tool_shed.webapp package
The Galaxy Tool Shed application.
- tool_shed.webapp.url_for(*args, **kwargs) str
Tries to resolve the URL using the routes module.
This only works in a WSGI app so a deprecation message is returned when running an ASGI app.
- tool_shed.webapp.expose(func)[source]
Decorator: mark a function as ‘exposed’ and thus web accessible
Subpackages
- tool_shed.webapp.api package
BaseShedAPIController
- Submodules
- tool_shed.webapp.api.authenticate module
- tool_shed.webapp.api.categories module
- tool_shed.webapp.api.configuration module
- tool_shed.webapp.api.groups module
- tool_shed.webapp.api.repositories module
RepositoriesController
RepositoriesController.add_repository_registry_entry()
RepositoriesController.get_ordered_installable_revisions()
RepositoriesController.get_repository_revision_install_info()
RepositoriesController.get_installable_revisions()
RepositoriesController.index()
RepositoriesController.remove_repository_registry_entry()
RepositoriesController.reset_metadata_on_repositories()
RepositoriesController.reset_metadata_on_repository()
RepositoriesController.show()
RepositoriesController.updates()
RepositoriesController.show_tools()
RepositoriesController.metadata()
RepositoriesController.update()
RepositoriesController.create()
RepositoriesController.create_changeset_revision()
RepositoriesController.app
- tool_shed.webapp.api.repository_revisions module
- tool_shed.webapp.api.tools module
- tool_shed.webapp.api.users module
- tool_shed.webapp.controllers package
- Submodules
- tool_shed.webapp.controllers.admin module
AdminController
AdminController.user_list_grid
AdminController.role_list_grid
AdminController.group_list_grid
AdminController.manage_category_grid
AdminController.repository_grid
AdminController.repository_metadata_grid
AdminController.delete_operation
AdminController.undelete_operation
AdminController.purge_operation
AdminController.browse_repositories()
AdminController.browse_repository_metadata()
AdminController.create_category()
AdminController.delete_repository()
AdminController.delete_repository_metadata()
AdminController.edit_category()
AdminController.manage_categories()
AdminController.regenerate_statistics()
AdminController.manage_role_associations()
AdminController.reset_metadata_on_selected_repositories_in_tool_shed()
AdminController.undelete_repository()
AdminController.mark_category_deleted()
AdminController.purge_category()
AdminController.undelete_category()
- tool_shed.webapp.controllers.groups module
- tool_shed.webapp.controllers.hg module
- tool_shed.webapp.controllers.repository module
get_mercurial_default_options_dict()
RepositoryController
RepositoryController.category_grid
RepositoryController.datatypes_grid
RepositoryController.deprecated_repositories_i_own_grid
RepositoryController.email_alerts_repository_grid
RepositoryController.docker_image_grid
RepositoryController.install_matched_repository_grid
RepositoryController.matched_repository_grid
RepositoryController.my_writable_repositories_grid
RepositoryController.my_writable_repositories_missing_tool_test_components_grid
RepositoryController.my_writable_repositories_with_invalid_tools_grid
RepositoryController.repositories_by_user_grid
RepositoryController.repositories_i_own_grid
RepositoryController.repositories_i_can_administer_grid
RepositoryController.repositories_in_category_grid
RepositoryController.repositories_missing_tool_test_components_grid
RepositoryController.repositories_with_invalid_tools_grid
RepositoryController.repository_dependencies_grid
RepositoryController.repository_grid
RepositoryController.repository_metadata_grid
RepositoryController.tool_dependencies_grid
RepositoryController.tools_grid
RepositoryController.valid_category_grid
RepositoryController.valid_repository_grid
