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galaxy.webapps.galaxy.controllers package

Galaxy web controllers.

Submodules

galaxy.webapps.galaxy.controllers.admin module

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

Bases: galaxy.webapps.base.controller.JSAppLauncher

__init__(app)

activate_operation = <galaxy.web.framework.helpers.grids.GridOperation object>

client(trans, **kwd)

Endpoint for admin clientside routes.

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

create_new_user(trans, **kwd)

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

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

data_tables_list(trans, **kwd)

data_types_list(trans, **kwd)

delete_operation = <galaxy.web.framework.helpers.grids.GridOperation object>

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

group_list_grid = <galaxy.webapps.galaxy.controllers.admin.GroupListGrid object>

groups_list(trans, **kwargs)

impersonate(trans, **kwd)

impersonate_operation = <galaxy.web.framework.helpers.grids.GridOperation object>

index(trans, **kwd)

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

manage_tool_dependencies(trans, install_dependencies=False, uninstall_dependencies=False, remove_unused_dependencies=False, selected_tool_ids=None, selected_environments_to_uninstall=None, viewkey='View tool-centric dependencies')

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

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

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

purge_operation = <galaxy.web.framework.helpers.grids.GridOperation object>

quota_list_grid = <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid object>

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

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

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

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

resend_activation_email = <galaxy.web.framework.helpers.grids.GridOperation object>

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

role_list_grid = <galaxy.webapps.galaxy.controllers.admin.RoleListGrid object>

roles_list(trans, **kwargs)

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

tool_version_list_grid = <galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid object>

tool_versions_list(trans, **kwd)

undelete_operation = <galaxy.web.framework.helpers.grids.GridOperation object>

user_list_grid = <galaxy.webapps.galaxy.controllers.admin.UserListGrid object>

users_list(trans, **kwd)

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

Bases: galaxy.web.framework.helpers.grids.Grid

class NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, group)

class RolesColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, group)

class StatusColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, group)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, group)

columns = [<galaxy.webapps.galaxy.controllers.admin.GroupListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_sort_key = 'name'

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.Group

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]

title = 'Groups'

title_id = 'groups-grid'

use_paging = True

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

Bases: galaxy.web.framework.helpers.grids.Grid

class AmountColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, quota)

class DescriptionColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, quota)

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, quota)

class NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, quota)

class StatusColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, quota)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, quota)

columns = [<galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DescriptionColumn 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.webapps.galaxy.controllers.admin.QuotaListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_sort_key = 'name'

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.Quota

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]

title = 'Quotas'

use_paging = True

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

Bases: galaxy.web.framework.helpers.grids.Grid

class DescriptionColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, role)

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, role)

class NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, role)

class StatusColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, role)

class TypeColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, role)

class UsersColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, role)

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.admin.RoleListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.TypeColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_sort_key = 'name'

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.Role

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]

title = 'Roles'

title_id = 'roles-grid'

use_paging = True

class galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class ToolIdColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, tool_version)

class ToolVersionsColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, tool_version)

build_initial_query(trans, **kwd)

columns = [<galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolIdColumn object>, <galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolVersionsColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_sort_key = 'tool_id'

model_class

alias of galaxy.model.tool_shed_install.ToolVersion

num_rows_per_page = 50

title = 'Tool versions'

use_paging = True

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

Bases: galaxy.web.framework.helpers.grids.Grid

class ActivatedColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class DiskUsageColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

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

class EmailColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, user)

class ExternalColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class GroupsColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class LastLoginColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

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

class RolesColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class StatusColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class TimeCreatedColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class UserNameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, user)

columns = [<galaxy.webapps.galaxy.controllers.admin.UserListGrid.EmailColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.UserNameColumn 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.webapps.galaxy.controllers.admin.UserListGrid.TimeCreatedColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.ActivatedColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.ExternalColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.PurgedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'purged': 'False'}

default_sort_key = 'email'

get_current_item(trans, **kwargs)

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.User

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]

title = 'Users'

title_id = 'users-grid'

use_default_filter = True

use_paging = True

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

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.get_role(trans, id)

Get a Role from the database by id.

