controllers Package

controllers Package

Galaxy web controllers.

admin Module

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

Bases: galaxy.web.base.controller.BaseUIController, galaxy.web.base.controllers.admin.Admin, galaxy.actions.admin.AdminActions, galaxy.web.base.controller.UsesQuotaMixin, galaxy.web.params.QuotaParamParser

check_for_tool_dependencies(trans, migration_stage)

create_quota(trans, *args, **kwargs)

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

display_applications(trans, *args, **kwargs)

edit_quota(trans, *args, **kwargs)

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

impersonate(trans, *args, **kwargs)

manage_users_and_groups_for_quota(trans, *args, **kwargs)

mark_quota_deleted(trans, *args, **kwargs)

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

purge_quota(trans, *args, **kwargs)

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

quotas(trans, *args, **kwargs)

recalculate_user_disk_usage(trans, *args, **kwargs)

reload_display_application(trans, *args, **kwargs)

rename_quota(trans, *args, **kwargs)

review_tool_migration_stages(trans, *args, **kwargs)

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

set_quota_default(trans, *args, **kwargs)

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

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

undelete_quota(trans, *args, **kwargs)

unset_quota_default(trans, *args, **kwargs)

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

view_datatypes_registry(trans, *args, **kwargs)

view_tool_data_tables(trans, *args, **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, inbound=False)

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

get_value(trans, grid, group)

class GroupListGrid.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, inbound=False)

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

get_value(trans, grid, group)

class GroupListGrid.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, inbound=False)

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

get_value(trans, grid, group)

class GroupListGrid.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, inbound=False)

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

get_value(trans, grid, group)

GroupListGrid.columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object at 0x7f85da4506d0>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f85dac2d5d0>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object at 0x7f85dac2d250>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f85dac2ded0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85dac2d290>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dac2d850>]

GroupListGrid.default_sort_key = 'name'

GroupListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85dac2da90>]

GroupListGrid.model_class

alias of Group

GroupListGrid.num_rows_per_page = 50

GroupListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2dd90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2dd10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d9d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d910>]

GroupListGrid.preserve_state = False

GroupListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2d790>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2df90>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2dad0>]

GroupListGrid.template = '/admin/dataset_security/group/grid.mako'

GroupListGrid.title = 'Groups'

GroupListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

class QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

class QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

class QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

class QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

class QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, quota)

QuotaListGrid.columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object at 0x7f85dac2de90>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object at 0x7f85dac2d990>, <galaxy.webapps.galaxy.controllers.admin.AmountColumn object at 0x7f85dac2d310>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f85dac2d810>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f85dac2d390>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f85dac2d6d0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85dac2dcd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dac2dc90>]

QuotaListGrid.default_sort_key = 'name'

QuotaListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85dac2df10>]

QuotaListGrid.model_class

alias of Quota

QuotaListGrid.num_rows_per_page = 50

QuotaListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d110>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d510>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2dc10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d750>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d210>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d610>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d1d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d2d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dac2d650>]

QuotaListGrid.preserve_state = False

QuotaListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2dd50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2dc50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85dac2da50>]

QuotaListGrid.template = '/admin/quota/grid.mako'

QuotaListGrid.title = 'Quotas'

QuotaListGrid.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, inbound=False)

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

get_value(trans, grid, role)

class RoleListGrid.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, inbound=False)

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

get_value(trans, grid, role)

class RoleListGrid.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, inbound=False)

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

get_value(trans, grid, role)

class RoleListGrid.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, inbound=False)

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

get_value(trans, grid, role)

class RoleListGrid.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, inbound=False)

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

get_value(trans, grid, role)

class RoleListGrid.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, inbound=False)

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

get_value(trans, grid, role)

RoleListGrid.apply_query_filter(trans, query, **kwargs)

RoleListGrid.columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object at 0x7f85da450610>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object at 0x7f85cd960f50>, <galaxy.webapps.galaxy.controllers.admin.TypeColumn object at 0x7f85cecd55d0>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f85da450990>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f85da450710>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f85da450910>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85da450890>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85da450a90>]

RoleListGrid.default_sort_key = 'name'

RoleListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85da450810>]

RoleListGrid.model_class

alias of Role

RoleListGrid.num_rows_per_page = 50

RoleListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85da450750>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85da450a10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85da4509d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85da4507d0>]

RoleListGrid.preserve_state = False

RoleListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85da450ad0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85da450650>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85da450950>]

RoleListGrid.template = '/admin/dataset_security/role/grid.mako'

RoleListGrid.title = 'Roles'

RoleListGrid.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, inbound=False)

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

get_value(trans, grid, tool_version)

class ToolVersionListGrid.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, inbound=False)

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

get_value(trans, grid, tool_version)

ToolVersionListGrid.build_initial_query(trans, **kwd)

ToolVersionListGrid.columns = [<galaxy.webapps.galaxy.controllers.admin.ToolIdColumn object at 0x7f85dac2d0d0>, <galaxy.webapps.galaxy.controllers.admin.ToolVersionsColumn object at 0x7f85dac2dbd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dac2d710>]

ToolVersionListGrid.default_filter = {}

ToolVersionListGrid.default_sort_key = 'tool_id'

ToolVersionListGrid.global_actions = []

ToolVersionListGrid.model_class

alias of ToolVersion

ToolVersionListGrid.num_rows_per_page = 50

ToolVersionListGrid.operations = []

ToolVersionListGrid.preserve_state = False

ToolVersionListGrid.standard_filters = []

ToolVersionListGrid.template = '/admin/tool_version/grid.mako'

ToolVersionListGrid.title = 'Tool versions'

ToolVersionListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

class UserListGrid.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, inbound=False)

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

get_value(trans, grid, user)

UserListGrid.columns = [<galaxy.webapps.galaxy.controllers.admin.EmailColumn object at 0x7f85d5b695d0>, <galaxy.webapps.galaxy.controllers.admin.UserNameColumn object at 0x7f85d5b693d0>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f85d5b69690>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object at 0x7f85d5b69e50>, <galaxy.webapps.galaxy.controllers.admin.ExternalColumn object at 0x7f85d5b69e90>, <galaxy.webapps.galaxy.controllers.admin.LastLoginColumn object at 0x7f85d5b69dd0>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f85d5b69450>, <galaxy.webapps.galaxy.controllers.admin.TimeCreatedColumn object at 0x7f85d5b69810>, <galaxy.webapps.galaxy.controllers.admin.ActivatedColumn object at 0x7f85d5b69290>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85d5b69610>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85d5b69f90>]

UserListGrid.default_sort_key = 'email'

UserListGrid.get_current_item(trans, **kwargs)

UserListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85d5b692d0>]

UserListGrid.model_class

alias of User

UserListGrid.num_rows_per_page = 50

UserListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d5b697d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d5b69850>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d5b69310>]

UserListGrid.preserve_state = False

UserListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85d5b69c50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85d5b69590>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85d5b69b50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85d5b69d10>]

UserListGrid.template = '/admin/user/grid.mako'

UserListGrid.title = 'Users'

UserListGrid.use_paging = True

admin_toolshed Module

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

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

activate_repository(trans, *args, **kwargs)

Activate a repository that was deactivated but not uninstalled.

browse_repositories(trans, *args, **kwargs)

browse_repository(trans, *args, **kwargs)

browse_tool_dependency(trans, *args, **kwargs)

browse_tool_shed(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.

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

manage_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.

repair_repository(trans, *args, **kwargs)

Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as each repository’s tool dependencies.

repair_tool_shed_repositories(trans, *args, **kwargs)

Repair specified tool shed repositories.

repository_installation_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid object>

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.

set_tool_versions(trans, *args, **kwargs)

Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the metadata for the repository’s revision in the Galaxy database.

tool_dependency_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid object>

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.

update_tool_shed_status_for_installed_repository(trans, *args, **kwargs)

view_tool_metadata(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.

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

cloudlaunch Module

data_admin Module

dataset Module

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

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, chunk=None, **kwd)

display_application(trans, dataset_id=None, user_id=None, app_name=None, link_name=None, app_action=None, action_param=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.

edit(trans, dataset_id=None, filename=None, hid=None, **kwd)

Allows user to modify parameters of an HDA.

errors(trans, id)

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

get_annotation_async(trans, id)

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, *args, **kwargs)

Returns dataset’s name and link.

