diff --git a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto index 9052c4c8..41027700 100644 --- a/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto +++ b/protos/ensembl/production/metadata/grpc/ensembl_metadata.proto @@ -248,7 +248,7 @@ message AttributesInfo { string genebuild_method = 1; string genebuild_method_display = 2; string genebuild_last_geneset_update = 3; - string genebuild_version = 4; + string genebuild_provider_version = 4; string genebuild_provider_name = 5; string genebuild_provider_url = 6; string genebuild_sample_gene = 7; @@ -383,15 +383,6 @@ message GenomeUUIDRequest { double release_version = 3; // Optional } -/* -Genome keyword filter. -If release_version is not given, the current version is used. - */ -message GenomeByKeywordRequest { - string keyword = 1; // Mandatory - double release_version = 2; // Optional -} - /* Genome specific keyword filter. If release_version is not given, the current version is used. diff --git a/src/ensembl/production/metadata/grpc/client_examples.py b/src/ensembl/production/metadata/grpc/client_examples.py index 4a76799a..819dc56c 100755 --- a/src/ensembl/production/metadata/grpc/client_examples.py +++ b/src/ensembl/production/metadata/grpc/client_examples.py @@ -426,10 +426,10 @@ def get_datasets_attributes_values_by_genome_uuid(stub): request3 = DatasetAttributesValuesRequest( genome_uuid="a73351f7-93e7-11ec-a39d-005056b38ce3", dataset_type="homologies", - attribute_name=["compara.homology_coverage"] + attribute_name=["compara.stats.homology_coverage"] ) attributes3 = stub.GetAttributesValuesByUUID(request3) - print("**** Dataset Attributes Values: By genome_uuid, dataset_type='homologies' and attribute_name=['compara.homology_coverage'] ****") + print("**** Dataset Attributes Values: By genome_uuid, dataset_type='homologies' and attribute_name=['compara.stats.homology_coverage'] ****") 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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^\n\x15GetDatasetInformation\x12\'.ensembl_metadata.GenomeDatatypeRequest\x1a\x1a.ensembl_metadata.Datasets\"\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\x12N\n\x0bGetFTPLinks\x12!.ensembl_metadata.FTPLinksRequest\x1a\x1a.ensembl_metadata.FTPLinks\"\x00\x12\x66\n\x17GetReleaseVersionByUUID\x12\'.ensembl_metadata.ReleaseVersionRequest\x1a .ensembl_metadata.ReleaseVersion\"\x00\x12z\n\x19GetAttributesValuesByUUID\x12\x30.ensembl_metadata.DatasetAttributesValuesRequest\x1a).ensembl_metadata.DatasetAttributesValues\"\x00\x62\x06proto3') _globals = globals() _builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) @@ -60,71 +60,69 @@ _globals['_ATTRIBUTE']._serialized_start=2111 _globals['_ATTRIBUTE']._serialized_end=2186 _globals['_ATTRIBUTESINFO']._serialized_start=2189 - _globals['_ATTRIBUTESINFO']._serialized_end=2606 - _globals['_GENOMESEQUENCE']._serialized_start=2608 - _globals['_GENOMESEQUENCE']._serialized_end=2721 - _globals['_ASSEMBLYREGION']._serialized_start=2723 - _globals['_ASSEMBLYREGION']._serialized_end=2837 - _globals['_GENOMEASSEMBLYSEQUENCEREGION']._serialized_start=2839 - _globals['_GENOMEASSEMBLYSEQUENCEREGION']._serialized_end=2953 - _globals['_DATASETINFO']._serialized_start=2956 - _globals['_DATASETINFO']._serialized_end=3287 - _globals['_DATASETS']._serialized_start=3289 - _globals['_DATASETS']._serialized_end=3369 - _globals['_GENOMEUUID']._serialized_start=3371 - _globals['_GENOMEUUID']._serialized_end=3404 - _globals['_ORGANISMSGROUP']._serialized_start=3406 - _globals['_ORGANISMSGROUP']._serialized_end=3527 - _globals['_ORGANISMSGROUPCOUNT']._serialized_start=3529 - _globals['_ORGANISMSGROUPCOUNT']._serialized_end=3640 - _globals['_FTPLINK']._serialized_start=3642 - _globals['_FTPLINK']._serialized_end=3687 - _globals['_FTPLINKS']._serialized_start=3689 - _globals['_FTPLINKS']._serialized_end=3741 - _globals['_RELEASEVERSION']._serialized_start=3743 - _globals['_RELEASEVERSION']._serialized_end=3784 - _globals['_DATASETATTRIBUTEVALUE']._serialized_start=3787 - _globals['_DATASETATTRIBUTEVALUE']._serialized_end=3928 - _globals['_DATASETATTRIBUTESVALUES']._serialized_start=3930 - _globals['_DATASETATTRIBUTESVALUES']._serialized_end=4041 - _globals['_GENOMEUUIDREQUEST']._serialized_start=4043 - _globals['_GENOMEUUIDREQUEST']._serialized_end=4108 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_start=4110 - _globals['_GENOMEBYKEYWORDREQUEST']._serialized_end=4176 - _globals['_GENOMEBYSPECIFICKEYWORDREQUEST']._serialized_start=4179 - _globals['_GENOMEBYSPECIFICKEYWORDREQUEST']._serialized_end=4436 - _globals['_GENOMENAMEREQUEST']._serialized_start=4438 - _globals['_GENOMENAMEREQUEST']._serialized_end=4523 - _globals['_ASSEMBLYIDREQUEST']._serialized_start=4525 - _globals['_ASSEMBLYIDREQUEST']._serialized_end=4592 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=4594 - _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=4675 - _globals['_ORGANISMIDREQUEST']._serialized_start=4677 - _globals['_ORGANISMIDREQUEST']._serialized_end=4734 - _globals['_RELEASEREQUEST']._serialized_start=4736 - _globals['_RELEASEREQUEST']._serialized_end=4818 - _globals['_GENOMESEQUENCEREQUEST']._serialized_start=4820 - _globals['_GENOMESEQUENCEREQUEST']._serialized_end=4890 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=4892 - _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4962 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4964 - _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=5052 - _globals['_DATASETSREQUEST']._serialized_start=5054 - _globals['_DATASETSREQUEST']._serialized_end=5117 - _globals['_GENOMEDATATYPEREQUEST']._serialized_start=5119 - _globals['_GENOMEDATATYPEREQUEST']._serialized_end=5185 - _globals['_GENOMEINFOREQUEST']._serialized_start=5188 - _globals['_GENOMEINFOREQUEST']._serialized_end=5325 - _globals['_ORGANISMSGROUPREQUEST']._serialized_start=5327 - _globals['_ORGANISMSGROUPREQUEST']._serialized_end=5375 - _globals['_GENOMETAGREQUEST']._serialized_start=5377 - _globals['_GENOMETAGREQUEST']._serialized_end=5415 - _globals['_FTPLINKSREQUEST']._serialized_start=5417 - _globals['_FTPLINKSREQUEST']._serialized_end=5502 - _globals['_RELEASEVERSIONREQUEST']._serialized_start=5504 - _globals['_RELEASEVERSIONREQUEST']._serialized_end=5595 - _globals['_DATASETATTRIBUTESVALUESREQUEST']._serialized_start=5598 - _globals['_DATASETATTRIBUTESVALUESREQUEST']._serialized_end=5743 - _globals['_ENSEMBLMETADATA']._serialized_start=5746 - _globals['_ENSEMBLMETADATA']._serialized_end=8158 + _globals['_ATTRIBUTESINFO']._serialized_end=2615 + _globals['_GENOMESEQUENCE']._serialized_start=2617 + _globals['_GENOMESEQUENCE']._serialized_end=2730 + _globals['_ASSEMBLYREGION']._serialized_start=2732 + _globals['_ASSEMBLYREGION']._serialized_end=2846 + _globals['_GENOMEASSEMBLYSEQUENCEREGION']._serialized_start=2848 + _globals['_GENOMEASSEMBLYSEQUENCEREGION']._serialized_end=2962 + _globals['_DATASETINFO']._serialized_start=2965 + _globals['_DATASETINFO']._serialized_end=3296 + _globals['_DATASETS']._serialized_start=3298 + _globals['_DATASETS']._serialized_end=3378 + _globals['_GENOMEUUID']._serialized_start=3380 + _globals['_GENOMEUUID']._serialized_end=3413 + _globals['_ORGANISMSGROUP']._serialized_start=3415 + _globals['_ORGANISMSGROUP']._serialized_end=3536 + _globals['_ORGANISMSGROUPCOUNT']._serialized_start=3538 + _globals['_ORGANISMSGROUPCOUNT']._serialized_end=3649 + _globals['_FTPLINK']._serialized_start=3651 + _globals['_FTPLINK']._serialized_end=3696 + _globals['_FTPLINKS']._serialized_start=3698 + _globals['_FTPLINKS']._serialized_end=3750 + _globals['_RELEASEVERSION']._serialized_start=3752 + _globals['_RELEASEVERSION']._serialized_end=3793 + _globals['_DATASETATTRIBUTEVALUE']._serialized_start=3796 + _globals['_DATASETATTRIBUTEVALUE']._serialized_end=3937 + _globals['_DATASETATTRIBUTESVALUES']._serialized_start=3939 + _globals['_DATASETATTRIBUTESVALUES']._serialized_end=4050 + _globals['_GENOMEUUIDREQUEST']._serialized_start=4052 + _globals['_GENOMEUUIDREQUEST']._serialized_end=4117 + _globals['_GENOMEBYSPECIFICKEYWORDREQUEST']._serialized_start=4120 + _globals['_GENOMEBYSPECIFICKEYWORDREQUEST']._serialized_end=4377 + _globals['_GENOMENAMEREQUEST']._serialized_start=4379 + _globals['_GENOMENAMEREQUEST']._serialized_end=4464 + _globals['_ASSEMBLYIDREQUEST']._serialized_start=4466 + _globals['_ASSEMBLYIDREQUEST']._serialized_end=4533 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_start=4535 + _globals['_ASSEMBLYACCESSIONIDREQUEST']._serialized_end=4616 + _globals['_ORGANISMIDREQUEST']._serialized_start=4618 + _globals['_ORGANISMIDREQUEST']._serialized_end=4675 + _globals['_RELEASEREQUEST']._serialized_start=4677 + _globals['_RELEASEREQUEST']._serialized_end=4759 + _globals['_GENOMESEQUENCEREQUEST']._serialized_start=4761 + _globals['_GENOMESEQUENCEREQUEST']._serialized_end=4831 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_start=4833 + _globals['_ASSEMBLYREGIONREQUEST']._serialized_end=4903 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_start=4905 + _globals['_GENOMEASSEMBLYSEQUENCEREGIONREQUEST']._serialized_end=4993 + _globals['_DATASETSREQUEST']._serialized_start=4995 + _globals['_DATASETSREQUEST']._serialized_end=5058 + _globals['_GENOMEDATATYPEREQUEST']._serialized_start=5060 + _globals['_GENOMEDATATYPEREQUEST']._serialized_end=5126 + _globals['_GENOMEINFOREQUEST']._serialized_start=5129 + _globals['_GENOMEINFOREQUEST']._serialized_end=5266 + _globals['_ORGANISMSGROUPREQUEST']._serialized_start=5268 + _globals['_ORGANISMSGROUPREQUEST']._serialized_end=5316 + _globals['_GENOMETAGREQUEST']._serialized_start=5318 + _globals['_GENOMETAGREQUEST']._serialized_end=5356 + _globals['_FTPLINKSREQUEST']._serialized_start=5358 + _globals['_FTPLINKSREQUEST']._serialized_end=5443 + _globals['_RELEASEVERSIONREQUEST']._serialized_start=5445 + _globals['_RELEASEVERSIONREQUEST']._serialized_end=5536 + _globals['_DATASETATTRIBUTESVALUESREQUEST']._serialized_start=5539 + _globals['_DATASETATTRIBUTESVALUESREQUEST']._serialized_end=5684 + _globals['_ENSEMBLMETADATA']._serialized_start=5687 + _globals['_ENSEMBLMETADATA']._serialized_end=8099 # @@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 0429f15f..9b34aad5 100644 --- a/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py +++ b/src/ensembl/production/metadata/grpc/protobuf_msg_factory.py @@ -201,7 +201,7 @@ def create_attributes_info(data=None): genebuild_method=required_attributes["genebuild.method"], genebuild_method_display=required_attributes["genebuild.method_display"], genebuild_last_geneset_update=required_attributes["genebuild.last_geneset_update"], - genebuild_version=required_attributes["genebuild.provider_version"], + genebuild_provider_version=required_attributes["genebuild.provider_version"], genebuild_provider_name=required_attributes["genebuild.provider_name"], genebuild_provider_url=required_attributes["genebuild.provider_url"], genebuild_sample_gene=required_attributes["genebuild.sample_gene"], @@ -399,7 +399,7 @@ def populate_dataset_info(data=None): dataset_source_type=ds_item.dataset.dataset_source.type if ds_item.dataset.dataset_source else "", dataset_type_name=ds_item.dataset.dataset_type.name, release_version=float(data.release.version) if data.release.version else None, - release_date=datetime.strftime(data.release.release_date, "%m/%d/%Y"), + release_date=datetime.strftime(data.release.release_date, "%m/%d/%Y") if data.release.release_date else None, release_type=data.release.release_type, ) ds_obj_list.append(ds_info) diff --git a/src/tests/databases/core_7/meta.txt b/src/tests/databases/core_7/meta.txt index 579ae4de..c36edf65 100644 --- a/src/tests/databases/core_7/meta.txt +++ b/src/tests/databases/core_7/meta.txt @@ -22,4 +22,4 @@ 24 1 genebuild.start_date 2023-08-Ensembl 25 1 genebuild.havana_datafreeze_date test2 26 \N schema_version 110 -27 1 assembly.total_coding_sequence_length 8989 \ No newline at end of file +27 1 assembly.stats.total_coding_sequence_length 8989 \ No newline at end of file diff --git a/src/tests/databases/core_9/meta.txt b/src/tests/databases/core_9/meta.txt index 1818c24c..89aea89e 100644 --- a/src/tests/databases/core_9/meta.txt +++ b/src/tests/databases/core_9/meta.txt @@ -20,6 +20,6 @@ 20 1 strain.type test 23 1 genome.genome_uuid a733550b-93e7-11ec-a39d-005056b38ce3 24 1 genebuild.havana_datafreeze_date test2 -25 1 assembly.total_genome_length 546 +25 1 assembly.stats.total_genome_length 546 26 1 genebuild.start_date 2023-07-Ensembl 27 \N schema_version 110 diff --git a/src/tests/databases/ensembl_genome_metadata/attribute.txt b/src/tests/databases/ensembl_genome_metadata/attribute.txt index 4f756f21..f3ace3e8 100644 --- a/src/tests/databases/ensembl_genome_metadata/attribute.txt +++ b/src/tests/databases/ensembl_genome_metadata/attribute.txt @@ -1,73 +1,73 @@ 1 assembly.accession assembly.accession assembly.accession string -2 assembly.chromosomes Chromosomes or plasmids Number of structures in cells containing DNA integer -3 assembly.component_sequences Component sequences Part of the primary sequences in assembly integer -4 assembly.contig_n50 