From eb405885c6a2dbb68195a95771e21816aeff23de Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 12:01:34 +0000 Subject: [PATCH 1/8] replace ensembl_name with production_name for GetGenomeUUID endpoint --- VERSION | 2 +- .../metadata/grpc/ensembl_metadata.proto | 2 +- .../metadata/grpc/adaptors/genome.py | 9 ++- .../metadata/grpc/client_examples.py | 74 +++++++++---------- .../metadata/grpc/ensembl_metadata_pb2.py | 21 +++--- .../production/metadata/grpc/servicer.py | 2 +- src/ensembl/production/metadata/grpc/utils.py | 18 +---- src/tests/test_utils.py | 12 +-- 8 files changed, 67 insertions(+), 73 deletions(-) diff --git a/VERSION b/VERSION index 359a5b95..50aea0e7 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.0.0 \ No newline at end of file +2.1.0 \ No newline at end of file diff --git a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto index 6b42c7cb..15804793 100644 --- a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto +++ b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto @@ -413,7 +413,7 @@ 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/grpc/adaptors/genome.py b/src/ensembl/production/metadata/grpc/adaptors/genome.py index 09551860..89e02356 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)) diff --git a/src/ensembl/production/metadata/grpc/client_examples.py b/src/ensembl/production/metadata/grpc/client_examples.py index 9ae64b04..75fcee15 100755 --- a/src/ensembl/production/metadata/grpc/client_examples.py +++ b/src/ensembl/production/metadata/grpc/client_examples.py @@ -272,15 +272,15 @@ 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) @@ -321,42 +321,42 @@ def get_genome_uuid_by_tag(stub): def run(): with grpc.insecure_channel("localhost:50051") as channel: stub = ensembl_metadata_pb2_grpc.EnsemblMetadataStub(channel) - print("---------------Get Species Information-----------") - get_species_information_by_uuid(stub) - print("---------------Get Assembly Information-----------") - get_assembly_information(stub) - print( - "---------------Get Genome Information from assembly accession-----------" - ) - get_genomes_by_assembly_accession(stub) - print("---------------Get Subspecies Information-----------") - get_sub_species_info(stub) - print("---------------Get Top Level Statistics-----------") - get_top_level_statistics(stub) - print("---------------Get Top Level Statistics By UUID-----------") - get_top_level_statistics_by_uuid(stub) - print("-------------- Get Genomes --------------") - get_genomes(stub) - print("-------------- List Genome Sequences --------------") - list_genome_sequences(stub) - print("-------------- List Genome Assembly Sequences --------------") - list_genome_assembly_sequences(stub) - print("-------------- List Region Info for Given Sequence Name --------------") - list_genome_assembly_sequences_region(stub) - print("-------------- List Releases --------------") - list_releases(stub) - print("-------------- List Releases for Genome --------------") - list_releases_by_uuid(stub) - print("---------------Get Datasets List-----------") - get_datasets_list_by_uuid(stub) - print("-------------- List Dataset information for Genome --------------") - get_dataset_infos_by_dataset_type(stub) + # print("---------------Get Species Information-----------") + # get_species_information_by_uuid(stub) + # print("---------------Get Assembly Information-----------") + # get_assembly_information(stub) + # print( + # "---------------Get Genome Information from assembly accession-----------" + # ) + # get_genomes_by_assembly_accession(stub) + # print("---------------Get Subspecies Information-----------") + # get_sub_species_info(stub) + # print("---------------Get Top Level Statistics-----------") + # get_top_level_statistics(stub) + # print("---------------Get Top Level Statistics By UUID-----------") + # get_top_level_statistics_by_uuid(stub) + # print("-------------- Get Genomes --------------") + # get_genomes(stub) + # print("-------------- List