galaxy.webapps.galaxy.controllers package

Galaxy web controllers.

Submodules

galaxy.webapps.galaxy.controllers.admin module

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

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

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 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)

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 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 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 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 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)

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 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 APIKeyColumn(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)

title = 'Users'

title_id = 'users-grid'

model_class

alias of galaxy.model.User

default_sort_key = 'email'

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

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

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>]

num_rows_per_page = 50

use_paging = True

get_current_item(trans, **kwargs)

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

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, role)

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 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 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 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 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)

title = 'Roles'

title_id = 'roles-grid'

model_class

alias of galaxy.model.Role

default_sort_key = 'name'

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

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

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>]

num_rows_per_page = 50

use_paging = True

apply_query_filter(trans, query, **kwargs)

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 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 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 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)

title = 'Groups'

title_id = 'groups-grid'

model_class

alias of galaxy.model.Group

default_sort_key = 'name'

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

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

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>]

num_rows_per_page = 50

use_paging = True

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

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, 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 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 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)

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)

title = 'Quotas'

model_class

alias of galaxy.model.Quota

default_sort_key = 'name'

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

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

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>]

num_rows_per_page = 50

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)

title = 'Tool versions'

model_class

alias of galaxy.model.tool_shed_install.ToolVersion

default_sort_key = 'tool_id'

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

global_actions = []

operations = []

standard_filters = []

default_filter = {}

num_rows_per_page = 50

use_paging = True

build_initial_query(trans, **kwd)

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

Bases: galaxy.web.base.controller.JSAppLauncher, galaxy.actions.admin.AdminActions, galaxy.web.base.controller.UsesQuotaMixin, galaxy.web.params.QuotaParamParser

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>

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

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

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

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

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

index(trans, *args, **kwargs)

client(trans, *args, **kwargs)

Endpoint for admin clientside routes.

data_tables_list(trans, *args, **kwargs)

data_types_list(trans, *args, **kwargs)

users_list(trans, *args, **kwargs)

quotas_list(trans, *args, **kwargs)

create_quota(trans, *args, **kwargs)

rename_quota(trans, *args, **kwargs)

manage_users_and_groups_for_quota(trans, *args, **kwargs)

edit_quota(trans, *args, **kwargs)

set_quota_default(trans, *args, **kwargs)

impersonate(trans, *args, **kwargs)

check_for_tool_dependencies(trans, migration_stage)

review_tool_migration_stages(trans, *args, **kwargs)

center(trans, *args, **kwargs)

tool_versions_list(trans, *args, **kwargs)

roles_list(trans, *args, **kwargs)

create_role(trans, *args, **kwargs)

rename_role(trans, *args, **kwargs)

manage_users_and_groups_for_role(trans, *args, **kwargs)

groups_list(trans, *args, **kwargs)

rename_group(trans, *args, **kwargs)

manage_users_and_roles_for_group(trans, *args, **kwargs)

create_group(trans, *args, **kwargs)

create_new_user(trans, *args, **kwargs)

reset_user_password(trans, *args, **kwargs)

manage_roles_and_groups_for_user(trans, *args, **kwargs)

jobs(trans, *args, **kwargs)

job_info(trans, *args, **kwargs)

manage_tool_dependencies(trans, *args, **kwargs)

sanitize_whitelist(trans, *args, **kwargs)

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

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

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

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

activate_repository(trans, *args, **kwargs)

Activate a repository that was deactivated but not uninstalled.

browse_repository(trans, *args, **kwargs)

browse_repositories(trans, *args, **kwargs)

restore_repository(trans, *args, **kwargs)

browse_tool_dependency(trans, *args, **kwargs)

browse_tool_shed(trans, *args, **kwargs)

browse_toolsheds(trans, *args, **kwargs)

browse_tool_sheds(trans, *args, **kwargs)

check_for_updates(trans, *args, **kwargs)

Send a request to the relevant tool shed to see if there are any updates.

deactivate_or_uninstall_repository(trans, *args, **kwargs)

Handle all changes when a tool shed repository is being deactivated or uninstalled. Notice that if the repository contents include a file named tool_data_table_conf.xml.sample, its entries are not removed from the defined config.shed_tool_data_table_config. This is because it becomes a bit complex to determine if other installed repositories include tools that require the same entry. For now we’ll never delete entries from config.shed_tool_data_table_config, but we may choose to do so in the future if it becomes necessary.