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

Get a User from the database by id.

galaxy.webapps.galaxy.controllers.admin_toolshed module

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

Bases: galaxy.webapps.galaxy.controllers.admin.AdminGalaxy

activate_repository(trans, **kwd)

Activate a repository that was deactivated but not uninstalled.

browse_repositories(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

get_file_contents(trans, file_path, repository_id)

get_tool_dependencies(trans, repository_id, repository_name, repository_owner, changeset_revision)

Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed.

get_updated_repository_information(trans, repository_id, repository_name, repository_owner, changeset_revision)

Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an uninstalled tool shed repository.

initiate_tool_dependency_installation(trans, tool_dependencies, **kwd)

Install specified dependencies for repository tools. The received list of tool_dependencies are the database records for those dependencies defined in the tool_dependencies.xml file (contained in the repository) that should be installed. This allows for filtering out dependencies that have not been checked for installation on the ‘Manage tool dependencies’ page for an installed tool shed repository.

install_latest_repository_revision(trans, **kwd)

Install the latest installable revision of a repository that has been previously installed.

install_repositories(trans, **kwd)

install_tool_dependencies_with_update(trans, **kwd)

Updating an installed tool shed repository where new tool dependencies but no new repository dependencies are included in the updated revision.

installed_repository_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid object>

manage_repository(trans, **kwd)

monitor_repository_installation(trans, **kwd)

prepare_for_install(trans, **kwd)

reinstall_repository(trans, **kwd)

Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository and tool dependencies of the repository.

repository_installation_status_updates(trans, ids=None, status_list=None)

reselect_tool_panel_section(trans, **kwd)

Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates available for the repository in the tool shed, the tool_dependencies and repository_dependencies associated with the updated changeset revision will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metadata from the Galaxy database will not be used since it is outdated.

restore_repository(trans, **kwd)

uninstall_tool_dependencies(trans, **kwd)

update_to_changeset_revision(trans, **kwd)

Update a cloned repository to the latest revision possible.

view_tool_metadata(trans, repository_id, tool_id, **kwd)

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

galaxy.webapps.galaxy.controllers.async module

Upload class

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

Bases: galaxy.webapps.base.controller.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: galaxy.webapps.base.controller.JSAppLauncher

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

create_user(trans, provider, **kwargs)

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

get_cilogon_idps(trans, **kwargs)

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

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)

logout(trans, provider, **kwargs)

galaxy.webapps.galaxy.controllers.data_manager module

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

Bases: galaxy.webapps.base.controller.BaseUIController

data_managers_list(trans, **kwd)

job_info(trans, **kwd)

jobs_list(trans, **kwd)

reload_tool_data_table(trans, **kwd)

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

tool_data_table_info(trans, **kwd)

tool_data_table_info_1(trans, **kwd)

tool_data_table_items(trans, **kwd)

galaxy.webapps.galaxy.controllers.dataset module

class galaxy.webapps.galaxy.controllers.dataset.DatasetInterface(app: galaxy.structured_app.StructuredApp)

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.item_attrs.UsesItemRatings, galaxy.webapps.base.controller.UsesExtendedMetadataMixin

__init__(app: galaxy.structured_app.StructuredApp)

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

copy_datasets(trans, source_history=None, source_content_ids='', target_history_id=None, target_history_ids='', new_history_name='', do_copy=False, **kwd)

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

delete(trans, dataset_id, filename, show_deleted_on_refresh=False)

delete_async(trans, dataset_id, filename)

display(trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)

display_application(trans, dataset_id=None, user_id=None, app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None, **kwds)

Access to external display applications

display_at(trans, dataset_id, filename=None, **kwd)

Sets up a dataset permissions so it is viewable at an external site

display_by_username_and_slug(trans, username, slug, filename=None, preview=True)

Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset’s id.

errors(trans, id)

exit_code(trans, dataset_id=None, **kwargs)

get_annotation_async(trans, id)

get_edit(trans, dataset_id=None, **kwd)

Produces the input definitions available to modify dataset attributes

get_embed_html_async(trans, id)

Returns HTML for embedding a dataset in a page.

get_item_content_async(trans, id)

Returns item content in HTML format.

get_metadata_file(trans, hda_id, metadata_name)

Allows the downloading of metadata files associated with datasets (eg. bai index for bam files)

get_name_and_link_async(trans, id=None)

Returns dataset’s name and link.

hda_deserializer = GalaxyTypeDepends(_do_resolve)

hda_manager = GalaxyTypeDepends(_do_resolve)

history_manager = GalaxyTypeDepends(_do_resolve)

imp(trans, dataset_id=None, **kwd)

Import another user’s dataset via a shared URL; dataset is added to user’s current history.

purge(trans, dataset_id, filename, show_deleted_on_refresh=False)

purge_async(trans, dataset_id, filename)

rate_async(trans, id, rating)

Rate a dataset asynchronously and return updated community data.

set_accessible_async(trans, id=None, accessible=False)

Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute.

