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galaxy.webapps.base package

Submodules

galaxy.webapps.base.controller module

Contains functionality needed in every web interface

class galaxy.webapps.base.controller.BaseAPIController(app)

Bases: galaxy.webapps.base.controller.BaseController

get_object(trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None)

not_implemented(trans, **kwd)

class galaxy.webapps.base.controller.BaseController(app)

Bases: object

Base class for Galaxy web application controllers.

__init__(app)

Initialize an interface for application ‘app’

decode_id(id)

encode_all_ids(trans, rval, recursive=False)

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

get_class(class_name)

Returns the class object that a string denotes. Without this method, we’d have to do eval(<class_name>).

get_group(trans, id, check_ownership=False, check_accessible=False, deleted=None)

get_object(trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None)

Convenience method to get a model object with the specified checks.

get_role(trans, id, check_ownership=False, check_accessible=False, deleted=None)

get_toolbox()

Returns the application toolbox

get_user(trans, id, check_ownership=False, check_accessible=False, deleted=None)

parse_filter_params(qdict, filter_attr_key='q', filter_value_key='qv', attr_op_split_char='-')

parse_limit_offset(qdict)

class galaxy.webapps.base.controller.BaseUIController(app)

Bases: galaxy.webapps.base.controller.BaseController

get_object(trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None)

message_exception(trans, message, sanitize=True)

class galaxy.webapps.base.controller.CreatesApiKeysMixin

Bases: object

Mixing centralizing logic for creating API keys for user objects.

Deprecated - please use api_keys.ApiKeyManager for new development.

create_api_key(trans, user)

class galaxy.webapps.base.controller.Datatype(extension, dtype, type_extension, mimetype, display_in_upload)

Bases: object

Used for storing in-memory list of datatypes currently in the datatypes registry.

__init__(extension, dtype, type_extension, mimetype, display_in_upload)

class galaxy.webapps.base.controller.JSAppLauncher(app)

Bases: galaxy.webapps.base.controller.BaseUIController

A controller that launches JavaScript web applications.

DEFAULT_ENTRY_FN = 'app'

JS_APP_MAKO_FILEPATH = '/js-app.mako'

USER_BOOTSTRAP_KEYS = ('id', 'email', 'username', 'is_admin', 'tags_used', 'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'preferences')

__init__(app)

client(trans, **kwd)

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.

template(trans, app_name: str, entry_fn: str = 'app', options=None, bootstrapped_data: typing.Optional[dict] = None, masthead: typing.Optional[bool] = True, **additional_options)

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.

galaxy.webapps.base.controller.Root

alias of galaxy.webapps.base.controller.BaseController

class galaxy.webapps.base.controller.SharableItemSecurityMixin

Bases: object

Mixin for handling security for sharable items.

security_check(trans, item, check_ownership=False, check_accessible=False)

Security checks for an item: checks if (a) user owns item or (b) item is accessible to user.

class galaxy.webapps.base.controller.SharableMixin

Bases: object

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

display_by_username_and_slug(trans, username, slug)

Display item by username and slug.

get_item(trans, id)

Return item based on id.

get_item_content_async(trans, id)

Returns item content in HTML format.

get_name_and_link_async(trans, id=None)

Returns item’s name and link.

manager = None

serializer = None

set_slug_async(trans, id, new_slug)

share(trans, id=None, email='', **kwd)

Handle sharing an item with a particular user.

slug_builder = <galaxy.managers.sharable.SlugBuilder object>

class galaxy.webapps.base.controller.UsesExtendedMetadataMixin

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin

Mixin for getting and setting item extended metadata.

create_extended_metadata(trans, extmeta)

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

delete_extended_metadata(trans, item)

get_item_extended_metadata_obj(trans, item)

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)

unset_item_extended_metadata_obj(trans, item, check_writable=False)

class galaxy.webapps.base.controller.UsesFormDefinitionsMixin

Bases: object

Mixin for controllers that use Galaxy form objects.

get_all_forms(trans, all_versions=False, filter=None, form_type='All')

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.

get_form_values(trans, user, form_definition, **kwd)

Returns the name:value dictionary containing all the form values

save_widget_field(trans, field_obj, widget_name, **kwd)

class galaxy.webapps.base.controller.UsesLibraryMixinItems

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin

can_current_user_add_to_library_item(trans, item)

check_user_can_add_to_library_item(trans, item, check_accessible=True)

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.

copy_hda_to_library_folder(trans, hda, library_folder, roles=None, ldda_message='', element_identifier=None)

get_library_dataset(trans, id, check_ownership=False, check_accessible=True)

get_library_dataset_dataset_association(trans, id, check_ownership=False, check_accessible=True)

get_library_folder(trans, id, check_ownership=False, check_accessible=True)

class galaxy.webapps.base.controller.UsesStoredWorkflowMixin

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin, galaxy.model.item_attrs.UsesAnnotations

Mixin for controllers that use StoredWorkflow objects.

get_stored_workflow(trans, id, check_ownership=True, check_accessible=False)

Get a StoredWorkflow from the database by id, verifying ownership.

