gpf_web package

Routes

• Common reports api
• Datasets api
• Enrichment api
• Family api
• Gene scores
• Gene sets
• Gene view
• Genomes api
• Genomic scores api
• Genotype browser
• Gpf instance
• Measures api
• Person sets api
• Pheno browser api
• Pheno tool api
• Query state save
• Sentry
• User queries

Subpackages

• common_reports_api package
  • Submodules
  • common_reports_api.common_reports_helper module
    • BaseCommonReportsHelper
    • CommonReportsHelper
  • common_reports_api.urls module
  • common_reports_api.views module
    • FamiliesDataDownloadView
    • FamilyCounterDownloadView
    • FamilyCounterListView
    • VariantReportsFullView
    • VariantReportsView
    • create_common_reports_helper()
  • Module contents
• 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.models module
    • Dataset
    • DatasetHierarchy
  • datasets_api.permissions module
    • IsDatasetAllowed
    • add_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()
    • remove_group_perm_from_dataset()
    • user_has_permission()
  • datasets_api.urls module
  • datasets_api.views module
    • BaseDatasetPermissionsView
    • DatasetDescriptionView
    • DatasetHierarchyView
    • DatasetPedigreeView
    • DatasetPermissionsSingleView
    • DatasetPermissionsView
    • DatasetView
    • FederationDatasetsView
    • VisibleDatasetsView
    • augment_accessibility()
    • augment_with_groups()
    • augment_with_parents()
    • get_description_etag()
  • Module contents
• datasets_api.migrations package
  • Submodules
  • datasets_api.migrations.0001_initial module
    • Migration
  • datasets_api.migrations.0002_dataset_groups module
    • Migration
  • datasets_api.migrations.0003_alter_dataset_options module
    • Migration
  • datasets_api.migrations.0004_dataset_broken module
    • Migration
  • datasets_api.migrations.0005_dataset_dataset_name module
    • Migration
  • datasets_api.migrations.0006_datasethierarchy module
    • Migration
  • datasets_api.migrations.0007_datasethierarchy_direct module
    • Migration
  • datasets_api.migrations.0008_datasethierarchy_instance_id module
    • Migration
  • Module contents
• enrichment_api package
  • Submodules
  • enrichment_api.enrichment_builder module
    • BaseEnrichmentBuilder
    • EnrichmentBuilder
  • enrichment_api.enrichment_helper module
    • BaseEnrichmentHelper
    • EnrichmentHelper
  • enrichment_api.enrichment_serializer module
    • EnrichmentSerializer
  • enrichment_api.urls module
  • enrichment_api.views module
    • EnrichmentModelsView
    • EnrichmentTestView
    • create_enrichment_builder()
    • create_enrichment_helper()
  • Module contents
• family_api package
  • Submodules
  • family_api.urls module
  • family_api.views module
    • AllMemberDetailsView
    • FamilyDetailsView
    • ListAllDetailsView
    • ListFamiliesView
    • ListMembersView
    • MemberDetailsView
    • TagsView
  • Module contents
• gene_profiles_api package
  • Submodules
  • gene_profiles_api.table_views module
    • GeneSymbolsView
    • TableRowsView
  • gene_profiles_api.urls module
  • gene_profiles_api.views module
    • ConfigurationView
    • ProfileView
  • Module contents
• gene_scores package
  • Submodules
  • gene_scores.urls module
  • gene_scores.views module
    • GeneScoresDownloadView
    • GeneScoresListView
    • GeneScoresPartitionsView
    • HistogramView
  • Module contents
• gene_sets package
  • Submodules
  • gene_sets.urls module
  • gene_sets.views module
    • DenovoGeneSetsDb
    • DenovoGeneSetsTypesView
    • GeneSetDownloadView
    • GeneSetsCollectionsView
    • GeneSetsHasDenovoView
    • GeneSetsView
  • Module contents
• gene_view package
  • Submodules
  • gene_view.urls module
  • gene_view.views module
    • ConfigView
    • DownloadSummaryVariantsView
    • QuerySummaryVariantsView
  • Module contents
• genomes_api package
  • Submodules
  • genomes_api.urls module
  • genomes_api.views module