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

Allows user to modify parameters of an HDA.

stderr(trans, dataset_id=None, **kwargs)

stdout(trans, dataset_id=None, **kwargs)

transfer_status(trans, dataset_id, filename=None)

Primarily used for the S3ObjectStore - get the status of data transfer if the file is not in cache

undelete(trans, dataset_id, filename)

undelete_async(trans, dataset_id, filename)

unhide(trans, dataset_id, filename)

galaxy.webapps.galaxy.controllers.error module

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

Bases: galaxy.webapps.base.controller.BaseUIController

index(trans)

galaxy.webapps.galaxy.controllers.forms module

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

Bases: galaxy.webapps.base.controller.BaseUIController

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

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

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

forms_list(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

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

Bases: galaxy.web.framework.helpers.grids.Grid

class DescriptionColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, form)

class NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, form)

class StatusColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, user)

class TypeColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, form)

build_initial_query(trans, **kwargs)

columns = [<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.webapps.galaxy.controllers.forms.FormsGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'deleted': 'False'}

default_sort_key = '-update_time'

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.FormDefinitionCurrent

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Forms'

use_paging = True

galaxy.webapps.galaxy.controllers.forms.get_form(trans, form_id)

Get a FormDefinition from the database by id.

galaxy.webapps.galaxy.controllers.history module

class galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class NameURLColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.PublicURLColumn, galaxy.webapps.galaxy.controllers.history.NameColumn

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid.NameURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'public_url': 'All', 'tags': 'All', 'username': 'All'}

default_sort_key = 'update_time'

model_class

alias of galaxy.model.History

num_rows_per_page = 50

title = 'Published Histories'

use_paging = True

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

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.SharableMixin, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.item_attrs.UsesItemRatings

__init__(app: galaxy.structured_app.StructuredApp)

adjust_hidden(trans, id=None, **kwd)

THIS METHOD IS A TEMPORARY ADDITION. It’ll allow us to fix the regression in history-wide actions, and will be removed in the first release after 17.01

as_xml(trans, id=None, show_deleted=None, show_hidden=None)

Return a history in xml format.

create_new_current(trans, name=None)

Create a new, current history for the current user

current_history_json(trans)

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

display_by_username_and_slug(trans, username, slug)

Display history based on a username and slug.

display_structured(trans, id=None)

Display a history as a nested structure showing the jobs and workflow invocations that created each dataset (if any).

get_item(trans, id)

get_name_and_link_async(trans, id=None)

Returns history’s name and link.

history_data(trans, history)

Return the given history in a serialized, dictionary form.

history_export_view = GalaxyTypeDepends(_do_resolve)

history_manager = GalaxyTypeDepends(_do_resolve)

history_serializer = GalaxyTypeDepends(_do_resolve)

index(trans)

list(trans, **kwargs)

List all available histories

list_as_xml(trans)

XML history list for functional tests

list_published(trans, **kwargs)

list_shared(trans, **kwargs)

List histories shared with current user by others

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.

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

Sets the permissions on a history.

published_list_grid = <galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid object>

purge_deleted_datasets(trans)

rate_async(trans, id, rating)

Rate a history asynchronously and return updated community data.

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

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

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

set_accessible_async(trans, id=None, accessible=False)

Set history’s importable attribute and slug.

set_as_current(trans, id)

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

shared_list_grid = <galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid object>

slug_builder = GalaxyTypeDepends(_do_resolve)

stored_list_grid = <galaxy.webapps.galaxy.controllers.history.HistoryListGrid object>

switch_to_history(trans, hist_id=None)

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

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.

view_multiple(trans, include_deleted_histories=False, order='update_time', limit=10)

class galaxy.webapps.galaxy.controllers.history.HistoryListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class DeletedColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.DeletedColumn

get_value(trans, grid, history)

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

class HistoryListNameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.webapps.galaxy.controllers.history.NameColumn

get_link(trans, grid, history)

class ItemCountColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, history)

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn object>, <galaxy.webapps.galaxy.controllers.history.HistoryListGrid.ItemCountColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <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.history.HistoryListGrid.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'deleted': 'False', 'name': 'All', 'sharing': 'All', 'tags': 'All'}

default_sort_key = '-update_time'

get_current_item(trans, **kwargs)

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

info_text = 'Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.'