get_stored_workflow_steps(trans, stored_workflow)

Restores states for a stored workflow’s steps.

slug_builder = <galaxy.managers.sharable.SlugBuilder object>

class galaxy.webapps.base.controller.UsesTagsMixin

Bases: galaxy.webapps.base.controller.SharableItemSecurityMixin

get_tag_handler(trans) → galaxy.model.tags.GalaxyTagHandler

get_user_tags_used(trans, user=None)

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.

set_tags_from_list(trans, item, new_tags_list, user=None)

class galaxy.webapps.base.controller.UsesVisualizationMixin

Bases: galaxy.webapps.base.controller.UsesLibraryMixinItems

Mixin for controllers that use Visualization objects.

add_visualization_revision(trans, visualization, config, title, dbkey)

Adds a new VisualizationRevision to the given visualization with the given parameters and set its parent visualization’s latest_revision to the new revision.

create_visualization(trans, type, title='Untitled Visualization', slug=None, dbkey=None, annotation=None, config=None, save=True)

Create visualiation and first revision.

get_hda(trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True)

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)

get_hda_or_ldda(trans, hda_ldda, dataset_id)

Returns either HDA or LDDA for hda/ldda and id combination.

get_new_track_config(trans, dataset)

Returns track configuration dict for a dataset.

get_published_visualizations(trans, exclude_user=None, order_by=None, query_only=False)

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.

get_tool_def(trans, hda)

Returns definition of an interactive tool for an HDA.

get_visualization(trans, id, check_ownership=True, check_accessible=False)

Get a Visualization from the database by id, verifying ownership.

get_visualization_config(trans, visualization)

Returns a visualization’s configuration. Only works for trackster visualizations right now.

get_visualization_dict(visualization)

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.

get_visualization_revision_dict(revision)

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.

get_visualization_summary_dict(visualization)

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.

get_visualizations_by_user(trans, user, order_by=None, query_only=False)

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.

get_visualizations_shared_with_user(trans, user, order_by=None, query_only=False)

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.

import_visualization(trans, id, user=None)

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.

save_visualization(trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None)

slug_builder = <galaxy.managers.sharable.SlugBuilder object>

galaxy.webapps.base.controller.sort_by_attr(seq, attr)

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.webapp module

class galaxy.webapps.base.webapp.GalaxyWebTransaction(environ: typing.Dict[str, typing.Any], app, webapp, session_cookie=None) → None

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: typing.Dict[str, typing.Any], app, webapp, session_cookie=None) → None

app

check_csrf_token(payload)

check_user_library_import_dir(user)

cookie_path

fill_template(filename, **kwargs)

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

fill_template_mako(filename, template_lookup=None, **kwargs)

get_cookie(name='galaxysession')

Convenience method for getting a session cookie

get_galaxy_session()

Return the current galaxy session

get_history(create=False, most_recent=False)

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.

get_message()

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

get_most_recent_history()

Gets the most recently updated history.

get_or_create_default_history()

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

get_or_create_remote_user(remote_user_email)

Create a remote user with the email remote_user_email and return it

get_user()

Return the current user if logged in or None.

handle_user_login(user)

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)

Logout the current user:

• invalidate the current session
• create a new session with no user associated

history

new_history(name=None)

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

qualified_url_for_path(path)

session_csrf_token

set_cookie(value, name='galaxysession', path='/', age=90, version='1')

set_cors_allow(name=None, value=None)

set_cors_headers()

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)

set_cors_origin(origin=None)

set_history(history)

set_message(message, type=None)

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

set_user(user)

Set the current user.

setup_i18n()

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

Convenience method for displaying an error message. See show_message.

show_message(message, type='info', refresh_frames=None, cont=None, use_panels=False, active_view='')

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_ok_message(message, refresh_frames=None, use_panels=False, active_view='')

Convenience method for displaying an ok message. See show_message.

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

Convenience method for displaying an warn message. See show_message.

template_context

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

url_builder

user

Return the current user if logged in or None.

user_checks(user)

This could contain more checks around a user upon login

class galaxy.webapps.base.webapp.WebApplication(galaxy_app, session_cookie='galaxysession', name=None)

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.

__init__(galaxy_app, session_cookie='galaxysession', name=None)

add_api_controllers(package_name, app)

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

add_ui_controllers(package_name, app)

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

create_mako_template_lookup(galaxy_app, name)

handle_controller_exception(e, trans, **kwargs)

injection_aware = False

make_body_iterable(trans, body)

transaction_chooser(environ, galaxy_app, session_cookie)

galaxy.webapps.base.webapp.build_native_uwsgi_app(paste_factory, config_section)

uwsgi can load paste factories with –ini-paste, but this builds non-paste uwsgi apps.

In particular these are useful with –yaml or –json for config.

galaxy.webapps.base.webapp.build_url_map(app, global_conf, **local_conf)

galaxy.webapps.base.webapp.config_allows_origin(origin_raw, config)

galaxy.webapps.base.webapp.default_url_path(path)

galaxy.webapps.base.webapp.url_builder(*args, **kwargs) → str

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