Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.webapps.base package

Submodules

galaxy.webapps.base.controller module

Contains functionality needed in every web interface

exception galaxy.webapps.base.controller.HTTPBadRequest(detail=None, headers=None, comment=None, body_template=None, json_formatter=None, **kw)[source]

Bases: webob.exc.HTTPClientError, paste.httpexceptions.HTTPBadRequest

explanation = 'The server could not comply with the request since it is either malformed or otherwise incorrect.'
class galaxy.webapps.base.controller.SharableMixin[source]

Bases: object

Mixin for a controller that manages an item that can be shared.

manager: Any = None
serializer: Any = None
slug_builder = <galaxy.managers.sharable.SlugBuilder object>
set_slug_async(trans, id, new_slug)[source]
share(trans, id=None, email='', **kwd)[source]

Handle sharing an item with a particular user.

display_by_username_and_slug(trans, username, slug)[source]

Display item by username and slug.

Returns item’s name and link.

get_item_content_async(trans, id)[source]

Returns item content in HTML format.

get_item(trans, id)[source]

Return item based on id.

galaxy.webapps.base.controller.sort_by_attr(seq, attr)[source]

Sort the sequence of objects by object’s attribute Arguments: seq - the list or any sequence (including immutable one) of objects to sort. attr - the name of attribute to sort by

galaxy.webapps.base.controller.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.

class galaxy.webapps.base.controller.UsesExtendedMetadataMixin[source]

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin

Mixin for getting and setting item extended metadata.

get_item_extended_metadata_obj(trans, item)[source]

Given an item object (such as a LibraryDatasetDatasetAssociation), find the object of the associated extended metadata

set_item_extended_metadata_obj(trans, item, extmeta_obj, check_writable=False)[source]
unset_item_extended_metadata_obj(trans, item, check_writable=False)[source]
create_extended_metadata(trans, extmeta)[source]

Create/index an extended metadata object. The returned object is not associated with any items

delete_extended_metadata(trans, item)[source]
class galaxy.webapps.base.controller.UsesFormDefinitionsMixin[source]

Bases: object

Mixin for controllers that use Galaxy form objects.

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.

save_widget_field(trans, field_obj, widget_name, **kwd)[source]
get_form_values(trans, user, form_definition, **kwd)[source]

Returns the name:value dictionary containing all the form values

class galaxy.webapps.base.controller.UsesTagsMixin[source]

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin

get_tag_handler(trans) galaxy.model.tags.GalaxyTagHandler[source]
set_tags_from_list(trans, item, new_tags_list, user=None)[source]
get_user_tags_used(trans, user=None)[source]

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.

galaxy.webapps.base.webapp module

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.

injection_aware: bool = False
__init__(galaxy_app, session_cookie='galaxysession', name=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).

build_apispec()[source]

Traverse all route paths starting with “api” and create an APISpec instance.

create_mako_template_lookup(galaxy_app, name)[source]
handle_controller_exception(e, trans, **kwargs)[source]

Allow handling of exceptions raised in controller methods.

make_body_iterable(trans, body)[source]
transaction_chooser(environ, galaxy_app, session_cookie)[source]
add_ui_controllers(package_name, app)[source]

Search for UI controllers in package_name and add them to the webapp.

add_api_controllers(package_name, app)[source]

Search for UI controllers in package_name and add them to the webapp.

galaxy.webapps.base.webapp.config_allows_origin(origin_raw, config)[source]
galaxy.webapps.base.webapp.url_builder(*args, **kwargs) str[source]

Wrapper around the WSGI version of the function for reversing URLs.

class galaxy.webapps.base.webapp.GalaxyWebTransaction(environ: Dict[str, Any], app, webapp, session_cookie=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)

__init__(environ: Dict[str, Any], app, webapp, session_cookie=None) None[source]
property app

Provide access to the Galaxy app object.

property url_builder

Provide access to Galaxy URLs (if available).

Parameters

qualified (bool) – if True, the fully qualified URL is returned, else a relative URL is returned (default False).

setup_i18n()[source]
set_cors_allow(name=None, value=None)[source]
set_cors_origin(origin=None)[source]
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)

get_user()[source]

Return the current user if logged in or None.

set_user(user)[source]

Set the current user.

property user

Return the current user if logged in or None.

Convenience method for getting a session cookie

Convenience method for setting a session cookie

get_or_create_remote_user(remote_user_email)[source]

Create a remote user with the email remote_user_email and return it

property cookie_path
check_user_library_import_dir(user)[source]
user_checks(user)[source]

This could contain more checks around a user upon login

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

handle_user_logout(logout_all=False)[source]
Logout the current user:
  • invalidate the current session

  • create a new session with no user associated

get_galaxy_session()[source]

Return the current galaxy session

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.

set_history(history)[source]
property history

Provide access to the user’s current history model object.

Return type

Optional[galaxy.model.History]

get_or_create_default_history()[source]

Gets or creates a default history and associates it with the current session.

get_most_recent_history()[source]

Gets the most recently updated history.

new_history(name=None)[source]

Create a new history and associate it with the current session and its associated user (if set).

template_context

Property that replaces itself with a calculated value the first time it is used.

set_message(message, type=None)[source]

Convenience method for setting the ‘message’ and ‘message_type’ element of the template context.

get_message()[source]

Convenience method for getting the ‘message’ element of the template context.

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

show_error_message(message, refresh_frames=None, use_panels=False, active_view='')[source]

Convenience method for displaying an error message. See show_message.

show_ok_message(message, refresh_frames=None, use_panels=False, active_view='')[source]

Convenience method for displaying an ok message. See show_message.

show_warn_message(message, refresh_frames=None, use_panels=False, active_view='')[source]

Convenience method for displaying an warn message. See show_message.

property session_csrf_token
check_csrf_token(payload)[source]
fill_template(filename, **kwargs)[source]

Fill in a template, putting any keyword arguments on the context.

fill_template_mako(filename, template_lookup=None, **kwargs)[source]
qualified_url_for_path(path)[source]
galaxy.webapps.base.webapp.default_url_path(path)[source]
galaxy.webapps.base.webapp.build_url_map(app, global_conf, **local_conf)[source]