Contig N50 Median size of contigs in a genome assembly bp +2 assembly.stats.chromosomes Chromosomes or plasmids Number of structures in cells containing DNA integer +3 assembly.stats.component_sequences Component sequences Part of the primary sequences in assembly integer +4 assembly.stats.contig_n50 Contig N50 Median size of contigs in a genome assembly bp 5 assembly.date assembly.date assembly.date string 6 assembly.default assembly.default assembly.default string -7 assembly.gc_percentage Average GC content Percentage of nucleotides in DNA that are G or C percent +7 assembly.stats.gc_percentage Average GC content Percentage of nucleotides in DNA that are G or C percent 8 assembly.is_reference assembly.is_reference assembly.is_reference string 9 assembly.level assembly.level assembly.level string 10 assembly.mapping assembly.mapping assembly.mapping string 11 assembly.name assembly.name assembly.name string 12 assembly.provider_name assembly.provider_name assembly.provider_name string 13 assembly.provider_url assembly.provider_url assembly.provider_url string -14 assembly.spanned_gaps Spanned gaps Number of gaps covered by sequencing reads integer +14 assembly.stats.spanned_gaps Spanned gaps Number of gaps covered by sequencing reads integer 15 assembly.tolid assembly.tolid assembly.tolid string -16 assembly.toplevel_sequences Top level sequences Primary sequences in a genome assembly integer -17 assembly.total_coding_sequence_length Total coding sequence length Total length of all coding sequences bp -18 assembly.total_gap_length Total gap length Total length of all gaps in a genome assembly bp -19 assembly.total_genome_length Total genome length Total length of all genomic sequences bp +16 assembly.stats.toplevel_sequences Top level sequences Primary sequences in a genome assembly integer +17 assembly.stats.total_coding_sequence_length Total coding sequence length Total length of all coding sequences bp +18 assembly.stats.total_gap_length Total gap length Total length of all gaps in a genome assembly bp +19 assembly.stats.total_genome_length Total genome length Total length of all genomic sequences bp 20 assembly.ucsc_alias assembly.ucsc_alias assembly.ucsc_alias string -21 genebuild.average_cds_length Average CDS length Average length of coding sequences float +21 genebuild.stats.average_cds_length Average CDS length Average length of coding sequences float 22 genebuild.average_coding_exons_per_coding_gene Average coding exons per coding gene Average coding exons per coding gene string -23 genebuild.average_coding_exons_per_transcript Average coding exons per transcript Average coding exons per coding transcript float -24 genebuild.average_coding_exon_length Average exon length per coding gene Average length of coding exons bp -25 genebuild.average_exon_length Average exon length Average length of exons bp -26 genebuild.average_genomic_span Average coding genomic span Average length of all genomic regions bp -27 genebuild.average_intron_length Average intron length Average intron length per coding gene bp +23 genebuild.stats.average_coding_exons_per_transcript Average coding exons per transcript Average coding exons per coding transcript float +24 genebuild.stats.average_coding_exon_length Average exon length per coding gene Average length of coding exons bp +25 genebuild.stats.average_exon_length Average exon length Average length of exons bp +26 genebuild.stats.average_genomic_span Average coding genomic span Average length of all genomic regions bp +27 genebuild.stats.average_intron_length Average intron length Average intron length per coding gene bp 28 genebuild.average_sequence_legth Average coding sequence length Average length of sequences in genome bp -29 genebuild.coding_genes Coding genes Genes that code for proteins integer -30 genebuild.coding_transcripts Coding transcripts Transcripts that code for proteins integer -31 genebuild.coding_transcripts_per_gene Average coding transcripts per gene Average coding transcripts per gene float +29 genebuild.stats.coding_genes Coding genes Genes that code for proteins integer +30 genebuild.stats.coding_transcripts Coding transcripts Transcripts that code for proteins integer +31 genebuild.stats.coding_transcripts_per_gene Average coding transcripts per gene Average coding transcripts per gene float 32 genebuild.hash genebuild.hash