GPF Development
- Release Notes
- dae Interface
- Genomic Resources
- Classes and Functions
- dae.genomic_resources package
- Subpackages
- Submodules
- dae.genomic_resources.aggregators module
- dae.genomic_resources.cached_repository module
- dae.genomic_resources.cli module
- dae.genomic_resources.draw_score_histograms module
- dae.genomic_resources.fsspec_protocol module
- dae.genomic_resources.genomic_context module
- dae.genomic_resources.genomic_context_cli module
- dae.genomic_resources.genomic_scores module
- dae.genomic_resources.group_repository module
- dae.genomic_resources.histogram module
- dae.genomic_resources.liftover_chain module
- dae.genomic_resources.reference_genome module
- dae.genomic_resources.repository module
GenomicResourceGenomicResourceProtocolRepoGenomicResourceRepoManifestManifestEntryManifestUpdateModeReadOnlyRepositoryProtocolReadWriteRepositoryProtocolResourceFileStateis_gr_id_token()is_version_constraint_satisfied()parse_gr_id_version_token()parse_resource_id_version()version_string_to_suffix()version_tuple_to_string()version_tuple_to_suffix()
- dae.genomic_resources.repository_factory module
- dae.genomic_resources.resource_implementation module
- dae.genomic_resources.testing module
build_filesystem_test_protocol()build_filesystem_test_repository()build_filesystem_test_resource()build_http_test_protocol()build_inmemory_test_protocol()build_inmemory_test_repository()build_inmemory_test_resource()build_s3_test_bucket()build_s3_test_filesystem()build_s3_test_protocol()convert_to_tab_separated()copy_proto_genomic_resources()proto_builder()resource_builder()s3_test_protocol()s3_test_server_endpoint()setup_bigwig()setup_dae_transmitted()setup_denovo()setup_directories()setup_empty_gene_models()setup_gene_models()setup_genome()setup_gzip()setup_pedigree()setup_tabix()setup_vcf()
- dae.genomic_resources.variant_utils module
- Module contents
- dae.genomic_resources package
- Classes and Functions
- Annotation
- Classes and Functions
- dae.annotation package
- Submodules
- dae.annotation.annotatable module
- dae.annotation.annotate_columns module
- dae.annotation.annotate_doc module
- dae.annotation.annotate_schema2_parquet module
- dae.annotation.annotate_utils module
- dae.annotation.annotate_vcf module
- dae.annotation.annotation_config module
- dae.annotation.annotation_factory module
build_annotation_pipeline()check_for_repeated_attributes_in_annotator()check_for_repeated_attributes_in_pipeline()check_for_unused_parameters()copy_annotation_pipeline()copy_reannotation_pipeline()get_annotator_factory()get_available_annotator_types()load_pipeline_from_file()load_pipeline_from_yaml()register_annotator_factory()resolve_repeated_attributes()
- dae.annotation.annotation_pipeline module
- dae.annotation.annotator_base module
- dae.annotation.cnv_collection_annotator module
- dae.annotation.debug_annotator module
- dae.annotation.docker_annotator module
- dae.annotation.effect_annotator module
- dae.annotation.format_handlers module
- dae.annotation.gene_score_annotator module
- dae.annotation.gene_set_annotator module
- dae.annotation.genomic_context module
- dae.annotation.liftover_annotator module
- dae.annotation.normalize_allele_annotator module
- dae.annotation.parquet module
- dae.annotation.reannotate_instance module
- dae.annotation.record_to_annotatable module
- dae.annotation.score_annotator module
- dae.annotation.simple_effect_annotator module
- Module contents
- dae.annotation package
- Classes and Functions
- Effect Annotation
- Classes and Functions
- dae.effect_annotation package
- Subpackages
- Submodules
- dae.effect_annotation.annotation_effects module
- dae.effect_annotation.annotation_request module
- dae.effect_annotation.annotator module
- dae.effect_annotation.cli module
- dae.effect_annotation.effect module
- dae.effect_annotation.gene_codes module
- dae.effect_annotation.variant module
- Module contents
- dae.effect_annotation package
