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galaxy.webapps.galaxy package¶
Subpackages¶
- galaxy.webapps.galaxy.api package
get_app()
get_app_with_request_session()
GalaxyTypeDepends
depends()
get_session_manager()
get_session()
get_api_user()
get_user()
UrlBuilder
GalaxyASGIRequest
GalaxyASGIResponse
get_current_history_from_session()
get_trans()
get_admin_user()
BaseGalaxyAPIController
RestVerb
Router
APIContentTypeRoute
as_form()
try_get_request_body_as_json()
IndexQueryTag
search_query_param()
- Submodules
- galaxy.webapps.galaxy.api.annotations module
- galaxy.webapps.galaxy.api.authenticate module
- galaxy.webapps.galaxy.api.cloud module
- galaxy.webapps.galaxy.api.cloudauthz module
- galaxy.webapps.galaxy.api.common module
- 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.get_structured_content()
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
- galaxy.webapps.galaxy.api.dynamic_tools module
- galaxy.webapps.galaxy.api.extended_metadata module
- galaxy.webapps.galaxy.api.folder_contents module
- galaxy.webapps.galaxy.api.folders module
- galaxy.webapps.galaxy.api.forms module
- galaxy.webapps.galaxy.api.genomes module
- galaxy.webapps.galaxy.api.group_roles module
- galaxy.webapps.galaxy.api.group_users module
- galaxy.webapps.galaxy.api.groups module
- galaxy.webapps.galaxy.api.histories module
DeleteHistoryPayload
CreateHistoryFormData
FastAPIHistories
FastAPIHistories.service
FastAPIHistories.index()
FastAPIHistories.count()
FastAPIHistories.index_deleted()
FastAPIHistories.published()
FastAPIHistories.shared_with_me()
FastAPIHistories.get_archived_histories()
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.archive_history()
FastAPIHistories.restore_archived_history()
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
- galaxy.webapps.galaxy.api.job_files module
- galaxy.webapps.galaxy.api.job_lock module
- galaxy.webapps.galaxy.api.job_ports module
- galaxy.webapps.galaxy.api.jobs module
FastAPIJobs
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
- 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
- galaxy.webapps.galaxy.api.metrics module
- galaxy.webapps.galaxy.api.page_revisions module
- 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
- galaxy.webapps.galaxy.api.provenance module
- galaxy.webapps.galaxy.api.quotas module
- galaxy.webapps.galaxy.api.remote_files module
- galaxy.webapps.galaxy.api.roles module
- galaxy.webapps.galaxy.api.sanitize_allow module
- galaxy.webapps.galaxy.api.search module
- galaxy.webapps.galaxy.api.short_term_storage module
- galaxy.webapps.galaxy.api.tags module
- galaxy.webapps.galaxy.api.tasks module
- galaxy.webapps.galaxy.api.tool_data module
- 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
- 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
- galaxy.webapps.galaxy.api.tools module
FormDataApiRoute
JsonApiRoute
FetchTools
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
- galaxy.webapps.galaxy.api.tours module
- galaxy.webapps.galaxy.api.trs_consumer module
- galaxy.webapps.galaxy.api.trs_search module
- galaxy.webapps.galaxy.api.uploads module
- galaxy.webapps.galaxy.api.users module
FastAPIUsers
FastAPIUsers.service
FastAPIUsers.user_serializer
FastAPIUsers.recalculate_disk_usage()
FastAPIUsers.get_or_create_api_key()
FastAPIUsers.get_api_key()
FastAPIUsers.create_api_key()
FastAPIUsers.delete_api_key()
FastAPIUsers.usage()
FastAPIUsers.usage_for()
FastAPIUsers.get_beacon()
FastAPIUsers.set_beacon()
FastAPIUsers.__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()
get_user_full()
- 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
- galaxy.webapps.galaxy.api.webhooks module
- galaxy.webapps.galaxy.api.workflows module
CreateInvocationFromStore
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
- 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.QuotaSourceLabelColumn
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
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
- galaxy.webapps.galaxy.controllers.async module
- galaxy.webapps.galaxy.controllers.authnz module
- galaxy.webapps.galaxy.controllers.data_manager module
- galaxy.webapps.galaxy.controllers.dataset module
DatasetInterface
DatasetInterface.history_manager
DatasetInterface.hda_manager
DatasetInterface.hda_deserializer
DatasetInterface.service
DatasetInterface.__init__()
DatasetInterface.default()
DatasetInterface.get_metadata_file()
