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galaxy.webapps.galaxy package

Subpackages

• galaxy.webapps.galaxy.api package
  • get_app()
  • get_app_with_request_session()
  • GalaxyTypeDepends
    • GalaxyTypeDepends.__init__()
  • depends()
  • get_session_manager()
  • get_session()
  • get_api_user()
  • get_user()
  • UrlBuilder
    • UrlBuilder.__init__()
  • GalaxyASGIRequest
    • GalaxyASGIRequest.__init__()
    • GalaxyASGIRequest.base
    • GalaxyASGIRequest.url_path
    • GalaxyASGIRequest.host
    • GalaxyASGIRequest.environ
  • GalaxyASGIResponse
    • GalaxyASGIResponse.__init__()
    • GalaxyASGIResponse.headers
  • get_current_history_from_session()
  • get_trans()
  • get_admin_user()
  • BaseGalaxyAPIController
    • BaseGalaxyAPIController.__init__()
  • RestVerb
    • RestVerb.get
    • RestVerb.head
    • RestVerb.post
    • RestVerb.put
    • RestVerb.patch
    • RestVerb.delete
    • RestVerb.options
  • Router
    • Router.wrap_with_alias()
    • Router.construct_aliases()
    • Router.get()
    • Router.patch()
    • Router.put()
    • Router.post()
    • Router.delete()
    • Router.options()
    • Router.head()
    • Router.cbv
  • APIContentTypeRoute
    • APIContentTypeRoute.match_content_type
    • APIContentTypeRoute.accept_matches()
    • APIContentTypeRoute.matches()
  • as_form()
  • try_get_request_body_as_json()
  • IndexQueryTag
    • IndexQueryTag.tag
    • IndexQueryTag.description
    • IndexQueryTag.alias
    • IndexQueryTag.admin_only
    • IndexQueryTag.as_markdown()
  • search_query_param()
  • Submodules
  • galaxy.webapps.galaxy.api.annotations module
    • BaseAnnotationsController
      • BaseAnnotationsController.tagged_item_id
      • BaseAnnotationsController.index()
      • BaseAnnotationsController.create()
      • BaseAnnotationsController.delete()
      • BaseAnnotationsController.undelete()
    • HistoryAnnotationsController
      • HistoryAnnotationsController.controller_name
      • HistoryAnnotationsController.tagged_item_id
      • HistoryAnnotationsController.history_manager
    • HistoryContentAnnotationsController
      • HistoryContentAnnotationsController.controller_name
      • HistoryContentAnnotationsController.tagged_item_id
      • HistoryContentAnnotationsController.hda_manager
    • WorkflowAnnotationsController
      • WorkflowAnnotationsController.controller_name
      • WorkflowAnnotationsController.tagged_item_id
  • galaxy.webapps.galaxy.api.authenticate module
    • AuthenticationController
      • AuthenticationController.authentication_service
      • AuthenticationController.options()
    • FastAPIAuthenticate
      • FastAPIAuthenticate.authentication_service
      • FastAPIAuthenticate.get_api_key()
      • FastAPIAuthenticate.__init__()
  • galaxy.webapps.galaxy.api.cloud module
    • CloudController
      • CloudController.__init__()
      • CloudController.index()
      • CloudController.get()
      • CloudController.send()
  • galaxy.webapps.galaxy.api.cloudauthz module
    • CloudAuthzController
      • CloudAuthzController.__init__()
      • CloudAuthzController.index()
      • CloudAuthzController.create()
      • CloudAuthzController.delete()
      • CloudAuthzController.update()
  • galaxy.webapps.galaxy.api.common module
    • parse_serialization_params()
    • query_serialization_params()
    • get_value_filter_query_params()
    • get_filter_query_params()
    • get_update_permission_payload()
    • get_query_parameters_from_request_excluding()
    • query_parameter_as_list()
  • galaxy.webapps.galaxy.api.configuration module
    • FastAPIConfiguration
      • FastAPIConfiguration.configuration_manager
      • FastAPIConfiguration.whoami()
      • FastAPIConfiguration.index()
      • FastAPIConfiguration.version()
      • FastAPIConfiguration.dynamic_tool_confs()
      • FastAPIConfiguration.decode_id()
      • FastAPIConfiguration.tool_lineages()
      • FastAPIConfiguration.reload_toolbox()
      • FastAPIConfiguration.__init__()
  • galaxy.webapps.galaxy.api.container_resolution module
    • ContainerResolutionAPIController
      • ContainerResolutionAPIController.__init__()
      • ContainerResolutionAPIController.index()
      • ContainerResolutionAPIController.show()
      • ContainerResolutionAPIController.resolve()
      • ContainerResolutionAPIController.resolve_toolbox()
      • ContainerResolutionAPIController.resolve_toolbox_with_install()
      • ContainerResolutionAPIController.resolve_with_install()
  • galaxy.webapps.galaxy.api.dataset_collections module
    • FastAPIDatasetCollections
      • FastAPIDatasetCollections.service
      • FastAPIDatasetCollections.create()
      • FastAPIDatasetCollections.copy()
      • FastAPIDatasetCollections.attributes()
      • FastAPIDatasetCollections.suitable_converters()
      • FastAPIDatasetCollections.show()
      • FastAPIDatasetCollections.contents()
      • FastAPIDatasetCollections.content()
      • FastAPIDatasetCollections.__init__()
  • galaxy.webapps.galaxy.api.datasets module
    • FastAPIDatasets
      • FastAPIDatasets.service
      • FastAPIDatasets.index()
      • FastAPIDatasets.show_storage()
      • FastAPIDatasets.show_inheritance_chain()
      • FastAPIDatasets.get_content_as_text()
      • FastAPIDatasets.converted_ext()
      • FastAPIDatasets.converted()
      • FastAPIDatasets.update_permissions()
      • FastAPIDatasets.extra_files()
      • FastAPIDatasets.display_history_content()
      • FastAPIDatasets.display()
      • FastAPIDatasets.get_metadata_file_history_content()
      • FastAPIDatasets.get_metadata_file_datasets()
      • FastAPIDatasets.show()
      • FastAPIDatasets.delete_batch()
      • FastAPIDatasets.compute_hash()
      • FastAPIDatasets.__init__()
  • galaxy.webapps.galaxy.api.datatypes module
    • FastAPIDatatypes
      • FastAPIDatatypes.datatypes_registry
      • FastAPIDatatypes.index()
      • FastAPIDatatypes.mapping()
      • FastAPIDatatypes.types_and_mapping()
      • FastAPIDatatypes.sniffers()
      • FastAPIDatatypes.converters()
      • FastAPIDatatypes.edam_formats()
      • FastAPIDatatypes.edam_formats_detailed()
      • FastAPIDatatypes.edam_data()
      • FastAPIDatatypes.edam_data_detailed()
      • FastAPIDatatypes.__init__()
  • galaxy.webapps.galaxy.api.display_applications module
    • DisplayApplicationsController
      • DisplayApplicationsController.manager
      • DisplayApplicationsController.index()
      • DisplayApplicationsController.reload()
  • galaxy.webapps.galaxy.api.dynamic_tools module
    • DynamicToolsController
      • DynamicToolsController.index()
      • DynamicToolsController.show()
      • DynamicToolsController.create()
      • DynamicToolsController.delete()
  • galaxy.webapps.galaxy.api.extended_metadata module
    • BaseExtendedMetadataController
      • BaseExtendedMetadataController.exmeta_item_id
      • BaseExtendedMetadataController.index()
      • BaseExtendedMetadataController.create()
    • LibraryDatasetExtendMetadataController
      • LibraryDatasetExtendMetadataController.controller_name
      • LibraryDatasetExtendMetadataController.exmeta_item_id
    • HistoryDatasetExtendMetadataController
      • HistoryDatasetExtendMetadataController.controller_name
      • HistoryDatasetExtendMetadataController.exmeta_item_id
      • HistoryDatasetExtendMetadataController.hda_manager
  • galaxy.webapps.galaxy.api.folder_contents module
    • FastAPILibraryFoldersContents
      • FastAPILibraryFoldersContents.service
      • FastAPILibraryFoldersContents.index()
      • FastAPILibraryFoldersContents.create()
      • FastAPILibraryFoldersContents.__init__()
  • galaxy.webapps.galaxy.api.folders module
    • FastAPILibraryFolders
      • FastAPILibraryFolders.service
      • FastAPILibraryFolders.show()
      • FastAPILibraryFolders.create()
      • FastAPILibraryFolders.update()
      • FastAPILibraryFolders.delete()
      • FastAPILibraryFolders.get_permissions()
      • FastAPILibraryFolders.set_permissions()
      • FastAPILibraryFolders.__init__()
  • galaxy.webapps.galaxy.api.forms module
    • FormDefinitionAPIController
      • FormDefinitionAPIController.index()
      • FormDefinitionAPIController.show()
      • FormDefinitionAPIController.create()
  • galaxy.webapps.galaxy.api.genomes module
    • get_id()
    • FastAPIGenomes
      • FastAPIGenomes.manager
      • FastAPIGenomes.index()
      • FastAPIGenomes.show()
      • FastAPIGenomes.indexes()
      • FastAPIGenomes.sequences()
      • FastAPIGenomes.__init__()
  • galaxy.webapps.galaxy.api.group_roles module
    • group_role_to_model()
    • FastAPIGroupRoles
      • FastAPIGroupRoles.manager
      • FastAPIGroupRoles.index()
      • FastAPIGroupRoles.show()
      • FastAPIGroupRoles.update()
      • FastAPIGroupRoles.delete()
      • FastAPIGroupRoles.__init__()
  • galaxy.webapps.galaxy.api.group_users module
    • group_user_to_model()
    • FastAPIGroupUsers
      • FastAPIGroupUsers.manager
      • FastAPIGroupUsers.index()
      • FastAPIGroupUsers.show()
      • FastAPIGroupUsers.update()