genebuild.hash string 33 genebuild.initial_release_date genebuild.initial_release_date genebuild.initial_release_date string 34 genebuild.last_geneset_update genebuild.last_geneset_update genebuild.last_geneset_update string 35 genebuild.level genebuild.level genebuild.level string -36 genebuild.longest_gene_length Longest coding gene Length of longest gene bp +36 genebuild.stats.longest_gene_length Longest coding gene Length of longest gene bp 37 genebuild.method genebuild.method genebuild.method string 38 genebuild.method_display genebuild.method_display genebuild.method_display string -39 genebuild.nc_average_exons_per_transcript Average exons per non-coding transcript Mean exon count per transcript float -40 genebuild.nc_average_exon_length Average exon length per non-coding transcript Mean exon length bp -41 genebuild.nc_average_genomic_span Average non-coding genomic span Mean length of all genomic regions bp -42 genebuild.nc_average_sequence_length Average non-coding sequence length Mean length of all sequences bp -43 genebuild.nc_longest_gene_length Longest non-coding gene Length of longest non-coding gene bp -44 genebuild.nc_long_non_coding_genes Long non-coding genes Long genes not coding for proteins integer -45 genebuild.nc_misc_non_coding_genes Misc. non-coding genes Miscellaneous non-coding genes integer -46 genebuild.nc_non_coding_genes Non-coding genes Genes that don't code for proteins integer -47 genebuild.nc_shortest_gene_length Shortest non-coding gene Length of shortest gene bp -48 genebuild.nc_small_non_coding_genes Small non-coding genes Small genes not coding for proteins integer -49 genebuild.nc_total_introns Introns in non-coding genes Total intron count integer -50 genebuild.nc_total_transcripts Non-coding transcripts Total RNA transcript count integer -51 genebuild.nc_transcripts_per_gene Average transcripts per non-coding gene Mean transcripts count per gene float -52 genebuild.ps_average_exons_per_transcript Average intron length per pseudogene Mean exon count per pseudogene transcript float -53 genebuild.ps_average_exon_length Average exon length per pseudogene Mean pseudogene exon length bp -54 genebuild.ps_average_genomic_span Average pseudogene genomic span Mean length of pseudogene regions bp -55 genebuild.ps_average_intron_length Average intron length per pseudogene Mean pseudogene intron length bp -56 genebuild.ps_average_sequence_length Average pseudogene sequence length Mean length of pseudogene sequences bp -57 genebuild.ps_longest_gene_length Longest pseudogene Length of longest pseudogene bp -58 genebuild.ps_pseudogenes Pseudogenes Genes which don't code functional protiens integer -59 genebuild.ps_shortest_gene_length Shortest pseudogene Length of shortest pseudogene bp -60 genebuild.ps_total_exons Exons in pseudogenes Total exon count in pseudogenes integer -61 genebuild.ps_total_introns Introns in pseudogenes Total intron count in pseudogenes integer -62 genebuild.ps_total_transcripts Transcripts in pseudogenes Total pseudogene RNA transcript count integer -63 genebuild.ps_transcripts_per_gene Average transcripts per pseudogene Mean pseudogene transcripts count per pseudogene float -64 genebuild.shortest_gene_length Shortest coding gene Length of shortest gene bp +39 genebuild.stats.nc_average_exons_per_transcript Average exons per non-coding transcript Mean exon count per transcript float +40 genebuild.stats.nc_average_exon_length Average exon length per non-coding transcript Mean exon length bp +41 genebuild.stats.nc_average_genomic_span Average non-coding genomic span Mean length of all genomic regions bp +42 genebuild.stats.nc_average_sequence_length Average non-coding sequence length Mean length of all sequences bp +43 genebuild.stats.nc_longest_gene_length Longest non-coding gene Length of longest non-coding gene bp +44 genebuild.stats.nc_long_non_coding_genes Long non-coding genes Long genes not coding for proteins integer +45 genebuild.stats.nc_misc_non_coding_genes Misc. non-coding genes Miscellaneous non-coding genes integer +46 genebuild.stats.nc_non_coding_genes Non-coding genes Genes that don't code for proteins integer +47 genebuild.stats.nc_shortest_gene_length Shortest non-coding gene Length of shortest gene bp +48 genebuild.stats.nc_small_non_coding_genes Small non-coding genes Small genes not coding for proteins integer +49 