RepositoryController.browse_categories()
RepositoryController.browse_datatypes()
RepositoryController.browse_deprecated_repositories_i_own()
RepositoryController.browse_my_writable_repositories()
RepositoryController.browse_my_writable_repositories_missing_tool_test_components()
RepositoryController.browse_my_writable_repositories_with_invalid_tools()
RepositoryController.browse_repositories()
RepositoryController.browse_repositories_by_user()
RepositoryController.browse_repositories_i_can_administer()
RepositoryController.browse_repositories_i_own()
RepositoryController.browse_repositories_in_category()
RepositoryController.browse_repositories_missing_tool_test_components()
RepositoryController.browse_repositories_with_invalid_tools()
RepositoryController.browse_repository()
RepositoryController.browse_repository_dependencies()
RepositoryController.browse_tools()
RepositoryController.browse_tool_dependencies()
RepositoryController.browse_valid_categories()
RepositoryController.browse_valid_repositories()
RepositoryController.create_galaxy_docker_image()
RepositoryController.create_repository()
RepositoryController.deprecate()
RepositoryController.display_image_in_repository()
RepositoryController.display_tool()
RepositoryController.download()
RepositoryController.export_via_api()
RepositoryController.find_tools()
RepositoryController.get_changeset_revision_and_ctx_rev()
RepositoryController.get_ctx_rev()
RepositoryController.get_file_contents()
RepositoryController.get_latest_downloadable_changeset_revision()
RepositoryController.get_readme_files()
RepositoryController.get_repository_dependencies()
RepositoryController.get_repository_id()
RepositoryController.get_repository_information()
RepositoryController.get_repository_type()
RepositoryController.get_required_repo_info_dict()
RepositoryController.get_tool_dependencies()
RepositoryController.get_tool_dependencies_config_contents()
RepositoryController.get_tool_dependency_definition_metadata()
RepositoryController.get_tool_versions()
RepositoryController.get_updated_repository_information()
RepositoryController.help()
RepositoryController.index()
RepositoryController.load_invalid_tool()
RepositoryController.manage_email_alerts()
RepositoryController.manage_repository()
RepositoryController.manage_repository_admins()
RepositoryController.multi_select_email_alerts()
RepositoryController.next_installable_changeset_revision()
RepositoryController.open_folder()
RepositoryController.preview_tools_in_changeset()
RepositoryController.previous_changeset_revisions()
RepositoryController.rate_repository()
RepositoryController.reset_all_metadata()
RepositoryController.reset_metadata_on_my_writable_repositories_in_tool_shed()
RepositoryController.set_email_alerts()
RepositoryController.set_malicious()
RepositoryController.sharable_owner()
RepositoryController.sharable_repository()
RepositoryController.sharable_repository_revision()
RepositoryController.updated_changeset_revisions()
RepositoryController.view_changelog()
RepositoryController.view_changeset()
RepositoryController.view_or_manage_repository()
RepositoryController.view_repository()
RepositoryController.view_tool_metadata()
RepositoryController.validate_changeset_revision()
get_first_repository_metadata()
get_current_repositories()
get_current_email_alert_repositories()
- tool_shed.webapp.controllers.repository_review module
- tool_shed.webapp.controllers.upload module
- tool_shed.webapp.controllers.user module
- tool_shed.webapp.framework package
- tool_shed.webapp.model package
now()
Base
APIKeys
User
User.id
User.create_time
User.update_time
User.username
User.active_repositories
User.galaxy_sessions
User.api_keys
User.reset_tokens
User.groups
User.dict_collection_visible_keys
User.dict_element_visible_keys