      • FastAPIGroupUsers.delete()
      • FastAPIGroupUsers.__init__()
  • galaxy.webapps.galaxy.api.groups module
    • GroupAPIController
      • GroupAPIController.manager
      • GroupAPIController.index()
      • GroupAPIController.create()
      • GroupAPIController.show()
      • GroupAPIController.update()
  • galaxy.webapps.galaxy.api.histories module
    • DeleteHistoryPayload
      • DeleteHistoryPayload.purge
    • CreateHistoryFormData
      • CreateHistoryFormData.as_form()
      • CreateHistoryFormData.name
      • CreateHistoryFormData.history_id
      • CreateHistoryFormData.all_datasets
      • CreateHistoryFormData.archive_source
      • CreateHistoryFormData.archive_type
      • CreateHistoryFormData.archive_file
    • FastAPIHistories
      • FastAPIHistories.service
      • FastAPIHistories.index()
      • FastAPIHistories.index_deleted()
      • FastAPIHistories.published()
      • FastAPIHistories.shared_with_me()
      • FastAPIHistories.show_recent()
      • FastAPIHistories.show()
      • FastAPIHistories.prepare_store_download()
      • FastAPIHistories.write_store()
      • FastAPIHistories.citations()
      • FastAPIHistories.create()
      • FastAPIHistories.delete()
      • FastAPIHistories.undelete()
      • FastAPIHistories.update()
      • FastAPIHistories.create_from_store()
      • FastAPIHistories.create_from_store_async()
      • FastAPIHistories.index_exports()
      • FastAPIHistories.archive_export()
      • FastAPIHistories.archive_download()
      • FastAPIHistories.get_custom_builds_metadata()
      • FastAPIHistories.sharing()
      • FastAPIHistories.enable_link_access()
      • FastAPIHistories.disable_link_access()
      • FastAPIHistories.publish()
      • FastAPIHistories.unpublish()
      • FastAPIHistories.share_with_users()
      • FastAPIHistories.set_slug()
      • FastAPIHistories.__init__()
  • galaxy.webapps.galaxy.api.history_contents module
    • ContentTypeQueryParam()
    • get_index_query_params()
    • parse_index_query_params()
    • get_legacy_index_query_params()
    • parse_legacy_index_query_params()
    • parse_content_types()
    • parse_dataset_details()
    • get_index_jobs_summary_params()
    • parse_index_jobs_summary_params()
    • FastAPIHistoryContents
      • FastAPIHistoryContents.service
      • FastAPIHistoryContents.index_typed()
      • FastAPIHistoryContents.index()
      • FastAPIHistoryContents.show_jobs_summary()
      • FastAPIHistoryContents.show()
      • FastAPIHistoryContents.show_legacy()
      • FastAPIHistoryContents.prepare_store_download()
      • FastAPIHistoryContents.write_store()
      • FastAPIHistoryContents.index_jobs_summary()
      • FastAPIHistoryContents.download_dataset_collection_history_content()
      • FastAPIHistoryContents.download_dataset_collection()
      • FastAPIHistoryContents.prepare_collection_download()
      • FastAPIHistoryContents.create_typed()
      • FastAPIHistoryContents.create()
      • FastAPIHistoryContents.update_permissions()
      • FastAPIHistoryContents.update_batch()
      • FastAPIHistoryContents.bulk_operation()
      • FastAPIHistoryContents.validate()
      • FastAPIHistoryContents.update_typed()
      • FastAPIHistoryContents.update_legacy()
      • FastAPIHistoryContents.delete_typed()
      • FastAPIHistoryContents.delete_legacy()
      • FastAPIHistoryContents.archive_named()
      • FastAPIHistoryContents.archive()
      • FastAPIHistoryContents.create_from_store()
      • FastAPIHistoryContents.materialize_dataset()
      • FastAPIHistoryContents.materialize_to_history()
      • FastAPIHistoryContents.__init__()
  • galaxy.webapps.galaxy.api.item_tags module
    • BaseItemTagsController
      • BaseItemTagsController.index()
      • BaseItemTagsController.show()
      • BaseItemTagsController.create()
      • BaseItemTagsController.update()
      • BaseItemTagsController.delete()
    • HistoryContentTagsController
      • HistoryContentTagsController.controller_name
      • HistoryContentTagsController.tagged_item_class
      • HistoryContentTagsController.tagged_item_id
    • HistoryTagsController
      • HistoryTagsController.controller_name
      • HistoryTagsController.tagged_item_class
      • HistoryTagsController.tagged_item_id
    • WorkflowTagsController
      • WorkflowTagsController.controller_name
      • WorkflowTagsController.tagged_item_class
      • WorkflowTagsController.tagged_item_id
  • galaxy.webapps.galaxy.api.job_files module
    • JobFilesAPIController
      • JobFilesAPIController.index()
      • JobFilesAPIController.create()
  • galaxy.webapps.galaxy.api.job_lock module
    • job_lock_status()
    • update_job_lock()
  • galaxy.webapps.galaxy.api.job_ports module
    • JobPortsAPIController
      • JobPortsAPIController.__init__()
      • JobPortsAPIController.create()
  • galaxy.webapps.galaxy.api.jobs module
    • FastAPIJobs
      • FastAPIJobs.service
      • FastAPIJobs.show()
      • FastAPIJobs.index()
      • FastAPIJobs.__init__()
    • JobController
      • JobController.job_manager
      • JobController.job_search
      • JobController.hda_manager
      • JobController.common_problems()
      • JobController.inputs()
      • JobController.outputs()
      • JobController.delete()
      • JobController.resume()
      • JobController.metrics()
      • JobController.destination_params()
      • JobController.parameters_display()
      • JobController.build_for_rerun()
      • JobController.create()
      • JobController.search()
      • JobController.error()
      • JobController.show_job_lock()
      • JobController.update_job_lock()
  • galaxy.webapps.galaxy.api.libraries module
    • FastAPILibraries
      • FastAPILibraries.service
      • FastAPILibraries.index()
      • FastAPILibraries.index_deleted()
      • FastAPILibraries.show()
      • FastAPILibraries.create()
      • FastAPILibraries.create_from_store()
      • FastAPILibraries.update()
      • FastAPILibraries.delete()
      • FastAPILibraries.get_permissions()
      • FastAPILibraries.set_permissions()
      • FastAPILibraries.__init__()
  • galaxy.webapps.galaxy.api.library_contents module
    • LibraryContentsController
      • LibraryContentsController.__init__()
      • LibraryContentsController.index()
      • LibraryContentsController.show()
      • LibraryContentsController.create()
      • LibraryContentsController.update()
      • LibraryContentsController.delete()
  • galaxy.webapps.galaxy.api.library_datasets module
    • LibraryDatasetsController
      • LibraryDatasetsController.__init__()
      • LibraryDatasetsController.show()
      • LibraryDatasetsController.show_version()
      • LibraryDatasetsController.show_roles()
      • LibraryDatasetsController.update()
      • LibraryDatasetsController.update_permissions()
      • LibraryDatasetsController.delete()
      • LibraryDatasetsController.load()
      • LibraryDatasetsController.download()
  • galaxy.webapps.galaxy.api.licenses module
    • FastAPILicenses
      • FastAPILicenses.licenses_manager
      • FastAPILicenses.index()
      • FastAPILicenses.get()
      • FastAPILicenses.__init__()
  • galaxy.webapps.galaxy.api.metrics module
    • FastAPIMetrics
      • FastAPIMetrics.manager
      • FastAPIMetrics.create()
      • FastAPIMetrics.__init__()
  • galaxy.webapps.galaxy.api.page_revisions module
    • PageRevisionsController
      • PageRevisionsController.manager
      • PageRevisionsController.index()
      • PageRevisionsController.create()
  • galaxy.webapps.galaxy.api.pages module
    • FastAPIPages
      • FastAPIPages.service
      • FastAPIPages.index()
      • FastAPIPages.create()
      • FastAPIPages.delete()
      • FastAPIPages.show_pdf()
      • FastAPIPages.prepare_pdf()
      • FastAPIPages.show()
      • FastAPIPages.sharing()
      • FastAPIPages.enable_link_access()
      • FastAPIPages.disable_link_access()
      • FastAPIPages.publish()
      • FastAPIPages.unpublish()
      • FastAPIPages.share_with_users()
      • FastAPIPages.set_slug()
      • FastAPIPages.__init__()
  • galaxy.webapps.galaxy.api.plugins module
    • PluginsController
      • PluginsController.hda_manager
      • PluginsController.history_manager
      • PluginsController.index()
      • PluginsController.show()
  • galaxy.webapps.galaxy.api.provenance module
    • BaseProvenanceController
      • BaseProvenanceController.index()
      • BaseProvenanceController.show()
      • BaseProvenanceController.create()
      • BaseProvenanceController.delete()
    • HDAProvenanceController
      • HDAProvenanceController.controller_name
      • HDAProvenanceController.provenance_item_class
      • HDAProvenanceController.provenance_item_id
      • HDAProvenanceController.hda_manager
    • LDDAProvenanceController
      • LDDAProvenanceController.controller_name
      • LDDAProvenanceController.provenance_item_class
      • LDDAProvenanceController.provenance_item_id
      • LDDAProvenanceController.hda_manager
  • galaxy.webapps.galaxy.api.quotas module
    • FastAPIQuota
      • FastAPIQuota.service