- Classes and Functions
- Genomic Variants
- Pedigrees Tools
- Classes and Functions
- dae.pedigrees package
- Submodules
- dae.pedigrees.drawing module
- dae.pedigrees.families_data module
- dae.pedigrees.family module
- dae.pedigrees.family_role_builder module
- dae.pedigrees.family_tag_builder module
FamilyTagsBuildercheck_affected_dad_family()check_affected_mom_family()check_affected_prb_family()check_affected_sib_family()check_control_family()check_family_tags_query()check_female_prb_family()check_male_prb_family()check_missing_dad_family()check_missing_mom_family()check_multiplex_family()check_nuclear_family()check_quad_family()check_simplex_family()check_tag()check_trio_family()check_unaffected_dad_family()check_unaffected_mom_family()check_unaffected_prb_family()check_unaffected_sib_family()set_attr()set_tag()tag_affected_dad_family()tag_affected_mom_family()tag_affected_prb_family()tag_affected_sib_family()tag_control_family()tag_female_prb_family()tag_male_prb_family()tag_missing_dad_family()tag_missing_mom_family()tag_multiplex_family()tag_nuclear_family()tag_quad_family()tag_simplex_family()tag_trio_family()tag_unaffected_dad_family()tag_unaffected_mom_family()tag_unaffected_prb_family()tag_unaffected_sib_family()unset_tag()
- dae.pedigrees.layout module
- dae.pedigrees.loader module
- dae.pedigrees.pedigrees module
- dae.pedigrees.testing module
- Module contents
- dae.pedigrees package
- Classes and Functions
- Variants Loaders
- dae.variants_loaders package
- dae.variants_loaders.raw package
- Submodules
- dae.variants_loaders.raw.flexible_variant_loader module
- dae.variants_loaders.raw.loader module
ArgumentTypeCLIArgumentCLILoaderFamiliesGenotypesVariantsGenotypesLoaderVariantsLoaderVariantsLoaderDecoratorVariantsLoaderDecorator.annotation_schemaVariantsLoaderDecorator.build_arguments_dict()VariantsLoaderDecorator.build_cli_arguments()VariantsLoaderDecorator.chromosomesVariantsLoaderDecorator.cli_arguments()VariantsLoaderDecorator.cli_defaults()VariantsLoaderDecorator.close()VariantsLoaderDecorator.get_attribute()
- Module contents
- dae.variants_loaders.dae package
- dae.variants_loaders.vcf package
- dae.variants_loaders.cnv package
- Import Tools
- What is Import Tools
- Import Tools config files
- Import Tools configuration format
- Working with the Import Tools CLI
- Running on a SGE cluster
- Running on a Kubernetes cluster
- Classes and Functions
- Genotype Data Parquet Writers
- dae.parquet package
- Subpackages
- Submodules
- dae.parquet.helpers module
- dae.parquet.parquet_writer module
- dae.parquet.partition_descriptor module
PartitionDescriptorPartitionDescriptor.dataset_family_partition()PartitionDescriptor.dataset_summary_partition()PartitionDescriptor.family_partition()PartitionDescriptor.get_variant_partitions()PartitionDescriptor.has_coding_bins()PartitionDescriptor.has_family_bins()PartitionDescriptor.has_family_partitions()PartitionDescriptor.has_frequency_bins()PartitionDescriptor.has_partitions()PartitionDescriptor.has_region_bins()PartitionDescriptor.has_summary_partitions()PartitionDescriptor.make_all_region_bins()PartitionDescriptor.make_coding_bin()PartitionDescriptor.make_family_bin()PartitionDescriptor.make_frequency_bin()PartitionDescriptor.make_region_bin()PartitionDescriptor.make_region_bins_regions()PartitionDescriptor.parse()PartitionDescriptor.parse_dict()PartitionDescriptor.parse_string()PartitionDescriptor.partition_directory()PartitionDescriptor.partition_filename()PartitionDescriptor.path_to_partitions()PartitionDescriptor.region_bins_count()PartitionDescriptor.region_to_region_bins()PartitionDescriptor.schema1_partition()PartitionDescriptor.serialize()PartitionDescriptor.summary_partition()PartitionDescriptor.to_dict()
- Module contents
- dae.parquet.schema2 package
- Submodules
- dae.parquet.schema2.parquet_io module