genebuild.stats.nc_total_introns Introns in non-coding genes Total intron count integer +50 genebuild.stats.nc_total_transcripts Non-coding transcripts Total RNA transcript count integer +51 genebuild.stats.nc_transcripts_per_gene Average transcripts per non-coding gene Mean transcripts count per gene float +52 genebuild.stats.ps_average_exons_per_transcript Average intron length per pseudogene Mean exon count per pseudogene transcript float +53 genebuild.stats.ps_average_exon_length Average exon length per pseudogene Mean pseudogene exon length bp +54 genebuild.stats.ps_average_genomic_span Average pseudogene genomic span Mean length of pseudogene regions bp +55 genebuild.stats.ps_average_intron_length Average intron length per pseudogene Mean pseudogene intron length bp +56 genebuild.stats.ps_average_sequence_length Average pseudogene sequence length Mean length of pseudogene sequences bp +57 genebuild.stats.ps_longest_gene_length Longest pseudogene Length of longest pseudogene bp +58 genebuild.stats.ps_pseudogenes Pseudogenes Genes which don't code functional protiens integer +59 genebuild.stats.ps_shortest_gene_length Shortest pseudogene Length of shortest pseudogene bp +60 genebuild.stats.ps_total_exons Exons in pseudogenes Total exon count in pseudogenes integer +61 genebuild.stats.ps_total_introns Introns in pseudogenes Total intron count in pseudogenes integer +62 genebuild.stats.ps_total_transcripts Transcripts in pseudogenes Total pseudogene RNA transcript count integer +63 genebuild.stats.ps_transcripts_per_gene Average transcripts per pseudogene Mean pseudogene transcripts count per pseudogene float +64 genebuild.stats.shortest_gene_length Shortest coding gene Length of shortest gene bp 65 genebuild.start_date genebuild.start_date genebuild.start_date string -66 genebuild.total_coding_exons Exons in coding genes Total number of coding exons integer -67 genebuild.total_exons Exons in genes Total number of exons integer -68 genebuild.total_introns Introns in coding genes Total number of introns integer -69 genebuild.total_transcripts Transcripts in coding genes Total number of RNA transcripts integer -70 genebuild.transcripts_per_gene Average transcripts per coding gene Average number of transcripts per gene float +66 genebuild.stats.total_coding_exons Exons in coding genes Total number of coding exons integer +67 genebuild.stats.total_exons Exons in genes Total number of exons integer +68 genebuild.stats.total_introns Introns in coding genes Total number of introns integer +69 genebuild.stats.total_transcripts Transcripts in coding genes Total number of RNA transcripts integer +70 genebuild.stats.transcripts_per_gene Average transcripts per coding gene Average number of transcripts per gene float 71 genebuild.version genebuild.version genebuild.version string 72 genebuild.sample_gene genebuild.sample_gene Sample Gene Data string 73 genebuild.sample_location genebuild.sample_location Sample Location Data string @@ -75,7 +75,7 @@ 75 assembly.web_accession_source assembly.web_accession_source assembly.web_accession_source string 76 assembly.web_accession_type assembly.web_accession_type assembly.web_accession_type string 77 genebuild.id genebuild.id genebuild.id string -78 genebuild.nc_average_intron_length Average intron length per non-coding transcript Mean intron length bp +78 genebuild.stats.nc_average_intron_length Average intron length per non-coding transcript Mean intron length bp 79 genebuild.projection_source_db genebuild.projection_source_db genebuild.projection_source_db string 80 assembly.long_name assembly.long_name assembly.long_name string 81 assembly.url_name assembly.url_name assembly.url_name string @@ -83,19 +83,19 @@ 83 assembly.version assembly.version assembly.version string 84 genebuild.provider_name genebuild.provider_name genebuild.provider_name string 85 genebuild.provider_url genebuild.provider_url genebuild.provider_url string -119 variation.short_variants Short variants Small-scale genetic variations integer +119 variation.stats.short_variants Short variants Small-scale genetic variations integer 120 variation.sample_variant variation.sample_variant variation.sample_variant string -123 variation.short_variants_with_phenotype_assertions Short variation with phenotype assertion Short variation with phenotype assertion string -161 compara.homology_coverage