      • FastAPIQuota.index()
      • FastAPIQuota.index_deleted()
      • FastAPIQuota.show()
      • FastAPIQuota.show_deleted()
      • FastAPIQuota.create()
      • FastAPIQuota.update()
      • FastAPIQuota.delete()
      • FastAPIQuota.undelete()
      • FastAPIQuota.__init__()
  • galaxy.webapps.galaxy.api.remote_files module
    • FastAPIRemoteFiles
      • FastAPIRemoteFiles.manager
      • FastAPIRemoteFiles.index()
      • FastAPIRemoteFiles.plugins()
      • FastAPIRemoteFiles.__init__()
  • galaxy.webapps.galaxy.api.roles module
    • role_to_model()
    • FastAPIRoles
      • FastAPIRoles.role_manager
      • FastAPIRoles.index()
      • FastAPIRoles.show()
      • FastAPIRoles.create()
      • FastAPIRoles.__init__()
  • galaxy.webapps.galaxy.api.sanitize_allow module
    • SanitizeAllowController
      • SanitizeAllowController.index()
      • SanitizeAllowController.create()
      • SanitizeAllowController.delete()
  • galaxy.webapps.galaxy.api.search module
    • SearchController
      • SearchController.create()
  • galaxy.webapps.galaxy.api.short_term_storage module
    • FastAPIShortTermStorage
      • FastAPIShortTermStorage.short_term_storage_monitor
      • FastAPIShortTermStorage.is_ready()
      • FastAPIShortTermStorage.serve()
      • FastAPIShortTermStorage.__init__()
  • galaxy.webapps.galaxy.api.tags module
    • FastAPITags
      • FastAPITags.manager
      • FastAPITags.update()
      • FastAPITags.__init__()
  • galaxy.webapps.galaxy.api.tasks module
    • FastAPITasks
      • FastAPITasks.manager
      • FastAPITasks.state()
      • FastAPITasks.__init__()
  • galaxy.webapps.galaxy.api.tool_data module
    • ImportToolDataBundle
      • ImportToolDataBundle.source
    • FastAPIToolData
      • FastAPIToolData.tool_data_manager
      • FastAPIToolData.index()
      • FastAPIToolData.create()
      • FastAPIToolData.show()
      • FastAPIToolData.reload()
      • FastAPIToolData.show_field()
      • FastAPIToolData.download_field_file()
      • FastAPIToolData.delete()
      • FastAPIToolData.__init__()
  • galaxy.webapps.galaxy.api.tool_dependencies module
    • ToolDependenciesAPIController
      • ToolDependenciesAPIController.__init__()
      • ToolDependenciesAPIController.index()
      • ToolDependenciesAPIController.show()
      • ToolDependenciesAPIController.update()
      • ToolDependenciesAPIController.resolver_dependency()
      • ToolDependenciesAPIController.install_dependency()
      • ToolDependenciesAPIController.manager_dependency()
      • ToolDependenciesAPIController.resolver_requirements()
      • ToolDependenciesAPIController.manager_requirements()
      • ToolDependenciesAPIController.clean()
      • ToolDependenciesAPIController.summarize_toolbox()
      • ToolDependenciesAPIController.toolbox_install()
      • ToolDependenciesAPIController.toolbox_uninstall()
      • ToolDependenciesAPIController.unused_dependency_paths()
      • ToolDependenciesAPIController.delete_unused_dependency_paths()
  • galaxy.webapps.galaxy.api.tool_entry_points module
    • ToolEntryPointsAPIController
      • ToolEntryPointsAPIController.__init__()
      • ToolEntryPointsAPIController.index()
      • ToolEntryPointsAPIController.access_entry_point()
      • ToolEntryPointsAPIController.stop_entry_point()
  • galaxy.webapps.galaxy.api.tool_shed_repositories module
    • get_message_for_no_shed_tool_config()
    • ToolShedRepositoriesController
      • ToolShedRepositoriesController.service
      • ToolShedRepositoriesController.install_repository_revision()
      • ToolShedRepositoriesController.install_repository_revisions()
      • ToolShedRepositoriesController.uninstall_repository()
      • ToolShedRepositoriesController.reset_metadata_on_selected_installed_repositories()
      • ToolShedRepositoriesController.reset_metadata_on_installed_repositories()
    • FastAPIToolShedRepositories
      • FastAPIToolShedRepositories.service
      • FastAPIToolShedRepositories.index()
      • FastAPIToolShedRepositories.check_for_updates()
      • FastAPIToolShedRepositories.show()
      • FastAPIToolShedRepositories.__init__()
  • galaxy.webapps.galaxy.api.tools module
    • FormDataApiRoute
      • FormDataApiRoute.match_content_type
      • FormDataApiRoute.methods
      • FormDataApiRoute.secure_cloned_response_field
      • FormDataApiRoute.response_fields
    • JsonApiRoute
      • JsonApiRoute.match_content_type
      • JsonApiRoute.methods
      • JsonApiRoute.secure_cloned_response_field
      • JsonApiRoute.response_fields
    • FetchTools
      • FetchTools.service
      • FetchTools.fetch_json()
      • FetchTools.fetch_form()
      • FetchTools.__init__()
    • ToolsController
      • ToolsController.history_manager
      • ToolsController.hda_manager
      • ToolsController.hdca_manager
      • ToolsController.service
      • ToolsController.index()
      • ToolsController.show()
      • ToolsController.build()
      • ToolsController.test_data_path()
      • ToolsController.test_data_download()
      • ToolsController.tests_summary()
      • ToolsController.test_data()
      • ToolsController.reload()
      • ToolsController.all_requirements()
      • ToolsController.requirements()
      • ToolsController.install_dependencies()
      • ToolsController.uninstall_dependencies()
      • ToolsController.build_dependency_cache()
      • ToolsController.diagnostics()
      • ToolsController.citations()
      • ToolsController.conversion()
      • ToolsController.xrefs()
      • ToolsController.download()
      • ToolsController.raw_tool_source()
      • ToolsController.error_stack()
      • ToolsController.create()
  • galaxy.webapps.galaxy.api.toolshed module
    • ToolShedController
      • ToolShedController.index()
      • ToolShedController.request()
  • galaxy.webapps.galaxy.api.tours module
    • FastAPITours
      • FastAPITours.registry
      • FastAPITours.index()
      • FastAPITours.show()
      • FastAPITours.update_tour()
      • FastAPITours.__init__()
  • galaxy.webapps.galaxy.api.trs_consumer module
    • TrsConsumeAPIController
      • TrsConsumeAPIController.get_servers()
      • TrsConsumeAPIController.get_tool()
      • TrsConsumeAPIController.get_versions()
      • TrsConsumeAPIController.get_version()
  • galaxy.webapps.galaxy.api.trs_search module
    • TrsSearchAPIController
      • TrsSearchAPIController.index()
  • galaxy.webapps.galaxy.api.uploads module
    • UploadsAPIController
      • UploadsAPIController.READ_CHUNK_SIZE
      • UploadsAPIController.hooks()
      • UploadsAPIController.index()
      • UploadsAPIController.create()
  • galaxy.webapps.galaxy.api.users module
    • FastAPIHistories
      • FastAPIHistories.service
      • FastAPIHistories.recalculate_disk_usage()
      • FastAPIHistories.get_or_create_api_key()
      • FastAPIHistories.get_api_key()
      • FastAPIHistories.create_api_key()
      • FastAPIHistories.delete_api_key()
      • FastAPIHistories.get_beacon()
      • FastAPIHistories.set_beacon()
      • FastAPIHistories.__init__()
    • UserAPIController
      • UserAPIController.user_manager
      • UserAPIController.user_serializer
      • UserAPIController.user_deserializer
      • UserAPIController.index()
      • UserAPIController.show()
      • UserAPIController.create()
      • UserAPIController.update()
      • UserAPIController.delete()
      • UserAPIController.undelete()
      • UserAPIController.anon_user_api_value()
      • UserAPIController.get_information()
      • UserAPIController.set_information()
      • UserAPIController.set_favorite()
      • UserAPIController.remove_favorite()
      • UserAPIController.set_theme()
      • UserAPIController.get_password()
      • UserAPIController.set_password()
      • UserAPIController.get_permissions()
      • UserAPIController.set_permissions()
      • UserAPIController.get_toolbox_filters()
      • UserAPIController.set_toolbox_filters()
      • UserAPIController.get_custom_builds()
      • UserAPIController.add_custom_builds()
      • UserAPIController.delete_custom_builds()
  • galaxy.webapps.galaxy.api.visualizations module
    • FastAPIVisualizations
      • FastAPIVisualizations.service
      • FastAPIVisualizations.sharing()
      • FastAPIVisualizations.enable_link_access()
      • FastAPIVisualizations.disable_link_access()
      • FastAPIVisualizations.publish()
      • FastAPIVisualizations.unpublish()
      • FastAPIVisualizations.share_with_users()
      • FastAPIVisualizations.set_slug()
      • FastAPIVisualizations.__init__()
    • VisualizationsController
      • VisualizationsController.service
      • VisualizationsController.index()
      • VisualizationsController.show()
      • VisualizationsController.create()
      • VisualizationsController.update()
  • galaxy.webapps.galaxy.api.webhooks module
    • WebhooksController
      • WebhooksController.all_webhooks()
      • WebhooksController.webhook_data()
  • galaxy.webapps.galaxy.api.workflows module
    • CreateInvocationFromStore
      • CreateInvocationFromStore.history_id
      • CreateInvocationFromStore.Config