Genome Sequences --------------") + # list_genome_sequences(stub) + # print("-------------- List Genome Assembly Sequences --------------") + # list_genome_assembly_sequences(stub) + # print("-------------- List Region Info for Given Sequence Name --------------") + # list_genome_assembly_sequences_region(stub) + # print("-------------- List Releases --------------") + # list_releases(stub) + # print("-------------- List Releases for Genome --------------") + # list_releases_by_uuid(stub) + # print("---------------Get Datasets List-----------") + # get_datasets_list_by_uuid(stub) + # print("-------------- List Dataset information for Genome --------------") + # get_dataset_infos_by_dataset_type(stub) print("-------------- Get Genome UUID --------------") get_genome_uuid(stub) - print("-------------- Get Organisms Group Count --------------") - get_organisms_group_count(stub) - print("-------------- Get Genome UUID By Tag --------------") - get_genome_uuid_by_tag(stub) + # print("-------------- Get Organisms Group Count --------------") + # get_organisms_group_count(stub) + # print("-------------- Get Genome UUID By Tag --------------") + # get_genome_uuid_by_tag(stub) if __name__ == "__main__": diff --git a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py index f17d2d39..4ec04a4c 100755 --- a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py +++ b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py @@ -1,6 +1,7 @@ # -*- coding: utf-8 -*- # Generated by the protocol buffer compiler. 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\x03(\t\x12\x17\n\x0frelease_version\x18\x02 \x03(\x01\x12\x14\n\x0c\x63urrent_only\x18\x03 \x01(\x08\"F\n\x15GenomeSequenceRequest\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12\x18\n\x10\x63hromosomal_only\x18\x02 \x01(\x08\"F\n\x15\x41ssemblyRegionRequest\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12\x18\n\x10\x63hromosomal_only\x18\x02 \x01(\x08\"X\n#GenomeAssemblySequenceRegionRequest\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12\x1c\n\x14sequence_region_name\x18\x02 \x01(\t\"?\n\x0f\x44\x61tasetsRequest\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12\x17\n\x0frelease_version\x18\x02 \x01(\x01\"B\n\x15GenomeDatatypeRequest\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12\x14\n\x0c\x64\x61taset_type\x18\x02 \x01(\t\"X\n\x11GenomeInfoRequest\x12\x17\n\x0fproduction_name\x18\x01 \x01(\t\x12\x15\n\rassembly_name\x18\x02 \x01(\t\x12\x13\n\x0buse_default\x18\x03 \x01(\x08\"0\n\x15OrganismsGroupRequest\x12\x17\n\x0frelease_version\x18\x01 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.ensembl_metadata.ReleaseRequest\x1a\x19.ensembl_metadata.Release\"\x00\x30\x01\x12V\n\x10GetReleaseByUUID\x12#.ensembl_metadata.GenomeUUIDRequest\x1a\x19.ensembl_metadata.Release\"\x00\x30\x01\x12\x62\n\x11GetGenomeSequence\x12\'.ensembl_metadata.GenomeSequenceRequest\x1a .ensembl_metadata.GenomeSequence\"\x00\x30\x01\x12\x62\n\x11GetAssemblyRegion\x12\'.ensembl_metadata.AssemblyRegionRequest\x1a .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\x62\x06proto3') _globals = globals() _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'ensembl.production.metadata.grpc.ensembl_metadata_pb2', _globals) if _descriptor._USE_C_DESCRIPTORS == False: DESCRIPTOR._options = None - _DATASETS_DATASETSENTRY._options = None - _DATASETS_DATASETSENTRY._serialized_options = b'8\001' + _globals['_DATASETS_DATASETSENTRY']._options = None + _globals['_DATASETS_DATASETSENTRY']._serialized_options = b'8\001' _globals['_GENOME']._serialized_start=78 _globals['_GENOME']._serialized_end=393 _globals['_SPECIES']._serialized_start=396 @@ -93,11 +94,11 @@ _globals['_GENOMEDATATYPEREQUEST']._serialized_start=4232 _globals['_GENOMEDATATYPEREQUEST']._serialized_end=4298 _globals['_GENOMEINFOREQUEST']._serialized_start=4300 - _globals['_GENOMEINFOREQUEST']._serialized_end=4385 - _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4387 - _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4435 - _globals['_GENOMETAGREQUEST']._serialized_start=4437 - _globals['_GENOMETAGREQUEST']._serialized_end=4475 - _globals['_ENSEMBLMETADATA']._serialized_start=4478 - _globals['_ENSEMBLMETADATA']._serialized_end=6352 + _globals['_GENOMEINFOREQUEST']._serialized_end=4388 + _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4390 + _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4438 + _globals['_GENOMETAGREQUEST']._serialized_start=4440 + _globals['_GENOMETAGREQUEST']._serialized_end=4478 + _globals['_ENSEMBLMETADATA']._serialized_start=4481 + _globals['_ENSEMBLMETADATA']._serialized_end=6355 # @@protoc_insertion_point(module_scope) diff --git a/src/ensembl/production/metadata/grpc/servicer.py b/src/ensembl/production/metadata/grpc/servicer.py index c7375a5e..9f040371 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 0c79a2ed..db559d01 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_utils.py b/src/tests/test_utils.py index 787893c2..87761621 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -683,21 +683,21 @@ 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", "GRCh38", False, {"genomeUuid": "a7335667-93e7-11ec-a39d-005056b38ce3"}), + ("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 )) From 7e7f3207aee861b29eccf1b5607351789215dfea Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 12:27:18 +0000 Subject: [PATCH 2/8] update production_name column in genome.txt sample to fix broken tests --- .../api/sample/ensembl_metadata/genome.txt | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) 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 From 888fd30d3bf092d6499ffdd374e0e8f760be4657 Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 12:33:28 +0000 Subject: [PATCH 3/8] remove one test case ehich isn't needed anymore --- src/tests/test_utils.py | 1 - 1 file changed, 1 deletion(-) diff --git a/src/tests/test_utils.py b/src/tests/test_utils.py index 87761621..7b309b24 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -688,7 +688,6 @@ def test_get_dataset_by_genome_id_no_results(self, genome_db_conn): ("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_production_name", "GRCh38", False, {"genomeUuid": "a7335667-93e7-11ec-a39d-005056b38ce3"}), ("random_production_name", "random_assembly_name", True, {}), ("random_production_name", "random_assembly_name", False, {}), ] From 11755444ecde12ece87bf65d08c910a5b563a02a Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 17:18:50 +0000 Subject: [PATCH 4/8] remove ensembl_name from GetOrganismsGroupCount() endpoint --- .../metadata/grpc/ensembl_metadata.proto | 9 +-- .../metadata/grpc/adaptors/genome.py | 2 - .../metadata/grpc/client_examples.py | 68 ++++++++--------- .../metadata/grpc/ensembl_metadata_pb2.py | 74 +++++++++---------- .../metadata/grpc/protobuf_msg_factory.py | 9 +-- src/tests/test_utils.py | 3 +- 6 files changed, 80 insertions(+), 85 deletions(-) diff --git a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto index 15804793..f15ef15e 100644 --- a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto +++ b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto @@ -290,11 +290,10 @@ 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 { diff --git a/src/ensembl/production/metadata/grpc/adaptors/genome.py b/src/ensembl/production/metadata/grpc/adaptors/genome.py index 89e02356..0328ea47 100644 --- a/src/ensembl/production/metadata/grpc/adaptors/genome.py +++ b/src/ensembl/production/metadata/grpc/adaptors/genome.py @@ -623,7 +623,6 @@ 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'), @@ -640,7 +639,6 @@ 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 75fcee15..ab3c61d2 100755 --- a/src/ensembl/production/metadata/grpc/client_examples.py +++ b/src/ensembl/production/metadata/grpc/client_examples.py @@ -321,42 +321,42 @@ def get_genome_uuid_by_tag(stub): def run(): with grpc.insecure_channel("localhost:50051") as channel: stub = ensembl_metadata_pb2_grpc.EnsemblMetadataStub(channel) - # print("---------------Get Species Information-----------") - # get_species_information_by_uuid(stub) - # print("---------------Get Assembly Information-----------") - # get_assembly_information(stub) - # print( - # "---------------Get Genome Information from assembly accession-----------" - # ) - # get_genomes_by_assembly_accession(stub) - # print("---------------Get Subspecies Information-----------") - # get_sub_species_info(stub) - # print("---------------Get Top Level Statistics-----------") - # get_top_level_statistics(stub) - # print("---------------Get Top Level Statistics By UUID-----------") - # get_top_level_statistics_by_uuid(stub) - # print("-------------- Get Genomes --------------") - # get_genomes(stub) - # print("-------------- List Genome Sequences --------------") - # list_genome_sequences(stub) - # print("-------------- List Genome Assembly Sequences --------------") - # list_genome_assembly_sequences(stub) - # print("-------------- List Region Info for Given Sequence Name --------------") - # list_genome_assembly_sequences_region(stub) - # print("-------------- List Releases --------------") - # list_releases(stub) - # print("-------------- List Releases for Genome --------------") - # list_releases_by_uuid(stub) - # print("---------------Get Datasets List-----------") - # get_datasets_list_by_uuid(stub) - # print("-------------- List Dataset information for Genome --------------") - # get_dataset_infos_by_dataset_type(stub) + print("---------------Get Species Information-----------") + get_species_information_by_uuid(stub) + print("---------------Get Assembly Information-----------") + get_assembly_information(stub) + print( + "---------------Get Genome Information from assembly accession-----------" + ) + get_genomes_by_assembly_accession(stub) + print("---------------Get Subspecies Information-----------") + get_sub_species_info(stub) + print("---------------Get Top Level Statistics-----------") + get_top_level_statistics(stub) + print("---------------Get Top Level Statistics By UUID-----------") + get_top_level_statistics_by_uuid(stub) + print("-------------- Get Genomes --------------") + get_genomes(stub) + print("-------------- List Genome Sequences --------------") + list_genome_sequences(stub) + print("-------------- List Genome Assembly Sequences --------------") + list_genome_assembly_sequences(stub) + print("-------------- List Region Info for Given Sequence Name --------------") + list_genome_assembly_sequences_region(stub) + print("-------------- List Releases --------------") + list_releases(stub) + print("-------------- List Releases for Genome --------------") + list_releases_by_uuid(stub) + print("---------------Get Datasets List-----------") + get_datasets_list_by_uuid(stub) + print("-------------- List Dataset information for Genome --------------") + get_dataset_infos_by_dataset_type(stub) print("-------------- Get Genome UUID --------------") get_genome_uuid(stub) - # print("-------------- Get Organisms Group Count --------------") - # get_organisms_group_count(stub) - # print("-------------- Get Genome UUID By Tag --------------") - # get_genome_uuid_by_tag(stub) + print("-------------- Get Organisms Group Count --------------") + get_organisms_group_count(stub) + print("-------------- Get Genome UUID By Tag --------------") + get_genome_uuid_by_tag(stub) if __name__ == "__main__": diff --git a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py index 4ec04a4c..b4e70ce4 100755 --- a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py +++ b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py @@ -14,7 +14,7 @@ -DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n7ensembl/production/metadata/grpc/ensembl_metadata.proto\x12\x10\x65nsembl_metadata\"\xbb\x02\n\x06Genome\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12,\n\x08\x61ssembly\x18\x02 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.ensembl_metadata.ReleaseRequest\x1a\x19.ensembl_metadata.Release\"\x00\x30\x01\x12V\n\x10GetReleaseByUUID\x12#.ensembl_metadata.GenomeUUIDRequest\x1a\x19.ensembl_metadata.Release\"\x00\x30\x01\x12\x62\n\x11GetGenomeSequence\x12\'.ensembl_metadata.GenomeSequenceRequest\x1a .ensembl_metadata.GenomeSequence\"\x00\x30\x01\x12\x62\n\x11GetAssemblyRegion\x12\'.ensembl_metadata.AssemblyRegionRequest\x1a .