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

find_tools_in_tool_shed(trans, *args, **kwargs)

find_workflows_in_tool_shed(trans, *args, **kwargs)

generate_workflow_image(trans, *args, **kwargs)

Return an svg image representation of a workflow dictionary created when the workflow was exported.

get_file_contents(trans, *args, **kwargs)

get_tool_dependencies(trans, *args, **kwargs)

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, *args, **kwargs)

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.

import_workflow(trans, *args, **kwargs)

Import a workflow contained in an installed tool shed repository into Galaxy.

initiate_tool_dependency_installation(trans, *args, **kwargs)

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, *args, **kwargs)

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

install_tool_dependencies_with_update(trans, *args, **kwargs)

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

install_repositories(trans, *args, **kwargs)

manage_repository(trans, *args, **kwargs)

manage_repository_tool_dependencies(trans, *args, **kwargs)

manage_tool_dependencies(trans, *args, **kwargs)

monitor_repository_installation(trans, *args, **kwargs)

open_folder(trans, *args, **kwargs)

prepare_for_install(trans, *args, **kwargs)

purge_repository(trans, *args, **kwargs)

Purge a “white ghost” repository from the database.

reinstall_repository(trans, *args, **kwargs)

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, *args, **kwargs)

reselect_tool_panel_section(trans, *args, **kwargs)

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.

reset_metadata_on_selected_installed_repositories(trans, *args, **kwargs)

reset_repository_metadata(trans, *args, **kwargs)

Reset all metadata on a single installed tool shed repository.

reset_to_install(trans, *args, **kwargs)

An error occurred while cloning the repository, so reset everything necessary to enable another attempt.

tool_dependency_status_updates(trans, *args, **kwargs)

uninstall_tool_dependencies(trans, *args, **kwargs)

update_to_changeset_revision(trans, *args, **kwargs)

Update a cloned repository to the latest revision possible.

view_tool_metadata(trans, *args, **kwargs)

update_tool_shed_status_for_installed_repository(trans, *args, **kwargs)

view_workflow(trans, *args, **kwargs)

Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.

galaxy.webapps.galaxy.controllers.async module

Upload class

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

Bases: galaxy.web.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.web.base.controller.JSAppLauncher

index(trans, *args, **kwargs)

GET /authnz/

returns a list of third-party identities associated with the user.

Parameters:

• trans (galaxy.web.framework.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, *args, **kwargs)

callback(trans, provider, **kwargs)

disconnect(trans, *args, **kwargs)

galaxy.webapps.galaxy.controllers.biostar module

galaxy.webapps.galaxy.controllers.data_manager module

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

Bases: galaxy.web.base.controller.BaseUIController

data_managers_list(trans, *args, **kwargs)

jobs_list(trans, *args, **kwargs)

job_info(trans, *args, **kwargs)

tool_data_table_info(trans, *args, **kwargs)

tool_data_table_info_1(trans, **kwd)

reload_tool_data_tables(trans, *args, **kwargs)

tool_data_table_items(trans, *args, **kwargs)

reload_tool_data_table(trans, *args, **kwargs)

galaxy.webapps.galaxy.controllers.dataset module

class galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid

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

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)

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, hda)

get_accepted_filters()

Returns a list of accepted filters for this column.

title = 'Saved Datasets'

model_class

alias of galaxy.model.HistoryDatasetAssociation

default_sort_key = '-update_time'