    • WorkflowsAPIController
      • WorkflowsAPIController.service
      • WorkflowsAPIController.invocations_service
      • WorkflowsAPIController.__init__()
      • WorkflowsAPIController.set_workflow_menu()
      • WorkflowsAPIController.show()
      • WorkflowsAPIController.create()
      • WorkflowsAPIController.workflow_dict()
      • WorkflowsAPIController.import_new_workflow_deprecated()
      • WorkflowsAPIController.update()
      • WorkflowsAPIController.refactor()
      • WorkflowsAPIController.build_module()
      • WorkflowsAPIController.get_tool_predictions()
      • WorkflowsAPIController.import_shared_workflow_deprecated()
      • WorkflowsAPIController.invoke()
      • WorkflowsAPIController.index_invocations()
      • WorkflowsAPIController.create_invocations_from_store()
      • WorkflowsAPIController.show_invocation()
      • WorkflowsAPIController.cancel_invocation()
      • WorkflowsAPIController.show_invocation_report()
      • WorkflowsAPIController.show_invocation_report_pdf()
      • WorkflowsAPIController.invocation_step()
      • WorkflowsAPIController.invocation_step_jobs_summary()
      • WorkflowsAPIController.invocation_jobs_summary()
      • WorkflowsAPIController.update_invocation_step()
    • FastAPIWorkflows
      • FastAPIWorkflows.service
      • FastAPIWorkflows.index()
      • FastAPIWorkflows.sharing()
      • FastAPIWorkflows.enable_link_access()
      • FastAPIWorkflows.disable_link_access()
      • FastAPIWorkflows.publish()
      • FastAPIWorkflows.unpublish()
      • FastAPIWorkflows.share_with_users()
      • FastAPIWorkflows.set_slug()
      • FastAPIWorkflows.delete_workflow()
      • FastAPIWorkflows.undelete_workflow()
      • FastAPIWorkflows.show_versions()
      • FastAPIWorkflows.get_workflow_menu()
      • FastAPIWorkflows.__init__()
    • FastAPIInvocations
      • FastAPIInvocations.invocations_service
      • FastAPIInvocations.prepare_store_download()
      • FastAPIInvocations.write_store()
      • FastAPIInvocations.export_invocation_bco()
      • FastAPIInvocations.download_invocation_bco()
      • FastAPIInvocations.__init__()
• galaxy.webapps.galaxy.controllers package
  • Submodules
  • galaxy.webapps.galaxy.controllers.admin module
    • UserListGrid
      • UserListGrid.EmailColumn
      • UserListGrid.UserNameColumn
      • UserListGrid.StatusColumn
      • UserListGrid.GroupsColumn
      • UserListGrid.RolesColumn
      • UserListGrid.ExternalColumn
      • UserListGrid.LastLoginColumn
      • UserListGrid.TimeCreatedColumn
      • UserListGrid.ActivatedColumn
      • UserListGrid.DiskUsageColumn
      • UserListGrid.title
      • UserListGrid.title_id
      • UserListGrid.model_class
      • UserListGrid.default_sort_key
      • UserListGrid.columns
      • UserListGrid.global_actions
      • UserListGrid.operations
      • UserListGrid.standard_filters
      • UserListGrid.num_rows_per_page
      • UserListGrid.use_paging
      • UserListGrid.default_filter
      • UserListGrid.use_default_filter
      • UserListGrid.get_current_item()
    • RoleListGrid
      • RoleListGrid.NameColumn
      • RoleListGrid.DescriptionColumn
      • RoleListGrid.TypeColumn
      • RoleListGrid.StatusColumn
      • RoleListGrid.GroupsColumn
      • RoleListGrid.UsersColumn
      • RoleListGrid.title
      • RoleListGrid.title_id
      • RoleListGrid.model_class
      • RoleListGrid.default_sort_key
      • RoleListGrid.columns
      • RoleListGrid.global_actions
      • RoleListGrid.operations
      • RoleListGrid.standard_filters
      • RoleListGrid.num_rows_per_page
      • RoleListGrid.use_paging
      • RoleListGrid.apply_query_filter()
    • GroupListGrid
      • GroupListGrid.NameColumn
      • GroupListGrid.StatusColumn
      • GroupListGrid.RolesColumn
      • GroupListGrid.UsersColumn
      • GroupListGrid.title
      • GroupListGrid.title_id
      • GroupListGrid.model_class
      • GroupListGrid.default_sort_key
      • GroupListGrid.columns
      • GroupListGrid.global_actions
      • GroupListGrid.operations
      • GroupListGrid.standard_filters
      • GroupListGrid.num_rows_per_page
      • GroupListGrid.use_paging
    • QuotaListGrid
      • QuotaListGrid.NameColumn
      • QuotaListGrid.DescriptionColumn
      • QuotaListGrid.AmountColumn
      • QuotaListGrid.StatusColumn
      • QuotaListGrid.UsersColumn
      • QuotaListGrid.GroupsColumn
      • QuotaListGrid.title
      • QuotaListGrid.model_class
      • QuotaListGrid.default_sort_key
      • QuotaListGrid.columns
      • QuotaListGrid.global_actions
      • QuotaListGrid.operations
      • QuotaListGrid.standard_filters
      • QuotaListGrid.num_rows_per_page
      • QuotaListGrid.use_paging
    • ToolVersionListGrid
      • ToolVersionListGrid.ToolIdColumn
      • ToolVersionListGrid.ToolVersionsColumn
      • ToolVersionListGrid.title
      • ToolVersionListGrid.model_class
      • ToolVersionListGrid.default_sort_key
      • ToolVersionListGrid.columns
      • ToolVersionListGrid.num_rows_per_page
      • ToolVersionListGrid.use_paging
      • ToolVersionListGrid.build_initial_query()
    • DatatypesEntryT
      • DatatypesEntryT.status
      • DatatypesEntryT.data
      • DatatypesEntryT.message
    • AdminGalaxy
      • AdminGalaxy.user_list_grid
      • AdminGalaxy.role_list_grid
      • AdminGalaxy.group_list_grid
      • AdminGalaxy.quota_list_grid
      • AdminGalaxy.tool_version_list_grid
      • AdminGalaxy.delete_operation
      • AdminGalaxy.undelete_operation
      • AdminGalaxy.purge_operation
      • AdminGalaxy.impersonate_operation
      • AdminGalaxy.activate_operation
      • AdminGalaxy.resend_activation_email
      • AdminGalaxy.__init__()
      • AdminGalaxy.data_tables_list()
      • AdminGalaxy.data_types_list()
      • AdminGalaxy.users_list()
      • AdminGalaxy.quotas_list()
      • AdminGalaxy.create_quota()
      • AdminGalaxy.rename_quota()
      • AdminGalaxy.manage_users_and_groups_for_quota()
      • AdminGalaxy.edit_quota()
      • AdminGalaxy.set_quota_default()
      • AdminGalaxy.impersonate()
      • AdminGalaxy.tool_versions_list()
      • AdminGalaxy.roles_list()
      • AdminGalaxy.create_role()
      • AdminGalaxy.rename_role()
      • AdminGalaxy.manage_users_and_groups_for_role()
      • AdminGalaxy.groups_list()
      • AdminGalaxy.rename_group()
      • AdminGalaxy.manage_users_and_roles_for_group()
      • AdminGalaxy.create_group()
      • AdminGalaxy.create_new_user()
      • AdminGalaxy.reset_user_password()
      • AdminGalaxy.manage_roles_and_groups_for_user()
    • build_select_input()
    • get_user()
    • get_role()
    • get_group()
    • get_quota()
  • galaxy.webapps.galaxy.controllers.admin_toolshed module
    • legacy_tool_shed_endpoint()
    • AdminToolshed
      • AdminToolshed.activate_repository()
      • AdminToolshed.restore_repository()
      • AdminToolshed.display_image_in_repository()
      • AdminToolshed.manage_repository_json()
      • AdminToolshed.quota_manager
  • galaxy.webapps.galaxy.controllers.async module
    • ASync
      • ASync.default()
      • ASync.index()
  • galaxy.webapps.galaxy.controllers.authnz module
    • OIDC
      • OIDC.index()
      • OIDC.login()
      • OIDC.callback()
      • OIDC.create_user()
      • OIDC.disconnect()
      • OIDC.logout()
      • OIDC.get_logout_url()
      • OIDC.get_cilogon_idps()
  • galaxy.webapps.galaxy.controllers.data_manager module
    • DataManager
      • DataManager.data_managers_list()
      • DataManager.jobs_list()
      • DataManager.job_info()
      • DataManager.tool_data_table_info()
      • DataManager.tool_data_table_info_1()
      • DataManager.reload_tool_data_tables()
      • DataManager.tool_data_table_items()
      • DataManager.reload_tool_data_table()
  • galaxy.webapps.galaxy.controllers.dataset module
    • DatasetInterface
      • DatasetInterface.history_manager
      • DatasetInterface.hda_manager
      • DatasetInterface.hda_deserializer
      • DatasetInterface.service
      • DatasetInterface.__init__()
      • DatasetInterface.stdout()
      • DatasetInterface.stderr()
      • DatasetInterface.exit_code()
      • DatasetInterface.default()
      • DatasetInterface.get_metadata_file()
      • DatasetInterface.transfer_status()
      • DatasetInterface.display()
      • DatasetInterface.get_edit()
      • DatasetInterface.set_edit()
      • DatasetInterface.imp()
      • DatasetInterface.get_name_and_link_async()
      • DatasetInterface.get_embed_html_async()
      • DatasetInterface.set_accessible_async()
      • DatasetInterface.display_by_username_and_slug()
      • DatasetInterface.annotate_async()
      • DatasetInterface.get_annotation_async()
      • DatasetInterface.display_at()
      • DatasetInterface.display_application()
      • DatasetInterface.delete()
      • DatasetInterface.delete_async()
      • DatasetInterface.undelete()
      • DatasetInterface.undelete_async()
      • DatasetInterface.unhide()
      • DatasetInterface.purge()
      • DatasetInterface.purge_async()
      • DatasetInterface.copy_datasets()
