gpf_web

• common_reports_api package
  • Subpackages
    • common_reports_api.tests package
      • Submodules
      • common_reports_api.tests.test_common_reports_api module
      • Module contents
  • Submodules
  • common_reports_api.common_reports_helper module
    • BaseCommonReportsHelper
      • BaseCommonReportsHelper.get_common_report()
      • BaseCommonReportsHelper.get_family_counter_list()
      • BaseCommonReportsHelper.get_family_counter_tsv()
      • BaseCommonReportsHelper.get_family_data_tsv()
      • BaseCommonReportsHelper.get_filtered_family_data_tsv()
      • BaseCommonReportsHelper.get_full_common_report()
    • CommonReportsHelper
      • CommonReportsHelper.get_common_report()
      • CommonReportsHelper.get_family_counter_list()
      • CommonReportsHelper.get_family_counter_tsv()
      • CommonReportsHelper.get_family_data_tsv()
      • CommonReportsHelper.get_filtered_family_data_tsv()
      • CommonReportsHelper.get_full_common_report()
      • CommonReportsHelper.make_tool()
  • common_reports_api.urls module
  • common_reports_api.views module
  • Module contents
• conftest module
• 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
      • Submodules
      • datasets_api.tests.conftest module
      • datasets_api.tests.test_datasets_api module
      • datasets_api.tests.test_permissions module
      • Module contents
  • Submodules
  • datasets_api.models module
  • datasets_api.permissions module
  • datasets_api.urls module
  • datasets_api.views module
  • Module contents
• enrichment_api package
  • Subpackages
    • enrichment_api.tests package
      • Submodules
      • enrichment_api.tests.conftest module
      • enrichment_api.tests.test_enrichment_api module
      • enrichment_api.tests.test_enrichment_builder module
      • enrichment_api.tests.test_enrichment_helper_simple module
      • enrichment_api.tests.test_enrichment_serializer module
      • enrichment_api.tests.test_t4c8_enrichment module
      • Module contents
  • Submodules
  • enrichment_api.enrichment_builder module
    • BaseEnrichmentBuilder
      • BaseEnrichmentBuilder.enrichment_test()
    • EnrichmentBuilder
      • EnrichmentBuilder.build()
      • EnrichmentBuilder.build_results()
      • EnrichmentBuilder.create_enrichment_description()
      • EnrichmentBuilder.enrichment_test()
      • EnrichmentBuilder.make_tool()
  • enrichment_api.enrichment_helper module
    • BaseEnrichmentHelper
      • BaseEnrichmentHelper.get_enrichment_models()
    • EnrichmentHelper
      • EnrichmentHelper.calc_enrichment_test()
      • EnrichmentHelper.collect_genotype_data_backgrounds()
      • EnrichmentHelper.create_background()
      • EnrichmentHelper.create_counter()
      • EnrichmentHelper.get_default_background_model()
      • EnrichmentHelper.get_default_counting_model()
      • EnrichmentHelper.get_enrichment_models()
      • EnrichmentHelper.get_selected_counting_models()
      • EnrichmentHelper.get_selected_person_set_collections()
      • EnrichmentHelper.make_tool()
  • enrichment_api.enrichment_serializer module
    • EnrichmentSerializer
      • EnrichmentSerializer.serialize()
      • EnrichmentSerializer.serialize_all()
      • EnrichmentSerializer.serialize_common_filter()
      • EnrichmentSerializer.serialize_enrichment_result()
      • EnrichmentSerializer.serialize_female()
      • EnrichmentSerializer.serialize_male()
      • EnrichmentSerializer.serialize_overlap_filter()
      • EnrichmentSerializer.serialize_people_groups()
      • EnrichmentSerializer.serialize_rec()
      • EnrichmentSerializer.serialize_rec_filter()
  • enrichment_api.urls module
  • enrichment_api.views module
  • Module contents
• family_api package
  • Subpackages
    • family_api.tests package
      • Submodules
      • family_api.tests.test_family_api module
      • Module contents
  • Submodules
  • family_api.urls module
  • family_api.views module
  • Module contents
• gene_profiles_api package
  • Subpackages
    • gene_profiles_api.tests package
      • Submodules
      • gene_profiles_api.tests.test_agp_api module
      • gene_profiles_api.tests.test_agp_api_configless module
      • Module contents
  • Submodules
  • gene_profiles_api.table_views module
  • gene_profiles_api.urls module
  • gene_profiles_api.views module
  • Module contents
• gene_scores package
  • Subpackages
    • gene_scores.tests package
      • Submodules
      • gene_scores.tests.conftest module
      • gene_scores.tests.test_gene_scores module
      • gene_scores.tests.test_gene_scores_db module