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.dataset.HistoryColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.webapps.galaxy.controllers.dataset.StatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

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

standard_filters = []

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

use_paging = True

num_rows_per_page = 50

build_initial_query(trans, **kwargs)

class galaxy.webapps.galaxy.controllers.dataset.DatasetInterface(app)

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

stored_list_grid = <galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid object>

__init__(app)

errors(trans, id)

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

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

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

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

get_metadata_file(trans, hda_id, metadata_name)

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

transfer_status(trans, *args, **kwargs)

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

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

get_edit(trans, *args, **kwargs)

Produces the input definitions available to modify dataset attributes

set_edit(trans, *args, **kwargs)

Allows user to modify parameters of an HDA.

list(trans, *args, **kwargs)

List all available datasets

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

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

get_name_and_link_async(trans, *args, **kwargs)

Returns dataset’s name and link.

get_embed_html_async(trans, id)

Returns HTML for embedding a dataset in a page.

set_accessible_async(trans, *args, **kwargs)

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

rate_async(trans, *args, **kwargs)

Rate a dataset asynchronously and return updated community data.

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.

get_item_content_async(trans, id)

Returns item content in HTML format.

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

get_annotation_async(trans, id)

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

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

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

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

delete_async(trans, dataset_id, filename)

undelete(trans, dataset_id, filename)

undelete_async(trans, dataset_id, filename)

unhide(trans, dataset_id, filename)

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

purge_async(trans, dataset_id, filename)

show_params(trans, dataset_id=None, from_noframe=None, **kwd)

Show the parameters used for the job associated with an HDA

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

galaxy.webapps.galaxy.controllers.error module

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

Bases: galaxy.web.base.controller.BaseUIController

index(trans)

galaxy.webapps.galaxy.controllers.forms module

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

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, form)

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 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)

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)

title = 'Forms'

model_class

alias of galaxy.model.FormDefinitionCurrent

default_sort_key = '-update_time'

num_rows_per_page = 50

use_paging = True

default_filter = {'deleted': 'False'}

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

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

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

build_initial_query(trans, **kwargs)

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

Bases: galaxy.web.base.controller.BaseUIController

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

forms_list(trans, *args, **kwargs)

create_form(trans, *args, **kwargs)

edit_form(trans, *args, **kwargs)

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.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.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.HistoryListGrid

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

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)

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 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)

build_initial_query(trans, **kwargs)

title = 'Saved Histories'

model_class

alias of galaxy.model.History

default_sort_key = '-update_time'

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

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

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>]

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

num_rows_per_page = 15

use_paging = True

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

get_current_item(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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)

title = 'Histories shared with you by others'

model_class

alias of galaxy.model.History

default_sort_key = '-update_time'

default_filter = {}

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

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

standard_filters = []

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

title = 'Published Histories'

model_class

alias of galaxy.model.History

default_sort_key = 'update_time'

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

use_paging = True

num_rows_per_page = 50

columns = [<galaxy.webapps.galaxy.controllers.history.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>]

operations = []

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

Bases: galaxy.web.base.controller.BaseUIController, galaxy.web.base.controller.SharableMixin, galaxy.model.item_attrs.UsesAnnotations, galaxy.model.item_attrs.UsesItemRatings, galaxy.web.base.controller.ExportsHistoryMixin, galaxy.web.base.controller.ImportsHistoryMixin

__init__(app)

index(trans)

list_as_xml(trans)

XML history list for functional tests

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

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

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

list_published(trans, *args, **kwargs)

list(trans, *args, **kwargs)

List all available histories

list_shared(trans, *args, **kwargs)

List histories shared with current user by others

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

Return a history in xml format.

display_structured(trans, *args, **kwargs)

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

view(trans, *args, **kwargs)

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

view_multiple(trans, *args, **kwargs)

display_by_username_and_slug(trans, username, slug)

Display history based on a username and slug.

permissions(trans, *args, **kwargs)

Sets the permissions on a history.

make_private(trans, *args, **kwargs)

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

share(trans, *args, **kwargs)

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

share_restricted(trans, *args, **kwargs)

purge_deleted_datasets(trans)

delete(trans, id, purge=False)

Delete the history – this does not require a logged in user.

