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galaxy.webapps.base package¶
Submodules¶
galaxy.webapps.base.controller module¶
Contains functionality needed in every web interface
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class
galaxy.webapps.base.controller.
BaseAPIController
(app)[source]¶
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class
galaxy.webapps.base.controller.
BaseController
(app)[source]¶ Bases:
object
Base class for Galaxy web application controllers.
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encode_all_ids
(trans, rval, recursive=False)[source]¶ Encodes all integer values in the dict rval whose keys are ‘id’ or end with ‘_id’
It might be useful to turn this in to a decorator
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get_class
(class_name)[source]¶ Returns the class object that a string denotes. Without this method, we’d have to do eval(<class_name>).
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get_object
(trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None)[source]¶ Convenience method to get a model object with the specified checks.
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class
galaxy.webapps.base.controller.
BaseUIController
(app)[source]¶
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class
galaxy.webapps.base.controller.
CreatesApiKeysMixin
[source]¶ Bases:
object
Mixing centralizing logic for creating API keys for user objects.
Deprecated - please use api_keys.ApiKeyManager for new development.
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class
galaxy.webapps.base.controller.
Datatype
(extension, dtype, type_extension, mimetype, display_in_upload)[source]¶ Bases:
object
Used for storing in-memory list of datatypes currently in the datatypes registry.
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class
galaxy.webapps.base.controller.
JSAppLauncher
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
A controller that launches JavaScript web applications.
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DEFAULT_ENTRY_FN
= 'app'¶
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JS_APP_MAKO_FILEPATH
= '/js-app.mako'¶
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USER_BOOTSTRAP_KEYS
= ('id', 'email', 'username', 'is_admin', 'tags_used', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'preferences')¶
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client
(trans, **kwd)[source]¶ Endpoint for clientside routes. This ships the primary SPA client.
Should not be used with url_for – see (https://github.com/galaxyproject/galaxy/issues/1878) for why.
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template
(trans, app_name: str, entry_fn: str = 'app', options=None, bootstrapped_data: typing.Optional[dict] = None, masthead: typing.Optional[bool] = True, **additional_options)[source]¶ Render and return the single page mako template that starts the app.
Parameters: - app_name – the first portion of the webpack bundle to as the app.
- entry_fn – the name of the window-scope function that starts the app. Defaults to ‘app’.
- bootstrapped_data – update containing any more data the app may need.
- masthead – include masthead elements in the initial page dom.
- additional_options – update to the options sent to the app.
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galaxy.webapps.base.controller.
Root
¶
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class
galaxy.webapps.base.controller.
SharableItemSecurityMixin
[source]¶ Bases:
object
Mixin for handling security for sharable items.
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class
galaxy.webapps.base.controller.
SharableMixin
[source]¶ Bases:
object
Mixin for a controller that manages an item that can be shared.
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manager
= None¶
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serializer
= None¶
Handle sharing an item with a particular user.
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slug_builder
= <galaxy.managers.sharable.SlugBuilder object>¶
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class
galaxy.webapps.base.controller.
UsesExtendedMetadataMixin
[source]¶ Bases:
galaxy.webapps.base.controller.SharableItemSecurityMixin
Mixin for getting and setting item extended metadata.
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create_extended_metadata
(trans, extmeta)[source]¶ Create/index an extended metadata object. The returned object is not associated with any items
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class
galaxy.webapps.base.controller.
UsesFormDefinitionsMixin
[source]¶ Bases:
object
Mixin for controllers that use Galaxy form objects.
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get_all_forms
(trans, all_versions=False, filter=None, form_type='All')[source]¶ Return all the latest forms from the form_definition_current table if all_versions is set to True. Otherwise return all the versions of all the forms from the form_definition table.
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class
galaxy.webapps.base.controller.
UsesLibraryMixinItems
[source]¶ Bases:
galaxy.webapps.base.controller.SharableItemSecurityMixin
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check_user_can_add_to_library_item
(trans, item, check_accessible=True)[source]¶ Raise exception if user cannot add to the specified library item (i.e. Folder). Can set check_accessible to False if folder was loaded with this check.