model_class

alias of galaxy.model.History

num_rows_per_page = 15

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]

title = 'Saved Histories'

use_paging = True

class galaxy.webapps.galaxy.controllers.history.NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, history)

class galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class DatasetsByStateColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, history)

class SharedByColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, history)

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.DatasetsByStateColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid.SharedByColumn object>]

default_sort_key = '-update_time'

model_class

alias of galaxy.model.History

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Histories shared with you by others'

galaxy.webapps.galaxy.controllers.interactive_environments module

API check for whether the current session’s interactive environment launch is ready

class galaxy.webapps.galaxy.controllers.interactive_environments.InteractiveEnvironmentsController(app)

Bases: galaxy.webapps.base.controller.BaseUIController

ready(trans, **kwd)

GET /interactive_environments/ready/

Queries the GIE proxy IPC to determine whether the current user’s session’s GIE launch is ready

Returns:true if ready else false Return type:boolean

galaxy.webapps.galaxy.controllers.library module

class galaxy.webapps.galaxy.controllers.library.Library(app)

Bases: galaxy.webapps.base.controller.BaseUIController

list(trans, **kwd)

galaxy.webapps.galaxy.controllers.openid module

galaxy.webapps.galaxy.controllers.page module

class galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid

Bases: galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Grid for selecting HDAs.

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

model_class

alias of galaxy.model.HistoryDatasetAssociation

title = 'Saved Datasets'

class galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid

Bases: galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Grid for selecting histories.

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

model_class

alias of galaxy.model.History

title = 'Saved Histories'

class galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Bases: galaxy.web.framework.helpers.grids.Grid

Base class for pages’ item selection grids.

class NameColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.TextColumn

get_value(trans, grid, item)

apply_query_filter(trans, query, **kwargs)

default_filter = {'deleted': 'False', 'sharing': 'All'}

default_sort_key = '-update_time'

num_rows_per_page = 10

show_item_checkboxes = True

use_paging = True

class galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'title': 'All', 'username': 'All'}

default_sort_key = 'update_time'

model_class

alias of galaxy.model.Page

title = 'Published Pages'

use_panels = True

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

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.SharableMixin, galaxy.webapps.base.controller.UsesStoredWorkflowMixin, galaxy.webapps.base.controller.UsesVisualizationMixin, galaxy.model.item_attrs.UsesItemRatings

__init__(app: galaxy.structured_app.StructuredApp)

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

Create a new page.

display(trans, id)

display_by_username_and_slug(trans, username, slug)

Display page based on a username and slug.

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

Edit a page’s attributes.

edit_content(trans, id)

Render the main page editor interface.

get_editor_iframe(trans)

Returns the document for the page editor’s iframe.

get_embed_html_async(trans, id)

Returns HTML for embedding a workflow in a page.

get_item(trans, id)

get_name_and_link_async(trans, id=None)

Returns page’s name and link.

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

Get a page from the database by id.

hda_manager = GalaxyTypeDepends(_do_resolve)

history_manager = GalaxyTypeDepends(_do_resolve)

history_serializer = GalaxyTypeDepends(_do_resolve)

list(trans, *args, **kwargs)

List user’s pages.

list_datasets_for_selection(trans, **kwargs)

Returns HTML that enables a user to select one or more datasets.

list_histories_for_selection(trans, **kwargs)

Returns HTML that enables a user to select one or more histories.

list_pages_for_selection(trans, **kwargs)

Returns HTML that enables a user to select one or more pages.

list_published(trans, *args, **kwargs)

list_visualizations_for_selection(trans, **kwargs)

Returns HTML that enables a user to select one or more visualizations.

list_workflows_for_selection(trans, **kwargs)

Returns HTML that enables a user to select one or more workflows.

page_manager = GalaxyTypeDepends(_do_resolve)

rate_async(trans, id, rating)

Rate a page asynchronously and return updated community data.

set_accessible_async(trans, id=None, accessible=False)

Set page’s importable attribute and slug.

slug_builder = GalaxyTypeDepends(_do_resolve)

workflow_manager = GalaxyTypeDepends(_do_resolve)

class galaxy.webapps.galaxy.controllers.page.PageListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class URLColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.PublicURLColumn

get_value(trans, grid, item)

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.page.PageListGrid.URLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'published': 'All', 'sharing': 'All', 'tags': 'All', 'title': 'All'}

default_sort_key = '-update_time'

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]

model_class

alias of galaxy.model.Page

operations = [<galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Pages'

use_panels = True

class galaxy.webapps.galaxy.controllers.page.PageSelectionGrid

Bases: galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Grid for selecting pages.