      • gene_scores.tests.test_gene_scores_views module
      • gene_scores.tests.test_scores_partitions module
      • Module contents
  • Submodules
  • gene_scores.urls module
  • gene_scores.views module
  • Module contents
• gene_sets package
  • Subpackages
    • gene_sets.tests package
      • Submodules
      • gene_sets.tests.test_gene_sets_api module
      • Module contents
  • Submodules
  • gene_sets.urls module
  • gene_sets.views module
  • Module contents
• gene_view package
  • Subpackages
    • gene_view.tests package
      • Submodules
      • gene_view.tests.test_gene_view module
      • Module contents
  • Submodules
  • gene_view.urls module
  • gene_view.views module
  • Module contents
• genomes_api package
  • Subpackages
    • genomes_api.tests package
      • Submodules
      • genomes_api.tests.test_gene_models_api module
      • Module contents
  • Submodules
  • genomes_api.urls module
  • genomes_api.views module
  • Module contents
• genomic_scores_api package
  • Subpackages
    • genomic_scores_api.tests package
      • Submodules
      • genomic_scores_api.tests.test_genomic_scores_api module
      • Module contents
  • Submodules
  • genomic_scores_api.urls module
  • genomic_scores_api.views module
  • Module contents
• genotype_browser package
  • Subpackages
    • genotype_browser.tests package
      • Submodules
      • genotype_browser.tests.conftest module
      • genotype_browser.tests.test_effect_types_download module
      • genotype_browser.tests.test_pheno_columns module
      • genotype_browser.tests.test_pheno_filters module
      • genotype_browser.tests.test_query_api module
      • Module contents
  • Submodules
  • genotype_browser.urls module
  • genotype_browser.views module
  • Module contents
• gpf_instance package
  • Subpackages
    • gpf_instance.tests package
      • Submodules
      • gpf_instance.tests.test_genome_view module
      • gpf_instance.tests.test_version_api module
      • gpf_instance.tests.test_wgpf_instance module
      • Module contents
  • Submodules
  • gpf_instance.apps module
    • WDAEConfig
      • WDAEConfig.name
      • WDAEConfig.ready()
  • gpf_instance.extension module
    • GPFExtensionBase
      • GPFExtensionBase.get_studies()
      • GPFExtensionBase.get_studies_ids()
      • GPFExtensionBase.get_tool()
      • GPFExtensionBase.setup()
    • GPFTool
      • GPFTool.make_tool()
      • GPFTool.tool_id
  • gpf_instance.gpf_instance module
    • get_wgpf_instance()
  • gpf_instance.urls module
  • gpf_instance.views module
  • Module contents
• gpf_web package
  • Submodules
  • gpf_web.default_settings module
    • CustomFormatter
      • CustomFormatter.FORMATS
      • CustomFormatter.bold_red
      • CustomFormatter.fmt_invert
      • CustomFormatter.fmt_normal
      • CustomFormatter.format()
      • CustomFormatter.grey
      • CustomFormatter.red
      • CustomFormatter.reset
      • CustomFormatter.time_fmt
      • CustomFormatter.yellow
  • gpf_web.eager_settings module
  • gpf_web.gunicorn_settings module
  • gpf_web.mypy_settings module
  • gpf_web.remote_settings module
  • gpf_web.settings module
  • gpf_web.silk_settings module
  • gpf_web.test_settings module
  • gpf_web.urls module
  • gpf_web.wdaemanage module
    • main()
  • gpf_web.wgpf module
    • cli()
  • gpf_web.wgpf_settings module
  • gpf_web.wsgi module
  • Module contents
• gpfjs package
  • Submodules
  • gpfjs.views module
    • favicon()
    • index()
  • Module contents
• groups_api package
  • Subpackages
    • groups_api.migrations package
      • Module contents
    • groups_api.tests package
      • Submodules
      • groups_api.tests.conftest module
      • groups_api.tests.test_groups_rest module
      • Module contents
  • Submodules
  • groups_api.serializers module
  • groups_api.urls module
  • groups_api.views module
  • Module contents
• measures_api package
  • Subpackages
    • measures_api.tests package
      • Submodules
      • measures_api.tests.test_measures_api module
      • Module contents
  • Submodules
  • measures_api.urls module
  • measures_api.views module
  • Module contents
• person_sets_api package
  • Subpackages
    • person_sets_api.tests package
      • Submodules
      • person_sets_api.tests.test_person_sets_api module
      • Module contents
  • Submodules
  • person_sets_api.urls module
  • person_sets_api.views module
  • Module contents
• pheno_browser_api package
  • Subpackages
    • pheno_browser_api.tests package
      • Submodules
      • pheno_browser_api.tests.test_pheno_browser_api module
