galaxy.webapps.galaxy.controllers package

Galaxy web controllers.

Submodules

galaxy.webapps.galaxy.controllers.admin module

class galaxy.webapps.galaxy.controllers.admin.UserListGrid

Bases: GridData

class StatusColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, user)

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, user)

class RolesColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, user)

class LastLoginColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, user)

sort(trans, query, ascending, column_name=None)

Sort query using this column.

class DiskUsageColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, user)

sort(trans, query, ascending, column_name=None)

Sort query using this column.

title = 'Users'

title_id = 'users-grid'

model_class

alias of User

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>]

apply_query_filter(query, **kwargs)

class galaxy.webapps.galaxy.controllers.admin.RoleListGrid

Bases: GridData

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, role)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, role)

title = 'Roles'

title_id = 'roles-grid'

model_class

alias of Role

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>]

apply_query_filter(query, **kwargs)

class galaxy.webapps.galaxy.controllers.admin.GroupListGrid

Bases: GridData

class RolesColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, group)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, group)

title = 'Groups'

title_id = 'groups-grid'

model_class

alias of Group

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>]

apply_query_filter(query, **kwargs)

class galaxy.webapps.galaxy.controllers.admin.QuotaListGrid

Bases: GridData

class AmountColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, quota)

class DefaultTypeColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, quota)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, quota)

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, quota)

title = 'Quotas'

model_class

alias of Quota

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>]

apply_query_filter(query, **kwargs)

class galaxy.webapps.galaxy.controllers.admin.DatatypesEntryT

Bases: TypedDict

status: str

data: list

message: str

class galaxy.webapps.galaxy.controllers.admin.AdminGalaxy(app: StructuredApp)

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)

Initialize an interface for application ‘app’

data_tables_list(trans, **kwd)

data_types_list(trans, **kwd) → DatatypesEntryT

users_list(trans, **kwd)

quotas_list(trans, payload=None, **kwargs)

create_quota(trans, payload=None, **kwd)

rename_quota(trans, payload=None, **kwd)

manage_users_and_groups_for_quota(trans, payload=None, **kwd)

edit_quota(trans, payload=None, **kwd)

set_quota_default(trans, payload=None, **kwd)

impersonate(trans, **kwd)

roles_list(trans, **kwargs)

create_role(trans, payload=None, **kwd)

rename_role(trans, payload=None, **kwd)

manage_users_and_groups_for_role(trans, payload=None, **kwd)

groups_list(trans, **kwargs)

rename_group(trans, payload=None, **kwd)

manage_users_and_roles_for_group(trans, payload=None, **kwd)

create_group(trans, payload=None, **kwd)

create_new_user(trans, **kwd)

reset_user_password(trans, payload=None, **kwd)

manage_roles_and_groups_for_user(trans, payload=None, **kwd)

galaxy.webapps.galaxy.controllers.admin.build_select_input(name, label, options, value)

galaxy.webapps.galaxy.controllers.admin.get_user(trans, user_id)

Get a User from the database by id.

galaxy.webapps.galaxy.controllers.admin.get_role(trans, id)

Get a Role from the database by id.

galaxy.webapps.galaxy.controllers.admin.get_group(trans, id)

Get a Group from the database by id.

galaxy.webapps.galaxy.controllers.admin.get_quota(trans, id)

Get a Quota from the database by id.

galaxy.webapps.galaxy.controllers.admin_toolshed module

galaxy.webapps.galaxy.controllers.admin_toolshed.legacy_tool_shed_endpoint(func)

class galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed(app: StructuredApp)

Bases: AdminGalaxy

activate_repository(trans, **kwd)

Activate a repository that was deactivated but not uninstalled.

restore_repository(trans, **kwd)

display_image_in_repository(trans, **kwd)

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

manage_repository_json(trans, **kwd)

quota_manager: QuotaManager

galaxy.webapps.galaxy.controllers.async module

Controller to handle communication of tools of type data_source_async

class galaxy.webapps.galaxy.controllers.async.ASync(app)

Bases: BaseUIController

default(trans, tool_id=None, data_id=None, data_secret=None, **kwd)

Catches the tool id and redirects as needed

index(trans, tool_id=None, data_secret=None, **kwd)

Manages ascynchronous connections

galaxy.webapps.galaxy.controllers.authnz module

OAuth 2.0 and OpenID Connect Authentication and Authorization Controller.

class galaxy.webapps.galaxy.controllers.authnz.OIDC(app)

Bases: JSAppLauncher

index(trans, **kwargs)

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.

