diff --git a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto index 4ee92a87..25b197b3 100644 --- a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto +++ b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto @@ -293,11 +293,10 @@ message GenomeUUID { message OrganismsGroup { uint32 species_taxonomy_id = 1; - string ensembl_name = 2; - string common_name = 3; - string scientific_name = 4; - uint32 order = 5; - uint32 count = 6; + string common_name = 2; + string scientific_name = 3; + uint32 order = 4; + uint32 count = 5; } message OrganismsGroupCount { @@ -420,7 +419,7 @@ message GenomeDatatypeRequest { Genome info filter used by Compara (EA-1090) */ message GenomeInfoRequest { - string ensembl_name = 1; // Mandatory + string production_name = 1; // Mandatory string assembly_name = 2; // Mandatory bool use_default = 3; // Optional } diff --git a/src/ensembl/production/metadata/api/sample/ensembl_metadata/genome.txt b/src/ensembl/production/metadata/api/sample/ensembl_metadata/genome.txt index 1705a258..44bc6c89 100644 --- a/src/ensembl/production/metadata/api/sample/ensembl_metadata/genome.txt +++ b/src/ensembl/production/metadata/api/sample/ensembl_metadata/genome.txt @@ -1,9 +1,9 @@ -1 a7335667-93e7-11ec-a39d-005056b38ce3 1 1 2023-05-12 13:30:58 0 test -2 3704ceb1-948d-11ec-a39d-005056b38ce3 2 1 2023-05-12 13:32:06 0 test1 -3 a73351f7-93e7-11ec-a39d-005056b38ce3 3 2 2023-05-12 13:32:14 0 test2 -4 a73356e1-93e7-11ec-a39d-005056b38ce3 4 3 2023-05-12 13:32:25 0 test3 -5 a73357ab-93e7-11ec-a39d-005056b38ce3 5 4 2023-05-12 13:32:36 0 test4 -6 a733574a-93e7-11ec-a39d-005056b38ce3 6 5 2023-05-12 13:32:46 0 test5 -7 a733550b-93e7-11ec-a39d-005056b38ce3 7 6 2023-05-12 13:32:52 0 test6 +1 a7335667-93e7-11ec-a39d-005056b38ce3 1 1 2023-05-12 13:30:58 0 homo_sapiens +2 3704ceb1-948d-11ec-a39d-005056b38ce3 2 1 2023-05-12 13:32:06 0 homo_sapiens_37 +3 a73351f7-93e7-11ec-a39d-005056b38ce3 3 2 2023-05-12 13:32:14 0 escherichia_coli_str_k_12_substr_mg1655 +4 a73356e1-93e7-11ec-a39d-005056b38ce3 4 3 2023-05-12 13:32:25 0 plasmodium_falciparum +5 a73357ab-93e7-11ec-a39d-005056b38ce3 5 4 2023-05-12 13:32:36 0 triticum_aestivum +6 a733574a-93e7-11ec-a39d-005056b38ce3 6 5 2023-05-12 13:32:46 0 saccharomyces_cerevisiae +7 a733550b-93e7-11ec-a39d-005056b38ce3 7 6 2023-05-12 13:32:52 0 caenorhabditis_elegans 8 a7335667-93e7-11ec-a39d-00aasab38ce3 8 1 2023-09-07 16:30:58 0 test7 9 90720316-006c-470b-a7dd-82d28f952264 9 8 2023-08-18 12:22:34 0 test8 diff --git a/src/ensembl/production/metadata/grpc/adaptors/genome.py b/src/ensembl/production/metadata/grpc/adaptors/genome.py index 728a6e9a..dcb62c02 100644 --- a/src/ensembl/production/metadata/grpc/adaptors/genome.py +++ b/src/ensembl/production/metadata/grpc/adaptors/genome.py @@ -80,8 +80,8 @@ def fetch_taxonomy_ids(self, taxonomy_names): def fetch_genomes(self, genome_id=None, genome_uuid=None, genome_tag=None, organism_uuid=None, assembly_uuid=None, assembly_accession=None, assembly_name=None, use_default_assembly=False, ensembl_name=None, - taxonomy_id=None, group=None, group_type=None, allow_unreleased=False, unreleased_only=False, - site_name=None, release_type=None, release_version=None, current_only=True): + production_name=None, taxonomy_id=None, group=None, group_type=None, allow_unreleased=False, + unreleased_only=False, site_name=None, release_type=None, release_version=None, current_only=True): """ Fetches genome information based on the specified parameters. @@ -95,6 +95,7 @@ def fetch_genomes(self, genome_id=None, genome_uuid=None, genome_tag=None, organ assembly_name (Union[str, List[str]]): The name(s) of the assembly(s) to