  • galaxy.webapps.galaxy.controllers.error module
    • Error
      • Error.index()
  • galaxy.webapps.galaxy.controllers.forms module
    • FormsGrid
      • FormsGrid.NameColumn
      • FormsGrid.DescriptionColumn
      • FormsGrid.TypeColumn
      • FormsGrid.StatusColumn
      • FormsGrid.title
      • FormsGrid.model_class
      • FormsGrid.default_sort_key
      • FormsGrid.num_rows_per_page
      • FormsGrid.use_paging
      • FormsGrid.default_filter
      • FormsGrid.columns
      • FormsGrid.operations
      • FormsGrid.global_actions
      • FormsGrid.build_initial_query()
    • Forms
      • Forms.forms_grid
      • Forms.forms_list()
      • Forms.create_form()
      • Forms.edit_form()
      • Forms.get_current_form()
      • Forms.save_form_definition()
    • get_form()
  • galaxy.webapps.galaxy.controllers.history module
    • NameColumn
      • NameColumn.get_value()
    • HistoryListGrid
      • HistoryListGrid.ItemCountColumn
      • HistoryListGrid.HistoryListNameColumn
      • HistoryListGrid.DeletedColumn
      • HistoryListGrid.build_initial_query()
      • HistoryListGrid.title
      • HistoryListGrid.model_class
      • HistoryListGrid.default_sort_key
      • HistoryListGrid.columns
      • HistoryListGrid.global_actions
      • HistoryListGrid.operations
      • HistoryListGrid.standard_filters
      • HistoryListGrid.default_filter
      • HistoryListGrid.num_rows_per_page
      • HistoryListGrid.use_paging
      • HistoryListGrid.info_text
      • HistoryListGrid.get_current_item()
      • HistoryListGrid.apply_query_filter()
    • SharedHistoryListGrid
      • SharedHistoryListGrid.DatasetsByStateColumn
      • SharedHistoryListGrid.SharedByColumn
      • SharedHistoryListGrid.title
      • SharedHistoryListGrid.model_class
      • SharedHistoryListGrid.default_sort_key
      • SharedHistoryListGrid.columns
      • SharedHistoryListGrid.operations
      • SharedHistoryListGrid.build_initial_query()
      • SharedHistoryListGrid.apply_query_filter()
    • HistoryController
      • HistoryController.history_manager
      • HistoryController.history_serializer
      • HistoryController.slug_builder
      • HistoryController.__init__()
      • HistoryController.index()
      • HistoryController.list_as_xml()
      • HistoryController.stored_list_grid
      • HistoryController.shared_list_grid
      • HistoryController.list()
      • HistoryController.list_shared()
      • HistoryController.as_xml()
      • HistoryController.view()
      • HistoryController.display_by_username_and_slug()
      • HistoryController.permissions()
      • HistoryController.make_private()
      • HistoryController.adjust_hidden()
      • HistoryController.purge_deleted_datasets()
      • HistoryController.resume_paused_jobs()
      • HistoryController.get_name_and_link_async()
      • HistoryController.set_accessible_async()
      • HistoryController.rename()
      • HistoryController.switch_to_history()
      • HistoryController.get_item()
      • HistoryController.history_data()
      • HistoryController.set_as_current()
      • HistoryController.current_history_json()
      • HistoryController.create_new_current()
  • galaxy.webapps.galaxy.controllers.library module
  • galaxy.webapps.galaxy.controllers.page module
    • format_bool()
    • PageListGrid
      • PageListGrid.URLColumn
      • PageListGrid.use_panels
      • PageListGrid.title
      • PageListGrid.model_class
      • PageListGrid.default_filter
      • PageListGrid.default_sort_key
      • PageListGrid.columns
      • PageListGrid.global_actions
      • PageListGrid.operations
      • PageListGrid.apply_query_filter()
    • PageAllPublishedGrid
      • PageAllPublishedGrid.use_panels
      • PageAllPublishedGrid.title
      • PageAllPublishedGrid.model_class
      • PageAllPublishedGrid.default_sort_key
      • PageAllPublishedGrid.default_filter
      • PageAllPublishedGrid.columns
      • PageAllPublishedGrid.build_initial_query()
      • PageAllPublishedGrid.apply_query_filter()
    • ItemSelectionGrid
      • ItemSelectionGrid.NameColumn
      • ItemSelectionGrid.show_item_checkboxes
      • ItemSelectionGrid.default_filter
      • ItemSelectionGrid.default_sort_key
      • ItemSelectionGrid.use_paging
      • ItemSelectionGrid.num_rows_per_page
      • ItemSelectionGrid.apply_query_filter()
    • HistorySelectionGrid
      • HistorySelectionGrid.title
      • HistorySelectionGrid.model_class
      • HistorySelectionGrid.columns
      • HistorySelectionGrid.apply_query_filter()
    • HistoryDatasetAssociationSelectionGrid
      • HistoryDatasetAssociationSelectionGrid.title
      • HistoryDatasetAssociationSelectionGrid.model_class
      • HistoryDatasetAssociationSelectionGrid.columns
      • HistoryDatasetAssociationSelectionGrid.apply_query_filter()
    • WorkflowSelectionGrid
      • WorkflowSelectionGrid.title
      • WorkflowSelectionGrid.model_class
      • WorkflowSelectionGrid.columns
    • PageSelectionGrid
      • PageSelectionGrid.title
      • PageSelectionGrid.model_class
      • PageSelectionGrid.columns
    • VisualizationSelectionGrid
      • VisualizationSelectionGrid.title
      • VisualizationSelectionGrid.model_class
      • VisualizationSelectionGrid.columns
    • PageController
      • PageController.page_manager
      • PageController.history_manager
      • PageController.history_serializer
      • PageController.hda_manager
      • PageController.workflow_manager
      • PageController.slug_builder
      • PageController.__init__()
      • PageController.list()
      • PageController.list_published()
      • PageController.create()
      • PageController.edit()
      • PageController.display()
      • PageController.display_by_username_and_slug()
      • PageController.set_accessible_async()
      • PageController.get_embed_html_async()
      • PageController.get_name_and_link_async()
      • PageController.list_histories_for_selection()
      • PageController.list_workflows_for_selection()
      • PageController.list_visualizations_for_selection()
      • PageController.list_pages_for_selection()
      • PageController.list_datasets_for_selection()
      • PageController.get_page()
      • PageController.get_item()
  • galaxy.webapps.galaxy.controllers.root module
    • RootController
      • RootController.history_manager
      • RootController.__init__()
      • RootController.default()
      • RootController.index()
      • RootController.login()
      • RootController.display_as()
      • RootController.welcome()
  • galaxy.webapps.galaxy.controllers.shed_tool_static module
    • ShedToolStatic
      • ShedToolStatic.index()
  • galaxy.webapps.galaxy.controllers.tag module
    • TagsController
      • TagsController.get_tagging_elt_async()
      • TagsController.add_tag_async()
      • TagsController.remove_tag_async()
      • TagsController.retag_async()
      • TagsController.tag_autocomplete_data()
  • galaxy.webapps.galaxy.controllers.tool_runner module
    • ToolRunner
      • ToolRunner.biomart()
      • ToolRunner.hapmapmart()
      • ToolRunner.default()
      • ToolRunner.index()
      • ToolRunner.rerun()
      • ToolRunner.data_source_redirect()
  • galaxy.webapps.galaxy.controllers.user module
    • User
      • User.user_manager
      • User.installed_len_files
      • User.__init__()
      • User.login()
      • User.resend_verification()
      • User.resend_activation_email()
      • User.is_outside_grace_period()
      • User.logout()
      • User.create()
      • User.activate()
      • User.change_password()
      • User.reset_password()
  • galaxy.webapps.galaxy.controllers.userskeys module
    • User
      • User.index()
      • User.admin_api_keys()
      • User.all_users()
      • User.get_all_users()
  • galaxy.webapps.galaxy.controllers.visualization module
    • HistoryDatasetsSelectionGrid
      • HistoryDatasetsSelectionGrid.DbKeyColumn
      • HistoryDatasetsSelectionGrid.HistoryColumn
      • HistoryDatasetsSelectionGrid.available_tracks
      • HistoryDatasetsSelectionGrid.title
      • HistoryDatasetsSelectionGrid.model_class
      • HistoryDatasetsSelectionGrid.default_filter
      • HistoryDatasetsSelectionGrid.default_sort_key
      • HistoryDatasetsSelectionGrid.columns
      • HistoryDatasetsSelectionGrid.build_initial_query()
      • HistoryDatasetsSelectionGrid.apply_query_filter()
    • LibraryDatasetsSelectionGrid
      • LibraryDatasetsSelectionGrid.available_tracks
      • LibraryDatasetsSelectionGrid.title
      • LibraryDatasetsSelectionGrid.model_class
      • LibraryDatasetsSelectionGrid.default_filter
      • LibraryDatasetsSelectionGrid.default_sort_key
      • LibraryDatasetsSelectionGrid.columns
      • LibraryDatasetsSelectionGrid.build_initial_query()
      • LibraryDatasetsSelectionGrid.apply_query_filter()
    • TracksterSelectionGrid
      • TracksterSelectionGrid.title
      • TracksterSelectionGrid.model_class
      • TracksterSelectionGrid.default_sort_key
      • TracksterSelectionGrid.use_paging
      • TracksterSelectionGrid.show_item_checkboxes