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

model_class

alias of galaxy.model.Page

title = 'Saved Pages'

class galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid

Bases: galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Grid for selecting visualizations.

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

model_class

alias of galaxy.model.Visualization

title = 'Saved Visualizations'

class galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid

Bases: galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid

Grid for selecting workflows.

columns = [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

model_class

alias of galaxy.model.StoredWorkflow

title = 'Saved Workflows'

galaxy.webapps.galaxy.controllers.page.format_bool(b)

galaxy.webapps.galaxy.controllers.root module

Contains the main interface in the Universe class

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

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

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

__init__(app: galaxy.structured_app.StructuredApp)

clear_history(trans)

Clears the history for a user.

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

Called on any url that does not match a controller method.

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

Returns a file in a format that can successfully be displayed in display_app.

history_add_to(trans, history_id=None, file_data=None, name='Data Added to History', info=None, ext='txt', dbkey='?', copy_access_from=None, **kwd)

Adds a POSTed file to a History.

history_import(trans, id=None, confirm=False, **kwd)

history_manager = GalaxyTypeDepends(_do_resolve)

history_new(trans, name=None)

Create a new history with the given name and refresh the history panel.

history_serializer = GalaxyTypeDepends(_do_resolve)

index(trans, 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, redirect=None, is_logout_redirect=False, **kwd)

User login path for client-side.

welcome(trans)

galaxy.webapps.galaxy.controllers.shed_tool_static module

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

Bases: galaxy.webapps.base.controller.BaseUIController

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

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: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.UsesTagsMixin

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

Add tag to an item.

get_tagging_elt_async(trans, item_id, item_class, elt_context='')

Returns HTML for editing an item’s tags.

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

Remove tag from an item.

retag_async(trans, item_id=None, item_class=None, new_tags=None)

Apply a new set of tags to an item; previous tags are deleted.

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

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: galaxy.webapps.base.controller.BaseUIController

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

Catches the tool id and redirects as needed

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

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

Catches the tool id and redirects as needed

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

Catches the tool id and redirects as needed

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

redirect(trans, redirect_url=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.

galaxy.webapps.galaxy.controllers.user module

Contains the user interface in the Universe class

class galaxy.webapps.galaxy.controllers.user.User(app: galaxy.structured_app.StructuredApp)

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.UsesFormDefinitionsMixin, galaxy.webapps.base.controller.CreatesApiKeysMixin

__init__(app: galaxy.structured_app.StructuredApp)

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)

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

installed_len_files = None

is_outside_grace_period(trans, create_time)

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

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

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

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.

resend_verification(trans)

Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.

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

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

user_manager = GalaxyTypeDepends(_do_resolve)

galaxy.webapps.galaxy.controllers.userskeys module

Contains the user interface in the Universe class

class galaxy.webapps.galaxy.controllers.userskeys.User(app)

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.UsesFormDefinitionsMixin

index(trans, cntrller, **kwd)

admin_api_keys(trans, uid, **kwd)

all_users(trans, **kwd)

get_all_users(trans)

galaxy.webapps.galaxy.controllers.visualization module

class galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class DbKeyColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

filter(trans, user, query, dbkey)

Filter by dbkey through a raw SQL b/c metadata is a BLOB.

class HistoryColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, hda)

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

Sort query using this column.

apply_query_filter(trans, query, **kwargs)

available_tracks = None

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn object>, <galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.DbKeyColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'deleted': 'False', 'shared': 'All'}

default_sort_key = '-hid'

model_class

alias of galaxy.model.HistoryDatasetAssociation

title = 'Add Datasets'

class galaxy.webapps.galaxy.controllers.visualization.LibraryDatasetsSelectionGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

available_tracks = None

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'deleted': 'False'}

default_sort_key = '-id'

model_class

alias of galaxy.model.LibraryDatasetDatasetAssociation

title = 'Add Datasets'

class galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]

default_sort_key = '-update_time'

model_class

alias of galaxy.model.Visualization

show_item_checkboxes = True

title = 'Insert into visualization'

use_paging = False

class galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'title': 'All', 'username': 'All'}

default_sort_key = 'update_time'

model_class

alias of galaxy.model.Visualization

title = 'Published Visualizations'

use_panels = True

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

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.SharableMixin, galaxy.webapps.base.controller.UsesVisualizationMixin, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.item_attrs.UsesItemRatings

__init__(app: galaxy.structured_app.StructuredApp)

circster(trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None)

Display a circster visualization.

copy(trans, id, **kwargs)

display_by_username_and_slug(trans, username, slug)

Display visualization based on a username and slug.