fetch. use_default_assembly (bool): Whether to use default assembly name or not. ensembl_name (Union[str, List[str]]): The Ensembl name(s) of the organism(s) to fetch. + production_name (Union[str, List[str]]): The production name(s) of the organism(s) to fetch. taxonomy_id (Union[int, List[int]]): The taxonomy ID(s) of the organism(s) to fetch. group (Union[str, List[str]]): The name(s) of the organism group(s) to filter by. group_type (Union[str, List[str]]): The type(s) of the organism group(s) to filter by. @@ -132,6 +133,7 @@ def fetch_genomes(self, genome_id=None, genome_uuid=None, genome_tag=None, organ assembly_accession = check_parameter(assembly_accession) assembly_name = check_parameter(assembly_name) ensembl_name = check_parameter(ensembl_name) + production_name = check_parameter(production_name) taxonomy_id = check_parameter(taxonomy_id) group = check_parameter(group) group_type = check_parameter(group_type) @@ -194,6 +196,9 @@ def fetch_genomes(self, genome_id=None, genome_uuid=None, genome_tag=None, organ if ensembl_name is not None: genome_select = genome_select.filter(Organism.ensembl_name.in_(ensembl_name)) + if production_name is not None: + genome_select = genome_select.filter(Genome.production_name.in_(production_name)) + if taxonomy_id is not None: genome_select = genome_select.filter(Organism.taxonomy_id.in_(taxonomy_id)) @@ -612,7 +617,6 @@ def fetch_organisms_group_counts(self, release_version=None, group_code='popular # Get latest released organisms query = db.select( o_species.species_taxonomy_id, - o_species.ensembl_name, o_species.common_name, o_species.scientific_name, OrganismGroupMember.order.label('order'), @@ -629,7 +633,6 @@ def fetch_organisms_group_counts(self, release_version=None, group_code='popular query = query.group_by( o_species.species_taxonomy_id, - o_species.ensembl_name, o_species.common_name, o_species.scientific_name, OrganismGroupMember.order diff --git a/src/ensembl/production/metadata/grpc/client_examples.py b/src/ensembl/production/metadata/grpc/client_examples.py index 5278fad7..68612980 100755 --- a/src/ensembl/production/metadata/grpc/client_examples.py +++ b/src/ensembl/production/metadata/grpc/client_examples.py @@ -273,15 +273,15 @@ def get_dataset_infos_by_dataset_type(stub): def get_genome_uuid(stub): request1 = GenomeInfoRequest( - ensembl_name="homo_sapiens_37", assembly_name="GRCh37.p13" + production_name="homo_sapiens_37", assembly_name="GRCh37.p13" ) genome_uuid1 = stub.GetGenomeUUID(request1) request2 = GenomeInfoRequest( - ensembl_name="homo_sapiens_37", assembly_name="GRCh37", use_default=True + production_name="homo_sapiens_37", assembly_name="GRCh37", use_default=True ) genome_uuid2 = stub.GetGenomeUUID(request2) request3 = GenomeInfoRequest( - ensembl_name="homo_sapiens_37", assembly_name="GRCh37.p13", use_default=True + production_name="homo_sapiens_37", assembly_name="GRCh37.p13", use_default=True ) genome_uuid3 = stub.GetGenomeUUID(request3) diff --git a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py index 6252279e..136b6eb0 100755 --- 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.ensembl_metadata.AssemblyRegion\"\x00\x30\x01\x12\x8a\x01\n\x1fGetGenomeAssemblySequenceRegion\x12\x35.ensembl_metadata.GenomeAssemblySequenceRegionRequest\x1a..ensembl_metadata.GenomeAssemblySequenceRegion\"\x00\x12X\n\x15GetDatasetsListByUUID\x12!.ensembl_metadata.DatasetsRequest\x1a\x1a.ensembl_metadata.Datasets\"\x00\x12\x62\n\x15GetDatasetInformation\x12\'.ensembl_metadata.GenomeDatatypeRequest\x1a\x1e.ensembl_metadata.DatasetInfos\"\x00\x12j\n\x16GetOrganismsGroupCount\x12\'.ensembl_metadata.OrganismsGroupRequest\x1a%.ensembl_metadata.OrganismsGroupCount\"\x00\x12X\n\x12GetGenomeUUIDByTag\x12\".ensembl_metadata.GenomeTagRequest\x1a\x1c.ensembl_metadata.GenomeUUID\"\x00\x12\x66\n\x17GetReleaseVersionByUUID\x12\'.ensembl_metadata.ReleaseVersionRequest\x1a .ensembl_metadata.ReleaseVersion\"\x00\x62\x06proto3') _globals = globals() _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) @@ -65,44 +65,44 @@ _globals['_DATASETS_DATASETSENTRY']._serialized_end=3120 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_globals['_GENOMEDATATYPEREQUEST']._serialized_start=4252 + _globals['_GENOMEDATATYPEREQUEST']._serialized_end=4318 + _globals['_GENOMEINFOREQUEST']._serialized_start=4320 + _globals['_GENOMEINFOREQUEST']._serialized_end=4408 + _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4410 + _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4458 + _globals['_GENOMETAGREQUEST']._serialized_start=4460 + _globals['_GENOMETAGREQUEST']._serialized_end=4498 + _globals['_RELEASEVERSIONREQUEST']._serialized_start=4500 + _globals['_RELEASEVERSIONREQUEST']._serialized_end=4591 + _globals['_ENSEMBLMETADATA']._serialized_start=4594 + _globals['_ENSEMBLMETADATA']._serialized_end=6572 # @@protoc_insertion_point(module_scope) diff --git a/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py b/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py index 00dccedb..d721747a 100644 --- a/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py +++ b/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py @@ -396,11 +396,10 @@ def create_organisms_group_count(data, release_version): for organism in data: created_organism_group = ensembl_metadata_pb2.OrganismsGroup( species_taxonomy_id=organism[0], - ensembl_name=organism[1], - common_name=organism[2], - scientific_name=organism[3], - order=organism[4], - count=organism[5], + common_name=organism[1], + scientific_name=organism[2], + order=organism[3], + count=organism[4], ) organisms_list.append(created_organism_group) diff --git a/src/ensembl/production/metadata/grpc/servicer.py b/src/ensembl/production/metadata/grpc/servicer.py index d8094dda..98e3f250 100644 --- a/src/ensembl/production/metadata/grpc/servicer.py +++ b/src/ensembl/production/metadata/grpc/servicer.py @@ -39,7 +39,7 @@ def GetTopLevelStatisticsByUUID(self, request, context): return utils.get_top_level_statistics_by_uuid(self.db, request.genome_uuid) def GetGenomeUUID(self, request, context): - return utils.get_genome_uuid(self.db, request.ensembl_name, request.assembly_name, request.use_default) + return utils.get_genome_uuid(self.db, request.production_name, request.assembly_name, request.use_default) def GetGenomeByUUID(self, request, context): return utils.get_genome_by_uuid(self.db, request.genome_uuid, request.release_version) diff --git a/src/ensembl/production/metadata/grpc/utils.py b/src/ensembl/production/metadata/grpc/utils.py index ccb1aa65..ca3f8296 100644 --- a/src/ensembl/production/metadata/grpc/utils.py +++ b/src/ensembl/production/metadata/grpc/utils.py @@ -179,12 +179,12 @@ def get_sub_species_info(db_conn, organism_uuid, group): return msg_factory.create_sub_species() -def get_genome_uuid(db_conn, ensembl_name, assembly_name, use_default=False): - if ensembl_name is None or assembly_name is None: +def get_genome_uuid(db_conn, production_name, assembly_name, use_default=False): + if production_name is None or assembly_name is None: return msg_factory.create_genome_uuid() genome_uuid_result = db_conn.fetch_genomes( - ensembl_name=ensembl_name, + production_name=production_name, assembly_name=assembly_name, use_default_assembly=use_default, allow_unreleased=cfg.allow_unreleased @@ -194,18 +194,6 @@ def get_genome_uuid(db_conn, ensembl_name, assembly_name, use_default=False): return msg_factory.create_genome_uuid( {"genome_uuid": genome_uuid_result[0].Genome.genome_uuid} ) - # PATCH: This is a special case, see EA-1112 for more details - elif len(genome_uuid_result) == 0: - # Try looking using only assembly_default (no ensembl_name is needed) - using_default_assembly_only_result = db_conn.fetch_genomes( - assembly_name=assembly_name, - use_default_assembly=True, - allow_unreleased=cfg.allow_unreleased - ) - if len(using_default_assembly_only_result) == 1: - return msg_factory.create_genome_uuid( - {"genome_uuid": using_default_assembly_only_result[0].Genome.genome_uuid} - ) return msg_factory.create_genome_uuid() diff --git a/src/tests/test_grpc.py b/src/tests/test_grpc.py index 23e0d6e5..80ed52c5 100644 --- a/src/tests/test_grpc.py +++ b/src/tests/test_grpc.py @@ -376,13 +376,13 @@ def test_fetch_organisms_group_counts(self, multi_dbs, species_taxonomy_id, expe test = conn.fetch_organisms_group_counts() # When fetching everything: # First result should be Human - assert test[0][2] == expected_organism + assert test[0][1] == expected_organism # We should have three assemblies associated with Human (Two for grch37.38 organism + one t2t) - assert test[0][5] == expected_assemblies_count + assert test[0][4] == expected_assemblies_count for data in test[1:]: # All others have only one genome in test DB - assert data[5] == 1 + assert data[4] == 1 @pytest.mark.parametrize( "organism_uuid, expected_assemblies_count", diff --git a/src/tests/test_protobuf_msg_factory.py b/src/tests/test_protobuf_msg_factory.py index 4236d411..0b4ba421 100644 --- a/src/tests/test_protobuf_msg_factory.py +++ b/src/tests/test_protobuf_msg_factory.py @@ -243,7 +243,6 @@ def test_create_organisms_group_count(self, multi_dbs, genome_db_conn): "organismsGroupCount": [ { "speciesTaxonomyId": 9606, - "ensemblName": "Homo_sapiens", "commonName": "Human", "scientificName": "Homo sapiens", "order": 1, diff --git a/src/tests/test_utils.py b/src/tests/test_utils.py index dc88c576..9f925f00 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -683,21 +683,20 @@ def test_get_dataset_by_genome_id_no_results(self, genome_db_conn): assert output == {} @pytest.mark.parametrize( - "ensembl_name, assembly_name, use_default, expected_output", + "production_name, assembly_name, use_default, expected_output", [ ("homo_sapiens", "GRCh38.p13", False, {"genomeUuid": "a7335667-93e7-11ec-a39d-005056b38ce3"}), ("homo_sapiens", "GRCh38.p13", True, {}), ("homo_sapiens", "GRCh38", True, {"genomeUuid": "a7335667-93e7-11ec-a39d-005056b38ce3"}), - ("random_ensembl_name", "GRCh38", False, {"genomeUuid": "a7335667-93e7-11ec-a39d-005056b38ce3"}), - ("random_ensembl_name", "random_assembly_name", True, {}), - ("random_ensembl_name", "random_assembly_name", False, {}), + ("random_production_name", "random_assembly_name", True, {}), + ("random_production_name", "random_assembly_name", False, {}), ] ) - def test_get_genome_uuid(self, genome_db_conn, ensembl_name, assembly_name, use_default, expected_output): + def test_get_genome_uuid(self, genome_db_conn, production_name, assembly_name, use_default, expected_output): output = json_format.MessageToJson( utils.get_genome_uuid( db_conn=genome_db_conn, - ensembl_name=ensembl_name, + production_name=production_name, assembly_name=assembly_name, use_default=use_default )) @@ -1109,7 +1108,6 @@ def test_get_organisms_group_count(self, genome_db_conn): "organismsGroupCount": [ { "speciesTaxonomyId": 9606, - "ensemblName": "Homo_sapiens", "commonName": "Human", "scientificName": "Homo sapiens", "order": 1,