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\x62\x06proto3') _globals = globals() _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) @@ -65,40 +65,40 @@ _globals['_DATASETS_DATASETSENTRY']._serialized_end=3120 _globals['_GENOMEUUID']._serialized_start=3122 _globals['_GENOMEUUID']._serialized_end=3155 - _globals['_ORGANISMSGROUP']._serialized_start=3158 - _globals['_ORGANISMSGROUP']._serialized_end=3301 - _globals['_ORGANISMSGROUPCOUNT']._serialized_start=3303 - _globals['_ORGANISMSGROUPCOUNT']._serialized_end=3414 - _globals['_GENOMEUUIDREQUEST']._serialized_start=3416 - _globals['_GENOMEUUIDREQUEST']._serialized_end=3481 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_start=3483 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_end=3549 - _globals['_GENOMENAMEREQUEST']._serialized_start=3551 - _globals['_GENOMENAMEREQUEST']._serialized_end=3636 - _globals['_ASSEMBLYIDREQUEST']._serialized_start=3638 - _globals['_ASSEMBLYIDREQUEST']._serialized_end=3705 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=3707 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=3788 - _globals['_ORGANISMIDREQUEST']._serialized_start=3790 - _globals['_ORGANISMIDREQUEST']._serialized_end=3847 - _globals['_RELEASEREQUEST']._serialized_start=3849 - _globals['_RELEASEREQUEST']._serialized_end=3931 - _globals['_GENOMESEQUENCEREQUEST']._serialized_start=3933 - _globals['_GENOMESEQUENCEREQUEST']._serialized_end=4003 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=4005 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4075 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4077 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=4165 - _globals['_DATASETSREQUEST']._serialized_start=4167 - _globals['_DATASETSREQUEST']._serialized_end=4230 - _globals['_GENOMEDATATYPEREQUEST']._serialized_start=4232 - _globals['_GENOMEDATATYPEREQUEST']._serialized_end=4298 - _globals['_GENOMEINFOREQUEST']._serialized_start=4300 - _globals['_GENOMEINFOREQUEST']._serialized_end=4388 - _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4390 - _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4438 - _globals['_GENOMETAGREQUEST']._serialized_start=4440 - _globals['_GENOMETAGREQUEST']._serialized_end=4478 - _globals['_ENSEMBLMETADATA']._serialized_start=4481 - _globals['_ENSEMBLMETADATA']._serialized_end=6355 + _globals['_ORGANISMSGROUP']._serialized_start=3157 + _globals['_ORGANISMSGROUP']._serialized_end=3278 + _globals['_ORGANISMSGROUPCOUNT']._serialized_start=3280 + _globals['_ORGANISMSGROUPCOUNT']._serialized_end=3391 + _globals['_GENOMEUUIDREQUEST']._serialized_start=3393 + _globals['_GENOMEUUIDREQUEST']._serialized_end=3458 + _globals['_GENOMEBYKEYWORDREQUEST']._serialized_start=3460 + _globals['_GENOMEBYKEYWORDREQUEST']._serialized_end=3526 + _globals['_GENOMENAMEREQUEST']._serialized_start=3528 + _globals['_GENOMENAMEREQUEST']._serialized_end=3613 + _globals['_ASSEMBLYIDREQUEST']._serialized_start=3615 + _globals['_ASSEMBLYIDREQUEST']._serialized_end=3682 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=3684 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=3765 + _globals['_ORGANISMIDREQUEST']._serialized_start=3767 + _globals['_ORGANISMIDREQUEST']._serialized_end=3824 + _globals['_RELEASEREQUEST']._serialized_start=3826 + _globals['_RELEASEREQUEST']._serialized_end=3908 + _globals['_GENOMESEQUENCEREQUEST']._serialized_start=3910 + _globals['_GENOMESEQUENCEREQUEST']._serialized_end=3980 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=3982 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4052 