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galaxy.webapps.galaxy.controllers package
Galaxy web controllers.
Submodules
galaxy.webapps.galaxy.controllers.admin module
- class galaxy.webapps.galaxy.controllers.admin.UserListGrid[source]
Bases:
GridData
- class StatusColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class RolesColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class LastLoginColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class DiskUsageColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- title = 'Users'
- title_id = 'users-grid'
- default_sort_key = 'email'
- columns: List[GridColumn] = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.DiskUsageColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
- class galaxy.webapps.galaxy.controllers.admin.RoleListGrid[source]
Bases:
GridData
- class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- title = 'Roles'
- title_id = 'roles-grid'
- default_sort_key = 'name'
- columns: List[GridColumn] = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
- class galaxy.webapps.galaxy.controllers.admin.GroupListGrid[source]
Bases:
GridData
- class RolesColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- title = 'Groups'
- title_id = 'groups-grid'
- default_sort_key = 'name'
- columns: List[GridColumn] = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
- class galaxy.webapps.galaxy.controllers.admin.QuotaListGrid[source]
Bases:
GridData
- class AmountColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class DefaultTypeColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- title = 'Quotas'
- default_sort_key = 'name'
- columns: List[GridColumn] = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.AmountColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.GroupsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DefaultTypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
- class galaxy.webapps.galaxy.controllers.admin.AdminGalaxy(app: StructuredApp)[source]
Bases:
JSAppLauncher
- user_list_grid = <galaxy.webapps.galaxy.controllers.admin.UserListGrid object>
- role_list_grid = <galaxy.webapps.galaxy.controllers.admin.RoleListGrid object>
- group_list_grid = <galaxy.webapps.galaxy.controllers.admin.GroupListGrid object>
- quota_list_grid = <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid object>
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- data_types_list(trans, **kwd) DatatypesEntryT [source]
- galaxy.webapps.galaxy.controllers.admin.get_user(trans, user_id)[source]
Get a User from the database by id.
- galaxy.webapps.galaxy.controllers.admin.get_role(trans, id)[source]
Get a Role from the database by id.
galaxy.webapps.galaxy.controllers.admin_toolshed module
- class galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed(app: StructuredApp)[source]
Bases:
AdminGalaxy
- activate_repository(trans, **kwd)[source]
Activate a repository that was deactivated but not uninstalled.
- display_image_in_repository(trans, **kwd)[source]
Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. .. image:: https://raw.github.com/galaxy/some_image.png .. image:: $PATH_TO_IMAGES/some_image.png .. image:: /static/images/some_image.gif .. image:: some_image.jpg .. image:: /deep/some_image.png
- quota_manager: QuotaManager
galaxy.webapps.galaxy.controllers.async module
Controller to handle communication of tools of type data_source_async
galaxy.webapps.galaxy.controllers.authnz module
OAuth 2.0 and OpenID Connect Authentication and Authorization Controller.
- class galaxy.webapps.galaxy.controllers.authnz.OIDC(app)[source]
Bases:
JSAppLauncher
- index(trans, **kwargs)[source]
- GET /authnz/
returns a list of third-party identities associated with the user.
- Parameters:
trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction.
kwargs – empty dict
- Return type:
list of dicts
- Returns:
a list of third-party identities associated with the user account.
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
- class galaxy.webapps.galaxy.controllers.forms.FormsGrid[source]
Bases:
GridData
- class NameColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class DescriptionColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- class TypeColumn(label, key=None, model_class=None, method=None, format=None, escape=True)[source]
Bases:
GridColumn
- title = 'Forms'
- model_class
alias of
FormDefinitionCurrent
- default_sort_key = 'update_time'
- columns: List[GridColumn] = [<galaxy.webapps.galaxy.controllers.forms.FormsGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.forms.FormsGrid.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.forms.FormsGrid.TypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
- class galaxy.webapps.galaxy.controllers.forms.Forms(app)[source]
Bases:
BaseUIController
- forms_grid = <galaxy.webapps.galaxy.controllers.forms.FormsGrid object>
galaxy.webapps.galaxy.controllers.history module
- class galaxy.webapps.galaxy.controllers.history.HistoryController(app: StructuredApp)[source]
Bases:
BaseUIController
,SharableMixin
,UsesAnnotations
,UsesItemRatings
- history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)
- history_serializer: HistorySerializer = GalaxyTypeDepends(_do_resolve)
- slug_builder: SlugBuilder = GalaxyTypeDepends(_do_resolve)
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- view(trans, id=None, show_deleted=False, show_hidden=False, use_panels=True)[source]
View a history. If a history is importable, then it is viewable by any user.