    • DefaultGeneModelsId
    • GeneModels
    • GeneSymbolsSearch
    • GeneSymbolsValidate
  • Module contents
• genomic_scores_api package
  • Submodules
  • genomic_scores_api.urls module
  • genomic_scores_api.views module
    • GenomicScoreDescsView
    • GenomicScoresView
  • Module contents
• genotype_browser package
  • Submodules
  • genotype_browser.urls module
  • genotype_browser.views module
    • GenotypeBrowserQueryDownloadView
    • GenotypeBrowserQueryView
  • Module contents
• gpf_instance package
  • Submodules
  • gpf_instance.apps module
    • WDAEConfig
  • gpf_instance.extension module
    • GPFExtensionBase
    • GPFTool
  • gpf_instance.gpf_instance module
    • get_wgpf_instance()
  • gpf_instance.urls module
  • gpf_instance.views module
    • AboutDescriptionView
    • DescriptionView
    • GenomeView
    • MarkdownFileView
    • get_about_etag()
    • get_description_etag()
    • version()
  • Module contents
• gpf_web package
  • Submodules
  • gpf_web.default_settings module
    • CustomFormatter
  • 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
  • Submodules
  • groups_api.serializers module
    • GroupCreateSerializer
    • GroupRetrieveSerializer
    • GroupSerializer
  • groups_api.urls module
  • groups_api.views module
    • GroupsViewSet
  • Module contents
• groups_api.migrations package
  • Module contents
• measures_api package
  • Submodules
  • measures_api.urls module
  • measures_api.views module
    • PhenoDataRoleListView
    • PhenoMeasureHistogramView
    • PhenoMeasureHistogramViewBeta
    • PhenoMeasureListView
    • PhenoMeasurePartitionsView
    • PhenoMeasureRegressionsView
    • PhenoMeasuresView
  • Module contents
• gpf_web
  • common_reports_api package
    • Submodules
    • common_reports_api.common_reports_helper module
    • common_reports_api.urls module
    • common_reports_api.views module
    • Module contents
  • 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
    • Submodules
    • datasets_api.models module
    • datasets_api.permissions module
    • datasets_api.urls module
    • datasets_api.views module
    • Module contents
  • enrichment_api package
    • Submodules
    • enrichment_api.enrichment_builder module
    • enrichment_api.enrichment_helper module
    • enrichment_api.enrichment_serializer module
    • enrichment_api.urls module
    • enrichment_api.views module
    • Module contents
  • family_api package
    • Submodules
    • family_api.urls module
    • family_api.views module
    • Module contents
  • gene_profiles_api package
    • Submodules
    • gene_profiles_api.table_views module
    • gene_profiles_api.urls module
    • gene_profiles_api.views module
    • Module contents
  • gene_scores package
    • Submodules
    • gene_scores.urls module
    • gene_scores.views module
    • Module contents
  • gene_sets package
    • Submodules
    • gene_sets.urls module
    • gene_sets.views module
    • Module contents
  • gene_view package
    • Submodules
    • gene_view.urls module
    • gene_view.views module
    • Module contents
  • genomes_api package
    • Submodules
    • genomes_api.urls module
    • genomes_api.views module
    • Module contents
  • genomic_scores_api package
    • Submodules
    • genomic_scores_api.urls module
    • genomic_scores_api.views module
    • Module contents
  • genotype_browser package
    • Submodules
    • genotype_browser.urls module
    • genotype_browser.views module
    • Module contents
  • gpf_instance package
    • Submodules
    • gpf_instance.apps module
    • gpf_instance.extension module
    • gpf_instance.gpf_instance module
    • gpf_instance.urls module
    • gpf_instance.views module
    • Module contents
  • gpf_web package
    • Submodules
    • gpf_web.default_settings module
    • 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
    • gpf_web.wgpf module
    • gpf_web.wgpf_settings module
    • gpf_web.wsgi module
    • Module contents
  • gpfjs package