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4054 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=4142 + _globals['_DATASETSREQUEST']._serialized_start=4144 + _globals['_DATASETSREQUEST']._serialized_end=4207 + _globals['_GENOMEDATATYPEREQUEST']._serialized_start=4209 + _globals['_GENOMEDATATYPEREQUEST']._serialized_end=4275 + _globals['_GENOMEINFOREQUEST']._serialized_start=4277 + _globals['_GENOMEINFOREQUEST']._serialized_end=4365 + _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4367 + _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4415 + _globals['_GENOMETAGREQUEST']._serialized_start=4417 + _globals['_GENOMETAGREQUEST']._serialized_end=4455 + _globals['_ENSEMBLMETADATA']._serialized_start=4458 + _globals['_ENSEMBLMETADATA']._serialized_end=6332 # @@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 05776016..72892206 100644 --- a/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py +++ b/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py @@ -369,11 +369,10 @@ 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/tests/test_utils.py b/src/tests/test_utils.py index 7b309b24..6920ba19 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -1108,7 +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, @@ -1118,7 +1117,7 @@ def test_get_organisms_group_count(self, genome_db_conn): } # make sure it returns 6 organisms json_output = json.loads(output) - assert len(json_output['organismsGroupCount']) == 6 + assert len(json_output['organismsGroupCount']) == 5 # and pick up the first element to check if it matches the expected output # I picked up only the first element for the sake of shortening the code assert json_output['organismsGroupCount'][0] == expected_output['organismsGroupCount'][0] From c68615cd0faa0e5d3deded9b68e38346540c1c75 Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 17:25:14 +0000 Subject: [PATCH 5/8] bump version to 2.1.1 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 50aea0e7..7c327287 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.1.0 \ No newline at end of file +2.1.1 \ No newline at end of file From 3300e34afdc544fe5d95e57077b4055d139e9a2c Mon Sep 17 00:00:00 2001 From: Bilal Date: Fri, 19 Jan 2024 17:29:52 +0000 Subject: [PATCH 6/8] fix broken tests --- src/tests/test_grpc.py | 6 +++--- src/tests/test_protobuf_msg_factory.py | 1 - src/tests/test_utils.py | 2 +- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/src/tests/test_grpc.py b/src/tests/test_grpc.py index 967c3af7..2a1b21f2 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 1e2b379c..a3d0c643 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 6920ba19..1d33f743 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -1117,7 +1117,7 @@ def test_get_organisms_group_count(self, genome_db_conn): } # make sure it returns 6 organisms json_output = json.loads(output) - assert len(json_output['organismsGroupCount']) == 5 + assert len(json_output['organismsGroupCount']) == 6 # and pick up the first element to check if it matches the expected output # I picked up only the first element for the sake of shortening the code assert json_output['organismsGroupCount'][0] == expected_output['organismsGroupCount'][0] From 9a37f0323ffda7d5045a47fb6dda6da57be7e552 Mon Sep 17 00:00:00 2001 From: Bilal Date: Wed, 24 Jan 2024 16:10:14 +0000 Subject: [PATCH 7/8] reverse back api version --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 7c327287..359a5b95 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.1.1 \ No newline at end of file +2.0.0 \ No newline at end of file From cc513f152de5954d9a4b52807e0ac0c4516bd93d Mon Sep 17 00:00:00 2001 From: Bilal Date: Wed, 24 Jan 2024 16:13:10 +0000 Subject: [PATCH 8/8] update pb2 file --- .../metadata/grpc/ensembl_metadata_pb2.py | 71 ++++++++++--------- 1 file changed, 37 insertions(+), 34 deletions(-) diff --git a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py index 34a0d98a..136b6eb0 100755 --- a/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py +++ b/src/ensembl/production/metadata/grpc/ensembl_metadata_pb2.py @@ -14,8 +14,7 @@ -DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n7ensembl/production/metadata/grpc/ensembl_metadata.proto\x12\x10\x65nsembl_metadata\"\xbb\x02\n\x06Genome\x12\x13\n\x0bgenome_uuid\x18\x01 \x01(\t\x12,\n\x08\x61ssembly\x18\x02 \x01(\x0b\x32\x1a.ensembl_metadata.Assembly\x12&\n\x05taxon\x18\x03 \x01(\x0b\x32\x17.ensembl_metadata.Taxon\x12\x0f\n\x07\x63reated\x18\x04 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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) @@ -70,36 +69,40 @@ _globals['_ORGANISMSGROUP']._serialized_end=3278 _globals['_ORGANISMSGROUPCOUNT']._serialized_start=3280 _globals['_ORGANISMSGROUPCOUNT']._serialized_end=3391 - _globals['_GENOMEUUIDREQUEST']._serialized_start=3393 - _globals['_GENOMEUUIDREQUEST']._serialized_end=3458 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_start=3460 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_end=3526 - _globals['_GENOMENAMEREQUEST']._serialized_start=3528 - _globals['_GENOMENAMEREQUEST']._serialized_end=3613 - _globals['_ASSEMBLYIDREQUEST']._serialized_start=3615 - _globals['_ASSEMBLYIDREQUEST']._serialized_end=3682 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=3684 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=3765 - _globals['_ORGANISMIDREQUEST']._serialized_start=3767 - _globals['_ORGANISMIDREQUEST']._serialized_end=3824 - _globals['_RELEASEREQUEST']._serialized_start=3826 - _globals['_RELEASEREQUEST']._serialized_end=3908 - _globals['_GENOMESEQUENCEREQUEST']._serialized_start=3910 - _globals['_GENOMESEQUENCEREQUEST']._serialized_end=3980 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=3982 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4052 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4054 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=4142 - _globals['_DATASETSREQUEST']._serialized_start=4144 - _globals['_DATASETSREQUEST']._serialized_end=4207 - _globals['_GENOMEDATATYPEREQUEST']._serialized_start=4209 - _globals['_GENOMEDATATYPEREQUEST']._serialized_end=4275 - _globals['_GENOMEINFOREQUEST']._serialized_start=4277 - _globals['_GENOMEINFOREQUEST']._serialized_end=4365 - _globals['_ORGANISMSGROUPREQUEST']._serialized_start=4367 - _globals['_ORGANISMSGROUPREQUEST']._serialized_end=4415 - _globals['_GENOMETAGREQUEST']._serialized_start=4417 - _globals['_GENOMETAGREQUEST']._serialized_end=4455 - _globals['_ENSEMBLMETADATA']._serialized_start=4458 - _globals['_ENSEMBLMETADATA']._serialized_end=6332 + _globals['_RELEASEVERSION']._serialized_start=3393 + _globals['_RELEASEVERSION']._serialized_end=3434 + _globals['_GENOMEUUIDREQUEST']._serialized_start=3436 + _globals['_GENOMEUUIDREQUEST']._serialized_end=3501 + _globals['_GENOMEBYKEYWORDREQUEST']._serialized_start=3503 + _globals['_GENOMEBYKEYWORDREQUEST']._serialized_end=3569 + _globals['_GENOMENAMEREQUEST']._serialized_start=3571 + _globals['_GENOMENAMEREQUEST']._serialized_end=3656 + _globals['_ASSEMBLYIDREQUEST']._serialized_start=3658 + _globals['_ASSEMBLYIDREQUEST']._serialized_end=3725 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=3727 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=3808 + _globals['_ORGANISMIDREQUEST']._serialized_start=3810 + _globals['_ORGANISMIDREQUEST']._serialized_end=3867 + _globals['_RELEASEREQUEST']._serialized_start=3869 + _globals['_RELEASEREQUEST']._serialized_end=3951 + _globals['_GENOMESEQUENCEREQUEST']._serialized_start=3953 + _globals['_GENOMESEQUENCEREQUEST']._serialized_end=4023 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=4025 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4095 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4097 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=4185 + _globals['_DATASETSREQUEST']._serialized_start=4187 + _globals['_DATASETSREQUEST']._serialized_end=4250 + _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)