      • TracksterSelectionGrid.columns
      • TracksterSelectionGrid.build_initial_query()
      • TracksterSelectionGrid.apply_query_filter()
    • VisualizationListGrid
      • VisualizationListGrid.get_url_args()
      • VisualizationListGrid.get_display_name()
      • VisualizationListGrid.title
      • VisualizationListGrid.model_class
      • VisualizationListGrid.default_sort_key
      • VisualizationListGrid.default_filter
      • VisualizationListGrid.columns
      • VisualizationListGrid.operations
      • VisualizationListGrid.apply_query_filter()
    • VisualizationAllPublishedGrid
      • VisualizationAllPublishedGrid.use_panels
      • VisualizationAllPublishedGrid.title
      • VisualizationAllPublishedGrid.model_class
      • VisualizationAllPublishedGrid.default_sort_key
      • VisualizationAllPublishedGrid.default_filter
      • VisualizationAllPublishedGrid.columns
      • VisualizationAllPublishedGrid.build_initial_query()
      • VisualizationAllPublishedGrid.apply_query_filter()
    • VisualizationController
      • VisualizationController.hda_manager
      • VisualizationController.slug_builder
      • VisualizationController.__init__()
      • VisualizationController.list_libraries()
      • VisualizationController.list_history_datasets()
      • VisualizationController.list_library_datasets()
      • VisualizationController.list_tracks()
      • VisualizationController.list_published()
      • VisualizationController.list()
      • VisualizationController.index()
      • VisualizationController.copy()
      • VisualizationController.set_accessible_async()
      • VisualizationController.imp()
      • VisualizationController.display_by_username_and_slug()
      • VisualizationController.get_name_and_link_async()
      • VisualizationController.save()
      • VisualizationController.edit()
      • VisualizationController.render()
      • VisualizationController.saved()
      • VisualizationController.trackster()
      • VisualizationController.circster()
      • VisualizationController.sweepster()
      • VisualizationController.get_item()
      • VisualizationController.phyloviz()
  • galaxy.webapps.galaxy.controllers.workflow module
    • StoredWorkflowListGrid
      • StoredWorkflowListGrid.StepsColumn
      • StoredWorkflowListGrid.use_panels
      • StoredWorkflowListGrid.title
      • StoredWorkflowListGrid.model_class
      • StoredWorkflowListGrid.default_filter
      • StoredWorkflowListGrid.default_sort_key
      • StoredWorkflowListGrid.columns
      • StoredWorkflowListGrid.operations
      • StoredWorkflowListGrid.apply_query_filter()
    • StoredWorkflowAllPublishedGrid
      • StoredWorkflowAllPublishedGrid.title
      • StoredWorkflowAllPublishedGrid.model_class
      • StoredWorkflowAllPublishedGrid.default_sort_key
      • StoredWorkflowAllPublishedGrid.default_filter
      • StoredWorkflowAllPublishedGrid.columns
      • StoredWorkflowAllPublishedGrid.operations
      • StoredWorkflowAllPublishedGrid.num_rows_per_page
      • StoredWorkflowAllPublishedGrid.use_paging
      • StoredWorkflowAllPublishedGrid.build_initial_query()
      • StoredWorkflowAllPublishedGrid.apply_query_filter()
    • SingleTagContentsParser
      • SingleTagContentsParser.__init__()
      • SingleTagContentsParser.handle_starttag()
      • SingleTagContentsParser.handle_data()
    • WorkflowController
      • WorkflowController.stored_list_grid
      • WorkflowController.published_list_grid
      • WorkflowController.slug_builder
      • WorkflowController.list_grid()
      • WorkflowController.list_published()
      • WorkflowController.display_by_username_and_slug()
      • WorkflowController.imp()
      • WorkflowController.rename_async()
      • WorkflowController.annotate_async()
      • WorkflowController.get_embed_html_async()
      • WorkflowController.get_name_and_link_async()
      • WorkflowController.gen_image()
      • WorkflowController.create()
      • WorkflowController.save_workflow_as()
      • WorkflowController.editor()
      • WorkflowController.load_workflow()
      • WorkflowController.export_to_myexp()
      • WorkflowController.for_direct_import()
      • WorkflowController.export_to_file()
      • WorkflowController.build_from_current_history()
      • WorkflowController.get_item()
• galaxy.webapps.galaxy.services package
  • Submodules
  • galaxy.webapps.galaxy.services.authenticate module
    • APIKeyResponse
      • APIKeyResponse.api_key
    • AuthenticationService
      • AuthenticationService.__init__()
      • AuthenticationService.get_api_key()
  • galaxy.webapps.galaxy.services.base module
    • ensure_celery_tasks_enabled()
    • ServiceBase
      • ServiceBase.__init__()
      • ServiceBase.decode_id()
      • ServiceBase.encode_id()
      • ServiceBase.decode_ids()
      • ServiceBase.encode_all_ids()
      • ServiceBase.build_order_by()
      • ServiceBase.get_class()
      • ServiceBase.get_object()
      • ServiceBase.check_user_is_authenticated()
      • ServiceBase.get_authenticated_user()
    • ServedExportStore
      • ServedExportStore.export_store
      • ServedExportStore.export_target
    • model_store_storage_target()
    • ServesExportStores
      • ServesExportStores.serve_export_store()
    • ConsumesModelStores
      • ConsumesModelStores.create_objects_from_store()
    • async_task_summary()
  • galaxy.webapps.galaxy.services.dataset_collections module
    • UpdateCollectionAttributePayload
      • UpdateCollectionAttributePayload.dbkey
      • UpdateCollectionAttributePayload.Config
    • DatasetCollectionAttributesResult
      • DatasetCollectionAttributesResult.dbkey
      • DatasetCollectionAttributesResult.extension
      • DatasetCollectionAttributesResult.model_class
      • DatasetCollectionAttributesResult.dbkeys
      • DatasetCollectionAttributesResult.extensions
      • DatasetCollectionAttributesResult.tags
    • SuitableConverter
      • SuitableConverter.tool_id
      • SuitableConverter.name
      • SuitableConverter.target_type
      • SuitableConverter.original_type
    • SuitableConverters
    • DatasetCollectionContentElements
    • DatasetCollectionsService
      • DatasetCollectionsService.__init__()
      • DatasetCollectionsService.create()
      • DatasetCollectionsService.copy()
      • DatasetCollectionsService.attributes()
      • DatasetCollectionsService.suitable_converters()
      • DatasetCollectionsService.show()
      • DatasetCollectionsService.dce_content()
      • DatasetCollectionsService.contents()
  • galaxy.webapps.galaxy.services.datasets module
    • RequestDataType
      • RequestDataType.state
      • RequestDataType.converted_datasets_state
      • RequestDataType.data
      • RequestDataType.features
      • RequestDataType.raw_data
      • RequestDataType.track_config
      • RequestDataType.genome_data
      • RequestDataType.in_use_state
    • DatasetStorageDetails
      • DatasetStorageDetails.object_store_id
      • DatasetStorageDetails.name
      • DatasetStorageDetails.description
      • DatasetStorageDetails.percent_used
      • DatasetStorageDetails.dataset_state
      • DatasetStorageDetails.hashes
      • DatasetStorageDetails.sources
    • DatasetInheritanceChainEntry
      • DatasetInheritanceChainEntry.name
      • DatasetInheritanceChainEntry.dep
    • DatasetInheritanceChain
    • ExtraFilesEntryClass
      • ExtraFilesEntryClass.Directory
      • ExtraFilesEntryClass.File
    • ExtraFileEntry
      • ExtraFileEntry.class_
      • ExtraFileEntry.path
    • DatasetTextContentDetails
      • DatasetTextContentDetails.item_data
      • DatasetTextContentDetails.truncated
      • DatasetTextContentDetails.item_url
    • ConvertedDatasetsMap
      • ConvertedDatasetsMap.Config
    • DataMode
      • DataMode.Coverage
      • DataMode.Auto
    • DataResult
      • DataResult.data
      • DataResult.dataset_type
      • DataResult.message
      • DataResult.extra_info
    • BamDataResult
      • BamDataResult.max_low
      • BamDataResult.max_high
    • DeleteDatasetBatchPayload
      • DeleteDatasetBatchPayload.datasets
      • DeleteDatasetBatchPayload.purge
    • ComputeDatasetHashPayload
      • ComputeDatasetHashPayload.hash_function
      • ComputeDatasetHashPayload.extra_files_path
      • ComputeDatasetHashPayload.Config
    • DatasetErrorMessage
      • DatasetErrorMessage.dataset
      • DatasetErrorMessage.error_message
    • DeleteDatasetBatchResult
      • DeleteDatasetBatchResult.success_count
      • DeleteDatasetBatchResult.errors
    • DatasetsService
      • DatasetsService.__init__()
      • DatasetsService.serializer_by_type
      • DatasetsService.dataset_manager_by_type
      • DatasetsService.index()
      • DatasetsService.show()
      • DatasetsService.show_storage()
      • DatasetsService.show_inheritance_chain()
      • DatasetsService.compute_hash()
      • DatasetsService.drs_dataset_instance()
      • DatasetsService.get_drs_object()
      • DatasetsService.update_permissions()
      • DatasetsService.extra_files()
      • DatasetsService.display()
      • DatasetsService.get_content_as_text()