ContinuousParquetFileWriterContinuousParquetFileWriter.BATCH_ROWSContinuousParquetFileWriter.DEFAULT_COMPRESSIONContinuousParquetFileWriter.append_family_allele()ContinuousParquetFileWriter.append_summary_allele()ContinuousParquetFileWriter.build_batch()ContinuousParquetFileWriter.build_table()ContinuousParquetFileWriter.close()ContinuousParquetFileWriter.data_reset()ContinuousParquetFileWriter.size()
VariantsParquetWriter
- dae.parquet.schema2.serializers module
AlleleParquetSerializerAlleleParquetSerializer.ENUM_PROPERTIESAlleleParquetSerializer.FAMILY_ALLELE_BASE_SCHEMAAlleleParquetSerializer.SUMMARY_ALLELE_BASE_SCHEMAAlleleParquetSerializer.build_family_allele_batch_dict()AlleleParquetSerializer.build_family_schema()AlleleParquetSerializer.build_summary_allele_batch_dict()AlleleParquetSerializer.build_summary_blob_schema()AlleleParquetSerializer.build_summary_schema()AlleleParquetSerializer.schema_familyAlleleParquetSerializer.schema_summary
JsonVariantsDataSerializerVariantsDataAvroSerializerVariantsDataSerializerconstruct_avro_family_schema()construct_avro_summary_schema()
- Module contents
- dae.parquet package
- Query Genomic Variants
- dae.query_variants package
- Subpackages
- Submodules
- dae.query_variants.attribute_queries module
AttributeQueryTransformerAttributeQueryTransformerFunctionAttributeQueryTransformerSQLAttributeQueryTransformerSQLLegacyCompoundStripTransformerMatcherQueryCompoundAdditionTransformerQueryCompoundAdditionTransformer.all()QueryCompoundAdditionTransformer.and_()QueryCompoundAdditionTransformer.any()QueryCompoundAdditionTransformer.compound()QueryCompoundAdditionTransformer.grouping()QueryCompoundAdditionTransformer.literal()QueryCompoundAdditionTransformer.neg()QueryCompoundAdditionTransformer.or_()
SyntaxSugarTransformercreate_and_node()create_or_node()transform_attribute_query_to_function()transform_attribute_query_to_sql_expression()transform_attribute_query_to_sql_expression_schema1()update_attribute_query_with_compounds()
- dae.query_variants.base_query_variants module
QueryVariantsQueryVariants.build_family_variants_query_runner()QueryVariants.build_summary_variants_query_runner()QueryVariants.has_affected_status_queries()QueryVariants.query_summary_variants()QueryVariants.query_variants()QueryVariants.tags_to_family_ids()QueryVariants.transform_roles_to_single_role_string()
QueryVariantsBase
- dae.query_variants.query_runners module
- Module contents
- dae.query_variants.sql package
- dae.query_variants.sql.schema2 package
- Submodules
- dae.query_variants.sql.schema2.base_query_builder module
- dae.query_variants.sql.schema2.base_variants module
- dae.query_variants.sql.schema2.family_builder module
- dae.query_variants.sql.schema2.sql_query_builder module
Db2LayoutQueryBuilderBaseQueryBuilderBase.GENE_REGIONS_HEURISTIC_CUTOFFQueryBuilderBase.GENE_REGIONS_HEURISTIC_EXTENDQueryBuilderBase.REGION_BINS_HEURISTIC_CUTOFFQueryBuilderBase.all_region_bins()QueryBuilderBase.build_gene_regions()QueryBuilderBase.build_schema()QueryBuilderBase.build_variant_types_query()QueryBuilderBase.calc_batched_heuristics()QueryBuilderBase.calc_coding_bins()QueryBuilderBase.calc_family_bins()QueryBuilderBase.calc_frequency_bins()QueryBuilderBase.calc_heuristics()QueryBuilderBase.calc_region_bins()QueryBuilderBase.check_inheritance_denovo_only()QueryBuilderBase.check_inheritance_query_value()QueryBuilderBase.check_roles_denovo_only()QueryBuilderBase.check_roles_query_value()QueryBuilderBase.check_variant_types_value()
QueryHeuristicsSqlQueryBuilderSqlQueryBuilder.apply_family_heuristics()SqlQueryBuilder.apply_summary_heuristics()SqlQueryBuilder.build()SqlQueryBuilder.build_family_variants_query()SqlQueryBuilder.build_summary_variants_query()SqlQueryBuilder.categorical_attr()SqlQueryBuilder.coding_bins()SqlQueryBuilder.effect_types()SqlQueryBuilder.family_base()SqlQueryBuilder.family_bins()SqlQueryBuilder.family_ids()SqlQueryBuilder.family_query()SqlQueryBuilder.family_variants()SqlQueryBuilder.frequency()SqlQueryBuilder.frequency_bins()SqlQueryBuilder.genes()SqlQueryBuilder.inheritance()SqlQueryBuilder.person_ids()SqlQueryBuilder.real_attr()SqlQueryBuilder.region_bins()SqlQueryBuilder.regions()SqlQueryBuilder.replace_tables()SqlQueryBuilder.resolve_tags()SqlQueryBuilder.roles()SqlQueryBuilder.sexes()SqlQueryBuilder.statuses()SqlQueryBuilder.summary_base()SqlQueryBuilder.summary_query()SqlQueryBuilder.summary_variants()SqlQueryBuilder.ultra_rare()