    • Submodules
    • gpfjs.views module
    • Module contents
  • groups_api package
    • Subpackages
    • Submodules
    • groups_api.serializers module
    • groups_api.urls module
    • groups_api.views module
    • Module contents
  • measures_api package
    • Submodules
    • measures_api.urls module
    • measures_api.views module
    • Module contents
  • person_sets_api package
    • Submodules
    • person_sets_api.urls module
    • person_sets_api.views module
    • Module contents
  • pheno_browser_api package
    • Submodules
    • pheno_browser_api.pheno_browser_helper module
    • pheno_browser_api.urls module
    • pheno_browser_api.views module
    • Module contents
  • pheno_tool_api package
    • Submodules
    • pheno_tool_api.adapter module
    • 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
    • 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
    • Submodules
    • sentry.urls module
    • sentry.views module
    • Module contents
  • studies package
    • Submodules
    • studies.conftest module
    • studies.query_transformer module
    • studies.response_transformer module
    • studies.study_wrapper module
    • Module contents
  • user_queries package
    • Subpackages
    • Submodules
    • user_queries.models module
    • user_queries.urls module
    • user_queries.views module
    • Module contents
  • users_api package
    • Subpackages
    • 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
    • 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
• person_sets_api package
  • Submodules
  • person_sets_api.urls module
  • person_sets_api.views module
    • CollectionConfigsView
    • CollectionDomainView
    • CollectionStatsView
  • Module contents
• pheno_browser_api package
  • Submodules
  • pheno_browser_api.pheno_browser_helper module
    • BasePhenoBrowserHelper
    • CountError
    • PhenoBrowserHelper
  • pheno_browser_api.urls module
  • pheno_browser_api.views module
    • PhenoImagesView
    • PhenoInstrumentsView
    • PhenoMeasureDescriptionView
    • PhenoMeasuresCount
    • PhenoMeasuresDownload
    • PhenoMeasuresInfoView
    • PhenoMeasuresView
    • create_pheno_browser_helper()
  • Module contents
• pheno_tool_api package
  • Submodules
  • pheno_tool_api.adapter module
    • PhenoToolAdapter
    • PhenoToolAdapterBase
  • pheno_tool_api.urls module
  • pheno_tool_api.views module
    • PhenoToolDownload
    • PhenoToolInstruments
    • PhenoToolMeasure
    • PhenoToolMeasures
    • PhenoToolPeopleValues
    • PhenoToolView
  • Module contents
• query_base package
  • Submodules
  • query_base.query_base module
    • DatasetAccessRightsView
    • QueryBaseView
  • Module contents
• query_state_save package
  • Subpackages
    • query_state_save.migrations package
  • Submodules
  • query_state_save.models module
    • QueryState
  • query_state_save.serializers module
    • QueryStateSerializer
  • query_state_save.urls module
  • query_state_save.views module
    • QueryStateDeleteView
    • QueryStateLoadView
    • QueryStateSaveView
  • Module contents
• query_state_save.migrations package
  • Submodules
  • query_state_save.migrations.0001_initial module
    • Migration
  • query_state_save.migrations.0002_auto_20190205_0736 module
    • Migration
  • query_state_save.migrations.0003_querystate_origin_querystate_timestamp module
    • Migration
  • Module contents
• sentry package
  • Submodules
  • sentry.urls module
  • sentry.views module
    • PlainTextParser
    • sentry()
  • Module contents
• studies package
  • Submodules
  • studies.conftest module
    • custom_query_transformer()
    • custom_response_transformer()
    • custom_wgpf()
    • custom_wgpf_module()
  • studies.query_transformer module
    • QueryTransformer
    • get_or_create_query_transformer()
    • make_query_transformer()
  • studies.response_transformer module
    • ResponseTransformer
    • get_or_create_response_transformer()