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

Edit a visualization’s attributes.

get_item(trans, id)

get_item_content_async(trans, id)

Returns item content in HTML format.

get_name_and_link_async(trans, id=None)

Returns visualization’s name and link.

gie_list(trans, **kwargs)

hda_manager = GalaxyTypeDepends(_do_resolve)

imp(trans, id)

Import a visualization into user’s workspace.

index(trans, *args, **kwargs)

Lists user’s saved visualizations.

list(trans, **kwargs)

list_history_datasets(trans, **kwargs)

List a history’s datasets that can be added to a visualization.

list_libraries(trans, **kwargs)

List all libraries that can be used for selecting datasets.

list_library_datasets(trans, **kwargs)

List a library’s datasets that can be added to a visualization.

list_published(trans, *args, **kwargs)

list_tracks(trans, **kwargs)

phyloviz(trans, id=None, dataset_id=None, tree_index=0, **kwargs)

rate_async(trans, id, rating)

Rate a visualization asynchronously and return updated community data.

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}

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

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

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

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

set_accessible_async(trans, id=None, accessible=False)

Set visualization’s importable attribute and slug.

slug_builder = GalaxyTypeDepends(_do_resolve)

sweepster(trans, id=None, hda_ldda=None, dataset_id=None, regions=None)

Displays a sweepster visualization using the incoming parameters. If id is available, get the visualization with the given id; otherwise, create a new visualization using a given dataset and regions.

trackster(trans, **kwargs)

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

class galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'deleted': 'False', 'sharing': 'All', 'tags': 'All', 'title': 'All'}

default_sort_key = '-update_time'

get_display_name(trans, item)

get_url_args(item)

Returns dictionary used to create item link.

model_class

alias of galaxy.model.Visualization

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Saved Visualizations'

galaxy.webapps.galaxy.controllers.workflow module

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

Bases: html.parser.HTMLParser

__init__(target_tag)

handle_data(text)

Called for each block of plain text.

handle_starttag(tag, attrs)

Called for each start tag.

class galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid

Bases: galaxy.web.framework.helpers.grids.Grid

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'public_url': 'All', 'tags': 'All', 'username': 'All'}

default_sort_key = 'update_time'

model_class

alias of galaxy.model.StoredWorkflow

num_rows_per_page = 50

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Published Workflows'

use_paging = True

class galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid

Bases: galaxy.web.framework.helpers.grids.Grid

class StepsColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)

Bases: galaxy.web.framework.helpers.grids.GridColumn

get_value(trans, grid, workflow)

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid.StepsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

default_filter = {'name': 'All', 'tags': 'All'}

default_sort_key = '-update_time'

model_class

alias of galaxy.model.StoredWorkflow

operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]

title = 'Saved Workflows'

use_panels = True

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

Bases: galaxy.webapps.base.controller.BaseUIController, galaxy.webapps.base.controller.SharableMixin, galaxy.webapps.base.controller.UsesStoredWorkflowMixin, galaxy.model.item_attrs.UsesItemRatings

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

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)

copy(trans, id, save_as_name=None)

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

delete(trans, id=None)

Mark a workflow as deleted

display_by_id(trans, id)

Display workflow based on id.

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

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

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

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.

export_to_file(trans, id)

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_myexp(trans, id, myexp_username, myexp_password)

Exports a workflow to myExperiment website.

for_direct_import(trans, id)

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.

gen_image(trans, id)

get_embed_html_async(trans, id)

Returns HTML for embedding a workflow in a page.

get_item(trans, id)

get_item_content_async(trans, id)

Returns item content in HTML format.

get_name_and_link_async(trans, id=None)

Returns workflow’s name and link.

imp(trans, id, **kwargs)

Imports a workflow shared by other users.

list(trans)

Render workflow main page (management of existing workflows)

list_grid(trans, **kwargs)

List user’s stored workflows.

list_published(trans, **kwargs)

load_workflow(trans, id, version=None)

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.

published_list_grid = <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid object>

rate_async(trans, id, rating)

Rate a workflow asynchronously and return updated community data.

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

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

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

set_accessible_async(trans, id=None, accessible=False)

Set workflow’s importable attribute and slug.

set_public_username(trans, id, username, **kwargs)

Set user’s public username and delegate to sharing()

share(trans, id, email='', use_panels=False)

sharing(trans, id, **kwargs)

Handle workflow sharing.

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

stored_list_grid = <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid object>