User.bootstrap_admin_user
User.roles
User.non_private_roles
User.__init__()
User.email
User.password
User.external
User.deleted
User.purged
User.new_repo_alert
User.current_galaxy_session
User.all_roles()
User.check_password()
User.get_disk_usage()
User.nice_total_disk_usage
User.set_disk_usage()
User.total_disk_usage
User.set_password_cleartext()
User.set_random_password()
User.table
PasswordResetToken
Group
Role
UserGroupAssociation
UserRoleAssociation
GroupRoleAssociation
RepositoryRoleAssociation
RepositoryRoleAssociation.id
RepositoryRoleAssociation.repository_id
RepositoryRoleAssociation.role_id
RepositoryRoleAssociation.create_time
RepositoryRoleAssociation.update_time
RepositoryRoleAssociation.__init__()
RepositoryRoleAssociation.repository
RepositoryRoleAssociation.role
RepositoryRoleAssociation.table
GalaxySession
GalaxySession.id
GalaxySession.create_time
GalaxySession.update_time
GalaxySession.user_id
GalaxySession.remote_host
GalaxySession.remote_addr
GalaxySession.referer
GalaxySession.session_key
GalaxySession.prev_session_id
GalaxySession.user
GalaxySession.__init__()
GalaxySession.is_valid
GalaxySession.last_action
GalaxySession.table
Repository
Repository.id
Repository.create_time
Repository.update_time
Repository.type
Repository.remote_repository_url
Repository.homepage_url
Repository.description
Repository.long_description
Repository.user_id
Repository.deleted
Repository.email_alerts
Repository.categories
Repository.ratings
Repository.downloadable_revisions
Repository.metadata_revisions
Repository.roles
Repository.dict_collection_visible_keys
Repository.dict_element_visible_keys
Repository.file_states
Repository.__init__()
Repository.private
Repository.times_downloaded
Repository.deprecated
Repository.name
Repository.user
Repository.hg_repo
Repository.admin_role
Repository.allow_push()
Repository.can_change_type()
Repository.can_change_type_to()
Repository.get_changesets_for_setting_metadata()
Repository.get_repository_dependencies()
Repository.get_type_class()
Repository.get_tool_dependencies()
Repository.installable_revisions()
Repository.is_new()
Repository.repo_path()
Repository.revision()
Repository.set_allow_push()
Repository.tip()
Repository.to_dict()
Repository.table
ItemRatingAssociation
RepositoryRatingAssociation
RepositoryRatingAssociation.id
RepositoryRatingAssociation.create_time
RepositoryRatingAssociation.update_time
RepositoryRatingAssociation.repository_id
RepositoryRatingAssociation.user_id
RepositoryRatingAssociation.rating
RepositoryRatingAssociation.comment
RepositoryRatingAssociation.repository
RepositoryRatingAssociation.user
RepositoryRatingAssociation.set_item()
RepositoryRatingAssociation.__init__()
RepositoryRatingAssociation.table
Category
RepositoryCategoryAssociation
Tag
RepositoryMetadata
RepositoryMetadata.create_time
RepositoryMetadata.repository
RepositoryMetadata.update_time
RepositoryMetadata.table
RepositoryMetadata.dict_collection_visible_keys
RepositoryMetadata.dict_element_visible_keys
RepositoryMetadata.__init__()
RepositoryMetadata.id
RepositoryMetadata.repository_id
RepositoryMetadata.numeric_revision
RepositoryMetadata.changeset_revision
RepositoryMetadata.metadata
RepositoryMetadata.tool_versions
RepositoryMetadata.malicious
RepositoryMetadata.downloadable
RepositoryMetadata.missing_test_components
RepositoryMetadata.has_repository_dependencies
RepositoryMetadata.includes_datatypes
RepositoryMetadata.includes_tools
RepositoryMetadata.includes_tool_dependencies
RepositoryMetadata.includes_workflows
RepositoryMetadata.includes_tools_for_display_in_tool_panel
RepositoryMetadata.repository_dependencies
sort_by_attr()
- Subpackages
- Submodules
- tool_shed.webapp.model.mapping module
- tool_shed.webapp.search package
- tool_shed.webapp.security package