compara.homology_coverage compara.homology_coverage float +123 variation.stats.short_variants_with_phenotype_assertions Short variation with phenotype assertion Short variation with phenotype assertion string +161 compara.stats.homology_coverage compara.stats.homology_coverage compara.stats.homology_coverage float 162 compara.homology_reference_species compara.homology_reference_species compara.homology_reference_species string 163 regulation.open_chromatin_count regulation.open_chromatin_count Number of open chromatin regions integer -164 regulation.promoter_count regulation.promoter_count Number of promoters integer -165 regulation.enhancer_count regulation.enhancer_count Number of enhancers integer -166 regulation.ctcf_count regulation.ctcf_count Number of CTCF binding sites integer +164 regulation.stats.promoter_count regulation.stats.promoter_count Number of promoters integer +165 regulation.stats.enhancer_count regulation.stats.enhancer_count Number of enhancers integer +166 regulation.stats.ctcf_count regulation.stats.ctcf_count Number of CTCF binding sites integer 167 regulation.tfbs_count regulation.tfbs_count Number of regions enriched for transcription factor binding integer 168 assembly.tol_id assembly.tol_id assembly.tol_id string 169 genebuild.annotation_source genebuild.annotation_source genebuild.annotation_source string -170 genebuild.nc_total_exons Exons in non-coding genes Total exon count integer +170 genebuild.stats.nc_total_exons Exons in non-coding genes Total exon count integer 179 assembly.description assembly.description assembly.description string 180 assembly.master_accession assembly.master_accession assembly.master_accession string 181 assembly.alt_accession assembly.alt_accession assembly.alt_accession string diff --git a/src/tests/test_dataset_factory.py b/src/tests/test_dataset_factory.py index 7268c1c6..1d078242 100644 --- a/src/tests/test_dataset_factory.py +++ b/src/tests/test_dataset_factory.py @@ -35,7 +35,7 @@ def test_update_dataset_attributes(self, test_dbs, dataset_factory): metadata_db = DBConnection(test_dbs['ensembl_genome_metadata'].dbc.url) with metadata_db.session_scope() as session: test_uuid = session.query(Dataset.dataset_uuid).filter(Dataset.dataset_id == 1).scalar() - test_attributes = {"assembly.contig_n50": "test1", "assembly.total_genome_length": "test2"} + test_attributes = {"assembly.stats.contig_n50": "test1", "assembly.stats.total_genome_length": "test2"} dataset_attribute = dataset_factory.update_dataset_attributes(test_uuid, test_attributes) for attrib in dataset_attribute: session.add(attrib) @@ -46,11 +46,11 @@ def test_update_dataset_attributes(self, test_dbs, dataset_factory): dataset_attribute = session.query(DatasetAttribute) \ .join(Attribute, DatasetAttribute.attribute_id == Attribute.attribute_id) \ .filter(DatasetAttribute.dataset_id == dataset.dataset_id, - Attribute.name == 'assembly.contig_n50', + Attribute.name == 'assembly.stats.contig_n50', DatasetAttribute.value == 'test1') \ .one_or_none() assert dataset_attribute is not None - test_attributes = {"assembly.gc_percentage": "test3", "genebuild.nc_longest_gene_length": "test4"} + test_attributes = {"assembly.stats.gc_percentage": "test3", "genebuild.stats.nc_longest_gene_length": "test4"} dataset_attribute = dataset_factory.update_dataset_attributes(test_uuid, test_attributes, session=session) for attrib in dataset_attribute: session.add(attrib) @@ -59,7 +59,7 @@ def test_update_dataset_attributes(self, test_dbs, dataset_factory): test_attribute = session.query(DatasetAttribute) \ .join(Attribute, DatasetAttribute.attribute_id == Attribute.attribute_id) \ .filter(DatasetAttribute.dataset_id == dataset.dataset_id, - Attribute.name == 'genebuild.nc_longest_gene_length', + Attribute.name == 'genebuild.stats.nc_longest_gene_length', DatasetAttribute.value == 'test4') \ .one_or_none() assert test_attribute is not None @@ -67,7 +67,7 @@ def test_update_dataset_attributes(self, test_dbs, dataset_factory): def test_create_dataset(self, test_dbs, dataset_factory): metadata_db = DBConnection(test_dbs['ensembl_genome_metadata'].dbc.url) with metadata_db.session_scope() as session: - test_attributes = {"assembly.contig_n50": "test1", "assembly.total_genome_length": "test2"} + test_attributes = {"assembly.stats.contig_n50": "test1", "assembly.stats.total_genome_length": "test2"} test_genome_uuid = session.query(Genome.genome_uuid).filter(Genome.genome_id == 4).scalar() # one human test_dataset_source = session.query(DatasetSource).filter( DatasetSource.name == 'homo_sapiens_gca018473315v1_core_110_1').one() @@ -96,7 +96,7 @@ def test_create_dataset(self, test_dbs, dataset_factory): test_attribute = session.query(DatasetAttribute) \ .join(Attribute, DatasetAttribute.attribute_id == Attribute.attribute_id) \ .filter(DatasetAttribute.dataset_id == created_dataset.dataset_id, - Attribute.name == 'genebuild.nc_longest_gene_length', + Attribute.name == 'genebuild.stats.nc_longest_gene_length', DatasetAttribute.value == 'test4') \ .all() assert test_attribute is not None diff --git a/src/tests/test_updater.py b/src/tests/test_updater.py index 8977eb30..e513d964 100644 --- a/src/tests/test_updater.py +++ b/src/tests/test_updater.py @@ -244,7 +244,7 @@ def test_update_released_force(self, test_dbs): assert count == 1 # Check that the old attributes are gone count = session.query(DatasetAttribute).join(Attribute).filter( - Attribute.name == 'assembly.total_coding_sequence_length', + Attribute.name == 'assembly.stats.total_coding_sequence_length', DatasetAttribute.value == '8989' ).count() assert count == 0 diff --git a/src/tests/test_utils.py b/src/tests/test_utils.py index 1b94dc30..746b1a1d 100644 --- a/src/tests/test_utils.py +++ b/src/tests/test_utils.py @@ -170,17 +170,17 @@ def test_get_top_level_statistics(self, genome_conn, allow_unreleased, organism_ 'statisticValue': 'GCA_900519105.1' } assembly_accession_stats = [stat for stat in output['statsByGenomeUuid'][0]['statistics'] if - stat['name'] == 'assembly.chromosomes'] + stat['name'] == 'assembly.stats.chromosomes'] assert len(assembly_accession_stats) == expected_count assert assembly_accession_stats[0] == { 'label': 'Chromosomes or plasmids', - 'name': 'assembly.chromosomes', + 'name': 'assembly.stats.chromosomes', 'statisticType': 'integer', 'statisticValue': '22' } assembly_homology_stats = [stat for stat in output['statsByGenomeUuid'][0]['statistics'] if - stat['name'] == 'compara.homology_coverage'] + stat['name'] == 'compara.stats.homology_coverage'] assert len(assembly_homology_stats) == 1 if not allow_unreleased else 2 def test_get_top_level_statistics_by_uuid(self, genome_conn): @@ -200,11 +200,11 @@ def test_get_top_level_statistics_by_uuid(self, genome_conn): 'statisticValue': 'GCA_900519105.1' } assembly_component_sequences = [stat for stat in output['statistics'] if - stat['name'] == 'assembly.component_sequences'] + stat['name'] == 'assembly.stats.component_sequences'] assert len(assembly_component_sequences) == 1 assert assembly_component_sequences[0] == { 'label': 'Component sequences', - 'name': 'assembly.component_sequences', + 'name': 'assembly.stats.component_sequences', 'statisticType': 'integer', 'statisticValue': '22' } @@ -390,7 +390,7 @@ def test_get_attributes_by_genome_uuid(self, genome_conn, allow_unreleased, geno 'genebuildMethod', 'genebuildMethodDisplay', 'genebuildLastGenesetUpdate', - 'genebuildVersion', + 'genebuildProviderVersion', 'genebuildProviderName', 'genebuildProviderUrl', 'genebuildSampleGene', @@ -475,7 +475,7 @@ def test_get_genomes_by_name(self, genome_conn): 'genebuildMethodDisplay': 'Mapping from reference', 'genebuildProviderName': 'Ensembl', 'genebuildProviderUrl': 'https://rapid.ensembl.org/info/genome/genebuild/full_genebuild.html', - 'genebuildVersion': 'ENS01', + 'genebuildProviderVersion': 'ENS01', 'variationSampleVariant': 'JAGYYT010000001.1:2643538:rs1423484253' Args: genome_conn: @@ -503,7 +503,7 @@ def test_get_genomes_by_name(self, genome_conn): 'genebuildMethodDisplay': 'Mapping from reference', 'genebuildProviderName': 'Ensembl', 'genebuildProviderUrl': 'https://rapid.ensembl.org/info/genome/genebuild/full_genebuild.html', - 'genebuildVersion': 'ENS01', + 'genebuildProviderVersion': 'ENS01', 'variationSampleVariant': 'JAGYYT010000001.1:2643538:rs1423484253' }, 'created': '2023-09-22 15:02:01', @@ -574,7 +574,7 @@ def test_get_genomes_by_name_release_unspecified(self, genome_conn): 'genebuildProviderUrl': 'https://wormbase.org/', 'genebuildSampleGene': 'WBGene00004893', 'genebuildSampleLocation': 'X:937766-957832', - 'genebuildVersion': 'EXT01' + 'genebuildProviderVersion': 'EXT01' }, 'created': '2023-09-22 15:06:58', 'genomeUuid': 'a733550b-93e7-11ec-a39d-005056b38ce3',