    • make_response_transformer()
    • members_in_order_get_family_structure()
  • studies.study_wrapper module
    • QueryTransformerProtocol
    • ResponseTransformerProtocol
    • WDAEAbstractStudy
    • WDAEStudy
    • WDAEStudyGroup
    • get_clean_config()
    • remove_none_values()
  • Module contents
• user_queries package
  • Subpackages
    • user_queries.migrations package
  • Submodules
  • user_queries.models module
    • UserQuery
  • user_queries.urls module
  • user_queries.views module
    • UserQueryCollectView
    • UserQuerySaveView
  • Module contents
• user_queries.migrations package
  • Submodules
  • user_queries.migrations.0001_initial module
    • Migration
  • Module contents
• users_api package
  • Subpackages
    • users_api.management package
    • users_api.migrations package
  • Submodules
  • users_api.forms module
    • WdaeLoginForm
    • WdaePasswordForgottenForm
    • WdaeRegisterPasswordForm
    • WdaeResetPasswordForm
  • users_api.models module
    • AuthenticationLog
    • BaseVerificationCode
    • GpUserState
    • ResetPasswordCode
    • SetPasswordCode
    • WdaeUser
    • WdaeUserManager
    • csrf_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
    • CreatableSlugRelatedField
    • DatasetSerializer
    • UserSerializer
    • UserWithoutEmailSerializer
  • users_api.urls module
  • users_api.validators module
    • SomeSuperuserLeftValidator
  • users_api.views module
    • BasePasswordView
    • FederationCredentials
    • ForgotPassword
    • RESTLoginView
    • ResetPassword
    • SetPassword
    • UserGpStateView
    • UserViewSet
    • WdaeLoginView
    • change_password()
    • check_verif_code()
    • get_user_info()
    • iterator_to_json()
    • logout()
    • register()
  • Module contents
• users_api.management package
  • Subpackages
    • users_api.management.commands package
  • Module contents
• users_api.management.commands package
  • Submodules
  • users_api.management.commands.dataset_groups module
    • Command
  • users_api.management.commands.dataset_mixin module
    • DatasetBaseMixin
  • users_api.management.commands.datasets_export module
    • Command
  • users_api.management.commands.datasets_restore module
    • Command
  • users_api.management.commands.datasets_show module
    • Command
  • users_api.management.commands.export_base module
    • ExportUsersBase
  • users_api.management.commands.import_base module
    • ImportUsersBase
  • users_api.management.commands.unlock_user module
    • Command
  • users_api.management.commands.user_create module
    • Command
  • users_api.management.commands.user_set_name module
    • Command
  • users_api.management.commands.user_setpasswd module
    • Command
  • users_api.management.commands.users_add module
    • Command
  • users_api.management.commands.users_export module
    • Command
  • users_api.management.commands.users_group_add module
    • Command
  • users_api.management.commands.users_group_remove module
    • Command
  • users_api.management.commands.users_remove module
    • Command
  • users_api.management.commands.users_restore module
    • Command
  • users_api.management.commands.users_show module
    • Command
  • Module contents
• users_api.migrations package
  • Submodules
  • users_api.migrations.0001_initial module
    • Migration
  • users_api.migrations.0002_auto_20190424_0751 module
    • Migration
  • users_api.migrations.0003_authenticationlog module
    • Migration
  • users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more module
    • Migration
  • users_api.migrations.0005_gpuserstate module
    • Migration
  • Module contents
• utils package
  • Submodules
  • utils.authentication module
    • GPFOAuth2Authentication
    • ReadOnlyDBAuthentication
    • SessionAuthenticationWithUnauthenticatedCSRF
    • SessionAuthenticationWithoutCSRF
    • 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
  • 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