- display_by_username_and_slug(trans, username, slug, **kwargs)[source]
Display history based on a username and slug.
- make_private(trans, history_id=None, all_histories=False, **kwd)[source]
Sets the datasets within a history to private. Also sets the default permissions for the history to private, for future datasets.
- resume_paused_jobs(trans, current=False, ids=None, **kwargs)[source]
Resume paused jobs for the active history – this does not require a logged in user.
- switch_to_history(trans, hist_id=None, **kwargs)[source]
Change the current user’s current history to one with hist_id.
- set_as_current(trans, id, **kwargs)[source]
Change the current user’s current history to one with id.
galaxy.webapps.galaxy.controllers.library module
galaxy.webapps.galaxy.controllers.page module
- class galaxy.webapps.galaxy.controllers.page.PageController(app: StructuredApp)[source]
Bases:
BaseUIController
,SharableMixin
,UsesStoredWorkflowMixin
,UsesVisualizationMixin
,UsesItemRatings
- page_manager: PageManager = GalaxyTypeDepends(_do_resolve)
- history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)
- history_serializer: HistorySerializer = GalaxyTypeDepends(_do_resolve)
- hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)
- workflow_manager: WorkflowsManager = GalaxyTypeDepends(_do_resolve)
- slug_builder: SlugBuilder = GalaxyTypeDepends(_do_resolve)
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
galaxy.webapps.galaxy.controllers.root module
Contains the main interface in the Universe class
- class galaxy.webapps.galaxy.controllers.root.RootController(app: StructuredApp)[source]
Bases:
JSAppLauncher
,UsesAnnotations
Controller class that maps to the url root of Galaxy (i.e. ‘/’).
- history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- default(trans, target1=None, target2=None, **kwd)[source]
Called on any url that does not match a controller method.
- index(trans: GalaxyWebTransaction, tool_id=None, workflow_id=None, history_id=None, m_c=None, m_a=None, **kwd)[source]
Root and entry point for client-side web app.
- Parameters:
tool_id (str or None) – load center panel with given tool if not None
workflow_id (encoded id or None) – load center panel with given workflow if not None
history_id (encoded id or None) – switch current history to given history if not None
m_c (str or None) – controller name (e.g. ‘user’)
m_a (str or None) – controller method/action (e.g. ‘dbkeys’)
If m_c and m_a are present, the center panel will be loaded using the controller and action as a url: (e.g. ‘user/dbkeys’).
- login(trans: GalaxyWebTransaction, redirect=None, is_logout_redirect=False, **kwd)[source]
User login path for client-side.
- display_as(trans: GalaxyWebTransaction, id=None, display_app=None, **kwd)[source]
Returns a file in a format that can successfully be displayed in display_app; if the file could not be returned, returns a message as a string.
- welcome(trans: GalaxyWebTransaction, **kwargs)[source]
galaxy.webapps.galaxy.controllers.shed_tool_static module
- class galaxy.webapps.galaxy.controllers.shed_tool_static.ShedToolStatic(app)[source]
Bases:
BaseUIController
- index(trans, shed, owner, repo, tool, version, image_file, **kwargs)[source]
Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. .. image:: https://raw.github.com/galaxy/some_image.png .. image:: $PATH_TO_IMAGES/some_image.png .. image:: /static/images/some_image.gif .. image:: some_image.jpg .. image:: /deep/some_image.png
galaxy.webapps.galaxy.controllers.tag module
Tags Controller: handles tagging/untagging of entities and provides autocomplete support.
