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galaxy.web.base package

Submodules

galaxy.web.base.controller module

Contains functionality needed in every web interface

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

Bases: object

Base class for Galaxy web application controllers.

__init__(app)

Initialize an interface for application ‘app’

get_toolbox()

Returns the application toolbox

get_class(class_name)

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

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

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

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

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

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

parse_limit_offset(qdict)

galaxy.web.base.controller.Root

alias of galaxy.web.base.controller.BaseController

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

Bases: galaxy.web.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.web.base.controller.BaseAPIController(app)

Bases: galaxy.web.base.controller.BaseController

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

validate_in_users_and_groups(trans, payload)

For convenience, in_users and in_groups can be encoded IDs or emails/group names in the API.

not_implemented(trans, **kwd)

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

Bases: galaxy.web.base.controller.BaseUIController

A controller that launches JavaScript web applications.

JS_APP_MAKO_FILEPATH = '/js-app.mako'

path to js app template

DEFAULT_ENTRY_FN = 'app'

window-scoped js function to call to start the app (will be passed options, bootstrapped)

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

keys used when serializing current user for bootstrapped data

__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, entry_fn='app', options=None, bootstrapped_data=None, masthead=True, **additional_options)

Render and return the single page mako template that starts the app.

app_name (string): the first portion of the webpack bundle to as the app. entry_fn (string): the name of the window-scope function that starts the

app. Defaults to ‘app’.

bootstrapped_data (dict): (optional) update containing any more data

the app may need.

masthead (boolean): (optional, default=True) include masthead elements in

the initial page dom.

additional_options (kwargs): update to the options sent to the app.

class galaxy.web.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.web.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.web.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.web.base.controller.ExportsHistoryMixin

Bases: object

serve_ready_history_export(trans, jeha)

queue_history_export(trans, history, gzip=True, include_hidden=False, include_deleted=False)

class galaxy.web.base.controller.ImportsHistoryMixin

Bases: object

queue_history_import(trans, archive_type, archive_source)

class galaxy.web.base.controller.UsesLibraryMixin

Bases: object

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

class galaxy.web.base.controller.UsesLibraryMixinItems

Bases: galaxy.web.base.controller.SharableItemSecurityMixin

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

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

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

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)

class galaxy.web.base.controller.UsesVisualizationMixin

Bases: galaxy.web.base.controller.UsesLibraryMixinItems

Mixin for controllers that use Visualization objects.

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

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

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.

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_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_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.

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.

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

Create visualiation and first revision.

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.

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

get_tool_def(trans, hda)

Returns definition of an interactive tool for an HDA.

get_visualization_config(trans, visualization)

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

get_new_track_config(trans, dataset)

Returns track configuration dict for a dataset.

get_hda_or_ldda(trans, hda_ldda, dataset_id)

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

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)

class galaxy.web.base.controller.UsesStoredWorkflowMixin

Bases: galaxy.web.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.

class galaxy.web.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.

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

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

Returns the name:value dictionary containing all the form values

class galaxy.web.base.controller.SharableMixin

Bases: object

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

manager = None

serializer = None

set_slug_async(trans, *args, **kwargs)

create_item_slug(sa_session, item)

Create/set item slug. Slug is unique among user’s importable items for item’s class. Returns true if item’s slug was set/changed; false otherwise.

sharing(trans, *args, **kwargs)

share(trans, *args, **kwargs)

Handle sharing an item with a particular user.

display_by_username_and_slug(trans, username, slug)

Display item by username and slug.

get_name_and_link_async(trans, *args, **kwargs)

Returns item’s name and link.

get_item_content_async(trans, *args, **kwargs)

Returns item content in HTML format.

get_item(trans, id)

Return item based on id.

class galaxy.web.base.controller.UsesQuotaMixin

Bases: object

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

class galaxy.web.base.controller.UsesTagsMixin

Bases: galaxy.web.base.controller.SharableItemSecurityMixin

get_tag_handler(trans)

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

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.

class galaxy.web.base.controller.UsesExtendedMetadataMixin

Bases: galaxy.web.base.controller.SharableItemSecurityMixin

Mixin for getting and setting item extended metadata.

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)

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)

exception galaxy.web.base.controller.ControllerUnavailable

Bases: exceptions.Exception

Deprecated: BaseController used to be available under the name Root

galaxy.web.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