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()
get_required_user()
UrlBuilder
GalaxyASGIRequest
GalaxyASGIResponse
get_current_history_from_session()
fix_url_for()
get_trans()
get_admin_user()
BaseGalaxyAPIController
RestVerb
FrameworkRouter
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.encode_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
- galaxy.webapps.galaxy.api.datasets module
- 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
- galaxy.webapps.galaxy.api.history_contents module
- 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
- 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.undelete()
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
get_files()
FetchTools
ToolsController
ToolsController.history_manager
ToolsController.hda_manager
ToolsController.hdca_manager
ToolsController.service
ToolsController.index()
ToolsController.panel_views()
ToolsController.panel_view()
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.recalculate_disk_usage_by_user_id()
FastAPIUsers.index_deleted()
FastAPIUsers.undelete()
FastAPIUsers.show_deleted()
FastAPIUsers.get_or_create_api_key()
FastAPIUsers.get_api_key()
FastAPIUsers.create_api_key()
FastAPIUsers.delete_api_key()
FastAPIUsers.usage()
FastAPIUsers.objectstore_usage()
FastAPIUsers.usage_for()
FastAPIUsers.get_beacon()
FastAPIUsers.set_beacon()
FastAPIUsers.remove_favorite()
FastAPIUsers.set_favorite()
FastAPIUsers.set_theme()
FastAPIUsers.add_custom_builds()
FastAPIUsers.get_custom_builds()
FastAPIUsers.delete_custom_builds()
FastAPIUsers.create()
FastAPIUsers.index()
FastAPIUsers.show()
FastAPIUsers.update()
FastAPIUsers.delete()
FastAPIUsers.send_activation_email()
FastAPIUsers.__init__()
UserAPIController
UserAPIController.service
UserAPIController.user_manager
UserAPIController.get_information()
UserAPIController.set_information()
UserAPIController.get_password()
UserAPIController.set_password()
UserAPIController.get_permissions()
UserAPIController.set_permissions()
UserAPIController.get_toolbox_filters()
UserAPIController.set_toolbox_filters()
- galaxy.webapps.galaxy.api.visualizations module
FastAPIVisualizations
FastAPIVisualizations.service
FastAPIVisualizations.index()
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
- galaxy.webapps.galaxy.controllers package
- Submodules
- galaxy.webapps.galaxy.controllers.admin module
UserListGrid
RoleListGrid
GroupListGrid
QuotaListGrid
DatatypesEntryT
AdminGalaxy
AdminGalaxy.user_list_grid
AdminGalaxy.role_list_grid
AdminGalaxy.group_list_grid
AdminGalaxy.quota_list_grid
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.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
- galaxy.webapps.galaxy.controllers.error module
- galaxy.webapps.galaxy.controllers.forms module
- galaxy.webapps.galaxy.controllers.history module
HistoryController
HistoryController.history_manager
HistoryController.history_serializer
HistoryController.slug_builder
HistoryController.__init__()
HistoryController.index()
HistoryController.view()
HistoryController.display_by_username_and_slug()
HistoryController.permissions()
HistoryController.make_private()
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
PageController
PageController.page_manager
PageController.history_manager
PageController.history_serializer
PageController.hda_manager
PageController.workflow_manager
PageController.slug_builder
PageController.__init__()
PageController.create()
PageController.edit()
PageController.display()
PageController.display_by_username_and_slug()
PageController.get_page()
- 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.visualization module
VisualizationController
VisualizationController.hda_manager
VisualizationController.slug_builder
VisualizationController.__init__()
VisualizationController.copy()
VisualizationController.imp()
VisualizationController.display_by_username_and_slug()
VisualizationController.save()
VisualizationController.edit()
VisualizationController.render()
VisualizationController.saved()
VisualizationController.trackster()
- galaxy.webapps.galaxy.controllers.workflow module
WorkflowController
WorkflowController.history_manager
WorkflowController.slug_builder
WorkflowController.__init__()
WorkflowController.display_by_username_and_slug()
WorkflowController.imp()
WorkflowController.gen_image()
WorkflowController.editor()
WorkflowController.load_workflow()
WorkflowController.for_direct_import()
WorkflowController.export_to_file()
WorkflowController.build_from_current_history()
- 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
- galaxy.webapps.galaxy.services.datasets module
- galaxy.webapps.galaxy.services.histories module
ShareableHistoryService
HistoriesService
HistoriesService.__init__()
HistoriesService.index()
HistoriesService.index_query()
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()
get_fasta_hdas_by_history()
- galaxy.webapps.galaxy.services.history_contents module
- 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
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()
UsersService.get_user()
UsersService.get_non_anonymous_user_full()
UsersService.get_user_full()
UsersService.show_user()
UsersService.user_to_detailed_model()
UsersService.get_index()
- 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: str | None = None)[source]
Bases:
WebApplication
- __init__(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None) None [source]
Create a new web application object. To actually connect some controllers use add_controller and add_route. Call finalize_config when all controllers and routes have been added and __call__ to handle a request (WSGI style).
- 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