Action
RBACAgent
RBACAgent.permitted_actions
RBACAgent.associate_components()
RBACAgent.associate_user_role()
RBACAgent.convert_permitted_action_strings()
RBACAgent.create_user_role()
RBACAgent.create_private_user_role()
RBACAgent.get_action()
RBACAgent.get_actions()
RBACAgent.get_item_actions()
RBACAgent.get_private_user_role()
CommunityRBACAgent
CommunityRBACAgent.__init__()
CommunityRBACAgent.sa_session
CommunityRBACAgent.allow_action()
CommunityRBACAgent.associate_components()
CommunityRBACAgent.associate_group_role()
CommunityRBACAgent.associate_user_group()
CommunityRBACAgent.associate_user_role()
CommunityRBACAgent.associate_repository_category()
CommunityRBACAgent.create_private_user_role()
CommunityRBACAgent.create_user_role()
CommunityRBACAgent.get_item_actions()
CommunityRBACAgent.get_private_user_role()
CommunityRBACAgent.set_entity_group_associations()
CommunityRBACAgent.set_entity_role_associations()
CommunityRBACAgent.set_entity_user_associations()
CommunityRBACAgent.usernames_that_can_push()
CommunityRBACAgent.can_push()
CommunityRBACAgent.user_can_administer_repository()
CommunityRBACAgent.user_can_import_repository_archive()
get_permitted_actions()
get_iuc_group()
- tool_shed.webapp.util package
Submodules
tool_shed.webapp.app module
- class tool_shed.webapp.app.UniverseApplication(**kwd)[source]
Bases:
ToolShedApp
,SentryClientMixin
,HaltableContainer
Encapsulates the state of a Universe application
- repository_types_registry: RepositoryTypesRegistry
- security_agent: CommunityRBACAgent
- hgweb_config_manager: HgWebConfigManager
- repository_registry: RepositoryRegistry
tool_shed.webapp.buildapp module
Provides factory methods to assemble the Galaxy web application
- class tool_shed.webapp.buildapp.ToolShedGalaxyWebTransaction(environ: Dict[str, Any], app: BasicSharedApp, webapp: WebApplication, session_cookie: str | None = None)[source]
Bases:
GalaxyWebTransaction
- class tool_shed.webapp.buildapp.CommunityWebApplication(galaxy_app: MinimalApp, session_cookie: str = 'galaxysession', name: str | None = None)[source]
Bases:
WebApplication
- transaction_chooser(environ, galaxy_app: BasicSharedApp, session_cookie: str)[source]
- tool_shed.webapp.buildapp.add_ui_controllers(webapp, app)[source]
Search for controllers in the ‘galaxy.webapps.controllers’ module and add them to the webapp.
- tool_shed.webapp.buildapp.app_factory(*args, **kwargs)[source]
Return a wsgi application serving the root object
tool_shed.webapp.config module
Universe configuration builder.
- class tool_shed.webapp.config.ToolShedAppConfiguration(**kwargs)[source]
Bases:
BaseAppConfiguration
,CommonConfigurationMixin
- default_config_file_name = 'tool_shed.yml'
- property shed_tool_data_path
- tool_shed.webapp.config.Configuration
alias of
ToolShedAppConfiguration
tool_shed.webapp.fast_app module
tool_shed.webapp.fast_factory module
Module containing factory class for building uvicorn app for the Galaxy Tool Shed.
Information on uvicorn, its various settings, and how to invoke it can be found at https://www.uvicorn.org/.
The Galaxy Tool Shed can be launched with uvicorn using the following invocation:
uvicorn --app-dir lib --factory tool_shed.webapp.fast_factory:factory
Use the environment variable TOOL_SHED_CONFIG_FILE
to specify a Tool Shed
configuration file.
TOOL_SHED_CONFIG_FILE=config/tool_shed.yml uvicorn --app-dir lib --factory tool_shed.webapp.fast_factory:factory
Note
Information on additional ways to configure uvicorn can be found at https://www.uvicorn.org/.
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 'tool_shed.webapp.fast_factory:factory()' --env TOOL_SHED_CONFIG_FILE=config/tool_shed.yml --pythonpath lib -w 4 -k uvicorn.workers.UvicornWorker --config lib/galaxy/web_stack/gunicorn_config.py