TagsQueryZygosityQuery
- dae.query_variants.sql.schema2.summary_builder module
- Module contents
- dae.query_variants package
- Genotype Storage
- dae.genotype_storage package
- Submodules
- dae.genotype_storage.genotype_storage module
- dae.genotype_storage.genotype_storage_registry module
GenotypeStorageRegistryGenotypeStorageRegistry.get_all_genotype_storage_ids()GenotypeStorageRegistry.get_all_genotype_storages()GenotypeStorageRegistry.get_default_genotype_storage()GenotypeStorageRegistry.get_genotype_storage()GenotypeStorageRegistry.register_default_storage()GenotypeStorageRegistry.register_genotype_storage()GenotypeStorageRegistry.register_storage_config()GenotypeStorageRegistry.register_storages_configs()GenotypeStorageRegistry.shutdown()
- Module contents
- dae.genotype_storage package
- In-Memory Genotype Storage
- dae.inmemory_storage package
- Submodules
- dae.inmemory_storage.annotation_serialization module
- dae.inmemory_storage.inmemory_genotype_storage module
- dae.inmemory_storage.inmemory_import_storage module
- dae.inmemory_storage.raw_variants module
RawFamilyVariantsRawFamilyVariants.build_family_variants_query_runner()RawFamilyVariants.build_summary_variants_query_runner()RawFamilyVariants.family_variant_filter_function()RawFamilyVariants.family_variants_iterator()RawFamilyVariants.filter_allele()RawFamilyVariants.filter_family_variant()RawFamilyVariants.filter_gene_effects()RawFamilyVariants.filter_real_attr()RawFamilyVariants.filter_regions()RawFamilyVariants.filter_summary_allele()RawFamilyVariants.filter_summary_variant()RawFamilyVariants.full_variants_iterator()RawFamilyVariants.query_summary_variants()RawFamilyVariants.query_variants()RawFamilyVariants.summary_variant_filter_function()RawFamilyVariants.summary_variants_iterator()
RawMemoryVariantsRawVariantsQueryRunner
- Module contents
- dae.inmemory_storage package
- Configuration
- Genotype Data
- Phenotype Data
- Pheno DB access
- Example usage of
PhenoDB - Classes and Functions
- dae.pheno package
- Subpackages
- Submodules
- dae.pheno.browser module
- dae.pheno.build_pheno_browser module
- dae.pheno.common module
- dae.pheno.db module
- dae.pheno.graphs module
- dae.pheno.import_tools module
- dae.pheno.pheno_data module
- dae.pheno.pheno_import module
ImportInstrumentMeasureReportadd_pheno_common_inference()collect_instruments()create_import_tasks()create_tables()determine_destination()generate_phenotype_data_config()get_gpf_instance()get_output_parquet_files_dir()handle_measure_inference_tasks()import_pheno_data()infer_measures()load_histogram_configs()load_inference_configs()load_instrument_description_file()load_instrument_descriptions()load_measure_description_file()load_measure_descriptions()main()merge_histogram_configs()merge_inference_configs()open_file()pheno_cli_parser()read_and_classify_measure()read_instrument_measure_names()read_pedigree()transform_cli_args()write_descriptions()write_reports_to_parquet()write_results()write_to_parquet()
- dae.pheno.prepare_data module
- dae.pheno.registry module
- dae.pheno.storage module
- dae.pheno.update_pheno_descriptions module
- Module contents
- dae.pheno package
- Phenotype tool
- Enrichment Tool
- dae
- dae package
- Subpackages
- dae.annotation package
- Submodules
- dae.annotation.annotatable module
- dae.annotation.annotate_columns module
- dae.annotation.annotate_doc module
- dae.annotation.annotate_schema2_parquet module
- dae.annotation.annotate_utils module
- dae.annotation.annotate_vcf module
- dae.annotation.annotation_config module
- dae.annotation.annotation_factory module