      • Module contents
  • Submodules
  • pheno_browser_api.pheno_browser_helper module
    • BasePhenoBrowserHelper
      • BasePhenoBrowserHelper.get_count()
      • BasePhenoBrowserHelper.get_image()
      • BasePhenoBrowserHelper.get_instruments()
      • BasePhenoBrowserHelper.get_measure_description()
      • BasePhenoBrowserHelper.get_measure_ids()
      • BasePhenoBrowserHelper.get_measures_info()
      • BasePhenoBrowserHelper.measures_count_status()
      • BasePhenoBrowserHelper.search_measures()
    • CountError
    • PhenoBrowserHelper
      • PhenoBrowserHelper.get_count()
      • PhenoBrowserHelper.get_image()
      • PhenoBrowserHelper.get_instruments()
      • PhenoBrowserHelper.get_measure_description()
      • PhenoBrowserHelper.get_measure_ids()
      • PhenoBrowserHelper.get_measures_info()
      • PhenoBrowserHelper.make_tool()
      • PhenoBrowserHelper.measures_count_status()
      • PhenoBrowserHelper.search_measures()
  • pheno_browser_api.urls module
  • pheno_browser_api.views module
  • Module contents
• pheno_tool_api package
  • Subpackages
    • pheno_tool_api.tests package
      • Submodules
      • pheno_tool_api.tests.test_pheno_tool_api module
      • pheno_tool_api.tests.test_pheno_tool_view_class_static_methods module
      • Module contents
  • Submodules
  • pheno_tool_api.adapter module
    • PhenoToolAdapter
      • PhenoToolAdapter.align_na_results()
      • PhenoToolAdapter.build_report_description()
      • PhenoToolAdapter.calc_by_effect()
      • PhenoToolAdapter.calc_variants()
      • PhenoToolAdapter.get_result_by_sex()
      • PhenoToolAdapter.make_tool()
      • PhenoToolAdapter.produce_download()
    • PhenoToolAdapterBase
      • PhenoToolAdapterBase.calc_variants()
      • PhenoToolAdapterBase.produce_download()
  • pheno_tool_api.urls module
  • pheno_tool_api.views module
  • Module contents
• query_base package
  • Submodules
  • query_base.query_base module
  • Module contents
• query_state_save package
  • Subpackages
    • query_state_save.migrations package
      • Submodules
      • query_state_save.migrations.0001_initial module
      • query_state_save.migrations.0002_auto_20190205_0736 module
      • query_state_save.migrations.0003_querystate_origin_querystate_timestamp module
      • Module contents
    • query_state_save.tests package
      • Submodules
      • query_state_save.tests.conftest module
      • query_state_save.tests.test_save_query_data module
      • Module contents
  • Submodules
  • query_state_save.models module
  • query_state_save.serializers module
  • query_state_save.urls module
  • query_state_save.views module
  • Module contents
• sentry package
  • Subpackages
    • sentry.tests package
      • Submodules
      • sentry.tests.test_sentry module
      • Module contents
  • Submodules
  • sentry.urls module
  • sentry.views module
    • PlainTextParser
      • PlainTextParser.media_type
      • PlainTextParser.parse()
    • sentry()
  • Module contents
• studies package
  • Subpackages
    • studies.tests package
      • Submodules
      • studies.tests.test_pheno_measures_columns module
      • studies.tests.test_query_transformer 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_person_sets module
      • studies.tests.test_study_wrapper_queries module
      • studies.tests.test_study_wrapper_unique_variants_query module
      • Module contents
  • Submodules
  • studies.conftest module
    • custom_query_transformer()
    • custom_response_transformer()
    • custom_wgpf()
    • custom_wgpf_module()
  • studies.query_transformer module
    • QueryTransformer
      • QueryTransformer.FILTER_RENAMES_MAP
      • QueryTransformer.extract_person_set_collection_query()
      • QueryTransformer.get_unique_family_variants()
      • QueryTransformer.transform_kwargs()
    • get_or_create_query_transformer()
    • make_query_transformer()
  • studies.response_transformer module
    • ResponseTransformer
      • ResponseTransformer.PHENOTYPE_ATTRS
      • ResponseTransformer.SPECIAL_ATTRS
      • ResponseTransformer.STREAMING_CHUNK_SIZE
      • ResponseTransformer.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
    • QueryTransformerProtocol
      • QueryTransformerProtocol.extract_person_set_collection_query()
      • QueryTransformerProtocol.get_unique_family_variants()
      • QueryTransformerProtocol.transform_kwargs()
    • ResponseTransformerProtocol
      • ResponseTransformerProtocol.build_variant_row()
      • ResponseTransformerProtocol.transform_gene_view_summary_variant()