      • DatasetsService.get_metadata_file()
      • DatasetsService.converted_ext()
      • DatasetsService.converted()
      • DatasetsService.delete_batch()
  • galaxy.webapps.galaxy.services.histories module
    • HistoriesService
      • HistoriesService.__init__()
      • HistoriesService.index()
      • HistoriesService.create()
      • HistoriesService.create_from_store()
      • HistoriesService.create_from_store_async()
      • HistoriesService.show()
      • HistoriesService.prepare_download()
      • HistoriesService.write_store()
      • HistoriesService.update()
      • HistoriesService.delete()
      • HistoriesService.undelete()
      • HistoriesService.shared_with_me()
      • HistoriesService.published()
      • HistoriesService.citations()
      • HistoriesService.index_exports()
      • HistoriesService.archive_export()
      • HistoriesService.get_ready_history_export()
      • HistoriesService.get_archive_download_path()
      • HistoriesService.get_archive_media_type()
      • HistoriesService.legacy_archive_download()
      • HistoriesService.get_custom_builds_metadata()
  • galaxy.webapps.galaxy.services.history_contents module
    • HistoryContentsIndexParams
      • HistoryContentsIndexParams.v
      • HistoryContentsIndexParams.dataset_details
    • LegacyHistoryContentsIndexParams
      • LegacyHistoryContentsIndexParams.ids
      • LegacyHistoryContentsIndexParams.types
      • LegacyHistoryContentsIndexParams.dataset_details
      • LegacyHistoryContentsIndexParams.deleted
      • LegacyHistoryContentsIndexParams.visible
    • HistoryContentsIndexJobsSummaryParams
      • HistoryContentsIndexJobsSummaryParams.ids
      • HistoryContentsIndexJobsSummaryParams.types
    • CreateHistoryContentPayloadBase
      • CreateHistoryContentPayloadBase.type
    • CreateHistoryContentPayloadFromCopy
      • CreateHistoryContentPayloadFromCopy.source
      • CreateHistoryContentPayloadFromCopy.content
    • CollectionElementIdentifier
      • CollectionElementIdentifier.name
      • CollectionElementIdentifier.src
      • CollectionElementIdentifier.id
      • CollectionElementIdentifier.tags
      • CollectionElementIdentifier.element_identifiers
      • CollectionElementIdentifier.collection_type
    • CreateHistoryContentFromStore
      • CreateHistoryContentFromStore.store_content_uri
      • CreateHistoryContentFromStore.store_dict
      • CreateHistoryContentFromStore.model_store_format
    • CreateHistoryContentPayloadFromCollection
      • CreateHistoryContentPayloadFromCollection.dbkey
      • CreateHistoryContentPayloadFromCollection.copy_elements
    • CreateHistoryContentPayload
      • CreateHistoryContentPayload.Config
      • CreateHistoryContentPayload.dbkey
      • CreateHistoryContentPayload.copy_elements
      • CreateHistoryContentPayload.source
      • CreateHistoryContentPayload.content
      • CreateHistoryContentPayload.type
    • HistoriesContentsService
      • HistoriesContentsService.__init__()
      • HistoriesContentsService.index()
      • HistoriesContentsService.show()
      • HistoriesContentsService.prepare_store_download()
      • HistoriesContentsService.write_store()
      • HistoriesContentsService.index_jobs_summary()
      • HistoriesContentsService.show_jobs_summary()
      • HistoriesContentsService.get_dataset_collection_archive_for_download()
      • HistoriesContentsService.prepare_collection_download()
      • HistoriesContentsService.create()
      • HistoriesContentsService.create_from_store()
      • HistoriesContentsService.materialize()
      • HistoriesContentsService.update_permissions()
      • HistoriesContentsService.update()
      • HistoriesContentsService.update_batch()
      • HistoriesContentsService.bulk_operation()
      • HistoriesContentsService.validate()
      • HistoriesContentsService.delete()
      • HistoriesContentsService.archive()
    • ItemOperation
      • ItemOperation.__init__()
    • HistoryItemOperator
      • HistoryItemOperator.__init__()
      • HistoryItemOperator.apply()
  • galaxy.webapps.galaxy.services.invocations module
    • InvocationSerializationView
      • InvocationSerializationView.element
      • InvocationSerializationView.collection
    • InvocationSerializationParams
      • InvocationSerializationParams.view
      • InvocationSerializationParams.step_details
      • InvocationSerializationParams.legacy_job_state
    • InvocationIndexPayload
      • InvocationIndexPayload.instance
    • PrepareStoreDownloadPayload
      • PrepareStoreDownloadPayload.model_store_format
      • PrepareStoreDownloadPayload.include_files
      • PrepareStoreDownloadPayload.include_deleted
      • PrepareStoreDownloadPayload.include_hidden
    • WriteInvocationStoreToPayload
      • WriteInvocationStoreToPayload.target_uri
      • WriteInvocationStoreToPayload.model_store_format
      • WriteInvocationStoreToPayload.include_files
      • WriteInvocationStoreToPayload.include_deleted
      • WriteInvocationStoreToPayload.include_hidden
    • InvocationsService
      • InvocationsService.__init__()
      • InvocationsService.index()
      • InvocationsService.prepare_store_download()
      • InvocationsService.write_store()
      • InvocationsService.serialize_workflow_invocation()
      • InvocationsService.serialize_workflow_invocations()
      • InvocationsService.deprecated_generate_invocation_bco()
  • galaxy.webapps.galaxy.services.jobs module
    • JobIndexViewEnum
      • JobIndexViewEnum.collection
      • JobIndexViewEnum.admin_job_list
    • JobIndexPayload
      • JobIndexPayload.view
    • JobsService
      • JobsService.__init__()
      • JobsService.job_manager
      • JobsService.job_search
      • JobsService.hda_manager
      • JobsService.show()
      • JobsService.index()
  • galaxy.webapps.galaxy.services.libraries module
    • LibrariesService
      • LibrariesService.__init__()
      • LibrariesService.index()
      • LibrariesService.show()
      • LibrariesService.create()
      • LibrariesService.create_from_store()
      • LibrariesService.update()
      • LibrariesService.delete()
      • LibrariesService.get_permissions()
      • LibrariesService.set_permissions()
      • LibrariesService.set_permissions_old()
  • galaxy.webapps.galaxy.services.library_folder_contents module
    • UserFolderPermissions
      • UserFolderPermissions.access
      • UserFolderPermissions.modify
      • UserFolderPermissions.add
      • UserFolderPermissions.manage
      • UserFolderPermissions.__init__()
    • LibraryFolderContentsService
      • LibraryFolderContentsService.__init__()
      • LibraryFolderContentsService.get_object()
      • LibraryFolderContentsService.index()
      • LibraryFolderContentsService.create()
  • galaxy.webapps.galaxy.services.library_folders module
    • LibraryFoldersService
      • LibraryFoldersService.__init__()
      • LibraryFoldersService.show()
      • LibraryFoldersService.create()
      • LibraryFoldersService.get_permissions()
      • LibraryFoldersService.set_permissions()
      • LibraryFoldersService.delete()
      • LibraryFoldersService.update()
  • galaxy.webapps.galaxy.services.pages module
    • PagesService
      • PagesService.__init__()
      • PagesService.index()
      • PagesService.create()
      • PagesService.delete()
      • PagesService.show()
      • PagesService.show_pdf()
      • PagesService.prepare_pdf()
  • galaxy.webapps.galaxy.services.quotas module
    • QuotasService
      • QuotasService.__init__()
      • QuotasService.index()
      • QuotasService.show()
      • QuotasService.create()
      • QuotasService.update()
      • QuotasService.delete()
      • QuotasService.undelete()
      • QuotasService.validate_in_users_and_groups()
  • galaxy.webapps.galaxy.services.sharable module
    • ShareableService
      • ShareableService.__init__()
      • ShareableService.set_slug()
      • ShareableService.sharing()
      • ShareableService.enable_link_access()
      • ShareableService.disable_link_access()
      • ShareableService.publish()
      • ShareableService.unpublish()
      • ShareableService.share_with_users()
  • galaxy.webapps.galaxy.services.tools module
    • ToolsService
      • ToolsService.__init__()
      • ToolsService.create_fetch()
  • galaxy.webapps.galaxy.services.users module
    • UsersService
      • UsersService.__init__()
      • UsersService.recalculate_disk_usage()
      • UsersService.get_api_key()
      • UsersService.get_or_create_api_key()
      • UsersService.create_api_key()
      • UsersService.delete_api_key()
  • galaxy.webapps.galaxy.services.visualizations module
    • VisualizationsService
      • VisualizationsService.__init__()
  • galaxy.webapps.galaxy.services.workflows module
    • WorkflowIndexPayload
      • WorkflowIndexPayload.missing_tools
    • WorkflowsService
      • WorkflowsService.__init__()
      • WorkflowsService.index()
      • WorkflowsService.delete()
      • WorkflowsService.undelete()
      • WorkflowsService.get_versions()
      • WorkflowsService.get_workflow_menu()