- dae.annotation.annotation_pipeline module
- dae.annotation.annotator_base module
- dae.annotation.cnv_collection_annotator module
- dae.annotation.debug_annotator module
- dae.annotation.docker_annotator module
- dae.annotation.effect_annotator module
- dae.annotation.format_handlers module
- dae.annotation.gene_score_annotator module
- dae.annotation.gene_set_annotator module
- dae.annotation.genomic_context module
- dae.annotation.liftover_annotator module
- dae.annotation.normalize_allele_annotator module
- dae.annotation.parquet module
- dae.annotation.reannotate_instance module
- dae.annotation.record_to_annotatable module
- dae.annotation.score_annotator module
- dae.annotation.simple_effect_annotator module
- Module contents
- dae.common_reports package
- dae.configuration package
- dae.dask package
- dae.duckdb_storage package
- Submodules
- dae.duckdb_storage.duckdb2_variants module
- dae.duckdb_storage.duckdb_connection_factory module
- dae.duckdb_storage.duckdb_genotype_storage module
- dae.duckdb_storage.duckdb_import_storage module
- dae.duckdb_storage.duckdb_legacy_genotype_storage module
- dae.duckdb_storage.duckdb_storage_config module
- dae.duckdb_storage.duckdb_storage_helpers module
- dae.duckdb_storage.duckdb_variants module
- Module contents
- dae.effect_annotation package
- Subpackages
- Submodules
- dae.effect_annotation.annotation_effects module
- dae.effect_annotation.annotation_request module
- dae.effect_annotation.annotator module
- dae.effect_annotation.cli module
- dae.effect_annotation.effect module
- dae.effect_annotation.gene_codes module
- dae.effect_annotation.variant module
- Module contents
- dae.enrichment_tool package
- Subpackages
- Submodules
- dae.enrichment_tool.base_enrichment_background module
- dae.enrichment_tool.build_coding_length_enrichment_background module
- dae.enrichment_tool.build_ur_synonymous_enrichment_background module
- dae.enrichment_tool.enrichment_builder module
- dae.enrichment_tool.enrichment_cache_builder module
- dae.enrichment_tool.enrichment_helper module
- dae.enrichment_tool.enrichment_serializer module
- dae.enrichment_tool.event_counters module
- dae.enrichment_tool.gene_weights_background module
- dae.enrichment_tool.genotype_helper module
- dae.enrichment_tool.samocha_background module
- Module contents
- dae.gene_profile package
- dae.gene_scores package
- dae.gene_sets package
- dae.genomic_resources package
- Subpackages
- Submodules
- dae.genomic_resources.aggregators module
- dae.genomic_resources.cached_repository module
- dae.genomic_resources.cli module
- dae.genomic_resources.draw_score_histograms module
- dae.genomic_resources.fsspec_protocol module
- dae.genomic_resources.genomic_context module
- dae.genomic_resources.genomic_context_cli module
- dae.genomic_resources.genomic_scores module
- dae.genomic_resources.group_repository module
- dae.genomic_resources.histogram module
- dae.genomic_resources.liftover_chain module
- dae.genomic_resources.reference_genome module
- dae.genomic_resources.repository module
- dae.genomic_resources.repository_factory module
- dae.genomic_resources.resource_implementation module
- dae.genomic_resources.testing module
- dae.genomic_resources.variant_utils module
- Module contents
- dae.genomic_scores package
- dae.genotype_storage package
- dae.gpf_instance package
- dae.gpf_instance_plugin package
- dae.import_tools package
- dae.inmemory_storage package
- dae.parquet package
- dae.parquet_storage package
- dae.pedigrees package
- Submodules
- dae.pedigrees.drawing module
- dae.pedigrees.families_data module
- dae.pedigrees.family module
- dae.pedigrees.family_role_builder module
- dae.pedigrees.family_tag_builder module
- dae.pedigrees.layout module
- dae.pedigrees.loader module
- dae.pedigrees.pedigrees module
- dae.pedigrees.testing module
- Module contents
- dae.person_filters package
- dae.person_sets package
- dae.pheno package
- Subpackages