- class galaxy.webapps.galaxy.controllers.tag.TagsController(app)[source]
Bases:
BaseUIController
,UsesTagsMixin
- add_tag_async(trans, item_id=None, item_class=None, new_tag=None, context=None, **kwargs)[source]
Add tag to an item.
galaxy.webapps.galaxy.controllers.tool_runner module
Controller handles external tool related requests
- class galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner(app)[source]
Bases:
BaseUIController
- rerun(trans, id=None, job_id=None, **kwd)[source]
Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in.
- data_source_redirect(trans, tool_id=None)[source]
Redirects a user accessing a Data Source tool to its target action link. This method will subvert mix-mode content blocking in several browsers when accessing non-https data_source tools from an https galaxy server.
Tested as working on Safari 7.0 and FireFox 26 Subverting did not work on Chrome 31
galaxy.webapps.galaxy.controllers.user module
Contains the user interface in the Universe class
- class galaxy.webapps.galaxy.controllers.user.User(app: StructuredApp)[source]
Bases:
BaseUIController
,UsesFormDefinitionsMixin
- user_manager: UserManager = GalaxyTypeDepends(_do_resolve)
- installed_len_files = None
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- resend_verification(trans, **kwargs)[source]
Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.
- resend_activation_email(trans, email, username)[source]
Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link.
- is_outside_grace_period(trans, create_time)[source]
Function checks whether the user is outside the config-defined grace period for inactive accounts.
- activate(trans, **kwd)[source]
Check whether token fits the user and then activate the user’s account.
- change_password(trans, payload=None, **kwd)[source]
Allows to change own password.
- Parameters:
payload (dict) – dictionary structure containing: * id: encoded user id * current: current user password * token: temporary token to change password (instead of id and current) * password: new password * confirm: new password (confirmation)
galaxy.webapps.galaxy.controllers.visualization module
- class galaxy.webapps.galaxy.controllers.visualization.VisualizationController(app: StructuredApp)[source]
Bases:
BaseUIController
,SharableMixin
,UsesVisualizationMixin
,UsesAnnotations
,UsesItemRatings
- hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)
- slug_builder: SlugBuilder = GalaxyTypeDepends(_do_resolve)
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- display_by_username_and_slug(trans, username, slug, **kwargs)[source]
Display visualization based on a username and slug.
- save(trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None, **kwargs)[source]
Save a visualization; if visualization does not have an ID, a new visualization is created. Returns JSON of visualization.
- render(trans, visualization_name, embedded=None, **kwargs)[source]
Render the appropriate visualization template, parsing the kwargs into appropriate variables and resources (such as ORM models) based on this visualizations param data in visualizations_conf.xml.
URL: /visualization/show/{visualization_name}
galaxy.webapps.galaxy.controllers.workflow module
- class galaxy.webapps.galaxy.controllers.workflow.WorkflowController(app: StructuredApp)[source]
Bases:
BaseUIController
,SharableMixin
,UsesStoredWorkflowMixin
,UsesItemRatings
- history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)
- slug_builder = <galaxy.managers.sharable.SlugBuilder object>
- __init__(app: StructuredApp)[source]
Initialize an interface for application ‘app’
- display_by_username_and_slug(trans, username, slug, format='html', **kwargs)[source]
Display workflow based on a username and slug. Format can be html, json, or json-download.
- editor(trans, id=None, workflow_id=None, version=None, **kwargs)[source]
Render the main workflow editor interface. The canvas is embedded as an iframe (necessary for scrolling to work properly), which is rendered by editor_canvas.
- load_workflow(trans, id, version=None, **kwargs)[source]
Get the latest Workflow for the StoredWorkflow identified by id and encode it as a json string that can be read by the workflow editor web interface.
- for_direct_import(trans, id, **kwargs)[source]
Get the latest Workflow for the StoredWorkflow identified by id and encode it as a json string that can be imported back into Galaxy
This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state.
- export_to_file(trans, id)[source]
Get the latest Workflow for the StoredWorkflow identified by id and export it to a JSON file that can be imported back into Galaxy.
This has slightly different information than the above. In particular, it does not attempt to decode forms and build UIs, it just stores the raw state.