Submodules

galaxy.webapps.galaxy.buildapp module

Provides factory methods to assemble the Galaxy web application

class galaxy.webapps.galaxy.buildapp.GalaxyWebApplication(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: Optional[str] = None)

Bases: WebApplication

injection_aware: bool = True

galaxy.webapps.galaxy.buildapp.app_factory(*args, **kwargs)

Return a wsgi application serving the root object

galaxy.webapps.galaxy.buildapp.app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs)

Return a wsgi application serving the root object and the Galaxy application.

When creating an app for asgi, set wsgi_preflight to False to allow FastAPI middleware to handle CORS options, etc..

galaxy.webapps.galaxy.buildapp.postfork_setup()

galaxy.webapps.galaxy.buildapp.populate_api_routes(webapp, app)

galaxy.webapps.galaxy.buildapp.wrap_in_middleware(app, global_conf, application_stack, **local_conf)

Based on the configuration wrap app in a set of common and useful middleware.

galaxy.webapps.galaxy.fast_app module

galaxy.webapps.galaxy.fast_app.add_galaxy_middleware(app: FastAPI, gx_app)

galaxy.webapps.galaxy.fast_app.initialize_fast_app(gx_wsgi_webapp, gx_app)

galaxy.webapps.galaxy.fast_factory module

Module containing factory class for building uvicorn app for Galaxy.

Information on uvicorn, its various settings, and how to invoke it can be found at https://www.uvicorn.org/.

Galaxy can be launched with uvicorn using the following invocation:

uvicorn --app-dir lib --factory galaxy.webapps.galaxy.fast_factory:factory

Use the environment variable GALAXY_CONFIG_FILE to specify a Galaxy configuration file. Galaxy configuration can be loading from a YAML or an .ini file (reads app:main currently but can be overridden with GALAXY_CONFIG_SECTION).

GALAXY_CONFIG_FILE=config/galaxy.yml uvicorn --app-dir lib --factory galaxy.webapps.galaxy.fast_factory:factory

Note

Information on additional ways to configure uvicorn can be found at https://www.uvicorn.org/.

Warning

If an ini file is supplied via GALAXY_CONFIG_FILE, the server properties such as host and port are not read from the file like older forms of configuring Galaxy.

Gunicorn is a server with more complex management options.

This factory function can be executed as a uvicorn worker managed with gunicorn with the following command-line.

gunicorn 'galaxy.webapps.galaxy.fast_factory:factory()' --env GALAXY_CONFIG_FILE=config/galaxy.ini --pythonpath lib -w 4 -k uvicorn.workers.UvicornWorker --config lib/galaxy/web_stack/gunicorn_config.py

galaxy.webapps.galaxy.fast_factory.factory()

galaxy.webapps.galaxy.workers module