- Submodules
- dae.pheno.browser module
- dae.pheno.build_pheno_browser module
- dae.pheno.common module
- dae.pheno.db module
- dae.pheno.graphs module
- dae.pheno.import_tools module
- dae.pheno.pheno_data module
- dae.pheno.pheno_import module
- dae.pheno.prepare_data module
- dae.pheno.registry module
- dae.pheno.storage module
- dae.pheno.update_pheno_descriptions module
- Module contents
- dae.pheno_tool package
- dae.query_variants package
- dae.schema2_storage package
- dae.studies package
- dae.task_graph package
- dae.testing package
- dae.tools package
- Submodules
- dae.tools.cnv_liftover module
- dae.tools.dae2vcf module
- dae.tools.dae_liftover module
- dae.tools.denovo2vcf module
- dae.tools.denovo_liftover module
- dae.tools.draw_pedigree module
- dae.tools.generate_common_report module
- dae.tools.generate_denovo_gene_sets module
- dae.tools.gpf_convert_study_config module
- dae.tools.gpf_validation_runner module
- dae.tools.grr_cache_repo module
- dae.tools.ped2ped module
- dae.tools.simple_study_import module
- dae.tools.to_gpf_gene_models_format module
- dae.tools.vcf2tsv module
- dae.tools.vcf_liftover module
- Module contents
- dae.utils package
- Submodules
- dae.utils.cnv_utils module
- dae.utils.dae_utils module
- dae.utils.debug_closing module
- dae.utils.dict_utils module
- dae.utils.filehash module
- dae.utils.fixtures module
- dae.utils.fs_utils module
- dae.utils.helpers module
- dae.utils.progress module
- dae.utils.regions module
- dae.utils.sql_utils module
- dae.utils.stats_collection module
- dae.utils.variant_utils module
- dae.utils.verbosity_configuration module
- Module contents
- dae.variants package
- dae.variants_loaders package
- dae.annotation package
- Module contents
- Subpackages
- dae package
- Genomic Resources
- wdae Interface
- Common reports api
- Datasets api
- Enrichment api
- Family api
- Gene scores
- Gene sets
- Gene view
- Genomes api
- Genomic scores api
- Genotype browser
- Gpf instance
- Groups api
- Measures api
- Person sets api
- Pheno browser api
- Pheno tool api
- Query state save
- Sentry
- User queries
- Users api
- wdae
- common_reports_api package
- conftest module
admin()admin_client()anonymous_client()datasets()enrichment_grr()hundred_groups()hundred_users()oauth_app()sample_dataset()session_t4c8_wgpf_instance()t4c8_dataset()t4c8_instance()t4c8_query_transformer()t4c8_response_transformer()t4c8_study_1()t4c8_study_1_wrapper()t4c8_study_2()t4c8_study_2_wrapper()t4c8_wgpf()t4c8_wgpf_instance()tokens()user()user_client()user_without_password()
- datasets_api package
- Subpackages
- datasets_api.migrations package
- Submodules
- datasets_api.migrations.0001_initial module
- datasets_api.migrations.0002_dataset_groups module
- datasets_api.migrations.0003_alter_dataset_options module
- datasets_api.migrations.0004_dataset_broken module
- datasets_api.migrations.0005_dataset_dataset_name module
- datasets_api.migrations.0006_datasethierarchy module
- datasets_api.migrations.0007_datasethierarchy_direct module
- datasets_api.migrations.0008_datasethierarchy_instance_id module
- Module contents
- datasets_api.tests package
- datasets_api.migrations package
- Submodules
- datasets_api.models module
DatasetDatasetHierarchyDatasetHierarchy.DoesNotExistDatasetHierarchy.MultipleObjectsReturnedDatasetHierarchy.add_relation()DatasetHierarchy.ancestorDatasetHierarchy.ancestor_idDatasetHierarchy.clear()DatasetHierarchy.descendantDatasetHierarchy.descendant_idDatasetHierarchy.directDatasetHierarchy.get_children()DatasetHierarchy.get_direct_datasets_parents()DatasetHierarchy.get_parents()DatasetHierarchy.idDatasetHierarchy.instance_idDatasetHierarchy.is_study()DatasetHierarchy.objects
- datasets_api.permissions module
IsDatasetAllowedadd_group_perm_to_dataset()add_group_perm_to_user()get_allowed_genotype_studies()get_dataset_groups()get_dataset_info()get_directly_allowed_genotype_data()get_instance_timestamp_etag()get_permissions_etag()get_user_groups()get_wdae_children()get_wdae_dataset()get_wdae_parents()handle_partial_permissions()user_has_permission()