      • ResponseTransformerProtocol.transform_gene_view_summary_variant_download()
      • ResponseTransformerProtocol.variant_transformer()
    • WDAEAbstractStudy
      • WDAEAbstractStudy.build_genotype_data_description()
      • WDAEAbstractStudy.config
      • WDAEAbstractStudy.config_columns
      • WDAEAbstractStudy.description
      • WDAEAbstractStudy.enrichment_cache_path
      • WDAEAbstractStudy.enrichment_config
      • WDAEAbstractStudy.families
      • WDAEAbstractStudy.genotype_data
      • WDAEAbstractStudy.get_children_ids()
      • WDAEAbstractStudy.get_gene_view_summary_variants()
      • WDAEAbstractStudy.get_gene_view_summary_variants_download()
      • WDAEAbstractStudy.get_measures()
      • WDAEAbstractStudy.get_measures_json()
      • WDAEAbstractStudy.get_person_set_collection()
      • WDAEAbstractStudy.get_studies_ids()
      • WDAEAbstractStudy.has_genotype_data
      • WDAEAbstractStudy.has_pheno_data
      • WDAEAbstractStudy.is_genotype
      • WDAEAbstractStudy.is_group
      • WDAEAbstractStudy.is_phenotype
      • WDAEAbstractStudy.make_config()
      • WDAEAbstractStudy.name
      • WDAEAbstractStudy.parents
      • WDAEAbstractStudy.person_set_collections
      • WDAEAbstractStudy.phenotype_data
      • WDAEAbstractStudy.query_variants_download_wdae()
      • WDAEAbstractStudy.query_variants_preview_wdae()
      • WDAEAbstractStudy.query_variants_wdae()
      • WDAEAbstractStudy.study_id
    • WDAEStudy
      • WDAEStudy.build_genotype_data_all_datasets()
      • WDAEStudy.build_genotype_data_description()
      • WDAEStudy.description
      • WDAEStudy.get_column_sources()
      • WDAEStudy.get_columns_as_sources()
      • WDAEStudy.get_gene_view_summary_variants()
      • WDAEStudy.get_gene_view_summary_variants_download()
      • WDAEStudy.get_measures_json()
      • WDAEStudy.query_variants_download_wdae()
      • WDAEStudy.query_variants_preview_wdae()
      • WDAEStudy.query_variants_raw()
      • WDAEStudy.query_variants_wdae()
    • WDAEStudyGroup
      • WDAEStudyGroup.get_children_ids()
      • WDAEStudyGroup.get_studies_ids()
    • get_clean_config()
    • remove_none_values()
  • Module contents
• user_queries package
  • Subpackages
    • user_queries.migrations package
      • Submodules
      • user_queries.migrations.0001_initial module
      • Module contents
  • Submodules
  • user_queries.models module
  • user_queries.urls module
  • user_queries.views module
  • Module contents
• users_api package
  • Subpackages
    • users_api.management package
      • Subpackages
      • Module contents
    • users_api.migrations package
      • Submodules
      • users_api.migrations.0001_initial module
      • users_api.migrations.0002_auto_20190424_0751 module
      • users_api.migrations.0003_authenticationlog module
      • users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more module
      • users_api.migrations.0005_gpuserstate module
      • Module contents
    • 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
  • users_api.serializers module
  • users_api.urls module
  • users_api.validators module
  • users_api.views module
  • Module contents
• utils package
  • Submodules
  • utils.authentication module
    • GPFOAuth2Authentication
      • GPFOAuth2Authentication.authenticate()
    • ReadOnlyDBAuthentication
      • ReadOnlyDBAuthentication.authenticate()
    • SessionAuthenticationWithUnauthenticatedCSRF
      • SessionAuthenticationWithUnauthenticatedCSRF.authenticate()
    • SessionAuthenticationWithoutCSRF
      • SessionAuthenticationWithoutCSRF.enforce_csrf()
    • oauth_cookie_to_header()
  • utils.datasets module
    • find_dataset_id_in_dict()
    • find_dataset_id_in_request()
  • utils.email_regex module
    • is_email_valid()
  • utils.expand_gene_set module
    • expand_gene_set()
    • expand_gene_syms()
  • utils.gene_sets module
    • get_denovo_gene_set_spec()
  • utils.logger module
    • log_filter()
    • request_logging()
    • request_logging_function_view()
  • utils.pagination module
    • WdaePageNumberPagination
      • WdaePageNumberPagination.get_paginated_response()
      • WdaePageNumberPagination.page_size_query_param
      • WdaePageNumberPagination.paginate_queryset()
  • utils.password_requirements module
    • is_password_valid()
  • utils.query_params module
    • parse_query_params()
  • utils.streaming_response_util module
    • convert()
    • iterator_to_json()
  • utils.testing module
    • setup_t4c8_grr()
    • setup_t4c8_instance()
    • setup_wgpf_instance()
  • Module contents