diff --git a/backend/cases_import/tests/snapshots/snap_test_models_executor.py b/backend/cases_import/tests/snapshots/snap_test_models_executor.py index ea8583b00..ece81c52a 100644 --- a/backend/cases_import/tests/snapshots/snap_test_models_executor.py +++ b/backend/cases_import/tests/snapshots/snap_test_models_executor.py @@ -32,3 +32,131 @@ "sex": 2, }, ] + +snapshots["ImportCreateWithSeqvarsVcfTest::test_run external files"] = [ + { + "available": None, + "designation": "variant_calls", + "file_attributes": { + "checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "variant_type": "seqvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "file://cases_import/tests/data/sample-brca1.vcf.gz", + }, + { + "available": None, + "designation": "variant_calls", + "file_attributes": { + "checksum": "sha256:6b137335b7803623c3389424e7b64d704fb1c9f3f55792db2916d312e2da27ef", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "variant_type": "seqvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "path": "file://cases_import/tests/data/sample-brca1.vcf.gz.tbi", + }, +] + +snapshots["ImportCreateWithSeqvarsVcfTest::test_run internal files"] = [ + { + "checksum": None, + "designation": "variant_calls/seqvars/orig-copy", + "file_attributes": { + "checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "variant_type": "seqvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/external-copy-0.vcf.gz", + }, + { + "checksum": None, + "designation": "variant_calls/seqvars/ingested-vcf", + "file_attributes": {}, + "identifier_map": {}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/ingested.vcf.gz", + }, + { + "checksum": None, + "designation": "variant_calls/seqvars/ingested-tbi", + "file_attributes": {}, + "identifier_map": {}, + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/seqvars/ingested.vcf.gz.tbi", + }, +] + +snapshots["ImportCreateWithStrucvarsVcfTest::test_run external files"] = [ + { + "available": None, + "designation": "variant_calls", + "file_attributes": { + "checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "variant_type": "strucvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "file://cases_import/tests/data/sample-brca1.vcf.gz", + }, + { + "available": None, + "designation": "variant_calls", + "file_attributes": { + "checksum": "sha256:6b137335b7803623c3389424e7b64d704fb1c9f3f55792db2916d312e2da27ef", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "variant_type": "strucvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "path": "file://cases_import/tests/data/sample-brca1.vcf.gz.tbi", + }, +] + +snapshots["ImportCreateWithStrucvarsVcfTest::test_run internal files"] = [ + { + "checksum": None, + "designation": "variant_calls/strucvars/orig-copy", + "file_attributes": { + "checksum": "sha256:4042c2afa59f24a327b3852bfcd0d8d991499d9c4eb81e7a7efe8d081e66af82", + "designation": "variant_calls", + "genomebuild": "grch37", + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "variant_type": "strucvars", + }, + "identifier_map": {"index": "NA12878-PCRF450-1"}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/external-copy-0.vcf.gz", + }, + { + "checksum": None, + "designation": "variant_calls/strucvars/ingested-vcf", + "file_attributes": {}, + "identifier_map": {}, + "mimetype": "text/plain+x-bgzip+x-variant-call-format", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/ingested.vcf.gz", + }, + { + "checksum": None, + "designation": "variant_calls/strucvars/ingested-tbi", + "file_attributes": {}, + "identifier_map": {}, + "mimetype": "application/octet-stream+x-tabix-tbi-index", + "path": "case-data/7a/1d7b28-2bf8-4340-81f3-5487d86c669f/c28a70a6-1c75-40a1-8d89-216ca16cffca/strucvars/ingested.vcf.gz.tbi", + }, +] diff --git a/backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py b/backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py new file mode 100644 index 000000000..d374f0db8 --- /dev/null +++ b/backend/ext_gestaltmatcher/migrations/0003_auto_20241009_0639.py @@ -0,0 +1,27 @@ +# Generated by Django 3.2.25 on 2024-10-09 06:39 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("ext_gestaltmatcher", "0002_smallvariantquerypediascores"), + ] + + operations = [ + migrations.AlterField( + model_name="smallvariantquerygestaltmatcherscores", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + migrations.AlterField( + model_name="smallvariantquerypediascores", + name="id", + field=models.BigAutoField( + auto_created=True, primary_key=True, serialize=False, verbose_name="ID" + ), + ), + ] diff --git a/backend/protos/seqvars/protos/output.proto b/backend/protos/seqvars/protos/output.proto index ea7ba8e9d..449abd7a4 100644 --- a/backend/protos/seqvars/protos/output.proto +++ b/backend/protos/seqvars/protos/output.proto @@ -166,12 +166,32 @@ message GeneRelatedConsequences { repeated seqvars.pbs.query.Consequence consequences = 3; } +// Enumerations with modes of inheritance from HPO. +enum ModeOfInheritance { + // Unspecified mode of inheritance. + MODE_OF_INHERITANCE_UNSPECIFIED = 0; + // Autosomal dominant inheritance (HP:0000006). + MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT = 1; + // Autosomal recessive inheritance (HP:0000007). + MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE = 2; + // X-linked dominant inheritance (HP:0001419). + MODE_OF_INHERITANCE_X_LINKED_DOMINANT = 3; + // X-linked recessive inheritance (HP:0001423). + MODE_OF_INHERITANCE_X_LINKED_RECESSIVE = 4; + // Y-linked inheritance (HP:0001450). + MODE_OF_INHERITANCE_Y_LINKED = 5; + // Mitochondrial inheritance (HP:0001427). + MODE_OF_INHERITANCE_MITOCHONDRIAL = 6; +} + // Phenotype-related information, if any. message GeneRelatedPhenotypes { // ACMG supplementary finding list. bool is_acmg_sf = 1; // Whether is a known disease gene. bool is_disease_gene = 2; + // Linked modes of inheritance. + repeated ModeOfInheritance mode_of_inheritances = 3; } // Gene-wise constraints. diff --git a/backend/seqvars/migrations/0010_auto_20240905_1017.py b/backend/seqvars/migrations/0010_auto_20240905_1017.py new file mode 100644 index 000000000..8ce2467c8 --- /dev/null +++ b/backend/seqvars/migrations/0010_auto_20240905_1017.py @@ -0,0 +1,32 @@ +# Generated by Django 3.2.25 on 2024-09-05 10:17 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ("seqvars", "0009_alter_seqvarsresultrow_genome_release"), + ] + + operations = [ + migrations.AlterModelOptions( + name="seqvarsqueryexecutionbackgroundjob", + options={"ordering": ["-pk"]}, + ), + migrations.AlterModelOptions( + name="seqvarsresultrow", + options={"ordering": ["chrom_no", "pos", "ref_allele", "alt_allele"]}, + ), + migrations.AlterModelOptions( + name="seqvarsresultset", + options={"ordering": ["-date_created"]}, + ), + migrations.AlterField( + model_name="seqvarsresultrow", + name="genome_release", + field=models.CharField( + choices=[("grch37", "GRCh37"), ("grch38", "GRCh38")], max_length=32 + ), + ), + ] diff --git a/backend/seqvars/models/base.py b/backend/seqvars/models/base.py index 2f935b851..073a99078 100644 --- a/backend/seqvars/models/base.py +++ b/backend/seqvars/models/base.py @@ -2055,6 +2055,17 @@ class GeneRelatedConsequencesPydantic(pydantic.BaseModel): consequences: list[SeqvarsVariantConsequenceChoice] +class SeqvarsModeOfInheritance(str, Enum): + """Mode of inheritance gene annotation.""" + + AUTOSOMAL_DOMINANT = "autosomal_dominant" + AUTOSOMAL_RECESSIVE = "autosomal_recessive" + X_LINKED_DOMINANT = "x_linked_dominant" + X_LINKED_RECESSIVE = "x_linked_recessive" + Y_LINKED = "y_linked" + MITOCHONDRIAL = "mitochondrial" + + class GeneRelatedPhenotypesPydantic(pydantic.BaseModel): """Phenotype-related information, if any.""" @@ -2062,6 +2073,8 @@ class GeneRelatedPhenotypesPydantic(pydantic.BaseModel): is_acmg_sf: bool = False #: Whether is a known disease gene. is_disease_gene: bool = False + #: Modes of inheritance. + mode_of_inheritances: list[SeqvarsModeOfInheritance] = [] class GnomadConstraintsPydantic(pydantic.BaseModel): @@ -2161,13 +2174,13 @@ class GeneRelatedAnnotationPydantic(pydantic.BaseModel): """Store gene-related annotation (always for a single gene).""" #: Gene ID information. - identity: GeneIdentityPydantic + identity: typing.Optional[GeneIdentityPydantic] #: Gene-related consequences, if any (none if intergenic). - consequences: GeneRelatedConsequencesPydantic + consequences: typing.Optional[GeneRelatedConsequencesPydantic] #: Gene-related phenotype information, if any. - phenotypes: GeneRelatedPhenotypesPydantic + phenotypes: typing.Optional[GeneRelatedPhenotypesPydantic] #: Gene-wise constraints on the gene, if any. - constraints: GeneRelatedConstraintsPydantic + constraints: typing.Optional[GeneRelatedConstraintsPydantic] class SeqvarsNuclearFrequencyPydantic(pydantic.BaseModel): @@ -2373,6 +2386,9 @@ def get_absolute_url(self) -> str: def __str__(self): return f"SeqvarsResultSet '{self.sodar_uuid}'" + class Meta: + ordering = ["-date_created"] + class SeqvarsResultRow(models.Model): """One entry in the result set.""" @@ -2414,6 +2430,9 @@ def __str__(self): f"{self.pos}-{self.ref_allele}-{self.alt_allele}'" ) + class Meta: + ordering = ["chrom_no", "pos", "ref_allele", "alt_allele"] + class SeqvarsQueryExecutionBackgroundJobManager(models.Manager): """Custom manager class that allows to create a ``SeqvarsQueryExeuctionBackgroundJob`` @@ -2478,3 +2497,6 @@ class SeqvarsQueryExecutionBackgroundJob(JobModelMessageMixin, models.Model): def get_human_readable_type(self): return self.task_desc + + class Meta: + ordering = ["-pk"] diff --git a/backend/seqvars/models/protobufs.py b/backend/seqvars/models/protobufs.py index 15873bc13..0b65932de 100644 --- a/backend/seqvars/models/protobufs.py +++ b/backend/seqvars/models/protobufs.py @@ -32,6 +32,7 @@ SeqvarsGnomadMitochondrialFrequencySettingsPydantic, SeqvarsHelixMtDbFrequencyPydantic, SeqvarsHelixMtDbFrequencySettingsPydantic, + SeqvarsModeOfInheritance, SeqvarsNuclearFrequencyPydantic, SeqvarsNuclearFrequencySettingsPydantic, SeqvarsOutputHeaderPydantic, @@ -84,6 +85,7 @@ GnomadConstraints, GnomadMitochondrialFrequency, HelixMtDbFrequency, + ModeOfInheritance, NuclearFrequency, OutputHeader, OutputRecord, @@ -772,10 +774,31 @@ def _consequences_from_protobuf( ) +MODE_OF_INHERITANCE_MAPPING: dict[ + ModeOfInheritance.ValueType : SeqvarsVariantScoreColumnTypeChoice +] = { + ModeOfInheritance.MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT: SeqvarsModeOfInheritance.AUTOSOMAL_DOMINANT, + ModeOfInheritance.MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE: SeqvarsModeOfInheritance.AUTOSOMAL_RECESSIVE, + ModeOfInheritance.MODE_OF_INHERITANCE_X_LINKED_DOMINANT: SeqvarsModeOfInheritance.X_LINKED_DOMINANT, + ModeOfInheritance.MODE_OF_INHERITANCE_X_LINKED_RECESSIVE: SeqvarsModeOfInheritance.X_LINKED_RECESSIVE, + ModeOfInheritance.MODE_OF_INHERITANCE_Y_LINKED: SeqvarsModeOfInheritance.Y_LINKED, + ModeOfInheritance.MODE_OF_INHERITANCE_MITOCHONDRIAL: SeqvarsModeOfInheritance.MITOCHONDRIAL, +} + + +def _mode_of_inheritance_from_protobuf( + mode_of_inheritance: ModeOfInheritance.ValueType, +) -> SeqvarsModeOfInheritance: + return MODE_OF_INHERITANCE_MAPPING[mode_of_inheritance] + + def _phenotypes_from_protobuf(phenotypes: GeneRelatedPhenotypes) -> GeneRelatedPhenotypesPydantic: return GeneRelatedPhenotypesPydantic( is_acmg_sf=phenotypes.is_acmg_sf, is_disease_gene=phenotypes.is_disease_gene, + mode_of_inheritances=list( + map(_mode_of_inheritance_from_protobuf, phenotypes.mode_of_inheritances) + ), ) diff --git a/backend/seqvars/protos/output_pb2.py b/backend/seqvars/protos/output_pb2.py index 12b6163da..55cec74c5 100644 --- a/backend/seqvars/protos/output_pb2.py +++ b/backend/seqvars/protos/output_pb2.py @@ -18,7 +18,7 @@ from seqvars.protos import query_pb2 as seqvars_dot_protos_dot_query__pb2 DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile( - b'\n\x1bseqvars/protos/output.proto\x12\x12seqvars.pbs.output\x1a\x1cgoogle/protobuf/struct.proto\x1a\x1fgoogle/protobuf/timestamp.proto\x1a\x1aseqvars/protos/query.proto"\xaa\x03\n\x0cOutputHeader\x12\x39\n\x0egenome_release\x18\x01 \x01(\x0e\x32!.seqvars.pbs.output.GenomeRelease\x12\x32\n\x08versions\x18\x02 \x03(\x0b\x32 .seqvars.pbs.output.VersionEntry\x12\x30\n\x05query\x18\x03 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) _globals = globals() @@ -26,14 +26,16 @@ _builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, "seqvars.protos.output_pb2", _globals) if _descriptor._USE_C_DESCRIPTORS == False: DESCRIPTOR._options = None - _globals["_VARIANTSCORECOLUMNTYPE"]._serialized_start = 4904 - _globals["_VARIANTSCORECOLUMNTYPE"]._serialized_end = 5047 - _globals["_GENOMERELEASE"]._serialized_start = 5049 - _globals["_GENOMERELEASE"]._serialized_end = 5150 - _globals["_CLINGENDOSAGESCORE"]._serialized_start = 5153 - _globals["_CLINGENDOSAGESCORE"]._serialized_end = 5478 - _globals["_AGGREGATEGERMLINEREVIEWSTATUS"]._serialized_start = 5481 - _globals["_AGGREGATEGERMLINEREVIEWSTATUS"]._serialized_end = 6221 + _globals["_VARIANTSCORECOLUMNTYPE"]._serialized_start = 4974 + _globals["_VARIANTSCORECOLUMNTYPE"]._serialized_end = 5117 + _globals["_GENOMERELEASE"]._serialized_start = 5119 + _globals["_GENOMERELEASE"]._serialized_end = 5220 + _globals["_MODEOFINHERITANCE"]._serialized_start = 5223 + _globals["_MODEOFINHERITANCE"]._serialized_end = 5528 + _globals["_CLINGENDOSAGESCORE"]._serialized_start = 5531 + _globals["_CLINGENDOSAGESCORE"]._serialized_end = 5856 + _globals["_AGGREGATEGERMLINEREVIEWSTATUS"]._serialized_start = 5859 + _globals["_AGGREGATEGERMLINEREVIEWSTATUS"]._serialized_end = 6599 _globals["_OUTPUTHEADER"]._serialized_start = 143 _globals["_OUTPUTHEADER"]._serialized_end = 569 _globals["_VARIANTSCORECOLUMN"]._serialized_start = 572 @@ -58,40 +60,40 @@ _globals["_GENEIDENTITY"]._serialized_end = 2171 _globals["_GENERELATEDCONSEQUENCES"]._serialized_start = 2174 _globals["_GENERELATEDCONSEQUENCES"]._serialized_end = 2317 - _globals["_GENERELATEDPHENOTYPES"]._serialized_start = 2319 - _globals["_GENERELATEDPHENOTYPES"]._serialized_end = 2387 - _globals["_GENERELATEDCONSTRAINTS"]._serialized_start = 2390 - _globals["_GENERELATEDCONSTRAINTS"]._serialized_end = 2771 - _globals["_GNOMADCONSTRAINTS"]._serialized_start = 2774 - _globals["_GNOMADCONSTRAINTS"]._serialized_end = 2956 - _globals["_DECIPHERCONSTRAINTS"]._serialized_start = 2958 - _globals["_DECIPHERCONSTRAINTS"]._serialized_end = 3011 - _globals["_RCNVCONSTRAINTS"]._serialized_start = 3013 - _globals["_RCNVCONSTRAINTS"]._serialized_end = 3065 - _globals["_SHETCONSTRAINTS"]._serialized_start = 3067 - _globals["_SHETCONSTRAINTS"]._serialized_end = 3099 - _globals["_CLINGENDOSAGEANNOTATION"]._serialized_start = 3102 - _globals["_CLINGENDOSAGEANNOTATION"]._serialized_end = 3238 - _globals["_VARIANTRELATEDANNOTATION"]._serialized_start = 3241 - _globals["_VARIANTRELATEDANNOTATION"]._serialized_end = 3546 - _globals["_FREQUENCYANNOTATION"]._serialized_start = 3549 - _globals["_FREQUENCYANNOTATION"]._serialized_end = 3984 - _globals["_NUCLEARFREQUENCY"]._serialized_start = 3986 - _globals["_NUCLEARFREQUENCY"]._serialized_end = 4074 - _globals["_GNOMADMITOCHONDRIALFREQUENCY"]._serialized_start = 4076 - _globals["_GNOMADMITOCHONDRIALFREQUENCY"]._serialized_end = 4159 - _globals["_HELIXMTDBFREQUENCY"]._serialized_start = 4161 - _globals["_HELIXMTDBFREQUENCY"]._serialized_end = 4234 - _globals["_DBIDS"]._serialized_start = 4236 - _globals["_DBIDS"]._serialized_end = 4279 - _globals["_CLINVARANNOTATION"]._serialized_start = 4282 - _globals["_CLINVARANNOTATION"]._serialized_end = 4503 - _globals["_SCOREANNOTATIONS"]._serialized_start = 4505 - _globals["_SCOREANNOTATIONS"]._serialized_end = 4572 - _globals["_SCOREENTRY"]._serialized_start = 4574 - _globals["_SCOREENTRY"]._serialized_end = 4653 - _globals["_CALLRELATEDANNOTATION"]._serialized_start = 4655 - _globals["_CALLRELATEDANNOTATION"]._serialized_end = 4734 - _globals["_SAMPLECALLINFO"]._serialized_start = 4737 - _globals["_SAMPLECALLINFO"]._serialized_end = 4901 + _globals["_GENERELATEDPHENOTYPES"]._serialized_start = 2320 + _globals["_GENERELATEDPHENOTYPES"]._serialized_end = 2457 + _globals["_GENERELATEDCONSTRAINTS"]._serialized_start = 2460 + _globals["_GENERELATEDCONSTRAINTS"]._serialized_end = 2841 + _globals["_GNOMADCONSTRAINTS"]._serialized_start = 2844 + _globals["_GNOMADCONSTRAINTS"]._serialized_end = 3026 + _globals["_DECIPHERCONSTRAINTS"]._serialized_start = 3028 + _globals["_DECIPHERCONSTRAINTS"]._serialized_end = 3081 + _globals["_RCNVCONSTRAINTS"]._serialized_start = 3083 + _globals["_RCNVCONSTRAINTS"]._serialized_end = 3135 + _globals["_SHETCONSTRAINTS"]._serialized_start = 3137 + _globals["_SHETCONSTRAINTS"]._serialized_end = 3169 + _globals["_CLINGENDOSAGEANNOTATION"]._serialized_start = 3172 + _globals["_CLINGENDOSAGEANNOTATION"]._serialized_end = 3308 + _globals["_VARIANTRELATEDANNOTATION"]._serialized_start = 3311 + _globals["_VARIANTRELATEDANNOTATION"]._serialized_end = 3616 + _globals["_FREQUENCYANNOTATION"]._serialized_start = 3619 + _globals["_FREQUENCYANNOTATION"]._serialized_end = 4054 + _globals["_NUCLEARFREQUENCY"]._serialized_start = 4056 + _globals["_NUCLEARFREQUENCY"]._serialized_end = 4144 + _globals["_GNOMADMITOCHONDRIALFREQUENCY"]._serialized_start = 4146 + _globals["_GNOMADMITOCHONDRIALFREQUENCY"]._serialized_end = 4229 + _globals["_HELIXMTDBFREQUENCY"]._serialized_start = 4231 + _globals["_HELIXMTDBFREQUENCY"]._serialized_end = 4304 + _globals["_DBIDS"]._serialized_start = 4306 + _globals["_DBIDS"]._serialized_end = 4349 + _globals["_CLINVARANNOTATION"]._serialized_start = 4352 + _globals["_CLINVARANNOTATION"]._serialized_end = 4573 + _globals["_SCOREANNOTATIONS"]._serialized_start = 4575 + _globals["_SCOREANNOTATIONS"]._serialized_end = 4642 + _globals["_SCOREENTRY"]._serialized_start = 4644 + _globals["_SCOREENTRY"]._serialized_end = 4723 + _globals["_CALLRELATEDANNOTATION"]._serialized_start = 4725 + _globals["_CALLRELATEDANNOTATION"]._serialized_end = 4804 + _globals["_SAMPLECALLINFO"]._serialized_start = 4807 + _globals["_SAMPLECALLINFO"]._serialized_end = 4971 # @@protoc_insertion_point(module_scope) diff --git a/backend/seqvars/protos/output_pb2.pyi b/backend/seqvars/protos/output_pb2.pyi index 59728f859..edcd72fdb 100644 --- a/backend/seqvars/protos/output_pb2.pyi +++ b/backend/seqvars/protos/output_pb2.pyi @@ -78,6 +78,49 @@ GENOME_RELEASE_GRCH38: GenomeRelease.ValueType # 2 """GRCh38.""" global___GenomeRelease = GenomeRelease +class _ModeOfInheritance: + ValueType = typing.NewType("ValueType", builtins.int) + V: typing_extensions.TypeAlias = ValueType + +class _ModeOfInheritanceEnumTypeWrapper( + google.protobuf.internal.enum_type_wrapper._EnumTypeWrapper[_ModeOfInheritance.ValueType], + builtins.type, +): # noqa: F821 + DESCRIPTOR: google.protobuf.descriptor.EnumDescriptor + MODE_OF_INHERITANCE_UNSPECIFIED: _ModeOfInheritance.ValueType # 0 + """Unspecified mode of inheritance.""" + MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT: _ModeOfInheritance.ValueType # 1 + """Autosomal dominant inheritance (HP:0000006).""" + MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE: _ModeOfInheritance.ValueType # 2 + """Autosomal recessive inheritance (HP:0000007).""" + MODE_OF_INHERITANCE_X_LINKED_DOMINANT: _ModeOfInheritance.ValueType # 3 + """X-linked dominant inheritance (HP:0001419).""" + MODE_OF_INHERITANCE_X_LINKED_RECESSIVE: _ModeOfInheritance.ValueType # 4 + """X-linked recessive inheritance (HP:0001423).""" + MODE_OF_INHERITANCE_Y_LINKED: _ModeOfInheritance.ValueType # 5 + """Y-linked inheritance (HP:0001450).""" + MODE_OF_INHERITANCE_MITOCHONDRIAL: _ModeOfInheritance.ValueType # 6 + """Mitochondrial inheritance (HP:0001427).""" + +class ModeOfInheritance(_ModeOfInheritance, metaclass=_ModeOfInheritanceEnumTypeWrapper): + """Enumerations with modes of inheritance from HPO.""" + +MODE_OF_INHERITANCE_UNSPECIFIED: ModeOfInheritance.ValueType # 0 +"""Unspecified mode of inheritance.""" +MODE_OF_INHERITANCE_AUTOSOMAL_DOMINANT: ModeOfInheritance.ValueType # 1 +"""Autosomal dominant inheritance (HP:0000006).""" +MODE_OF_INHERITANCE_AUTOSOMAL_RECESSIVE: ModeOfInheritance.ValueType # 2 +"""Autosomal recessive inheritance (HP:0000007).""" +MODE_OF_INHERITANCE_X_LINKED_DOMINANT: ModeOfInheritance.ValueType # 3 +"""X-linked dominant inheritance (HP:0001419).""" +MODE_OF_INHERITANCE_X_LINKED_RECESSIVE: ModeOfInheritance.ValueType # 4 +"""X-linked recessive inheritance (HP:0001423).""" +MODE_OF_INHERITANCE_Y_LINKED: ModeOfInheritance.ValueType # 5 +"""Y-linked inheritance (HP:0001450).""" +MODE_OF_INHERITANCE_MITOCHONDRIAL: ModeOfInheritance.ValueType # 6 +"""Mitochondrial inheritance (HP:0001427).""" +global___ModeOfInheritance = ModeOfInheritance + class _ClingenDosageScore: ValueType = typing.NewType("ValueType", builtins.int) V: typing_extensions.TypeAlias = ValueType @@ -897,20 +940,37 @@ class GeneRelatedPhenotypes(google.protobuf.message.Message): IS_ACMG_SF_FIELD_NUMBER: builtins.int IS_DISEASE_GENE_FIELD_NUMBER: builtins.int + MODE_OF_INHERITANCES_FIELD_NUMBER: builtins.int is_acmg_sf: builtins.bool """ACMG supplementary finding list.""" is_disease_gene: builtins.bool """Whether is a known disease gene.""" + @property + def mode_of_inheritances( + self, + ) -> google.protobuf.internal.containers.RepeatedScalarFieldContainer[ + global___ModeOfInheritance.ValueType + ]: + """Linked modes of inheritance.""" + def __init__( self, *, is_acmg_sf: builtins.bool = ..., is_disease_gene: builtins.bool = ..., + mode_of_inheritances: ( + collections.abc.Iterable[global___ModeOfInheritance.ValueType] | None + ) = ..., ) -> None: ... def ClearField( self, field_name: typing_extensions.Literal[ - "is_acmg_sf", b"is_acmg_sf", "is_disease_gene", b"is_disease_gene" + "is_acmg_sf", + b"is_acmg_sf", + "is_disease_gene", + b"is_disease_gene", + "mode_of_inheritances", + b"mode_of_inheritances", ], ) -> None: ... diff --git a/backend/seqvars/tasks.py b/backend/seqvars/tasks.py index c9d5601d2..81512805a 100644 --- a/backend/seqvars/tasks.py +++ b/backend/seqvars/tasks.py @@ -1,8 +1,10 @@ -from cases_import import models from config.celery import app +from seqvars.models import executors @app.task(bind=True) def run_seqvarsqueryexecutionbackgroundjob(_self, *, seqvarsqueryexecutionbackgroundjob_pk: int): """Task to execute a ``cases_import.models.SeqvarsQueryExecutionBackgroundJob``.""" - return models.run_seqvarsqueryexecutionbackgroundjob(pk=seqvarsqueryexecutionbackgroundjob_pk) + return executors.run_seqvarsqueryexecutionbackgroundjob( + pk=seqvarsqueryexecutionbackgroundjob_pk + ) diff --git a/backend/seqvars/tests/snapshots/snap_test_views_api.py b/backend/seqvars/tests/snapshots/snap_test_views_api.py index 1c30d6eea..3c13e8ec7 100644 --- a/backend/seqvars/tests/snapshots/snap_test_views_api.py +++ b/backend/seqvars/tests/snapshots/snap_test_views_api.py @@ -7,6 +7,7 @@ snapshots = Snapshot() snapshots["TestQueryPresetsFactoryDefaultsViewSet::test_list 1"] = { + "count": 3, "next": None, "previous": None, "results": [ diff --git a/backend/seqvars/tests/test_permissions_api.py b/backend/seqvars/tests/test_permissions_api.py index aaddc645b..713cb0954 100644 --- a/backend/seqvars/tests/test_permissions_api.py +++ b/backend/seqvars/tests/test_permissions_api.py @@ -2261,7 +2261,7 @@ def test_list(self): url = reverse( "seqvars:api-resultset-list", kwargs={ - "query": self.query.sodar_uuid, + "queryexecution": self.queryexecution.sodar_uuid, }, ) good_users = [ @@ -2281,7 +2281,7 @@ def test_retrieve(self): url = reverse( "seqvars:api-resultset-detail", kwargs={ - "query": self.query.sodar_uuid, + "queryexecution": self.queryexecution.sodar_uuid, "resultset": self.resultset.sodar_uuid, }, ) diff --git a/backend/seqvars/tests/test_views_api.py b/backend/seqvars/tests/test_views_api.py index c89461cfd..84e7c5db5 100644 --- a/backend/seqvars/tests/test_views_api.py +++ b/backend/seqvars/tests/test_views_api.py @@ -110,6 +110,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -266,6 +267,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -415,6 +417,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -551,6 +554,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -687,6 +691,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -823,6 +828,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -959,6 +965,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1095,6 +1102,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1231,6 +1239,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1367,6 +1376,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1503,6 +1513,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1635,6 +1646,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -1811,6 +1823,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -2094,6 +2107,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -2161,9 +2175,10 @@ def test_start(self): new_seqvarqueryexecution = SeqvarsQueryExecution.objects.exclude( pk=self.queryexecution.pk ).first() + # Note: will fail as execution of worker in test fails. self.assertEqual( new_seqvarqueryexecution.state, - SeqvarsQueryExecution.STATE_QUEUED, + SeqvarsQueryExecution.STATE_FAILED, ) @@ -2186,7 +2201,7 @@ def test_list(self): reverse( "seqvars:api-resultset-list", kwargs={ - "query": self.query.sodar_uuid, + "queryexecution": self.queryexecution.sodar_uuid, }, ) ) @@ -2195,6 +2210,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], @@ -2207,7 +2223,7 @@ def test_retrieve_existing(self): reverse( "seqvars:api-resultset-detail", kwargs={ - "query": self.query.sodar_uuid, + "queryexecution": self.queryexecution.sodar_uuid, "resultset": self.resultset.sodar_uuid, }, ) @@ -2218,7 +2234,7 @@ def test_retrieve_existing(self): @parameterized.expand( [ - [{"query": "00000000-0000-0000-0000-000000000000"}], + [{"queryexecution": "00000000-0000-0000-0000-000000000000"}], [{"resultset": "00000000-0000-0000-0000-000000000000"}], ] ) @@ -2229,7 +2245,7 @@ def test_retrieve_nonexisting(self, kwargs_override: dict[str, Any]): "seqvars:api-resultset-detail", kwargs={ **{ - "query": self.query.sodar_uuid, + "queryexecution": self.queryexecution.sodar_uuid, "resultset": self.resultset.sodar_uuid, }, **kwargs_override, @@ -2268,6 +2284,7 @@ def test_list(self): self.assertDictEqual( response.json(), { + "count": 1, "next": None, "previous": None, "results": [result_json], diff --git a/backend/seqvars/urls.py b/backend/seqvars/urls.py index c2ea3d6d7..931f1c054 100644 --- a/backend/seqvars/urls.py +++ b/backend/seqvars/urls.py @@ -81,7 +81,7 @@ basename="api-queryexecution", ) router.register( - r"api/resultset/(?P[0-9a-f-]+)", + r"api/resultset/(?P[0-9a-f-]+)", views_api.SeqvarsResultSetViewSet, basename="api-resultset", ) diff --git a/backend/seqvars/views_api.py b/backend/seqvars/views_api.py index b919cbf97..c4455d6ee 100644 --- a/backend/seqvars/views_api.py +++ b/backend/seqvars/views_api.py @@ -5,13 +5,13 @@ from django.db import transaction from django.shortcuts import get_object_or_404 from drf_spectacular.openapi import AutoSchema -from drf_spectacular.utils import extend_schema +from drf_spectacular.utils import OpenApiParameter, extend_schema from modelcluster.queryset import FakeQuerySet from projectroles.models import Project from projectroles.views_api import SODARAPIProjectPermission from rest_framework import serializers, viewsets from rest_framework.decorators import action -from rest_framework.pagination import CursorPagination +from rest_framework.pagination import PageNumberPagination from rest_framework.response import Response from cases_analysis.models import CaseAnalysisSession @@ -56,11 +56,12 @@ SeqvarsResultRowSerializer, SeqvarsResultSetSerializer, ) +from seqvars.tasks import run_seqvarsqueryexecutionbackgroundjob from varfish.api_utils import VarfishApiRenderer, VarfishApiVersioning from variants.models.case import Case -class StandardPagination(CursorPagination): +class StandardPagination(PageNumberPagination): """Standard cursor navigation for the API.""" page_size = 100 @@ -89,6 +90,11 @@ def get_project(kwargs): elif "query" in kwargs: query = get_object_or_404(SeqvarsQuery.objects.all(), sodar_uuid=kwargs["query"]) project = query.session.caseanalysis.case.project + elif "queryexecution" in kwargs: + queryexecution = get_object_or_404( + SeqvarsQueryExecution.objects.all(), sodar_uuid=kwargs["queryexecution"] + ) + project = queryexecution.query.session.caseanalysis.case.project elif "resultset" in kwargs: resultset = get_object_or_404( SeqvarsResultSet.objects.all(), sodar_uuid=kwargs["resultset"] @@ -536,7 +542,6 @@ class SeqvarsQueryExecutionViewSet(BaseReadOnlyViewSet): @extend_schema(request=serializers.Serializer) @action(methods=["post"], detail=False) - @transaction.atomic() def start(self, *args, **kwargs): """Create a new query execution for the given query. @@ -545,15 +550,17 @@ def start(self, *args, **kwargs): query = None # TODO: check permissions on the source's project query = SeqvarsQuery.objects.get(sodar_uuid=self.kwargs["query"]) - queryexecution = SeqvarsQueryExecution.objects.create( - state=SeqvarsQueryExecution.STATE_QUEUED, - query=query, - querysettings=query.settings.make_clone(), - ) - SeqvarsQueryExecutionBackgroundJob.objects.create_full( - seqvarsqueryexecution=queryexecution, - user=self.request.user, - ) + with transaction.atomic(): + queryexecution = SeqvarsQueryExecution.objects.create( + state=SeqvarsQueryExecution.STATE_QUEUED, + query=query, + querysettings=query.settings.make_clone(), + ) + bgjob = SeqvarsQueryExecutionBackgroundJob.objects.create_full( + seqvarsqueryexecution=queryexecution, + user=self.request.user, + ) + run_seqvarsqueryexecutionbackgroundjob.delay(seqvarsqueryexecutionbackgroundjob_pk=bgjob.pk) serializer = self.get_serializer(queryexecution) return Response(serializer.data) @@ -582,7 +589,7 @@ def get_queryset(self): if sys.argv[:2] == ["manage.py", "spectacular"]: return result # short circuit in schema generation result = result.filter( - queryexecution__query__sodar_uuid=self.kwargs["query"], + queryexecution__sodar_uuid=self.kwargs["queryexecution"], ) return result @@ -603,6 +610,15 @@ class SeqvarsResultRowViewSet(BaseReadOnlyViewSet): #: Override pagination as rows do not have ``date_created``. pagination_class = SeqvarsResultRowPagination + @extend_schema( + parameters=[ + OpenApiParameter(name="order_by", type=str), + OpenApiParameter(name="order_dir", type=str), + ] + ) + def list(self, *args, **kwargs): + return super().list(*args, **kwargs) + def get_queryset(self): """Return queryset with all ``ResultRow`` records for the given result set.""" result = SeqvarsResultRow.objects.all() diff --git a/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml b/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml index 7d17f9bf0..79f53d6e9 100644 --- a/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml +++ b/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml @@ -2189,12 +2189,12 @@ paths: operationId: seqvars_api_predefinedquery_list description: ViewSet for the ``PredefinedQuery`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -2396,12 +2396,12 @@ paths: operationId: seqvars_api_query_list description: Allow CRUD of the user's queries. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -2639,12 +2639,12 @@ paths: operationId: seqvars_api_queryexecution_list description: ViewSet for retrieving ``QueryExecution`` records. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -2732,12 +2732,12 @@ paths: operationId: seqvars_api_querypresetsclinvar_list description: ViewSet for the ``QueryPresetsClinvar`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -2939,12 +2939,12 @@ paths: operationId: seqvars_api_querypresetscolumns_list description: ViewSet for the ``QueryPresetsColumns`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -3146,12 +3146,12 @@ paths: operationId: seqvars_api_querypresetsconsequence_list description: ViewSet for the ``QueryPresetsConsequence`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -3356,12 +3356,12 @@ paths: This is a public view, no permissions are required. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -3415,12 +3415,12 @@ paths: operationId: seqvars_api_querypresetsfrequency_list description: ViewSet for the ``QueryPresetsFrequency`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -3622,12 +3622,12 @@ paths: operationId: seqvars_api_querypresetslocus_list description: ViewSet for the ``QueryPresetsLocus`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -3829,12 +3829,12 @@ paths: operationId: seqvars_api_querypresetsphenotypeprio_list description: ViewSet for the ``QueryPresetsPhenotypePrio`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -4036,12 +4036,12 @@ paths: operationId: seqvars_api_querypresetsquality_list description: ViewSet for the ``QueryPresetsQuality`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -4243,12 +4243,12 @@ paths: operationId: seqvars_api_querypresetsset_list description: ViewSet for the ``QueryPresetsSet`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -4492,12 +4492,12 @@ paths: operationId: seqvars_api_querypresetssetversion_list description: ViewSet for the ``QueryPresetsSetVersion`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -4738,12 +4738,12 @@ paths: operationId: seqvars_api_querypresetsvariantprio_list description: ViewSet for the ``QueryPresetsVariantPrio`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -4945,12 +4945,12 @@ paths: operationId: seqvars_api_querysettings_list description: ViewSet for the ``QuerySettings`` model. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -5152,12 +5152,20 @@ paths: operationId: seqvars_api_resultrow_list description: ViewSet for retrieving ``ResultRow`` records. parameters: - - name: cursor + - in: query + name: order_by + schema: + type: string + - in: query + name: order_dir + schema: + type: string + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -5213,17 +5221,17 @@ paths: schema: $ref: '#/components/schemas/SeqvarsResultRow' description: '' - /seqvars/api/resultset/{query}/: + /seqvars/api/resultset/{queryexecution}/: get: operationId: seqvars_api_resultset_list description: ViewSet for retrieving ``ResultSet`` records. parameters: - - name: cursor + - name: page required: false in: query - description: The pagination cursor value. + description: A page number within the paginated result set. schema: - type: string + type: integer - name: page_size required: false in: query @@ -5231,7 +5239,7 @@ paths: schema: type: integer - in: path - name: query + name: queryexecution schema: type: string pattern: ^[0-9a-f-]+$ @@ -5249,13 +5257,13 @@ paths: schema: $ref: '#/components/schemas/PaginatedSeqvarsResultSetList' description: '' - /seqvars/api/resultset/{query}/{resultset}/: + /seqvars/api/resultset/{queryexecution}/{resultset}/: get: operationId: seqvars_api_resultset_retrieve description: ViewSet for retrieving ``ResultSet`` records. parameters: - in: path - name: query + name: queryexecution schema: type: string pattern: ^[0-9a-f-]+$ @@ -7412,13 +7420,21 @@ components: description: Store gene-related annotation (always for a single gene). properties: identity: - $ref: '#/components/schemas/GeneIdentityPydantic' + anyOf: + - $ref: '#/components/schemas/GeneIdentityPydantic' + - type: 'null' consequences: - $ref: '#/components/schemas/GeneRelatedConsequencesPydantic' + anyOf: + - $ref: '#/components/schemas/GeneRelatedConsequencesPydantic' + - type: 'null' phenotypes: - $ref: '#/components/schemas/GeneRelatedPhenotypesPydantic' + anyOf: + - $ref: '#/components/schemas/GeneRelatedPhenotypesPydantic' + - type: 'null' constraints: - $ref: '#/components/schemas/GeneRelatedConstraintsPydantic' + anyOf: + - $ref: '#/components/schemas/GeneRelatedConstraintsPydantic' + - type: 'null' required: - identity - consequences @@ -7489,6 +7505,12 @@ components: default: false title: Is Disease Gene type: boolean + mode_of_inheritances: + default: [] + items: + $ref: '#/components/schemas/SeqvarsModeOfInheritance' + title: Mode Of Inheritances + type: array title: GeneRelatedPhenotypesPydantic type: object GenomeRegionPydantic: @@ -7750,12 +7772,19 @@ components: PaginatedSeqvarsPredefinedQueryList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7763,12 +7792,19 @@ components: PaginatedSeqvarsQueryExecutionList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7776,12 +7812,19 @@ components: PaginatedSeqvarsQueryList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7789,12 +7832,19 @@ components: PaginatedSeqvarsQueryPresetsClinvarList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7802,12 +7852,19 @@ components: PaginatedSeqvarsQueryPresetsColumnsList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7815,12 +7872,19 @@ components: PaginatedSeqvarsQueryPresetsConsequenceList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7828,12 +7892,19 @@ components: PaginatedSeqvarsQueryPresetsFrequencyList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7841,12 +7912,19 @@ components: PaginatedSeqvarsQueryPresetsLocusList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7854,12 +7932,19 @@ components: PaginatedSeqvarsQueryPresetsPhenotypePrioList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7867,12 +7952,19 @@ components: PaginatedSeqvarsQueryPresetsQualityList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7880,12 +7972,19 @@ components: PaginatedSeqvarsQueryPresetsSetList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7893,12 +7992,19 @@ components: PaginatedSeqvarsQueryPresetsSetVersionList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7906,12 +8012,19 @@ components: PaginatedSeqvarsQueryPresetsVariantPrioList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7919,12 +8032,19 @@ components: PaginatedSeqvarsQuerySettingsList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7932,12 +8052,19 @@ components: PaginatedSeqvarsResultRowList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -7945,12 +8072,19 @@ components: PaginatedSeqvarsResultSetList: type: object properties: + count: + type: integer + example: 123 next: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=4 previous: type: string nullable: true + format: uri + example: http://api.example.org/accounts/?page=2 results: type: array items: @@ -9979,6 +10113,17 @@ components: title: Frequency title: SeqvarsHelixMtDbFrequencySettingsPydantic type: object + SeqvarsModeOfInheritance: + description: Mode of inheritance gene annotation. + enum: + - autosomal_dominant + - autosomal_recessive + - x_linked_dominant + - x_linked_recessive + - y_linked + - mitochondrial + title: SeqvarsModeOfInheritance + type: string SeqvarsNuclearFrequencyPydantic: description: Store gnomAD and in-house nuclear frequency information. properties: diff --git a/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz new file mode 100644 index 000000000..e52a7e281 --- /dev/null +++ b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e326d77b7cc2ce80ac3662bf3f25797ba5576dbe1b5c74ae52d76edff3c99da1 +size 19060169 diff --git a/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi new file mode 100644 index 000000000..163c5de9b --- /dev/null +++ b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.gatk_hc.vcf.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:52045b80f3cc92cbcb921d27657f894b67715ea479db7bafb27fba82821229f0 +size 532600 diff --git a/backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl new file mode 120000 index 000000000..b418c6835 --- /dev/null +++ b/backend/varfish/users/management/commands/data/Case_1_exons.grch37.yaml.tpl @@ -0,0 +1 @@ +Case_1.grch37.yaml.tpl \ No newline at end of file diff --git a/backend/varfish/users/management/commands/data/Case_1_exons.ped b/backend/varfish/users/management/commands/data/Case_1_exons.ped new file mode 120000 index 000000000..01312d94f --- /dev/null +++ b/backend/varfish/users/management/commands/data/Case_1_exons.ped @@ -0,0 +1 @@ +Case_1.ped \ No newline at end of file diff --git a/backend/varfish/users/management/commands/initdev.py b/backend/varfish/users/management/commands/initdev.py index 8424e45b5..470b78607 100644 --- a/backend/varfish/users/management/commands/initdev.py +++ b/backend/varfish/users/management/commands/initdev.py @@ -63,7 +63,7 @@ def add_arguments(self, parser): parser.add_argument( "--data-case", default="Case_1", - choices=["Case_1"], + choices=["Case_1", "Case_1_exons"], help="Name of case to use when adding data or import job", ) parser.add_argument( diff --git a/frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts b/frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts index 621a9b05c..1437725c6 100644 --- a/frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts +++ b/frontend/ext/varfish-api/src/lib/@tanstack/vue-query.gen.ts @@ -2,8 +2,8 @@ import type { Options } from '@hey-api/client-fetch'; import { queryOptions, infiniteQueryOptions, type InfiniteData, type UseMutationOptions } from '@tanstack/vue-query'; -import type { CasesAnalysisApiCaseanalysisListData, CasesAnalysisApiCaseanalysisListError, CasesAnalysisApiCaseanalysisListResponse, CasesAnalysisApiCaseanalysisRetrieveData, CasesAnalysisApiCaseanalysissessionListData, CasesAnalysisApiCaseanalysissessionListError, CasesAnalysisApiCaseanalysissessionListResponse, CasesAnalysisApiCaseanalysissessionRetrieveData, CasesImportApiCaseImportActionListCreateListData, CasesImportApiCaseImportActionListCreateListError, CasesImportApiCaseImportActionListCreateListResponse, CasesImportApiCaseImportActionListCreateCreateData, CasesImportApiCaseImportActionListCreateCreateError, CasesImportApiCaseImportActionListCreateCreateResponse, CasesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveData, CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateData, CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateError, CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateResponse, CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateData, CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateError, CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateResponse, CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyData, CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyError, CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyResponse, CasesQcApiCaseqcRetrieveRetrieveData, CasesQcApiVarfishstatsRetrieveRetrieveData, CasesApiAnnotationReleaseInfoListListData, CasesApiCaseCommentListCreateListData, CasesApiCaseCommentListCreateCreateData, CasesApiCaseCommentListCreateCreateError, CasesApiCaseCommentListCreateCreateResponse, CasesApiCasePhenotypeTermsListCreateListData, CasesApiCasePhenotypeTermsListCreateCreateData, CasesApiCasePhenotypeTermsListCreateCreateError, CasesApiCasePhenotypeTermsListCreateCreateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyRetrieveData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyResponse, CasesApiCaseCountRetrieveData, CasesApiCaseListListData, CasesApiCaseListListError, CasesApiCaseListListResponse, CasesApiCaseRetrieveUpdateDestroyRetrieveData, CasesApiCaseRetrieveUpdateDestroyUpdateData, CasesApiCaseRetrieveUpdateDestroyUpdateError, CasesApiCaseRetrieveUpdateDestroyUpdateResponse, CasesApiCaseRetrieveUpdateDestroyPartialUpdateData, CasesApiCaseRetrieveUpdateDestroyPartialUpdateError, CasesApiCaseRetrieveUpdateDestroyPartialUpdateResponse, CasesApiCaseRetrieveUpdateDestroyDestroyData, CasesApiCaseRetrieveUpdateDestroyDestroyError, CasesApiCaseRetrieveUpdateDestroyDestroyResponse, CasesApiSvAnnotationReleaseInfoListListData, ProjectApiCreateCreateData, ProjectApiCreateCreateError, ProjectApiCreateCreateResponse, ProjectApiInvitesCreateCreateData, ProjectApiInvitesCreateCreateError, ProjectApiInvitesCreateCreateResponse, ProjectApiInvitesListListData, ProjectApiInvitesResendCreateData, ProjectApiInvitesResendCreateError, ProjectApiInvitesResendCreateResponse, ProjectApiInvitesRevokeCreateData, ProjectApiInvitesRevokeCreateError, ProjectApiInvitesRevokeCreateResponse, ProjectApiRemoteGetRetrieveData, ProjectApiRetrieveRetrieveData, ProjectApiRolesCreateCreateData, ProjectApiRolesCreateCreateError, ProjectApiRolesCreateCreateResponse, ProjectApiRolesDestroyDestroyData, ProjectApiRolesDestroyDestroyError, ProjectApiRolesDestroyDestroyResponse, ProjectApiRolesOwnerTransferCreateData, ProjectApiRolesOwnerTransferCreateError, ProjectApiRolesOwnerTransferCreateResponse, ProjectApiRolesUpdateUpdateData, ProjectApiRolesUpdateUpdateError, ProjectApiRolesUpdateUpdateResponse, ProjectApiRolesUpdatePartialUpdateData, ProjectApiRolesUpdatePartialUpdateError, ProjectApiRolesUpdatePartialUpdateResponse, ProjectApiSettingsRetrieveRetrieveData, ProjectApiSettingsSetCreateData, ProjectApiSettingsSetCreateError, ProjectApiSettingsSetCreateResponse, ProjectApiSettingsSetUserCreateError, ProjectApiSettingsSetUserCreateResponse, ProjectApiUpdateUpdateData, ProjectApiUpdateUpdateError, ProjectApiUpdateUpdateResponse, ProjectApiUpdatePartialUpdateData, ProjectApiUpdatePartialUpdateError, ProjectApiUpdatePartialUpdateResponse, SeqmetaApiEnrichmentkitListCreateCreateData, SeqmetaApiEnrichmentkitListCreateCreateError, SeqmetaApiEnrichmentkitListCreateCreateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyRetrieveData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyResponse, SeqmetaApiTargetbedfileListCreateListData, SeqmetaApiTargetbedfileListCreateCreateData, SeqmetaApiTargetbedfileListCreateCreateError, SeqmetaApiTargetbedfileListCreateCreateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyRetrieveData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyResponse, SeqvarsApiPredefinedqueryListData, SeqvarsApiPredefinedqueryListError, SeqvarsApiPredefinedqueryListResponse, SeqvarsApiPredefinedqueryCreateData, SeqvarsApiPredefinedqueryCreateError, SeqvarsApiPredefinedqueryCreateResponse, SeqvarsApiPredefinedqueryRetrieveData, SeqvarsApiPredefinedqueryUpdateData, SeqvarsApiPredefinedqueryUpdateError, SeqvarsApiPredefinedqueryUpdateResponse, SeqvarsApiPredefinedqueryPartialUpdateData, SeqvarsApiPredefinedqueryPartialUpdateError, SeqvarsApiPredefinedqueryPartialUpdateResponse, SeqvarsApiPredefinedqueryDestroyData, SeqvarsApiPredefinedqueryDestroyError, SeqvarsApiPredefinedqueryDestroyResponse, SeqvarsApiQueryListData, SeqvarsApiQueryListError, SeqvarsApiQueryListResponse, SeqvarsApiQueryCreateData, SeqvarsApiQueryCreateError, SeqvarsApiQueryCreateResponse, SeqvarsApiQueryRetrieveData, SeqvarsApiQueryUpdateData, SeqvarsApiQueryUpdateError, SeqvarsApiQueryUpdateResponse, SeqvarsApiQueryPartialUpdateData, SeqvarsApiQueryPartialUpdateError, SeqvarsApiQueryPartialUpdateResponse, SeqvarsApiQueryDestroyData, SeqvarsApiQueryDestroyError, SeqvarsApiQueryDestroyResponse, SeqvarsApiQueryCreateFromCreateData, SeqvarsApiQueryCreateFromCreateError, SeqvarsApiQueryCreateFromCreateResponse, SeqvarsApiQueryexecutionListData, SeqvarsApiQueryexecutionListError, SeqvarsApiQueryexecutionListResponse, SeqvarsApiQueryexecutionRetrieveData, SeqvarsApiQueryexecutionStartCreateData, SeqvarsApiQueryexecutionStartCreateError, SeqvarsApiQueryexecutionStartCreateResponse, SeqvarsApiQuerypresetsclinvarListData, SeqvarsApiQuerypresetsclinvarListError, SeqvarsApiQuerypresetsclinvarListResponse, SeqvarsApiQuerypresetsclinvarCreateData, SeqvarsApiQuerypresetsclinvarCreateError, SeqvarsApiQuerypresetsclinvarCreateResponse, SeqvarsApiQuerypresetsclinvarRetrieveData, SeqvarsApiQuerypresetsclinvarUpdateData, SeqvarsApiQuerypresetsclinvarUpdateError, SeqvarsApiQuerypresetsclinvarUpdateResponse, SeqvarsApiQuerypresetsclinvarPartialUpdateData, SeqvarsApiQuerypresetsclinvarPartialUpdateError, SeqvarsApiQuerypresetsclinvarPartialUpdateResponse, SeqvarsApiQuerypresetsclinvarDestroyData, SeqvarsApiQuerypresetsclinvarDestroyError, SeqvarsApiQuerypresetsclinvarDestroyResponse, SeqvarsApiQuerypresetscolumnsListData, SeqvarsApiQuerypresetscolumnsListError, SeqvarsApiQuerypresetscolumnsListResponse, SeqvarsApiQuerypresetscolumnsCreateData, SeqvarsApiQuerypresetscolumnsCreateError, SeqvarsApiQuerypresetscolumnsCreateResponse, SeqvarsApiQuerypresetscolumnsRetrieveData, SeqvarsApiQuerypresetscolumnsUpdateData, SeqvarsApiQuerypresetscolumnsUpdateError, SeqvarsApiQuerypresetscolumnsUpdateResponse, SeqvarsApiQuerypresetscolumnsPartialUpdateData, SeqvarsApiQuerypresetscolumnsPartialUpdateError, SeqvarsApiQuerypresetscolumnsPartialUpdateResponse, SeqvarsApiQuerypresetscolumnsDestroyData, SeqvarsApiQuerypresetscolumnsDestroyError, SeqvarsApiQuerypresetscolumnsDestroyResponse, SeqvarsApiQuerypresetsconsequenceListData, SeqvarsApiQuerypresetsconsequenceListError, SeqvarsApiQuerypresetsconsequenceListResponse, SeqvarsApiQuerypresetsconsequenceCreateData, SeqvarsApiQuerypresetsconsequenceCreateError, SeqvarsApiQuerypresetsconsequenceCreateResponse, SeqvarsApiQuerypresetsconsequenceRetrieveData, SeqvarsApiQuerypresetsconsequenceUpdateData, SeqvarsApiQuerypresetsconsequenceUpdateError, SeqvarsApiQuerypresetsconsequenceUpdateResponse, SeqvarsApiQuerypresetsconsequencePartialUpdateData, SeqvarsApiQuerypresetsconsequencePartialUpdateError, SeqvarsApiQuerypresetsconsequencePartialUpdateResponse, SeqvarsApiQuerypresetsconsequenceDestroyData, SeqvarsApiQuerypresetsconsequenceDestroyError, SeqvarsApiQuerypresetsconsequenceDestroyResponse, SeqvarsApiQuerypresetsfactorydefaultsListData, SeqvarsApiQuerypresetsfactorydefaultsListError, SeqvarsApiQuerypresetsfactorydefaultsListResponse, SeqvarsApiQuerypresetsfactorydefaultsRetrieveData, SeqvarsApiQuerypresetsfrequencyListData, SeqvarsApiQuerypresetsfrequencyListError, SeqvarsApiQuerypresetsfrequencyListResponse, SeqvarsApiQuerypresetsfrequencyCreateData, SeqvarsApiQuerypresetsfrequencyCreateError, SeqvarsApiQuerypresetsfrequencyCreateResponse, SeqvarsApiQuerypresetsfrequencyRetrieveData, SeqvarsApiQuerypresetsfrequencyUpdateData, SeqvarsApiQuerypresetsfrequencyUpdateError, SeqvarsApiQuerypresetsfrequencyUpdateResponse, SeqvarsApiQuerypresetsfrequencyPartialUpdateData, SeqvarsApiQuerypresetsfrequencyPartialUpdateError, SeqvarsApiQuerypresetsfrequencyPartialUpdateResponse, SeqvarsApiQuerypresetsfrequencyDestroyData, SeqvarsApiQuerypresetsfrequencyDestroyError, SeqvarsApiQuerypresetsfrequencyDestroyResponse, SeqvarsApiQuerypresetslocusListData, SeqvarsApiQuerypresetslocusListError, SeqvarsApiQuerypresetslocusListResponse, SeqvarsApiQuerypresetslocusCreateData, SeqvarsApiQuerypresetslocusCreateError, SeqvarsApiQuerypresetslocusCreateResponse, SeqvarsApiQuerypresetslocusRetrieveData, SeqvarsApiQuerypresetslocusUpdateData, SeqvarsApiQuerypresetslocusUpdateError, SeqvarsApiQuerypresetslocusUpdateResponse, SeqvarsApiQuerypresetslocusPartialUpdateData, SeqvarsApiQuerypresetslocusPartialUpdateError, SeqvarsApiQuerypresetslocusPartialUpdateResponse, SeqvarsApiQuerypresetslocusDestroyData, SeqvarsApiQuerypresetslocusDestroyError, SeqvarsApiQuerypresetslocusDestroyResponse, SeqvarsApiQuerypresetsphenotypeprioListData, SeqvarsApiQuerypresetsphenotypeprioListError, SeqvarsApiQuerypresetsphenotypeprioListResponse, SeqvarsApiQuerypresetsphenotypeprioCreateData, SeqvarsApiQuerypresetsphenotypeprioCreateError, SeqvarsApiQuerypresetsphenotypeprioCreateResponse, SeqvarsApiQuerypresetsphenotypeprioRetrieveData, SeqvarsApiQuerypresetsphenotypeprioUpdateData, SeqvarsApiQuerypresetsphenotypeprioUpdateError, SeqvarsApiQuerypresetsphenotypeprioUpdateResponse, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateData, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateError, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateResponse, SeqvarsApiQuerypresetsphenotypeprioDestroyData, SeqvarsApiQuerypresetsphenotypeprioDestroyError, SeqvarsApiQuerypresetsphenotypeprioDestroyResponse, SeqvarsApiQuerypresetsqualityListData, SeqvarsApiQuerypresetsqualityListError, SeqvarsApiQuerypresetsqualityListResponse, SeqvarsApiQuerypresetsqualityCreateData, SeqvarsApiQuerypresetsqualityCreateError, SeqvarsApiQuerypresetsqualityCreateResponse, SeqvarsApiQuerypresetsqualityRetrieveData, SeqvarsApiQuerypresetsqualityUpdateData, SeqvarsApiQuerypresetsqualityUpdateError, SeqvarsApiQuerypresetsqualityUpdateResponse, SeqvarsApiQuerypresetsqualityPartialUpdateData, SeqvarsApiQuerypresetsqualityPartialUpdateError, SeqvarsApiQuerypresetsqualityPartialUpdateResponse, SeqvarsApiQuerypresetsqualityDestroyData, SeqvarsApiQuerypresetsqualityDestroyError, SeqvarsApiQuerypresetsqualityDestroyResponse, SeqvarsApiQuerypresetssetListData, SeqvarsApiQuerypresetssetListError, SeqvarsApiQuerypresetssetListResponse, SeqvarsApiQuerypresetssetCreateData, SeqvarsApiQuerypresetssetCreateError, SeqvarsApiQuerypresetssetCreateResponse, SeqvarsApiQuerypresetssetRetrieveData, SeqvarsApiQuerypresetssetUpdateData, SeqvarsApiQuerypresetssetUpdateError, SeqvarsApiQuerypresetssetUpdateResponse, SeqvarsApiQuerypresetssetPartialUpdateData, SeqvarsApiQuerypresetssetPartialUpdateError, SeqvarsApiQuerypresetssetPartialUpdateResponse, SeqvarsApiQuerypresetssetDestroyData, SeqvarsApiQuerypresetssetDestroyError, SeqvarsApiQuerypresetssetDestroyResponse, SeqvarsApiQuerypresetssetCopyFromCreateData, SeqvarsApiQuerypresetssetCopyFromCreateError, SeqvarsApiQuerypresetssetCopyFromCreateResponse, SeqvarsApiQuerypresetssetversionListData, SeqvarsApiQuerypresetssetversionListError, SeqvarsApiQuerypresetssetversionListResponse, SeqvarsApiQuerypresetssetversionCreateData, SeqvarsApiQuerypresetssetversionCreateError, SeqvarsApiQuerypresetssetversionCreateResponse, SeqvarsApiQuerypresetssetversionRetrieveData, SeqvarsApiQuerypresetssetversionUpdateData, SeqvarsApiQuerypresetssetversionUpdateError, SeqvarsApiQuerypresetssetversionUpdateResponse, SeqvarsApiQuerypresetssetversionPartialUpdateData, SeqvarsApiQuerypresetssetversionPartialUpdateError, SeqvarsApiQuerypresetssetversionPartialUpdateResponse, SeqvarsApiQuerypresetssetversionDestroyData, SeqvarsApiQuerypresetssetversionDestroyError, SeqvarsApiQuerypresetssetversionDestroyResponse, SeqvarsApiQuerypresetssetversionCopyFromCreateData, SeqvarsApiQuerypresetssetversionCopyFromCreateError, SeqvarsApiQuerypresetssetversionCopyFromCreateResponse, SeqvarsApiQuerypresetsvariantprioListData, SeqvarsApiQuerypresetsvariantprioListError, SeqvarsApiQuerypresetsvariantprioListResponse, SeqvarsApiQuerypresetsvariantprioCreateData, SeqvarsApiQuerypresetsvariantprioCreateError, SeqvarsApiQuerypresetsvariantprioCreateResponse, SeqvarsApiQuerypresetsvariantprioRetrieveData, SeqvarsApiQuerypresetsvariantprioUpdateData, SeqvarsApiQuerypresetsvariantprioUpdateError, SeqvarsApiQuerypresetsvariantprioUpdateResponse, SeqvarsApiQuerypresetsvariantprioPartialUpdateData, SeqvarsApiQuerypresetsvariantprioPartialUpdateError, SeqvarsApiQuerypresetsvariantprioPartialUpdateResponse, SeqvarsApiQuerypresetsvariantprioDestroyData, SeqvarsApiQuerypresetsvariantprioDestroyError, SeqvarsApiQuerypresetsvariantprioDestroyResponse, SeqvarsApiQuerysettingsListData, SeqvarsApiQuerysettingsListError, SeqvarsApiQuerysettingsListResponse, SeqvarsApiQuerysettingsCreateData, SeqvarsApiQuerysettingsCreateError, SeqvarsApiQuerysettingsCreateResponse, SeqvarsApiQuerysettingsRetrieveData, SeqvarsApiQuerysettingsUpdateData, SeqvarsApiQuerysettingsUpdateError, SeqvarsApiQuerysettingsUpdateResponse, SeqvarsApiQuerysettingsPartialUpdateData, SeqvarsApiQuerysettingsPartialUpdateError, SeqvarsApiQuerysettingsPartialUpdateResponse, SeqvarsApiQuerysettingsDestroyData, SeqvarsApiQuerysettingsDestroyError, SeqvarsApiQuerysettingsDestroyResponse, SeqvarsApiResultrowListData, SeqvarsApiResultrowListError, SeqvarsApiResultrowListResponse, SeqvarsApiResultrowRetrieveData, SeqvarsApiResultsetListData, SeqvarsApiResultsetListError, SeqvarsApiResultsetListResponse, SeqvarsApiResultsetRetrieveData } from '../types.gen'; -import { client, casesAnalysisApiCaseanalysisList, casesAnalysisApiCaseanalysisRetrieve, casesAnalysisApiCaseanalysissessionList, casesAnalysisApiCaseanalysissessionRetrieve, casesImportApiCaseImportActionListCreateList, casesImportApiCaseImportActionListCreateCreate, casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieve, casesImportApiCaseImportActionRetrieveUpdateDestroyUpdate, casesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdate, casesImportApiCaseImportActionRetrieveUpdateDestroyDestroy, casesQcApiCaseqcRetrieveRetrieve, casesQcApiVarfishstatsRetrieveRetrieve, casesApiAnnotationReleaseInfoListList, casesApiCaseCommentListCreateList, casesApiCaseCommentListCreateCreate, casesApiCasePhenotypeTermsListCreateList, casesApiCasePhenotypeTermsListCreateCreate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyRetrieve, casesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroy, casesApiCaseCountRetrieve, casesApiCaseListList, casesApiCaseRetrieveUpdateDestroyRetrieve, casesApiCaseRetrieveUpdateDestroyUpdate, casesApiCaseRetrieveUpdateDestroyPartialUpdate, casesApiCaseRetrieveUpdateDestroyDestroy, casesApiSvAnnotationReleaseInfoListList, casesApiUserAndGlobalSettingsRetrieve, genepanelsApiGenepanelCategoryListList, genepanelsApiLookupGenepanelRetrieve, projectApiCreateCreate, projectApiInvitesCreateCreate, projectApiInvitesListList, projectApiInvitesResendCreate, projectApiInvitesRevokeCreate, projectApiListRetrieve, projectApiRemoteGetRetrieve, projectApiRetrieveRetrieve, projectApiRolesCreateCreate, projectApiRolesDestroyDestroy, projectApiRolesOwnerTransferCreate, projectApiRolesUpdateUpdate, projectApiRolesUpdatePartialUpdate, projectApiSettingsRetrieveRetrieve, projectApiSettingsRetrieveUserRetrieve, projectApiSettingsSetCreate, projectApiSettingsSetUserCreate, projectApiUpdateUpdate, projectApiUpdatePartialUpdate, projectApiUsersCurrentRetrieve, projectApiUsersListList, seqmetaApiEnrichmentkitListCreateList, seqmetaApiEnrichmentkitListCreateCreate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyRetrieve, seqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroy, seqmetaApiTargetbedfileListCreateList, seqmetaApiTargetbedfileListCreateCreate, seqmetaApiTargetbedfileRetrieveUpdateDestroyRetrieve, seqmetaApiTargetbedfileRetrieveUpdateDestroyUpdate, seqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdate, seqmetaApiTargetbedfileRetrieveUpdateDestroyDestroy, seqvarsApiPredefinedqueryList, seqvarsApiPredefinedqueryCreate, seqvarsApiPredefinedqueryRetrieve, seqvarsApiPredefinedqueryUpdate, seqvarsApiPredefinedqueryPartialUpdate, seqvarsApiPredefinedqueryDestroy, seqvarsApiQueryList, seqvarsApiQueryCreate, seqvarsApiQueryRetrieve, seqvarsApiQueryUpdate, seqvarsApiQueryPartialUpdate, seqvarsApiQueryDestroy, seqvarsApiQueryCreateFromCreate, seqvarsApiQueryexecutionList, seqvarsApiQueryexecutionRetrieve, seqvarsApiQueryexecutionStartCreate, seqvarsApiQuerypresetsclinvarList, seqvarsApiQuerypresetsclinvarCreate, seqvarsApiQuerypresetsclinvarRetrieve, seqvarsApiQuerypresetsclinvarUpdate, seqvarsApiQuerypresetsclinvarPartialUpdate, seqvarsApiQuerypresetsclinvarDestroy, seqvarsApiQuerypresetscolumnsList, seqvarsApiQuerypresetscolumnsCreate, seqvarsApiQuerypresetscolumnsRetrieve, seqvarsApiQuerypresetscolumnsUpdate, seqvarsApiQuerypresetscolumnsPartialUpdate, seqvarsApiQuerypresetscolumnsDestroy, seqvarsApiQuerypresetsconsequenceList, seqvarsApiQuerypresetsconsequenceCreate, seqvarsApiQuerypresetsconsequenceRetrieve, seqvarsApiQuerypresetsconsequenceUpdate, seqvarsApiQuerypresetsconsequencePartialUpdate, seqvarsApiQuerypresetsconsequenceDestroy, seqvarsApiQuerypresetsfactorydefaultsList, seqvarsApiQuerypresetsfactorydefaultsRetrieve, seqvarsApiQuerypresetsfrequencyList, seqvarsApiQuerypresetsfrequencyCreate, seqvarsApiQuerypresetsfrequencyRetrieve, seqvarsApiQuerypresetsfrequencyUpdate, seqvarsApiQuerypresetsfrequencyPartialUpdate, seqvarsApiQuerypresetsfrequencyDestroy, seqvarsApiQuerypresetslocusList, seqvarsApiQuerypresetslocusCreate, seqvarsApiQuerypresetslocusRetrieve, seqvarsApiQuerypresetslocusUpdate, seqvarsApiQuerypresetslocusPartialUpdate, seqvarsApiQuerypresetslocusDestroy, seqvarsApiQuerypresetsphenotypeprioList, seqvarsApiQuerypresetsphenotypeprioCreate, seqvarsApiQuerypresetsphenotypeprioRetrieve, seqvarsApiQuerypresetsphenotypeprioUpdate, seqvarsApiQuerypresetsphenotypeprioPartialUpdate, seqvarsApiQuerypresetsphenotypeprioDestroy, seqvarsApiQuerypresetsqualityList, seqvarsApiQuerypresetsqualityCreate, seqvarsApiQuerypresetsqualityRetrieve, seqvarsApiQuerypresetsqualityUpdate, seqvarsApiQuerypresetsqualityPartialUpdate, seqvarsApiQuerypresetsqualityDestroy, seqvarsApiQuerypresetssetList, seqvarsApiQuerypresetssetCreate, seqvarsApiQuerypresetssetRetrieve, seqvarsApiQuerypresetssetUpdate, seqvarsApiQuerypresetssetPartialUpdate, seqvarsApiQuerypresetssetDestroy, seqvarsApiQuerypresetssetCopyFromCreate, seqvarsApiQuerypresetssetversionList, seqvarsApiQuerypresetssetversionCreate, seqvarsApiQuerypresetssetversionRetrieve, seqvarsApiQuerypresetssetversionUpdate, seqvarsApiQuerypresetssetversionPartialUpdate, seqvarsApiQuerypresetssetversionDestroy, seqvarsApiQuerypresetssetversionCopyFromCreate, seqvarsApiQuerypresetsvariantprioList, seqvarsApiQuerypresetsvariantprioCreate, seqvarsApiQuerypresetsvariantprioRetrieve, seqvarsApiQuerypresetsvariantprioUpdate, seqvarsApiQuerypresetsvariantprioPartialUpdate, seqvarsApiQuerypresetsvariantprioDestroy, seqvarsApiQuerysettingsList, seqvarsApiQuerysettingsCreate, seqvarsApiQuerysettingsRetrieve, seqvarsApiQuerysettingsUpdate, seqvarsApiQuerysettingsPartialUpdate, seqvarsApiQuerysettingsDestroy, seqvarsApiResultrowList, seqvarsApiResultrowRetrieve, seqvarsApiResultsetList, seqvarsApiResultsetRetrieve } from '../services.gen'; +import type { CasesAnalysisApiCaseanalysisListData, CasesAnalysisApiCaseanalysisListError, CasesAnalysisApiCaseanalysisListResponse, CasesAnalysisApiCaseanalysisRetrieveData, CasesAnalysisApiCaseanalysissessionListData, CasesAnalysisApiCaseanalysissessionListError, CasesAnalysisApiCaseanalysissessionListResponse, CasesAnalysisApiCaseanalysissessionRetrieveData, CasesImportApiCaseImportActionListData, CasesImportApiCaseImportActionListError, CasesImportApiCaseImportActionListResponse, CasesImportApiCaseImportActionCreateData, CasesImportApiCaseImportActionCreateError, CasesImportApiCaseImportActionCreateResponse, CasesImportApiCaseImportActionRetrieveData, CasesImportApiCaseImportActionUpdateData, CasesImportApiCaseImportActionUpdateError, CasesImportApiCaseImportActionUpdateResponse, CasesImportApiCaseImportActionPartialUpdateData, CasesImportApiCaseImportActionPartialUpdateError, CasesImportApiCaseImportActionPartialUpdateResponse, CasesImportApiCaseImportActionDestroyData, CasesImportApiCaseImportActionDestroyError, CasesImportApiCaseImportActionDestroyResponse, CasesQcApiCaseqcRetrieveRetrieveData, CasesQcApiVarfishstatsRetrieveRetrieveData, CasesApiAnnotationReleaseInfoListListData, CasesApiCaseCommentListCreateListData, CasesApiCaseCommentListCreateCreateData, CasesApiCaseCommentListCreateCreateError, CasesApiCaseCommentListCreateCreateResponse, CasesApiCasePhenotypeTermsListCreateListData, CasesApiCasePhenotypeTermsListCreateCreateData, CasesApiCasePhenotypeTermsListCreateCreateError, CasesApiCasePhenotypeTermsListCreateCreateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyRetrieveData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdateResponse, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyData, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyError, CasesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroyResponse, CasesApiCaseCountRetrieveData, CasesApiCaseListListData, CasesApiCaseListListError, CasesApiCaseListListResponse, CasesApiCaseRetrieveUpdateDestroyRetrieveData, CasesApiCaseRetrieveUpdateDestroyUpdateData, CasesApiCaseRetrieveUpdateDestroyUpdateError, CasesApiCaseRetrieveUpdateDestroyUpdateResponse, CasesApiCaseRetrieveUpdateDestroyPartialUpdateData, CasesApiCaseRetrieveUpdateDestroyPartialUpdateError, CasesApiCaseRetrieveUpdateDestroyPartialUpdateResponse, CasesApiCaseRetrieveUpdateDestroyDestroyData, CasesApiCaseRetrieveUpdateDestroyDestroyError, CasesApiCaseRetrieveUpdateDestroyDestroyResponse, CasesApiSvAnnotationReleaseInfoListListData, ProjectApiCreateCreateData, ProjectApiCreateCreateError, ProjectApiCreateCreateResponse, ProjectApiInvitesCreateCreateData, ProjectApiInvitesCreateCreateError, ProjectApiInvitesCreateCreateResponse, ProjectApiInvitesListListData, ProjectApiInvitesResendCreateData, ProjectApiInvitesResendCreateError, ProjectApiInvitesResendCreateResponse, ProjectApiInvitesRevokeCreateData, ProjectApiInvitesRevokeCreateError, ProjectApiInvitesRevokeCreateResponse, ProjectApiRemoteGetRetrieveData, ProjectApiRetrieveRetrieveData, ProjectApiRolesCreateCreateData, ProjectApiRolesCreateCreateError, ProjectApiRolesCreateCreateResponse, ProjectApiRolesDestroyDestroyData, ProjectApiRolesDestroyDestroyError, ProjectApiRolesDestroyDestroyResponse, ProjectApiRolesOwnerTransferCreateData, ProjectApiRolesOwnerTransferCreateError, ProjectApiRolesOwnerTransferCreateResponse, ProjectApiRolesUpdateUpdateData, ProjectApiRolesUpdateUpdateError, ProjectApiRolesUpdateUpdateResponse, ProjectApiRolesUpdatePartialUpdateData, ProjectApiRolesUpdatePartialUpdateError, ProjectApiRolesUpdatePartialUpdateResponse, ProjectApiSettingsRetrieveRetrieveData, ProjectApiSettingsSetCreateData, ProjectApiSettingsSetCreateError, ProjectApiSettingsSetCreateResponse, ProjectApiSettingsSetUserCreateError, ProjectApiSettingsSetUserCreateResponse, ProjectApiUpdateUpdateData, ProjectApiUpdateUpdateError, ProjectApiUpdateUpdateResponse, ProjectApiUpdatePartialUpdateData, ProjectApiUpdatePartialUpdateError, ProjectApiUpdatePartialUpdateResponse, SeqmetaApiEnrichmentkitListCreateCreateData, SeqmetaApiEnrichmentkitListCreateCreateError, SeqmetaApiEnrichmentkitListCreateCreateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyRetrieveData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdateResponse, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyData, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyError, SeqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroyResponse, SeqmetaApiTargetbedfileListCreateListData, SeqmetaApiTargetbedfileListCreateCreateData, SeqmetaApiTargetbedfileListCreateCreateError, SeqmetaApiTargetbedfileListCreateCreateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyRetrieveData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyUpdateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdateResponse, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyData, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyError, SeqmetaApiTargetbedfileRetrieveUpdateDestroyDestroyResponse, SeqvarsApiPredefinedqueryListData, SeqvarsApiPredefinedqueryListError, SeqvarsApiPredefinedqueryListResponse, SeqvarsApiPredefinedqueryCreateData, SeqvarsApiPredefinedqueryCreateError, SeqvarsApiPredefinedqueryCreateResponse, SeqvarsApiPredefinedqueryRetrieveData, SeqvarsApiPredefinedqueryUpdateData, SeqvarsApiPredefinedqueryUpdateError, SeqvarsApiPredefinedqueryUpdateResponse, SeqvarsApiPredefinedqueryPartialUpdateData, SeqvarsApiPredefinedqueryPartialUpdateError, SeqvarsApiPredefinedqueryPartialUpdateResponse, SeqvarsApiPredefinedqueryDestroyData, SeqvarsApiPredefinedqueryDestroyError, SeqvarsApiPredefinedqueryDestroyResponse, SeqvarsApiQueryListData, SeqvarsApiQueryListError, SeqvarsApiQueryListResponse, SeqvarsApiQueryCreateData, SeqvarsApiQueryCreateError, SeqvarsApiQueryCreateResponse, SeqvarsApiQueryRetrieveData, SeqvarsApiQueryUpdateData, SeqvarsApiQueryUpdateError, SeqvarsApiQueryUpdateResponse, SeqvarsApiQueryPartialUpdateData, SeqvarsApiQueryPartialUpdateError, SeqvarsApiQueryPartialUpdateResponse, SeqvarsApiQueryDestroyData, SeqvarsApiQueryDestroyError, SeqvarsApiQueryDestroyResponse, SeqvarsApiQueryCreateFromCreateData, SeqvarsApiQueryCreateFromCreateError, SeqvarsApiQueryCreateFromCreateResponse, SeqvarsApiQueryexecutionListData, SeqvarsApiQueryexecutionListError, SeqvarsApiQueryexecutionListResponse, SeqvarsApiQueryexecutionRetrieveData, SeqvarsApiQueryexecutionStartCreateData, SeqvarsApiQueryexecutionStartCreateError, SeqvarsApiQueryexecutionStartCreateResponse, SeqvarsApiQuerypresetsclinvarListData, SeqvarsApiQuerypresetsclinvarListError, SeqvarsApiQuerypresetsclinvarListResponse, SeqvarsApiQuerypresetsclinvarCreateData, SeqvarsApiQuerypresetsclinvarCreateError, SeqvarsApiQuerypresetsclinvarCreateResponse, SeqvarsApiQuerypresetsclinvarRetrieveData, SeqvarsApiQuerypresetsclinvarUpdateData, SeqvarsApiQuerypresetsclinvarUpdateError, SeqvarsApiQuerypresetsclinvarUpdateResponse, SeqvarsApiQuerypresetsclinvarPartialUpdateData, SeqvarsApiQuerypresetsclinvarPartialUpdateError, SeqvarsApiQuerypresetsclinvarPartialUpdateResponse, SeqvarsApiQuerypresetsclinvarDestroyData, SeqvarsApiQuerypresetsclinvarDestroyError, SeqvarsApiQuerypresetsclinvarDestroyResponse, SeqvarsApiQuerypresetscolumnsListData, SeqvarsApiQuerypresetscolumnsListError, SeqvarsApiQuerypresetscolumnsListResponse, SeqvarsApiQuerypresetscolumnsCreateData, SeqvarsApiQuerypresetscolumnsCreateError, SeqvarsApiQuerypresetscolumnsCreateResponse, SeqvarsApiQuerypresetscolumnsRetrieveData, SeqvarsApiQuerypresetscolumnsUpdateData, SeqvarsApiQuerypresetscolumnsUpdateError, SeqvarsApiQuerypresetscolumnsUpdateResponse, SeqvarsApiQuerypresetscolumnsPartialUpdateData, SeqvarsApiQuerypresetscolumnsPartialUpdateError, SeqvarsApiQuerypresetscolumnsPartialUpdateResponse, SeqvarsApiQuerypresetscolumnsDestroyData, SeqvarsApiQuerypresetscolumnsDestroyError, SeqvarsApiQuerypresetscolumnsDestroyResponse, SeqvarsApiQuerypresetsconsequenceListData, SeqvarsApiQuerypresetsconsequenceListError, SeqvarsApiQuerypresetsconsequenceListResponse, SeqvarsApiQuerypresetsconsequenceCreateData, SeqvarsApiQuerypresetsconsequenceCreateError, SeqvarsApiQuerypresetsconsequenceCreateResponse, SeqvarsApiQuerypresetsconsequenceRetrieveData, SeqvarsApiQuerypresetsconsequenceUpdateData, SeqvarsApiQuerypresetsconsequenceUpdateError, SeqvarsApiQuerypresetsconsequenceUpdateResponse, SeqvarsApiQuerypresetsconsequencePartialUpdateData, SeqvarsApiQuerypresetsconsequencePartialUpdateError, SeqvarsApiQuerypresetsconsequencePartialUpdateResponse, SeqvarsApiQuerypresetsconsequenceDestroyData, SeqvarsApiQuerypresetsconsequenceDestroyError, SeqvarsApiQuerypresetsconsequenceDestroyResponse, SeqvarsApiQuerypresetsfactorydefaultsListData, SeqvarsApiQuerypresetsfactorydefaultsListError, SeqvarsApiQuerypresetsfactorydefaultsListResponse, SeqvarsApiQuerypresetsfactorydefaultsRetrieveData, SeqvarsApiQuerypresetsfrequencyListData, SeqvarsApiQuerypresetsfrequencyListError, SeqvarsApiQuerypresetsfrequencyListResponse, SeqvarsApiQuerypresetsfrequencyCreateData, SeqvarsApiQuerypresetsfrequencyCreateError, SeqvarsApiQuerypresetsfrequencyCreateResponse, SeqvarsApiQuerypresetsfrequencyRetrieveData, SeqvarsApiQuerypresetsfrequencyUpdateData, SeqvarsApiQuerypresetsfrequencyUpdateError, SeqvarsApiQuerypresetsfrequencyUpdateResponse, SeqvarsApiQuerypresetsfrequencyPartialUpdateData, SeqvarsApiQuerypresetsfrequencyPartialUpdateError, SeqvarsApiQuerypresetsfrequencyPartialUpdateResponse, SeqvarsApiQuerypresetsfrequencyDestroyData, SeqvarsApiQuerypresetsfrequencyDestroyError, SeqvarsApiQuerypresetsfrequencyDestroyResponse, SeqvarsApiQuerypresetslocusListData, SeqvarsApiQuerypresetslocusListError, SeqvarsApiQuerypresetslocusListResponse, SeqvarsApiQuerypresetslocusCreateData, SeqvarsApiQuerypresetslocusCreateError, SeqvarsApiQuerypresetslocusCreateResponse, SeqvarsApiQuerypresetslocusRetrieveData, SeqvarsApiQuerypresetslocusUpdateData, SeqvarsApiQuerypresetslocusUpdateError, SeqvarsApiQuerypresetslocusUpdateResponse, SeqvarsApiQuerypresetslocusPartialUpdateData, SeqvarsApiQuerypresetslocusPartialUpdateError, SeqvarsApiQuerypresetslocusPartialUpdateResponse, SeqvarsApiQuerypresetslocusDestroyData, SeqvarsApiQuerypresetslocusDestroyError, SeqvarsApiQuerypresetslocusDestroyResponse, SeqvarsApiQuerypresetsphenotypeprioListData, SeqvarsApiQuerypresetsphenotypeprioListError, SeqvarsApiQuerypresetsphenotypeprioListResponse, SeqvarsApiQuerypresetsphenotypeprioCreateData, SeqvarsApiQuerypresetsphenotypeprioCreateError, SeqvarsApiQuerypresetsphenotypeprioCreateResponse, SeqvarsApiQuerypresetsphenotypeprioRetrieveData, SeqvarsApiQuerypresetsphenotypeprioUpdateData, SeqvarsApiQuerypresetsphenotypeprioUpdateError, SeqvarsApiQuerypresetsphenotypeprioUpdateResponse, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateData, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateError, SeqvarsApiQuerypresetsphenotypeprioPartialUpdateResponse, SeqvarsApiQuerypresetsphenotypeprioDestroyData, SeqvarsApiQuerypresetsphenotypeprioDestroyError, SeqvarsApiQuerypresetsphenotypeprioDestroyResponse, SeqvarsApiQuerypresetsqualityListData, SeqvarsApiQuerypresetsqualityListError, SeqvarsApiQuerypresetsqualityListResponse, SeqvarsApiQuerypresetsqualityCreateData, SeqvarsApiQuerypresetsqualityCreateError, SeqvarsApiQuerypresetsqualityCreateResponse, SeqvarsApiQuerypresetsqualityRetrieveData, SeqvarsApiQuerypresetsqualityUpdateData, SeqvarsApiQuerypresetsqualityUpdateError, SeqvarsApiQuerypresetsqualityUpdateResponse, SeqvarsApiQuerypresetsqualityPartialUpdateData, SeqvarsApiQuerypresetsqualityPartialUpdateError, SeqvarsApiQuerypresetsqualityPartialUpdateResponse, SeqvarsApiQuerypresetsqualityDestroyData, SeqvarsApiQuerypresetsqualityDestroyError, SeqvarsApiQuerypresetsqualityDestroyResponse, SeqvarsApiQuerypresetssetListData, SeqvarsApiQuerypresetssetListError, SeqvarsApiQuerypresetssetListResponse, SeqvarsApiQuerypresetssetCreateData, SeqvarsApiQuerypresetssetCreateError, SeqvarsApiQuerypresetssetCreateResponse, SeqvarsApiQuerypresetssetRetrieveData, SeqvarsApiQuerypresetssetUpdateData, SeqvarsApiQuerypresetssetUpdateError, SeqvarsApiQuerypresetssetUpdateResponse, SeqvarsApiQuerypresetssetPartialUpdateData, SeqvarsApiQuerypresetssetPartialUpdateError, SeqvarsApiQuerypresetssetPartialUpdateResponse, SeqvarsApiQuerypresetssetDestroyData, SeqvarsApiQuerypresetssetDestroyError, SeqvarsApiQuerypresetssetDestroyResponse, SeqvarsApiQuerypresetssetCopyFromCreateData, SeqvarsApiQuerypresetssetCopyFromCreateError, SeqvarsApiQuerypresetssetCopyFromCreateResponse, SeqvarsApiQuerypresetssetversionListData, SeqvarsApiQuerypresetssetversionListError, SeqvarsApiQuerypresetssetversionListResponse, SeqvarsApiQuerypresetssetversionCreateData, SeqvarsApiQuerypresetssetversionCreateError, SeqvarsApiQuerypresetssetversionCreateResponse, SeqvarsApiQuerypresetssetversionRetrieveData, SeqvarsApiQuerypresetssetversionUpdateData, SeqvarsApiQuerypresetssetversionUpdateError, SeqvarsApiQuerypresetssetversionUpdateResponse, SeqvarsApiQuerypresetssetversionPartialUpdateData, SeqvarsApiQuerypresetssetversionPartialUpdateError, SeqvarsApiQuerypresetssetversionPartialUpdateResponse, SeqvarsApiQuerypresetssetversionDestroyData, SeqvarsApiQuerypresetssetversionDestroyError, SeqvarsApiQuerypresetssetversionDestroyResponse, SeqvarsApiQuerypresetssetversionCopyFromCreateData, SeqvarsApiQuerypresetssetversionCopyFromCreateError, SeqvarsApiQuerypresetssetversionCopyFromCreateResponse, SeqvarsApiQuerypresetsvariantprioListData, SeqvarsApiQuerypresetsvariantprioListError, SeqvarsApiQuerypresetsvariantprioListResponse, SeqvarsApiQuerypresetsvariantprioCreateData, SeqvarsApiQuerypresetsvariantprioCreateError, SeqvarsApiQuerypresetsvariantprioCreateResponse, SeqvarsApiQuerypresetsvariantprioRetrieveData, SeqvarsApiQuerypresetsvariantprioUpdateData, SeqvarsApiQuerypresetsvariantprioUpdateError, SeqvarsApiQuerypresetsvariantprioUpdateResponse, SeqvarsApiQuerypresetsvariantprioPartialUpdateData, SeqvarsApiQuerypresetsvariantprioPartialUpdateError, SeqvarsApiQuerypresetsvariantprioPartialUpdateResponse, SeqvarsApiQuerypresetsvariantprioDestroyData, SeqvarsApiQuerypresetsvariantprioDestroyError, SeqvarsApiQuerypresetsvariantprioDestroyResponse, SeqvarsApiQuerysettingsListData, SeqvarsApiQuerysettingsListError, SeqvarsApiQuerysettingsListResponse, SeqvarsApiQuerysettingsCreateData, SeqvarsApiQuerysettingsCreateError, SeqvarsApiQuerysettingsCreateResponse, SeqvarsApiQuerysettingsRetrieveData, SeqvarsApiQuerysettingsUpdateData, SeqvarsApiQuerysettingsUpdateError, SeqvarsApiQuerysettingsUpdateResponse, SeqvarsApiQuerysettingsPartialUpdateData, SeqvarsApiQuerysettingsPartialUpdateError, SeqvarsApiQuerysettingsPartialUpdateResponse, SeqvarsApiQuerysettingsDestroyData, SeqvarsApiQuerysettingsDestroyError, SeqvarsApiQuerysettingsDestroyResponse, SeqvarsApiResultrowListData, SeqvarsApiResultrowListError, SeqvarsApiResultrowListResponse, SeqvarsApiResultrowRetrieveData, SeqvarsApiResultsetListData, SeqvarsApiResultsetListError, SeqvarsApiResultsetListResponse, SeqvarsApiResultsetRetrieveData } from '../types.gen'; +import { client, casesAnalysisApiCaseanalysisList, casesAnalysisApiCaseanalysisRetrieve, casesAnalysisApiCaseanalysissessionList, casesAnalysisApiCaseanalysissessionRetrieve, casesImportApiCaseImportActionList, casesImportApiCaseImportActionCreate, casesImportApiCaseImportActionRetrieve, casesImportApiCaseImportActionUpdate, casesImportApiCaseImportActionPartialUpdate, casesImportApiCaseImportActionDestroy, casesQcApiCaseqcRetrieveRetrieve, casesQcApiVarfishstatsRetrieveRetrieve, casesApiAnnotationReleaseInfoListList, casesApiCaseCommentListCreateList, casesApiCaseCommentListCreateCreate, casesApiCasePhenotypeTermsListCreateList, casesApiCasePhenotypeTermsListCreateCreate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyRetrieve, casesApiCasePhenotypeTermsRetrieveUpdateDestroyUpdate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyPartialUpdate, casesApiCasePhenotypeTermsRetrieveUpdateDestroyDestroy, casesApiCaseCountRetrieve, casesApiCaseListList, casesApiCaseRetrieveUpdateDestroyRetrieve, casesApiCaseRetrieveUpdateDestroyUpdate, casesApiCaseRetrieveUpdateDestroyPartialUpdate, casesApiCaseRetrieveUpdateDestroyDestroy, casesApiSvAnnotationReleaseInfoListList, casesApiUserAndGlobalSettingsRetrieve, genepanelsApiGenepanelCategoryListList, genepanelsApiLookupGenepanelRetrieve, projectApiCreateCreate, projectApiInvitesCreateCreate, projectApiInvitesListList, projectApiInvitesResendCreate, projectApiInvitesRevokeCreate, projectApiListRetrieve, projectApiRemoteGetRetrieve, projectApiRetrieveRetrieve, projectApiRolesCreateCreate, projectApiRolesDestroyDestroy, projectApiRolesOwnerTransferCreate, projectApiRolesUpdateUpdate, projectApiRolesUpdatePartialUpdate, projectApiSettingsRetrieveRetrieve, projectApiSettingsRetrieveUserRetrieve, projectApiSettingsSetCreate, projectApiSettingsSetUserCreate, projectApiUpdateUpdate, projectApiUpdatePartialUpdate, projectApiUsersCurrentRetrieve, projectApiUsersListList, seqmetaApiEnrichmentkitListCreateList, seqmetaApiEnrichmentkitListCreateCreate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyRetrieve, seqmetaApiEnrichmentkitRetrieveUpdateDestroyUpdate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyPartialUpdate, seqmetaApiEnrichmentkitRetrieveUpdateDestroyDestroy, seqmetaApiTargetbedfileListCreateList, seqmetaApiTargetbedfileListCreateCreate, seqmetaApiTargetbedfileRetrieveUpdateDestroyRetrieve, seqmetaApiTargetbedfileRetrieveUpdateDestroyUpdate, seqmetaApiTargetbedfileRetrieveUpdateDestroyPartialUpdate, seqmetaApiTargetbedfileRetrieveUpdateDestroyDestroy, seqvarsApiPredefinedqueryList, seqvarsApiPredefinedqueryCreate, seqvarsApiPredefinedqueryRetrieve, seqvarsApiPredefinedqueryUpdate, seqvarsApiPredefinedqueryPartialUpdate, seqvarsApiPredefinedqueryDestroy, seqvarsApiQueryList, seqvarsApiQueryCreate, seqvarsApiQueryRetrieve, seqvarsApiQueryUpdate, seqvarsApiQueryPartialUpdate, seqvarsApiQueryDestroy, seqvarsApiQueryCreateFromCreate, seqvarsApiQueryexecutionList, seqvarsApiQueryexecutionRetrieve, seqvarsApiQueryexecutionStartCreate, seqvarsApiQuerypresetsclinvarList, seqvarsApiQuerypresetsclinvarCreate, seqvarsApiQuerypresetsclinvarRetrieve, seqvarsApiQuerypresetsclinvarUpdate, seqvarsApiQuerypresetsclinvarPartialUpdate, seqvarsApiQuerypresetsclinvarDestroy, seqvarsApiQuerypresetscolumnsList, seqvarsApiQuerypresetscolumnsCreate, seqvarsApiQuerypresetscolumnsRetrieve, seqvarsApiQuerypresetscolumnsUpdate, seqvarsApiQuerypresetscolumnsPartialUpdate, seqvarsApiQuerypresetscolumnsDestroy, seqvarsApiQuerypresetsconsequenceList, seqvarsApiQuerypresetsconsequenceCreate, seqvarsApiQuerypresetsconsequenceRetrieve, seqvarsApiQuerypresetsconsequenceUpdate, seqvarsApiQuerypresetsconsequencePartialUpdate, seqvarsApiQuerypresetsconsequenceDestroy, seqvarsApiQuerypresetsfactorydefaultsList, seqvarsApiQuerypresetsfactorydefaultsRetrieve, seqvarsApiQuerypresetsfrequencyList, seqvarsApiQuerypresetsfrequencyCreate, seqvarsApiQuerypresetsfrequencyRetrieve, seqvarsApiQuerypresetsfrequencyUpdate, seqvarsApiQuerypresetsfrequencyPartialUpdate, seqvarsApiQuerypresetsfrequencyDestroy, seqvarsApiQuerypresetslocusList, seqvarsApiQuerypresetslocusCreate, seqvarsApiQuerypresetslocusRetrieve, seqvarsApiQuerypresetslocusUpdate, seqvarsApiQuerypresetslocusPartialUpdate, seqvarsApiQuerypresetslocusDestroy, seqvarsApiQuerypresetsphenotypeprioList, seqvarsApiQuerypresetsphenotypeprioCreate, seqvarsApiQuerypresetsphenotypeprioRetrieve, seqvarsApiQuerypresetsphenotypeprioUpdate, seqvarsApiQuerypresetsphenotypeprioPartialUpdate, seqvarsApiQuerypresetsphenotypeprioDestroy, seqvarsApiQuerypresetsqualityList, seqvarsApiQuerypresetsqualityCreate, seqvarsApiQuerypresetsqualityRetrieve, seqvarsApiQuerypresetsqualityUpdate, seqvarsApiQuerypresetsqualityPartialUpdate, seqvarsApiQuerypresetsqualityDestroy, seqvarsApiQuerypresetssetList, seqvarsApiQuerypresetssetCreate, seqvarsApiQuerypresetssetRetrieve, seqvarsApiQuerypresetssetUpdate, seqvarsApiQuerypresetssetPartialUpdate, seqvarsApiQuerypresetssetDestroy, seqvarsApiQuerypresetssetCopyFromCreate, seqvarsApiQuerypresetssetversionList, seqvarsApiQuerypresetssetversionCreate, seqvarsApiQuerypresetssetversionRetrieve, seqvarsApiQuerypresetssetversionUpdate, seqvarsApiQuerypresetssetversionPartialUpdate, seqvarsApiQuerypresetssetversionDestroy, seqvarsApiQuerypresetssetversionCopyFromCreate, seqvarsApiQuerypresetsvariantprioList, seqvarsApiQuerypresetsvariantprioCreate, seqvarsApiQuerypresetsvariantprioRetrieve, seqvarsApiQuerypresetsvariantprioUpdate, seqvarsApiQuerypresetsvariantprioPartialUpdate, seqvarsApiQuerypresetsvariantprioDestroy, seqvarsApiQuerysettingsList, seqvarsApiQuerysettingsCreate, seqvarsApiQuerysettingsRetrieve, seqvarsApiQuerysettingsUpdate, seqvarsApiQuerysettingsPartialUpdate, seqvarsApiQuerysettingsDestroy, seqvarsApiResultrowList, seqvarsApiResultrowRetrieve, seqvarsApiResultsetList, seqvarsApiResultsetRetrieve } from '../services.gen'; type QueryKey = [ Pick & { @@ -65,10 +65,10 @@ export const casesAnalysisApiCaseanalysisListInfiniteOptions = (options: Options const { data } = await casesAnalysisApiCaseanalysisList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -137,10 +137,10 @@ export const casesAnalysisApiCaseanalysissessionListInfiniteOptions = (options: const { data } = await casesAnalysisApiCaseanalysissessionList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -176,43 +176,43 @@ export const casesAnalysisApiCaseanalysissessionRetrieveOptions = (options: Opti queryKey: casesAnalysisApiCaseanalysissessionRetrieveQueryKey(options) }); }; -export const casesImportApiCaseImportActionListCreateListQueryKey = (options: Options) => [ - createQueryKey("casesImportApiCaseImportActionListCreateList", options) +export const casesImportApiCaseImportActionListQueryKey = (options: Options) => [ + createQueryKey("casesImportApiCaseImportActionList", options) ]; -export const casesImportApiCaseImportActionListCreateListOptions = (options: Options) => { return queryOptions({ +export const casesImportApiCaseImportActionListOptions = (options: Options) => { return queryOptions({ queryFn: async ({ queryKey }) => { - const { data } = await casesImportApiCaseImportActionListCreateList({ + const { data } = await casesImportApiCaseImportActionList({ ...options, ...queryKey[0], throwOnError: true }); return data; }, - queryKey: casesImportApiCaseImportActionListCreateListQueryKey(options) + queryKey: casesImportApiCaseImportActionListQueryKey(options) }); }; -export const casesImportApiCaseImportActionListCreateListInfiniteQueryKey = (options: Options): QueryKey> => [ - createQueryKey("casesImportApiCaseImportActionListCreateList", options, true) +export const casesImportApiCaseImportActionListInfiniteQueryKey = (options: Options): QueryKey> => [ + createQueryKey("casesImportApiCaseImportActionList", options, true) ]; -export const casesImportApiCaseImportActionListCreateListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const casesImportApiCaseImportActionListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore - const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { + const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { page: pageParam } }; - const { data } = await casesImportApiCaseImportActionListCreateList({ + const { data } = await casesImportApiCaseImportActionList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -229,28 +229,28 @@ export const casesImportApiCaseImportActionListCreateListInfiniteOptions = (opti }); return data; }, - queryKey: casesImportApiCaseImportActionListCreateListInfiniteQueryKey(options) + queryKey: casesImportApiCaseImportActionListInfiniteQueryKey(options) }); }; -export const casesImportApiCaseImportActionListCreateCreateQueryKey = (options: Options) => [ - createQueryKey("casesImportApiCaseImportActionListCreateCreate", options) +export const casesImportApiCaseImportActionCreateQueryKey = (options: Options) => [ + createQueryKey("casesImportApiCaseImportActionCreate", options) ]; -export const casesImportApiCaseImportActionListCreateCreateOptions = (options: Options) => { return queryOptions({ +export const casesImportApiCaseImportActionCreateOptions = (options: Options) => { return queryOptions({ queryFn: async ({ queryKey }) => { - const { data } = await casesImportApiCaseImportActionListCreateCreate({ + const { data } = await casesImportApiCaseImportActionCreate({ ...options, ...queryKey[0], throwOnError: true }); return data; }, - queryKey: casesImportApiCaseImportActionListCreateCreateQueryKey(options) + queryKey: casesImportApiCaseImportActionCreateQueryKey(options) }); }; -export const casesImportApiCaseImportActionListCreateCreateMutation = () => { const mutationOptions: UseMutationOptions> = { +export const casesImportApiCaseImportActionCreateMutation = () => { const mutationOptions: UseMutationOptions> = { mutationFn: async (options) => { - const { data } = await casesImportApiCaseImportActionListCreateCreate({ + const { data } = await casesImportApiCaseImportActionCreate({ ...options, throwOnError: true }); @@ -258,25 +258,25 @@ export const casesImportApiCaseImportActionListCreateCreateMutation = () => { co } }; return mutationOptions; }; -export const casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveQueryKey = (options: Options) => [ - createQueryKey("casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieve", options) +export const casesImportApiCaseImportActionRetrieveQueryKey = (options: Options) => [ + createQueryKey("casesImportApiCaseImportActionRetrieve", options) ]; -export const casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveOptions = (options: Options) => { return queryOptions({ +export const casesImportApiCaseImportActionRetrieveOptions = (options: Options) => { return queryOptions({ queryFn: async ({ queryKey }) => { - const { data } = await casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieve({ + const { data } = await casesImportApiCaseImportActionRetrieve({ ...options, ...queryKey[0], throwOnError: true }); return data; }, - queryKey: casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveQueryKey(options) + queryKey: casesImportApiCaseImportActionRetrieveQueryKey(options) }); }; -export const casesImportApiCaseImportActionRetrieveUpdateDestroyUpdateMutation = () => { const mutationOptions: UseMutationOptions> = { +export const casesImportApiCaseImportActionUpdateMutation = () => { const mutationOptions: UseMutationOptions> = { mutationFn: async (options) => { - const { data } = await casesImportApiCaseImportActionRetrieveUpdateDestroyUpdate({ + const { data } = await casesImportApiCaseImportActionUpdate({ ...options, throwOnError: true }); @@ -284,9 +284,9 @@ export const casesImportApiCaseImportActionRetrieveUpdateDestroyUpdateMutation = } }; return mutationOptions; }; -export const casesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateMutation = () => { const mutationOptions: UseMutationOptions> = { +export const casesImportApiCaseImportActionPartialUpdateMutation = () => { const mutationOptions: UseMutationOptions> = { mutationFn: async (options) => { - const { data } = await casesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdate({ + const { data } = await casesImportApiCaseImportActionPartialUpdate({ ...options, throwOnError: true }); @@ -294,9 +294,9 @@ export const casesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateMut } }; return mutationOptions; }; -export const casesImportApiCaseImportActionRetrieveUpdateDestroyDestroyMutation = () => { const mutationOptions: UseMutationOptions> = { +export const casesImportApiCaseImportActionDestroyMutation = () => { const mutationOptions: UseMutationOptions> = { mutationFn: async (options) => { - const { data } = await casesImportApiCaseImportActionRetrieveUpdateDestroyDestroy({ + const { data } = await casesImportApiCaseImportActionDestroy({ ...options, throwOnError: true }); @@ -531,10 +531,10 @@ export const casesApiCaseListListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiPredefinedqueryListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiPredefinedqueryList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -1374,23 +1374,23 @@ export const seqvarsApiQueryListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQueryListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQueryList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -1528,23 +1528,23 @@ export const seqvarsApiQueryexecutionListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQueryexecutionListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQueryexecutionList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -1626,23 +1626,23 @@ export const seqvarsApiQuerypresetsclinvarListInfiniteQueryKey = (options: Optio createQueryKey("seqvarsApiQuerypresetsclinvarList", options, true) ]; -export const seqvarsApiQuerypresetsclinvarListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsclinvarListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsclinvarList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -1754,23 +1754,23 @@ export const seqvarsApiQuerypresetscolumnsListInfiniteQueryKey = (options: Optio createQueryKey("seqvarsApiQuerypresetscolumnsList", options, true) ]; -export const seqvarsApiQuerypresetscolumnsListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetscolumnsListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetscolumnsList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -1882,23 +1882,23 @@ export const seqvarsApiQuerypresetsconsequenceListInfiniteQueryKey = (options: O createQueryKey("seqvarsApiQuerypresetsconsequenceList", options, true) ]; -export const seqvarsApiQuerypresetsconsequenceListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsconsequenceListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsconsequenceList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2010,23 +2010,23 @@ export const seqvarsApiQuerypresetsfactorydefaultsListInfiniteQueryKey = (option createQueryKey("seqvarsApiQuerypresetsfactorydefaultsList", options, true) ]; -export const seqvarsApiQuerypresetsfactorydefaultsListInfiniteOptions = (options?: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsfactorydefaultsListInfiniteOptions = (options?: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsfactorydefaultsList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2082,23 +2082,23 @@ export const seqvarsApiQuerypresetsfrequencyListInfiniteQueryKey = (options: Opt createQueryKey("seqvarsApiQuerypresetsfrequencyList", options, true) ]; -export const seqvarsApiQuerypresetsfrequencyListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsfrequencyListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsfrequencyList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2210,23 +2210,23 @@ export const seqvarsApiQuerypresetslocusListInfiniteQueryKey = (options: Options createQueryKey("seqvarsApiQuerypresetslocusList", options, true) ]; -export const seqvarsApiQuerypresetslocusListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetslocusListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetslocusList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2338,23 +2338,23 @@ export const seqvarsApiQuerypresetsphenotypeprioListInfiniteQueryKey = (options: createQueryKey("seqvarsApiQuerypresetsphenotypeprioList", options, true) ]; -export const seqvarsApiQuerypresetsphenotypeprioListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsphenotypeprioListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsphenotypeprioList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2466,23 +2466,23 @@ export const seqvarsApiQuerypresetsqualityListInfiniteQueryKey = (options: Optio createQueryKey("seqvarsApiQuerypresetsqualityList", options, true) ]; -export const seqvarsApiQuerypresetsqualityListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsqualityListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsqualityList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2594,23 +2594,23 @@ export const seqvarsApiQuerypresetssetListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetssetListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetssetList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2748,23 +2748,23 @@ export const seqvarsApiQuerypresetssetversionListInfiniteQueryKey = (options: Op createQueryKey("seqvarsApiQuerypresetssetversionList", options, true) ]; -export const seqvarsApiQuerypresetssetversionListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetssetversionListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetssetversionList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -2902,23 +2902,23 @@ export const seqvarsApiQuerypresetsvariantprioListInfiniteQueryKey = (options: O createQueryKey("seqvarsApiQuerypresetsvariantprioList", options, true) ]; -export const seqvarsApiQuerypresetsvariantprioListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerypresetsvariantprioListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerypresetsvariantprioList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -3030,23 +3030,23 @@ export const seqvarsApiQuerysettingsListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiQuerysettingsListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiQuerysettingsList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -3158,23 +3158,23 @@ export const seqvarsApiResultrowListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiResultrowListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiResultrowList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -3230,23 +3230,23 @@ export const seqvarsApiResultsetListInfiniteQueryKey = (options: Options) => { return infiniteQueryOptions, QueryKey>, string | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( +export const seqvarsApiResultsetListInfiniteOptions = (options: Options) => { return infiniteQueryOptions, QueryKey>, number | Pick>[0], 'body' | 'headers' | 'path' | 'query'>>( // @ts-ignore { queryFn: async ({ pageParam, queryKey }) => { // @ts-ignore const page: Pick>[0], 'body' | 'headers' | 'path' | 'query'> = typeof pageParam === "object" ? pageParam : { query: { - cursor: pageParam + page: pageParam } }; const { data } = await seqvarsApiResultsetList({ ...options, ...queryKey[0], - body: { - ...queryKey[0].body as any, - ...page.body as any - }, + // body: { + // ...queryKey[0].body as any, + // ...page.body as any + // }, headers: { ...queryKey[0].headers, ...page.headers @@ -3280,4 +3280,4 @@ export const seqvarsApiResultsetRetrieveOptions = (options: Options(options: Options) => { return (options?.client ?? client).get({ +export const casesImportApiCaseImportActionList = (options: Options) => { return (options?.client ?? client).get({ ...options, - url: '/cases-import/api/case-import-action/list-create/{project}/' + url: '/cases-import/api/case-import-action/{project}/' }); }; /** - * API view mixin for generic DRF API views with serializers, SODAR project - * context and permission checkin. - * - * Unless overriding ``permission_classes`` with their own implementation, the - * user MUST supply a ``permission_required`` attribute. - * - * Replace ``lookup_url_kwarg`` with your view's url kwarg (SODAR project - * compatible model name in lowercase). + * Override to ensure creation happens in a transaction. * - * If the lookup is done via a foreign key, change the ``lookup_field`` - * attribute of your class into ``foreignkey__sodar_uuid``, e.g. - * ``project__sodar_uuid`` for lists. - * - * If your object(s) don't have a direct ``project`` relation, update the - * ``queryset_project_field`` to point to the field, e.g. - * ``someothermodel__project``. + * This is important so we can rely on the serializer validation to be consistent + * with the creation (e.g., on collision checks). */ -export const casesImportApiCaseImportActionListCreateCreate = (options: Options) => { return (options?.client ?? client).post({ +export const casesImportApiCaseImportActionCreate = (options: Options) => { return (options?.client ?? client).post({ ...options, - url: '/cases-import/api/case-import-action/list-create/{project}/' + url: '/cases-import/api/case-import-action/{project}/' }); }; /** - * API view mixin for generic DRF API views with serializers, SODAR project - * context and permission checkin. - * - * Unless overriding ``permission_classes`` with their own implementation, the - * user MUST supply a ``permission_required`` attribute. - * - * Replace ``lookup_url_kwarg`` with your view's url kwarg (SODAR project - * compatible model name in lowercase). - * - * If the lookup is done via a foreign key, change the ``lookup_field`` - * attribute of your class into ``foreignkey__sodar_uuid``, e.g. - * ``project__sodar_uuid`` for lists. - * - * If your object(s) don't have a direct ``project`` relation, update the - * ``queryset_project_field`` to point to the field, e.g. - * ``someothermodel__project``. + * Base class for app view sets having project from URL kwarg as context. */ -export const casesImportApiCaseImportActionRetrieveUpdateDestroyRetrieve = (options: Options) => { return (options?.client ?? client).get({ +export const casesImportApiCaseImportActionRetrieve = (options: Options) => { return (options?.client ?? client).get({ ...options, - url: '/cases-import/api/case-import-action/retrieve-update-destroy/{caseimportaction}/' + url: '/cases-import/api/case-import-action/{project}/{caseimportaction}/' }); }; /** - * API view mixin for generic DRF API views with serializers, SODAR project - * context and permission checkin. + * Override to ensure creation happens in a transaction. * - * Unless overriding ``permission_classes`` with their own implementation, the - * user MUST supply a ``permission_required`` attribute. - * - * Replace ``lookup_url_kwarg`` with your view's url kwarg (SODAR project - * compatible model name in lowercase). - * - * If the lookup is done via a foreign key, change the ``lookup_field`` - * attribute of your class into ``foreignkey__sodar_uuid``, e.g. - * ``project__sodar_uuid`` for lists. - * - * If your object(s) don't have a direct ``project`` relation, update the - * ``queryset_project_field`` to point to the field, e.g. - * ``someothermodel__project``. + * This is important so we can rely on the serializer validation to be consistent + * with the creation (e.g., on collision checks). */ -export const casesImportApiCaseImportActionRetrieveUpdateDestroyUpdate = (options: Options) => { return (options?.client ?? client).put({ +export const casesImportApiCaseImportActionUpdate = (options: Options) => { return (options?.client ?? client).put({ ...options, - url: '/cases-import/api/case-import-action/retrieve-update-destroy/{caseimportaction}/' + url: '/cases-import/api/case-import-action/{project}/{caseimportaction}/' }); }; /** - * API view mixin for generic DRF API views with serializers, SODAR project - * context and permission checkin. - * - * Unless overriding ``permission_classes`` with their own implementation, the - * user MUST supply a ``permission_required`` attribute. - * - * Replace ``lookup_url_kwarg`` with your view's url kwarg (SODAR project - * compatible model name in lowercase). - * - * If the lookup is done via a foreign key, change the ``lookup_field`` - * attribute of your class into ``foreignkey__sodar_uuid``, e.g. - * ``project__sodar_uuid`` for lists. - * - * If your object(s) don't have a direct ``project`` relation, update the - * ``queryset_project_field`` to point to the field, e.g. - * ``someothermodel__project``. + * Base class for app view sets having project from URL kwarg as context. */ -export const casesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdate = (options: Options) => { return (options?.client ?? client).patch({ +export const casesImportApiCaseImportActionPartialUpdate = (options: Options) => { return (options?.client ?? client).patch({ ...options, - url: '/cases-import/api/case-import-action/retrieve-update-destroy/{caseimportaction}/' + url: '/cases-import/api/case-import-action/{project}/{caseimportaction}/' }); }; /** - * API view mixin for generic DRF API views with serializers, SODAR project - * context and permission checkin. - * - * Unless overriding ``permission_classes`` with their own implementation, the - * user MUST supply a ``permission_required`` attribute. - * - * Replace ``lookup_url_kwarg`` with your view's url kwarg (SODAR project - * compatible model name in lowercase). - * - * If the lookup is done via a foreign key, change the ``lookup_field`` - * attribute of your class into ``foreignkey__sodar_uuid``, e.g. - * ``project__sodar_uuid`` for lists. - * - * If your object(s) don't have a direct ``project`` relation, update the - * ``queryset_project_field`` to point to the field, e.g. - * ``someothermodel__project``. + * Override to prevent destruction unless state is draft. */ -export const casesImportApiCaseImportActionRetrieveUpdateDestroyDestroy = (options: Options) => { return (options?.client ?? client).delete({ +export const casesImportApiCaseImportActionDestroy = (options: Options) => { return (options?.client ?? client).delete({ ...options, - url: '/cases-import/api/case-import-action/retrieve-update-destroy/{caseimportaction}/' + url: '/cases-import/api/case-import-action/{project}/{caseimportaction}/' }); }; /** @@ -1668,7 +1584,7 @@ export const seqvarsApiResultrowRetrieve = (options: Options) => { return (options?.client ?? client).get({ ...options, - url: '/seqvars/api/resultset/{query}/' + url: '/seqvars/api/resultset/{queryexecution}/' }); }; /** @@ -1676,5 +1592,5 @@ export const seqvarsApiResultsetList = (op */ export const seqvarsApiResultsetRetrieve = (options: Options) => { return (options?.client ?? client).get({ ...options, - url: '/seqvars/api/resultset/{query}/{resultset}/' + url: '/seqvars/api/resultset/{queryexecution}/{resultset}/' }); }; \ No newline at end of file diff --git a/frontend/ext/varfish-api/src/lib/types.gen.ts b/frontend/ext/varfish-api/src/lib/types.gen.ts index 8b2ad9ed8..79dfd0139 100644 --- a/frontend/ext/varfish-api/src/lib/types.gen.ts +++ b/frontend/ext/varfish-api/src/lib/types.gen.ts @@ -881,10 +881,10 @@ export type GenePydanticList = Array<{ * Store gene-related annotation (always for a single gene). */ export type GeneRelatedAnnotationPydantic = { - identity: GeneIdentityPydantic; - consequences: GeneRelatedConsequencesPydantic; - phenotypes: GeneRelatedPhenotypesPydantic; - constraints: GeneRelatedConstraintsPydantic; + identity: (GeneIdentityPydantic | null); + consequences: (GeneRelatedConsequencesPydantic | null); + phenotypes: (GeneRelatedPhenotypesPydantic | null); + constraints: (GeneRelatedConstraintsPydantic | null); }; /** @@ -913,6 +913,7 @@ export type GeneRelatedConstraintsPydantic = { export type GeneRelatedPhenotypesPydantic = { is_acmg_sf?: boolean; is_disease_gene?: boolean; + mode_of_inheritances?: Array; }; /** @@ -1019,96 +1020,112 @@ export type PaginatedCaseSerializerNgList = { }; export type PaginatedSeqvarsPredefinedQueryList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryExecutionList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsClinvarList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsColumnsList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsConsequenceList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsFrequencyList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsLocusList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsPhenotypePrioList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsQualityList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsSetList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsSetVersionList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQueryPresetsVariantPrioList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsQuerySettingsList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsResultRowList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; }; export type PaginatedSeqvarsResultSetList = { + count?: number; next?: (string) | null; previous?: (string) | null; results?: Array; @@ -2016,6 +2033,11 @@ export type SeqvarsHelixMtDbFrequencySettingsPydantic = { frequency?: (number | null); }; +/** + * Mode of inheritance gene annotation. + */ +export type SeqvarsModeOfInheritance = 'autosomal_dominant' | 'autosomal_recessive' | 'x_linked_dominant' | 'x_linked_recessive' | 'y_linked' | 'mitochondrial'; + /** * Store gnomAD and in-house nuclear frequency information. */ @@ -2908,7 +2930,7 @@ export type SeqvarsQuerySettingsGenotype = { * Pydantic representation of ``SeqvarsQuerySettingsGenotype``. */ export type SeqvarsQuerySettingsGenotypePydantic = { - recessive_mode?: (SeqvarsRecessiveModeChoice); + recessive_mode?: SeqvarsRecessiveModeChoice; sample_genotypes?: Array; }; @@ -3378,7 +3400,7 @@ export type CasesAnalysisApiCaseanalysissessionRetrieveResponse = (CaseAnalysisS export type CasesAnalysisApiCaseanalysissessionRetrieveError = unknown; -export type CasesImportApiCaseImportActionListCreateListData = { +export type CasesImportApiCaseImportActionListData = { path: { project: string; }; @@ -3394,62 +3416,66 @@ export type CasesImportApiCaseImportActionListCreateListData = { }; }; -export type CasesImportApiCaseImportActionListCreateListResponse = (PaginatedCaseImportActionList); +export type CasesImportApiCaseImportActionListResponse = (PaginatedCaseImportActionList); -export type CasesImportApiCaseImportActionListCreateListError = unknown; +export type CasesImportApiCaseImportActionListError = unknown; -export type CasesImportApiCaseImportActionListCreateCreateData = { +export type CasesImportApiCaseImportActionCreateData = { body: CaseImportActionRequest; path: { project: string; }; }; -export type CasesImportApiCaseImportActionListCreateCreateResponse = (CaseImportAction); +export type CasesImportApiCaseImportActionCreateResponse = (CaseImportAction); -export type CasesImportApiCaseImportActionListCreateCreateError = unknown; +export type CasesImportApiCaseImportActionCreateError = unknown; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveData = { +export type CasesImportApiCaseImportActionRetrieveData = { path: { caseimportaction: string; + project: string; }; }; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveResponse = (CaseImportAction); +export type CasesImportApiCaseImportActionRetrieveResponse = (CaseImportAction); -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyRetrieveError = unknown; +export type CasesImportApiCaseImportActionRetrieveError = unknown; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateData = { +export type CasesImportApiCaseImportActionUpdateData = { body: CaseImportActionRequest; path: { caseimportaction: string; + project: string; }; }; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateResponse = (CaseImportAction); +export type CasesImportApiCaseImportActionUpdateResponse = (CaseImportAction); -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyUpdateError = unknown; +export type CasesImportApiCaseImportActionUpdateError = unknown; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateData = { +export type CasesImportApiCaseImportActionPartialUpdateData = { body?: PatchedCaseImportActionRequest; path: { caseimportaction: string; + project: string; }; }; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateResponse = (CaseImportAction); +export type CasesImportApiCaseImportActionPartialUpdateResponse = (CaseImportAction); -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyPartialUpdateError = unknown; +export type CasesImportApiCaseImportActionPartialUpdateError = unknown; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyData = { +export type CasesImportApiCaseImportActionDestroyData = { path: { caseimportaction: string; + project: string; }; }; -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyResponse = (void); +export type CasesImportApiCaseImportActionDestroyResponse = (void); -export type CasesImportApiCaseImportActionRetrieveUpdateDestroyDestroyError = unknown; +export type CasesImportApiCaseImportActionDestroyError = unknown; export type CasesQcApiCaseqcRetrieveRetrieveData = { path: { @@ -3972,9 +3998,9 @@ export type SeqvarsApiPredefinedqueryListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4049,9 +4075,9 @@ export type SeqvarsApiQueryListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4137,9 +4163,9 @@ export type SeqvarsApiQueryexecutionListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4178,9 +4204,9 @@ export type SeqvarsApiQuerypresetsclinvarListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4255,9 +4281,9 @@ export type SeqvarsApiQuerypresetscolumnsListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4332,9 +4358,9 @@ export type SeqvarsApiQuerypresetsconsequenceListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4406,9 +4432,9 @@ export type SeqvarsApiQuerypresetsconsequenceDestroyError = unknown; export type SeqvarsApiQuerypresetsfactorydefaultsListData = { query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4436,9 +4462,9 @@ export type SeqvarsApiQuerypresetsfrequencyListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4513,9 +4539,9 @@ export type SeqvarsApiQuerypresetslocusListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4590,9 +4616,9 @@ export type SeqvarsApiQuerypresetsphenotypeprioListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4667,9 +4693,9 @@ export type SeqvarsApiQuerypresetsqualityListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4744,9 +4770,9 @@ export type SeqvarsApiQuerypresetssetListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4833,9 +4859,9 @@ export type SeqvarsApiQuerypresetssetversionListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4922,9 +4948,9 @@ export type SeqvarsApiQuerypresetsvariantprioListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -4999,9 +5025,9 @@ export type SeqvarsApiQuerysettingsListData = { }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -5075,10 +5101,12 @@ export type SeqvarsApiResultrowListData = { resultset: string; }; query?: { + order_by?: string; + order_dir?: string; /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -5103,13 +5131,13 @@ export type SeqvarsApiResultrowRetrieveError = unknown; export type SeqvarsApiResultsetListData = { path: { - query: string; + queryexecution: string; }; query?: { /** - * The pagination cursor value. + * A page number within the paginated result set. */ - cursor?: string; + page?: number; /** * Number of results to return per page. */ @@ -5123,7 +5151,7 @@ export type SeqvarsApiResultsetListError = unknown; export type SeqvarsApiResultsetRetrieveData = { path: { - query: string; + queryexecution: string; resultset: string; }; }; diff --git a/frontend/src/cases/components/CaseListTable/CaseListTable.vue b/frontend/src/cases/components/CaseListTable/CaseListTable.vue index 220ca00e0..b62fdd62c 100644 --- a/frontend/src/cases/components/CaseListTable/CaseListTable.vue +++ b/frontend/src/cases/components/CaseListTable/CaseListTable.vue @@ -129,6 +129,9 @@ watch( item-value="name" @update:options="updateQueryDebounced" > +