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

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

rate_async(trans, *args, **kwargs)

Rate a history asynchronously and return updated community data.

export_archive(trans, id=None, gzip=True, include_hidden=False, include_deleted=False, preview=False)

Export a history to an archive.

get_name_and_link_async(trans, *args, **kwargs)

Returns history’s name and link.

set_accessible_async(trans, *args, **kwargs)

Set history’s importable attribute and slug.

rename(trans, *args, **kwargs)

switch_to_history(trans, *args, **kwargs)

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

get_item(trans, id)

history_data(trans, history)

Return the given history in a serialized, dictionary form.

set_as_current(trans, *args, **kwargs)

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

current_history_json(trans, *args, **kwargs)

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

create_new_current(trans, *args, **kwargs)

Create a new, current history for the current user

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.web.base.controller.BaseUIController

ready(trans, *args, **kwargs)

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.web.base.controller.BaseUIController

list(trans, **kwd)

galaxy.webapps.galaxy.controllers.page module

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

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)

use_panels = True

title = 'Pages'

model_class

alias of galaxy.model.Page

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

default_sort_key = '-update_time'

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.page.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>]

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

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>]

apply_query_filter(trans, query, **kwargs)

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

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

use_panels = True

title = 'Published Pages'

model_class

alias of galaxy.model.Page

default_sort_key = 'update_time'

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

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>]

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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)

show_item_checkboxes = True

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

default_sort_key = '-update_time'

use_paging = True

num_rows_per_page = 10

apply_query_filter(trans, query, **kwargs)

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

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

Grid for selecting histories.

title = 'Saved Histories'

model_class

alias of galaxy.model.History

columns = [<galaxy.webapps.galaxy.controllers.page.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>]

apply_query_filter(trans, query, **kwargs)

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

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

Grid for selecting HDAs.

title = 'Saved Datasets'

model_class

alias of galaxy.model.HistoryDatasetAssociation

columns = [<galaxy.webapps.galaxy.controllers.page.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>]

apply_query_filter(trans, query, **kwargs)

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

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

Grid for selecting workflows.

title = 'Saved Workflows'

model_class

alias of galaxy.model.StoredWorkflow

columns = [<galaxy.webapps.galaxy.controllers.page.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>]

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

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

Grid for selecting pages.

title = 'Saved Pages'

model_class

alias of galaxy.model.Page

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>]

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

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

Grid for selecting visualizations.

title = 'Saved Visualizations'

model_class

alias of galaxy.model.Visualization

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>]

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

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

__init__(app)

list(trans, *args, **kwargs)

List user’s pages.

list_published(trans, *args, **kwargs)

create(trans, *args, **kwargs)

Create a new page.

edit(trans, *args, **kwargs)

Edit a page’s attributes.

edit_content(trans, *args, **kwargs)

Render the main page editor interface.

share(trans, *args, **kwargs)

Handle sharing with an individual user.

save(trans, *args, **kwargs)

display(trans, *args, **kwargs)

display_by_username_and_slug(trans, username, slug)

Display page based on a username and slug.

set_accessible_async(trans, *args, **kwargs)

Set page’s importable attribute and slug.

rate_async(trans, *args, **kwargs)

Rate a page asynchronously and return updated community data.

get_embed_html_async(trans, id)

Returns HTML for embedding a workflow in a page.

get_name_and_link_async(trans, *args, **kwargs)

Returns page’s name and link.

list_histories_for_selection(trans, *args, **kwargs)

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

list_workflows_for_selection(trans, *args, **kwargs)

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

list_visualizations_for_selection(trans, *args, **kwargs)

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

list_pages_for_selection(trans, *args, **kwargs)

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

list_datasets_for_selection(trans, *args, **kwargs)

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

get_editor_iframe(trans)

Returns the document for the page editor’s iframe.