- datasets_api.urls module
- datasets_api.views module
- Module contents
- Subpackages
- enrichment_api package
- family_api package
- gene_profiles_api package
- gene_scores package
- gene_sets package
- gene_view package
- genomes_api package
- genomic_scores_api package
- genotype_browser package
- gpf_instance package
- gpfjs package
- groups_api package
- Subpackages
- Submodules
- groups_api.serializers module
- groups_api.urls module
- groups_api.views module
GroupsViewSetGroupsViewSet.authentication_classesGroupsViewSet.basenameGroupsViewSet.descriptionGroupsViewSet.detailGroupsViewSet.filter_backendsGroupsViewSet.get_queryset()GroupsViewSet.get_serializer_class()GroupsViewSet.lookup_fieldGroupsViewSet.nameGroupsViewSet.permission_classesGroupsViewSet.search_fieldsGroupsViewSet.serializer_classGroupsViewSet.suffix
- Module contents
- measures_api package
- person_sets_api package
- pheno_browser_api package
- pheno_tool_api package
- query_base package
- query_state_save package
- sentry package
- studies package
- Subpackages
- studies.tests package
- Submodules
- studies.tests.test_pheno_measures_columns module
- studies.tests.test_query_transformer_family_tags module
- studies.tests.test_query_transformer_present_in_child_and_parent module
- studies.tests.test_response_transformer_columns module
- studies.tests.test_study_config_genotype_browser_columns module
- studies.tests.test_study_group_person_sets_queries module
- studies.tests.test_study_query_request module
- studies.tests.test_study_wrapper module
- studies.tests.test_study_wrapper_queries module
- Module contents
- studies.tests package
- Submodules
- studies.query_transformer module
- studies.response_transformer module
ResponseTransformerResponseTransformer.PHENOTYPE_ATTRSResponseTransformer.SPECIAL_ATTRSResponseTransformer.STREAMING_CHUNK_SIZEResponseTransformer.build_variant_row()ResponseTransformer.transform_gene_view_summary_variant()ResponseTransformer.transform_gene_view_summary_variant_download()ResponseTransformer.variant_transformer()
get_or_create_response_transformer()make_response_transformer()members_in_order_get_family_structure()
- studies.study_wrapper module
QueryTransformerProtocolResponseTransformerProtocolWDAEAbstractStudyWDAEAbstractStudy.configWDAEAbstractStudy.config_columnsWDAEAbstractStudy.descriptionWDAEAbstractStudy.familiesWDAEAbstractStudy.genotype_dataWDAEAbstractStudy.get_children_ids()WDAEAbstractStudy.has_pheno_dataWDAEAbstractStudy.is_genotypeWDAEAbstractStudy.is_groupWDAEAbstractStudy.is_phenotypeWDAEAbstractStudy.make_config()WDAEAbstractStudy.nameWDAEAbstractStudy.parentsWDAEAbstractStudy.person_set_collectionsWDAEAbstractStudy.phenotype_dataWDAEAbstractStudy.query_variants_wdae_streaming()WDAEAbstractStudy.study_id
WDAEStudyWDAEStudyGroupget_clean_config()remove_none_values()
- Module contents
- Subpackages
- user_queries package
- users_api package
- Subpackages
- users_api.management package
- users_api.migrations package
- users_api.tests package
- Submodules
- users_api.tests.conftest module
- users_api.tests.test_commands module
- users_api.tests.test_commands_datasets module
- users_api.tests.test_federation_credentials_api module
- users_api.tests.test_users_api module
- users_api.tests.test_users_authentication module
- users_api.tests.test_users_groups module
- users_api.tests.test_users_researcher_registration module
- users_api.tests.test_users_rest module
- users_api.tests.test_users_with_password module
- users_api.tests.test_users_without_password module
- Module contents
- Submodules
- users_api.forms module
- users_api.models module