login(trans, provider, idphint=None)

callback(trans, provider, idphint=None, **kwargs)

create_user(trans, provider, **kwargs)

disconnect(trans, provider, email=None, **kwargs)

logout(trans, provider, **kwargs)

get_logout_url(trans, provider=None, **kwargs)

get_cilogon_idps(trans, **kwargs)

galaxy.webapps.galaxy.controllers.data_manager module

class galaxy.webapps.galaxy.controllers.data_manager.DataManager(app)

Bases: BaseUIController

data_managers_list(trans, **kwd)

jobs_list(trans, **kwd)

job_info(trans, **kwd)

tool_data_table_info(trans, **kwd)

tool_data_table_info_1(trans, **kwd)

reload_tool_data_tables(trans, table_name=None, **kwd)

tool_data_table_items(trans, **kwd)

reload_tool_data_table(trans, **kwd)

galaxy.webapps.galaxy.controllers.dataset module

galaxy.webapps.galaxy.controllers.error module

class galaxy.webapps.galaxy.controllers.error.Error(app)

Bases: BaseUIController

index(trans)

galaxy.webapps.galaxy.controllers.forms module

class galaxy.webapps.galaxy.controllers.forms.FormsGrid

Bases: GridData

class NameColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, form)

class DescriptionColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, form)

class TypeColumn(label, key=None, model_class=None, method=None, format=None, escape=True)

Bases: GridColumn

get_value(trans, grid, form)

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>]

apply_query_filter(query, **kwargs)

class galaxy.webapps.galaxy.controllers.forms.Forms(app)

Bases: BaseUIController

forms_grid = <galaxy.webapps.galaxy.controllers.forms.FormsGrid object>

forms_list(trans, payload=None, **kwd)

create_form(trans, payload=None, **kwd)

edit_form(trans, payload=None, **kwd)

get_current_form(trans, payload=None, **kwd)

This method gets all the unsaved user-entered form details and returns a dictionary containing the name, desc, type, layout & fields of the form

save_form_definition(trans, form_id=None, payload=None, **kwd)

This method saves a form given an id

galaxy.webapps.galaxy.controllers.history module

class galaxy.webapps.galaxy.controllers.history.HistoryController(app: StructuredApp)

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)

Initialize an interface for application ‘app’

index(trans)

view(trans, id=None, show_deleted=False, show_hidden=False, use_panels=True)

View a history. If a history is importable, then it is viewable by any user.

display_by_username_and_slug(trans, username, slug, **kwargs)

Display history based on a username and slug.

permissions(trans, payload=None, **kwd)

Sets the permissions on a history.

make_private(trans, history_id=None, all_histories=False, **kwd)

Sets the datasets within a history to private. Also sets the default permissions for the history to private, for future datasets.

purge_deleted_datasets(trans)

resume_paused_jobs(trans, current=False, ids=None, **kwargs)

Resume paused jobs the active history – this does not require a logged in user.

rename(trans, payload=None, **kwd)

switch_to_history(trans, hist_id=None, **kwargs)

Change the current user’s current history to one with hist_id.

get_item(trans, id)

Return item based on id.

history_data(trans, history)

Return the given history in a serialized, dictionary form.

set_as_current(trans, id, **kwargs)

Change the current user’s current history to one with id.

current_history_json(trans, since=None, **kwargs)

Return the current user’s current history in a serialized, dictionary form.

create_new_current(trans, name=None, **kwargs)

Create a new, current history for the current user

galaxy.webapps.galaxy.controllers.library module

galaxy.webapps.galaxy.controllers.page module

class galaxy.webapps.galaxy.controllers.page.PageController(app: StructuredApp)

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)

Initialize an interface for application ‘app’

create(trans, payload=None, **kwd)

Create a new page.

edit(trans, payload=None, **kwd)

Edit a page’s attributes.

display(trans, id, **kwargs)

display_by_username_and_slug(trans, username, slug, **kwargs)

Display page based on a username and slug.