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copy_hda_to_library_folder
(trans, hda, library_folder, roles=None, ldda_message='', element_identifier=None)[source]¶
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class
galaxy.webapps.base.controller.
UsesStoredWorkflowMixin
[source]¶ Bases:
galaxy.webapps.base.controller.SharableItemSecurityMixin
,galaxy.model.item_attrs.UsesAnnotations
Mixin for controllers that use StoredWorkflow objects.
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get_stored_workflow
(trans, id, check_ownership=True, check_accessible=False)[source]¶ Get a StoredWorkflow from the database by id, verifying ownership.
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get_stored_workflow_steps
(trans, stored_workflow)[source]¶ Restores states for a stored workflow’s steps.
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slug_builder
= <galaxy.managers.sharable.SlugBuilder object>¶
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class
galaxy.webapps.base.controller.
UsesTagsMixin
[source]¶ Bases:
galaxy.webapps.base.controller.SharableItemSecurityMixin
Return a list of distinct ‘user_tname:user_value’ strings that the given user has used.
user defaults to trans.user. Returns an empty list if no user is given and trans.user is anonymous.
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class
galaxy.webapps.base.controller.
UsesVisualizationMixin
[source]¶ Bases:
galaxy.webapps.base.controller.UsesLibraryMixinItems
Mixin for controllers that use Visualization objects.
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add_visualization_revision
(trans, visualization, config, title, dbkey)[source]¶ Adds a new VisualizationRevision to the given visualization with the given parameters and set its parent visualization’s latest_revision to the new revision.
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create_visualization
(trans, type, title='Untitled Visualization', slug=None, dbkey=None, annotation=None, config=None, save=True)[source]¶ Create visualiation and first revision.
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get_hda
(trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True)[source]¶ Get an HDA object by id performing security checks using the current transaction.
Deprecated in lieu to galaxy.managers.hdas.HDAManager.get_accessible(decoded_id, user)
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get_hda_or_ldda
(trans, hda_ldda, dataset_id)[source]¶ Returns either HDA or LDDA for hda/ldda and id combination.
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get_published_visualizations
(trans, exclude_user=None, order_by=None, query_only=False)[source]¶ Return query or query results for published visualizations optionally excluding the user in exclude_user.
Set order_by to a column or list of columns to change the order returned. Defaults to DEFAULT_ORDER_BY. Set query_only to return just the query for further filtering or processing.
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get_visualization
(trans, id, check_ownership=True, check_accessible=False)[source]¶ Get a Visualization from the database by id, verifying ownership.
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get_visualization_config
(trans, visualization)[source]¶ Returns a visualization’s configuration. Only works for trackster visualizations right now.
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get_visualization_dict
(visualization)[source]¶ Return a set of detailed attributes for a visualization in dictionary form. The visualization’s latest_revision is returned in its own sub-dictionary. NOTE: that encoding ids isn’t done here should happen at the caller level.
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get_visualization_revision_dict
(revision)[source]¶ Return a set of detailed attributes for a visualization in dictionary form. NOTE: that encoding ids isn’t done here should happen at the caller level.
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get_visualization_summary_dict
(visualization)[source]¶ Return a set of summary attributes for a visualization in dictionary form. NOTE: that encoding ids isn’t done here should happen at the caller level.
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get_visualizations_by_user
(trans, user, order_by=None, query_only=False)[source]¶ Return query or query results of visualizations filtered by a user.
Set order_by to a column or list of columns to change the order returned. Defaults to DEFAULT_ORDER_BY. Set query_only to return just the query for further filtering or processing.
Return query or query results for visualizations shared with the given user.
Set order_by to a column or list of columns to change the order returned. Defaults to DEFAULT_ORDER_BY. Set query_only to return just the query for further filtering or processing.
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import_visualization
(trans, id, user=None)[source]¶ Copy the visualization with the given id and associate the copy with the given user (defaults to trans.user).
Raises ItemAccessibilityException if user is not passed and the current user is anonymous, and if the visualization is not importable. Raises ItemDeletionException if the visualization has been deleted.