AuthenticationLogAuthenticationLog.DoesNotExistAuthenticationLog.MultipleObjectsReturnedAuthenticationLog.emailAuthenticationLog.failed_attemptAuthenticationLog.get_last_login_for()AuthenticationLog.get_locked_out_error()AuthenticationLog.get_next_by_time()AuthenticationLog.get_previous_by_time()AuthenticationLog.get_remaining_lockout_time()AuthenticationLog.idAuthenticationLog.is_user_locked_out()AuthenticationLog.log_authentication_attempt()AuthenticationLog.objectsAuthenticationLog.time
BaseVerificationCodeBaseVerificationCode.MetaBaseVerificationCode.create()BaseVerificationCode.created_atBaseVerificationCode.get_code()BaseVerificationCode.get_next_by_created_at()BaseVerificationCode.get_previous_by_created_at()BaseVerificationCode.pathBaseVerificationCode.userBaseVerificationCode.user_idBaseVerificationCode.validate()
GpUserStateResetPasswordCodeResetPasswordCode.DoesNotExistResetPasswordCode.MultipleObjectsReturnedResetPasswordCode.created_atResetPasswordCode.get_next_by_created_at()ResetPasswordCode.get_previous_by_created_at()ResetPasswordCode.idResetPasswordCode.objectsResetPasswordCode.pathResetPasswordCode.userResetPasswordCode.user_idResetPasswordCode.validate()
SetPasswordCodeSetPasswordCode.DoesNotExistSetPasswordCode.MultipleObjectsReturnedSetPasswordCode.created_atSetPasswordCode.get_next_by_created_at()SetPasswordCode.get_previous_by_created_at()SetPasswordCode.idSetPasswordCode.objectsSetPasswordCode.pathSetPasswordCode.userSetPasswordCode.user_idSetPasswordCode.validate()
WdaeUserWdaeUser.DoesNotExistWdaeUser.MultipleObjectsReturnedWdaeUser.REQUIRED_FIELDSWdaeUser.SUPERUSER_GROUPWdaeUser.UMLIMITED_DOWNLOAD_GROUPWdaeUser.USERNAME_FIELDWdaeUser.allowed_datasetsWdaeUser.auth_tokenWdaeUser.change_password()WdaeUser.date_joinedWdaeUser.deauthenticate()WdaeUser.emailWdaeUser.email_user()WdaeUser.gpuserstateWdaeUser.groupsWdaeUser.has_unlimited_downloadWdaeUser.idWdaeUser.is_activeWdaeUser.is_staffWdaeUser.is_superuserWdaeUser.last_loginWdaeUser.nameWdaeUser.oauth2_provider_accesstokenWdaeUser.oauth2_provider_applicationWdaeUser.oauth2_provider_grantWdaeUser.oauth2_provider_idtokenWdaeUser.oauth2_provider_refreshtokenWdaeUser.objectsWdaeUser.passwordWdaeUser.register_preexisting_user()WdaeUser.reset_password()WdaeUser.resetpasswordcodeWdaeUser.set_password()WdaeUser.set_unusable_password()WdaeUser.setpasswordcodeWdaeUser.user_permissionsWdaeUser.userquery_set
WdaeUserManagercsrf_clear()get_default_application()group_post_delete()group_pre_delete()send_already_existing_email()send_reset_email()send_reset_inactive_acc_email()send_verif_email()staff_update()
- users_api.serializers module
- users_api.urls module
- users_api.validators module
- users_api.views module
BasePasswordViewFederationCredentialsForgotPasswordRESTLoginViewResetPasswordSetPasswordUserGpStateViewUserViewSetUserViewSet.authentication_classesUserViewSet.basenameUserViewSet.create()UserViewSet.descriptionUserViewSet.destroy()UserViewSet.detailUserViewSet.filter_backendsUserViewSet.get_serializer_class()UserViewSet.list()UserViewSet.nameUserViewSet.partial_update()UserViewSet.password_reset()UserViewSet.permission_classesUserViewSet.querysetUserViewSet.retrieve()UserViewSet.search_fieldsUserViewSet.serializer_classUserViewSet.streaming_search()UserViewSet.suffixUserViewSet.update()
WdaeLoginViewchange_password()check_verif_code()get_user_info()iterator_to_json()logout()register()
- Module contents
- Subpackages
- utils package
- Submodules
- utils.authentication module
- utils.datasets module
- utils.email_regex module
- utils.expand_gene_set module
- utils.gene_sets module
- utils.logger module
- utils.pagination module
- utils.password_requirements module
- utils.query_params module
- utils.streaming_response_util module
- utils.testing module
- Module contents
- wdae package
- Submodules
- wdae.default_settings module
- wdae.eager_settings module
- wdae.gunicorn_settings module
- wdae.remote_settings module
- wdae.settings module
- wdae.silk_settings module
- wdae.test_settings module
- wdae.urls module
- wdae.wdaemanage module
- wdae.wgpf module
- wdae.wgpf_settings module
- wdae.wsgi module
- Module contents