {}, 'b': {}}, ), ) self.assertTrue(result == ['a', 'b', 'c']) @@ -257,16 +268,54 @@ def test_get_datasets_to_update_select_different(self): enums={'a': {}, 'b': {}}, # 'a' has extra select, 'b' has different select, 'c' is missing select in ht2_globals selects={ - 'a': {'field1', 'field2'}, - 'b': {'test_select'}, - 'c': set('test_select'), + 'a': {'field1': hl.tint32, 'field2': hl.tint32}, + 'b': {'test_select': hl.tint32}, + 'c': {'test_select': hl.tint32}, }, ), ht2_globals=Globals( paths={'a': 'a_path', 'b': 'b_path'}, versions={'a': 'v1', 'b': 'v2'}, enums={'a': {}, 'b': {}}, - selects={'a': {'field1'}, 'b': {'test_select_2'}}, + selects={'a': {'field1': hl.tint32}, 'b': {'test_select_2': hl.tint32}}, ), ) self.assertTrue(result == ['a', 'b', 'c']) + + def test_get_datasets_to_update_select_type_validation(self): + self.assertRaisesRegex( + ValueError, + "Unexpected field types detected in a: \\[\\('field1', dtype\\('int32'\\)\\)\\]", + get_datasets_to_update, + ht1_globals=Globals( + paths={'a': 'a_path'}, + versions={'a': 'v1'}, + enums={'a': {}}, + selects={ + 'a': {'field1': hl.tarray(hl.tint32)}, + }, + ), + ht2_globals=Globals( + paths={'a': 'a_path'}, + versions={'a': 'v1'}, + enums={'a': {}}, + selects={'a': {'field1': hl.tint32, 'field2': hl.tint32}}, + ), + ) + result = get_datasets_to_update( + ht1_globals=Globals( + paths={'a': 'a_path'}, + versions={'a': 'v1'}, + enums={'a': {}}, + selects={ + 'a': {'field1': hl.tarray(hl.tint32)}, + }, + ), + ht2_globals=Globals( + paths={'a': 'a_path'}, + versions={'a': 'v1'}, + enums={'a': {}}, + selects={'a': {'field1': hl.tarray(hl.tint32), 'field2': hl.tint32}}, + ), + ) + self.assertTrue(result == ['a']) diff --git a/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py b/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py index 842686c5c..67a5492bf 100644 --- a/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py +++ b/v03_pipeline/lib/tasks/reference_data/update_variant_annotations_table_with_updated_reference_dataset_test.py @@ -45,7 +45,7 @@ hl.tstruct( locus=hl.tlocus('GRCh38'), alleles=hl.tarray(hl.tstr), - PHRED=hl.tint32, + PHRED=hl.tfloat32, ), key=['locus', 'alleles'], globals=hl.Struct( @@ -760,7 +760,7 @@ def test_update_vat_with_updated_rdc_snv_indel_38( conditions=None, ), dbnsfp=hl.Struct( - REVEL_score=0.043, + REVEL_score=0.0430000014603138, SIFT_score=None, Polyphen2_HVAR_score=None, MutationTaster_pred_id=0, @@ -1168,7 +1168,7 @@ def test_update_vat_with_updated_rdc_snv_indel_37( conditions=None, ), dbnsfp=hl.Struct( - REVEL_score=0.043, + REVEL_score=0.0430000014603138, SIFT_score=None, Polyphen2_HVAR_score=None, MutationTaster_pred_id=0, diff --git a/v03_pipeline/var/test/reference_data/test_combined_1.ht/.README.txt.crc b/v03_pipeline/var/test/reference_data/test_combined_1.ht/.README.txt.crc index a98fcdead..1c47b9a3c 100644 Binary files a/v03_pipeline/var/test/reference_data/test_combined_1.ht/.README.txt.crc and b/v03_pipeline/var/test/reference_data/test_combined_1.ht/.README.txt.crc differ diff --git a/v03_pipeline/var/test/reference_data/test_combined_1.ht/.metadata.json.gz.crc b/v03_pipeline/var/test/reference_data/test_combined_1.ht/.metadata.json.gz.crc index b2ace029a..db7a7824c 100644 Binary files a/v03_pipeline/var/test/reference_data/test_combined_1.ht/.metadata.json.gz.crc and b/v03_pipeline/var/test/reference_data/test_combined_1.ht/.metadata.json.gz.crc differ diff --git a/v03_pipeline/var/test/reference_data/test_combined_1.ht/README.txt b/v03_pipeline/var/test/reference_data/test_combined_1.ht/README.txt index 856600d4e..e46de4296 100644 --- a/v03_pipeline/var/test/reference_data/test_combined_1.ht/README.txt +++ b/v03_pipeline/var/test/reference_data/test_combined_1.ht/README.txt @@ -1,3 +1,3 @@ This folder comprises a Hail (www.hail.is) native Table or MatrixTable. - Written with version 0.2.128-eead8100a1c1 - Created at 2024/05/09 20:02:21 \ No newline at end of file + Written with version 0.2.130-bea04d9c79b5 + Created at 2024/05/20 13:48:16 \ No newline at end of file diff --git a/v03_pipeline/var/test/reference_data/test_combined_1.ht/index/part-0-963ef6be-cd5f-443a-970c-8b5cf2bcd090.idx/.index.crc b/v03_pipeline/var/test/reference_data/test_combined_1.ht/index/part-0-6a5a9d6a-4ded-424b-9735-922a5346e7ad.idx/.index.crc similarity index 100% rename from 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