DatasetInterface.display()
DatasetInterface.get_edit()
DatasetInterface.set_edit()
DatasetInterface.imp()
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
- 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
get_form()
- galaxy.webapps.galaxy.controllers.history module
NameColumn
HistoryListGrid
HistoryListGrid.ItemCountColumn
HistoryListGrid.HistoryListNameColumn
HistoryListGrid.StatusColumn
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.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
PageAllPublishedGrid
ItemSelectionGrid
HistorySelectionGrid
HistoryDatasetAssociationSelectionGrid
WorkflowSelectionGrid
PageSelectionGrid
VisualizationSelectionGrid
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.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
- galaxy.webapps.galaxy.controllers.shed_tool_static module
- galaxy.webapps.galaxy.controllers.tag module
- galaxy.webapps.galaxy.controllers.tool_runner module
- galaxy.webapps.galaxy.controllers.user module
- galaxy.webapps.galaxy.controllers.userskeys module
- 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.imp()
VisualizationController.display_by_username_and_slug()
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
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.gen_image()
WorkflowController.create()
WorkflowController.save_workflow_as()
WorkflowController.editor()
WorkflowController.load_workflow()
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
- galaxy.webapps.galaxy.services.base module
ensure_celery_tasks_enabled()
SecurityNotProvidedError
ServiceBase
ServiceBase.__init__()
ServiceBase.security
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
model_store_storage_target()
ServesExportStores
ConsumesModelStores
async_task_summary()
- galaxy.webapps.galaxy.services.dataset_collections module
UpdateCollectionAttributePayload
DatasetCollectionAttributesResult
SuitableConverter
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
DatasetContentType
ConcreteObjectStoreQuotaSourceDetails
DatasetStorageDetails
DatasetStorageDetails.object_store_id
DatasetStorageDetails.name
DatasetStorageDetails.description
DatasetStorageDetails.percent_used
DatasetStorageDetails.dataset_state
DatasetStorageDetails.hashes
DatasetStorageDetails.sources
DatasetStorageDetails.shareable
DatasetStorageDetails.quota
DatasetStorageDetails.badges
DatasetInheritanceChainEntry
DatasetInheritanceChain
ExtraFilesEntryClass
ExtraFileEntry
DatasetTextContentDetails
ConvertedDatasetsMap
DataMode
DataResult
BamDataResult
DeleteDatasetBatchPayload
ComputeDatasetHashPayload
DatasetErrorMessage
DeleteDatasetBatchResult
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()
DatasetsService.get_structured_content()
- 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.count()
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()
HistoriesService.archive_history()
HistoriesService.restore_archived_history()
HistoriesService.get_archived_histories()
- galaxy.webapps.galaxy.services.history_contents module
HistoryContentsIndexParams
LegacyHistoryContentsIndexParams
HistoryContentsIndexJobsSummaryParams
CreateHistoryContentPayloadBase
CreateHistoryContentPayloadFromCopy
CollectionElementIdentifier
CreateHistoryContentFromStore
CreateHistoryContentPayloadFromCollection
CreateHistoryContentPayload
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
HistoryItemOperator
- galaxy.webapps.galaxy.services.invocations module
- galaxy.webapps.galaxy.services.jobs module
- 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
- galaxy.webapps.galaxy.services.library_folders module
- galaxy.webapps.galaxy.services.pages module
- galaxy.webapps.galaxy.services.quotas module
- galaxy.webapps.galaxy.services.sharable module
- galaxy.webapps.galaxy.services.tools module
- galaxy.webapps.galaxy.services.users module
- galaxy.webapps.galaxy.services.visualizations module
- galaxy.webapps.galaxy.services.workflows module
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)[source]¶
Bases:
WebApplication
- galaxy.webapps.galaxy.buildapp.app_factory(*args, **kwargs)[source]¶
Return a wsgi application serving the root object
- galaxy.webapps.galaxy.buildapp.app_pair(global_conf, load_app_kwds=None, wsgi_preflight=True, **kwargs)[source]¶
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.fast_app module¶
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