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

Get a page from the database by id.

galaxy.webapps.galaxy.controllers.root module

Contains the main interface in the Universe class

class galaxy.webapps.galaxy.controllers.root.RootController(app: StructuredApp)

Bases: JSAppLauncher, UsesAnnotations

Controller class that maps to the url root of Galaxy (i.e. ‘/’).

history_manager: HistoryManager = GalaxyTypeDepends(_do_resolve)

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

default(trans, target1=None, target2=None, **kwd)

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)

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)

User login path for client-side.

display_as(trans: GalaxyWebTransaction, id=None, display_app=None, **kwd)

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)

galaxy.webapps.galaxy.controllers.shed_tool_static module

class galaxy.webapps.galaxy.controllers.shed_tool_static.ShedToolStatic(app)

Bases: BaseUIController

index(trans, shed, owner, repo, tool, version, image_file, **kwargs)

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)

Bases: BaseUIController, UsesTagsMixin

add_tag_async(trans, item_id=None, item_class=None, new_tag=None, context=None, **kwargs)

Add tag to an item.

remove_tag_async(trans, item_id=None, item_class=None, tag_name=None, context=None, **kwargs)

Remove tag from an item.

tag_autocomplete_data(trans, q=None, limit=None, timestamp=None, item_id=None, item_class=None, **kwargs)

Get autocomplete data for an item’s tags.

galaxy.webapps.galaxy.controllers.tool_runner module

Controller handles external tool related requests

class galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner(app)

Bases: BaseUIController

biomart(trans, tool_id='biomart', **kwd)

Catches the tool id and redirects as needed

hapmapmart(trans, tool_id='hapmapmart', **kwd)

Catches the tool id and redirects as needed

default(trans, tool_id=None, **kwd)

Catches the tool id and redirects as needed

index(trans, tool_id=None, from_noframe=None, **kwd)

rerun(trans, id=None, job_id=None, **kwd)

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)

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)

Bases: BaseUIController, UsesFormDefinitionsMixin

user_manager: UserManager = GalaxyTypeDepends(_do_resolve)

installed_len_files = None

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

login(trans, payload=None, **kwd)

resend_verification(trans, **kwargs)

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)

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)

Function checks whether the user is outside the config-defined grace period for inactive accounts.

logout(trans, logout_all=False, **kwd)

create(trans, payload=None, **kwd)

activate(trans, **kwd)

Check whether token fits the user and then activate the user’s account.

change_password(trans, payload=None, **kwd)

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)

reset_password(trans, payload=None, **kwd)

Reset the user’s password. Send an email with token that allows a password change.

galaxy.webapps.galaxy.controllers.visualization module

class galaxy.webapps.galaxy.controllers.visualization.VisualizationController(app: StructuredApp)

Bases: BaseUIController, SharableMixin, UsesVisualizationMixin, UsesAnnotations, UsesItemRatings

hda_manager: HDAManager = GalaxyTypeDepends(_do_resolve)

slug_builder: SlugBuilder = GalaxyTypeDepends(_do_resolve)

__init__(app: StructuredApp)

Initialize an interface for application ‘app’

copy(trans, id, **kwargs)

imp(trans, id, **kwargs)

Import a visualization into user’s workspace.

display_by_username_and_slug(trans, username, slug, **kwargs)

Display visualization based on a username and slug.

save(trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None, **kwargs)

Save a visualization; if visualization does not have an ID, a new visualization is created. Returns JSON of visualization.

edit(trans, payload=None, **kwd)

Edit a visualization’s attributes.

render(trans, visualization_name, embedded=None, **kwargs)

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}

saved(trans, id=None, revision=None, type=None, config=None, title=None, **kwargs)

Save (on POST) or load (on GET) a visualization then render.

trackster(trans, **kwargs)

Display browser for the visualization denoted by id and add the datasets listed in dataset_ids.

galaxy.webapps.galaxy.controllers.workflow module

class galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser(target_tag)

Bases: HTMLParser

__init__(target_tag)

Initialize and reset this instance.

If convert_charrefs is True (the default), all character references are automatically converted to the corresponding Unicode characters.

handle_starttag(tag, attrs)

Called for each start tag.

handle_data(text)

Called for each block of plain text.

class galaxy.webapps.galaxy.controllers.workflow.WorkflowController(app)

Bases: BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings

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

display_by_username_and_slug(trans, username, slug, format='html', **kwargs)

Display workflow based on a username and slug. Format can be html, json, or json-download.

imp(trans, id, **kwargs)

Imports a workflow shared by other users.

rename_async(trans, id, new_name=None, **kwargs)

annotate_async(trans, id, new_annotation=None, **kwargs)

gen_image(trans, id, embed='false', version='', **kwargs)

create(trans, payload=None, **kwd)

save_workflow_as(trans, workflow_name, workflow_data, workflow_annotation='', from_tool_form=False, **kwargs)

Creates a new workflow based on Save As command. It is a new workflow, but is created with workflow_data already present.

editor(trans, id=None, workflow_id=None, version=None, **kwargs)

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)

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)

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)

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.

build_from_current_history(trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None, **kwargs)