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

Get a page from the database by id.

get_item(trans, id)

galaxy.webapps.galaxy.controllers.root module

Contains the main interface in the Universe class

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

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

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

__init__(app)

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

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

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, **kwd)

User login path for client-side.

tool_search(trans, *args, **kwargs)

Searches the tool database and returns data for any tool whose text matches the query.

Data are returned in JSON format.

tool_help(trans, id)

Return help page for tool identified by ‘id’ if available

display(trans, id=None, hid=None, tofile=None, toext='.txt', encoded_id=None, **kwd)

Returns data directly into the browser.

Sets the mime-type according to the extension.

Used by the twill tool test driver - used anywhere else? Would like to drop hid argument and path if unneeded now. Likewise, would like to drop encoded_id=XXX and use assume id is encoded (likely id wouldn’t be coming in encoded if this is used anywhere else though.)

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

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

history_delete(trans, id)

Backward compatibility with check_galaxy script.

clear_history(trans)

Clears the history for a user.

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

history_new(trans, name=None)

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

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.

dataset_make_primary(trans, id=None)

Copies a dataset and makes primary.

welcome(trans)

bucket_proxy(trans, bucket=None, **kwd)

echo(trans, **kwd)

Echos parameters (debugging).

echo_json(trans, *args, **kwargs)

Echos parameters as JSON (debugging).

Attempts to parse values passed as boolean, float, then int. Defaults to string. Non-recursive (will not parse lists).

generate_error(trans, code=500)

Raises an exception (debugging).

generate_json_error(trans, *args, **kwargs)

Raises an exception (debugging).

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.web.base.controller.BaseUIController, galaxy.web.base.controller.UsesTagsMixin

get_tagging_elt_async(trans, *args, **kwargs)

Returns HTML for editing an item’s tags.

add_tag_async(trans, *args, **kwargs)

Add tag to an item.

remove_tag_async(trans, *args, **kwargs)

Remove tag from an item.

retag_async(trans, *args, **kwargs)

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

tag_autocomplete_data(trans, *args, **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: galaxy.web.base.controller.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

redirect(trans, redirect_url=None, **kwd)

galaxy.webapps.galaxy.controllers.user module

Contains the user interface in the Universe class

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

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

installed_len_files = None

__init__(app)

login(trans, *args, **kwargs)

resend_verification(trans)

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, *args, **kwargs)

activate(trans, **kwd)

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

change_password(trans, *args, **kwargs)

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, *args, **kwargs)

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

galaxy.webapps.galaxy.controllers.userskeys module

Contains the user interface in the Universe class

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

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

index(trans, *args, **kwargs)

admin_api_keys(trans, *args, **kwargs)

all_users(trans, *args, **kwargs)

get_all_users(trans, *args, **kwargs)

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.

available_tracks = None

title = 'Add Datasets'

model_class

alias of galaxy.model.HistoryDatasetAssociation

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

default_sort_key = '-hid'

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.HistoryColumn object>, <galaxy.webapps.galaxy.controllers.visualization.DbKeyColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

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

available_tracks = None

title = 'Add Datasets'

model_class

alias of galaxy.model.LibraryDatasetDatasetAssociation

default_filter = {'deleted': 'False'}

default_sort_key = '-id'

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>]

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

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

title = 'Insert into visualization'

model_class

alias of galaxy.model.Visualization

default_sort_key = '-update_time'

use_paging = False

show_item_checkboxes = True

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

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

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

get_url_args(item)

Returns dictionary used to create item link.

get_display_name(trans, item)

title = 'Saved Visualizations'

model_class

alias of galaxy.model.Visualization

default_sort_key = '-update_time'

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

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>]