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save_visualization
(trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None)[source]¶
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slug_builder
= <galaxy.managers.sharable.SlugBuilder object>¶
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galaxy.webapps.base.webapp module¶
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class
galaxy.webapps.base.webapp.
GalaxyWebTransaction
(environ: typing.Dict[str, typing.Any], app, webapp, session_cookie=None) → None[source]¶ Bases:
galaxy.web.framework.base.DefaultWebTransaction
,galaxy.managers.context.ProvidesHistoryContext
Encapsulates web transaction specific state for the Galaxy application (specifically the user’s “cookie” session and history)
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app
¶
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fill_template
(filename, **kwargs)[source]¶ Fill in a template, putting any keyword arguments on the context.
Convenience method for getting a session cookie
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get_history
(create=False, most_recent=False)[source]¶ Load the current history.
- If that isn’t available, we find the most recently updated history.
- If that isn’t available, we get or create the default history.
Transactions will not always have an active history (API requests), so None is a valid response.
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get_message
()[source]¶ Convenience method for getting the ‘message’ element of the template context.
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get_or_create_default_history
()[source]¶ Gets or creates a default history and associates it with the current session.
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get_or_create_remote_user
(remote_user_email)[source]¶ Create a remote user with the email remote_user_email and return it
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handle_user_login
(user)[source]¶ - Login a new user (possibly newly created)
- do some ‘system’ checks (if any) for this user
- create a new session
- associate new session with user
- if old session had a history and it was not associated with a user, associate it with the new session, otherwise associate the current session’s history with the user
- add the disk usage of the current session to the user’s total disk usage
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handle_user_logout
(logout_all=False)[source]¶ - Logout the current user:
- invalidate the current session
- create a new session with no user associated
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history
¶
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new_history
(name=None)[source]¶ Create a new history and associate it with the current session and its associated user (if set).
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session_csrf_token
¶
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set_cors_headers
()[source]¶ Allow CORS requests if configured to do so by echoing back the request’s ‘Origin’ header (if any) as the response header ‘Access-Control-Allow-Origin’
Preflight OPTIONS requests to the API work by routing all OPTIONS requests to a single method in the authenticate API (options method), setting CORS headers, and responding OK.
NOTE: raising some errors (such as httpexceptions), will remove the header (e.g. client will get both CORS error and 404 inside that)
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set_message
(message, type=None)[source]¶ Convenience method for setting the ‘message’ and ‘message_type’ element of the template context.
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show_error_message
(message, refresh_frames=None, use_panels=False, active_view='')[source]¶ Convenience method for displaying an error message. See show_message.
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show_message
(message, type='info', refresh_frames=None, cont=None, use_panels=False, active_view='')[source]¶ Convenience method for displaying a simple page with a single message.
- type: one of “error”, “warning”, “info”, or “done”; determines the
- type of dialog box and icon displayed with the message
- refresh_frames: names of frames in the interface that should be
- refreshed when the message is displayed
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show_ok_message
(message, refresh_frames=None, use_panels=False, active_view='')[source]¶ Convenience method for displaying an ok message. See show_message.
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show_warn_message
(message, refresh_frames=None, use_panels=False, active_view='')[source]¶ Convenience method for displaying an warn message. See show_message.
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template_context
¶ Property that replaces itself with a calculated value the first time it is used.
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url_builder
¶
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user
¶ Return the current user if logged in or None.
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class
galaxy.webapps.base.webapp.
WebApplication
(galaxy_app, session_cookie='galaxysession', name=None)[source]¶ Bases:
galaxy.web.framework.base.WebApplication
Base WSGI application instantiated for all Galaxy webapps.
A web application that:
- adds API and UI controllers by scanning given directories and importing all modules found there.
- has a security object.
- builds mako template lookups.
- generates GalaxyWebTransactions.
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add_api_controllers
(package_name, app)[source]¶ Search for UI controllers in package_name and add them to the webapp.
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add_ui_controllers
(package_name, app)[source]¶ Search for UI controllers in package_name and add them to the webapp.
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injection_aware
= False¶