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>]

apply_query_filter(trans, query, **kwargs)

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

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

use_panels = True

title = 'Published Visualizations'

model_class

alias of galaxy.model.Visualization

default_sort_key = 'update_time'

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

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>]

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

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

__init__(app)

list_libraries(trans, *args, **kwargs)

List all libraries that can be used for selecting datasets.

list_history_datasets(trans, *args, **kwargs)

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

list_library_datasets(trans, *args, **kwargs)

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

list_tracks(trans, *args, **kwargs)

list_published(trans, *args, **kwargs)

list(trans, *args, **kwargs)

index(trans, *args, **kwargs)

Lists user’s saved visualizations.

copy(trans, *args, **kwargs)

set_accessible_async(trans, *args, **kwargs)

Set visualization’s importable attribute and slug.

rate_async(trans, *args, **kwargs)

Rate a visualization asynchronously and return updated community data.

imp(trans, *args, **kwargs)

Import a visualization into user’s workspace.

share(trans, *args, **kwargs)

Handle sharing a visualization with a particular user.

display_by_username_and_slug(trans, username, slug)

Display visualization based on a username and slug.

get_name_and_link_async(trans, *args, **kwargs)

Returns visualization’s name and link.

get_item_content_async(trans, id)

Returns item content in HTML format.

save(trans, *args, **kwargs)

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

edit(trans, *args, **kwargs)

Edit a visualization’s attributes.

render(trans, *args, **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, *args, **kwargs)

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

trackster(trans, *args, **kwargs)

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

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

Display a circster visualization.

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.

get_item(trans, id)

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

gie_list(trans, *args, **kwargs)

bookmarks_from_dataset(trans, *args, **kwargs)

galaxy.webapps.galaxy.controllers.workflow module

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)

use_panels = True

title = 'Saved Workflows'

model_class

alias of galaxy.model.StoredWorkflow

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

default_sort_key = '-update_time'

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

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>]

apply_query_filter(trans, query, **kwargs)

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

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

title = 'Published Workflows'

model_class

alias of galaxy.model.StoredWorkflow

default_sort_key = 'update_time'

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

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>]

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

num_rows_per_page = 50

use_paging = True

build_initial_query(trans, **kwargs)

apply_query_filter(trans, query, **kwargs)

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

Bases: HTMLParser.HTMLParser

__init__(target_tag)

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

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

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

list_grid(trans, *args, **kwargs)

List user’s stored workflows.

list(trans, *args, **kwargs)

Render workflow main page (management of existing workflows)

list_published(trans, *args, **kwargs)

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.

display_by_id(trans, id)

Display workflow based on id.

get_item_content_async(trans, id)

Returns item content in HTML format.

share(trans, *args, **kwargs)

sharing(trans, *args, **kwargs)

Handle workflow sharing.

set_public_username(trans, *args, **kwargs)

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

imp(trans, *args, **kwargs)

Imports a workflow shared by other users.

rename_async(trans, *args, **kwargs)

annotate_async(trans, *args, **kwargs)

rate_async(trans, *args, **kwargs)

Rate a workflow asynchronously and return updated community data.

set_accessible_async(trans, *args, **kwargs)

Set workflow’s importable attribute and slug.

get_embed_html_async(trans, id)

Returns HTML for embedding a workflow in a page.

get_name_and_link_async(trans, *args, **kwargs)

Returns workflow’s name and link.

gen_image(trans, *args, **kwargs)

copy(trans, *args, **kwargs)

create(trans, *args, **kwargs)

save_workflow_as(trans, *args, **kwargs)

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

delete(trans, id=None)

Mark a workflow as deleted

editor(trans, *args, **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, *args, **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.

export_to_myexp(trans, *args, **kwargs)

Exports a workflow to myExperiment website.

for_direct_import(trans, *args, **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, *args, **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.

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)

get_item(trans, id)

tag_outputs(trans, id, **kwargs)