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

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

list(trans, *args, **kwargs)

List all available datasets

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

purge_async(trans, dataset_id, filename)

rate_async(trans, *args, **kwargs)

Rate a dataset asynchronously and return updated community data.

report_error(trans, id, email='', message='', **kwd)

set_accessible_async(trans, *args, **kwargs)

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

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

Show the parameters used for the job associated with an HDA

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

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

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

transfer_status(trans, *args, **kwargs)

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)

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, inbound=False)

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

get_value(trans, grid, hda)

class HistoryDatasetAssociationListGrid.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, inbound=False)

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

get_accepted_filters()

Returns a list of accepted filters for this column.

get_value(trans, grid, hda)

HistoryDatasetAssociationListGrid.build_initial_query(trans, **kwargs)

HistoryDatasetAssociationListGrid.columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85ccc1a950>, <galaxy.webapps.galaxy.controllers.dataset.HistoryColumn object at 0x7f85cc9bee90>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cc9bee10>, <galaxy.webapps.galaxy.controllers.dataset.StatusColumn object at 0x7f85cc9beed0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc9bef10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cc9bef50>]

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

HistoryDatasetAssociationListGrid.default_sort_key = '-update_time'

HistoryDatasetAssociationListGrid.model_class

alias of HistoryDatasetAssociation

HistoryDatasetAssociationListGrid.num_rows_per_page = 50

HistoryDatasetAssociationListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cc9bef90>]

HistoryDatasetAssociationListGrid.preserve_state = False

HistoryDatasetAssociationListGrid.standard_filters = []

HistoryDatasetAssociationListGrid.template = '/dataset/grid.mako'

HistoryDatasetAssociationListGrid.title = 'Saved Datasets'

HistoryDatasetAssociationListGrid.use_async = True

HistoryDatasetAssociationListGrid.use_paging = True

error Module

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

Bases: galaxy.web.base.controller.BaseUIController

index(trans)

external_service Module

class galaxy.webapps.galaxy.controllers.external_service.ExternalService(app)

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

browse_external_services(trans, *args, **kwargs)

create_external_service(trans, *args, **kwargs)

delete_external_service(trans, *args, **kwargs)

edit_external_service(trans, *args, **kwargs)

edit_external_service_form_definition(trans, *args, **kwargs)

external_service_grid = <galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid object>

get_external_service_type(trans, external_service_type_id, action='browse_external_services')

reload_external_service_types(trans, *args, **kwargs)

undelete_external_service(trans, *args, **kwargs)

update_external_service_form_definition(trans, *args, **kwargs)

view_external_service(trans, *args, **kwargs)

class galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid

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

class ExternalServiceTypeColumn(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, inbound=False)

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

get_value(trans, grid, external_service)

class ExternalServiceGrid.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, inbound=False)

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

get_value(trans, grid, external_service)

ExternalServiceGrid.columns = [<galaxy.webapps.galaxy.controllers.external_service.NameColumn object at 0x7f85db92ed10>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85dc5e7250>, <galaxy.webapps.galaxy.controllers.external_service.ExternalServiceTypeColumn object at 0x7f85dc5e7350>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85dc5e7dd0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85dc5e7a10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dc5e7890>]

ExternalServiceGrid.default_filter = {'deleted': 'False'}

ExternalServiceGrid.default_sort_key = '-create_time'

ExternalServiceGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85dc5e7ed0>, <galaxy.web.framework.helpers.grids.GridAction object at 0x7f85dc5e7990>]

ExternalServiceGrid.model_class

alias of ExternalService

ExternalServiceGrid.num_rows_per_page = 50

ExternalServiceGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7710>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7050>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7fd0>]

ExternalServiceGrid.preserve_state = True

ExternalServiceGrid.template = 'admin/external_service/grid.mako'

ExternalServiceGrid.title = 'External Services'

ExternalServiceGrid.use_paging = True

external_services Module

class galaxy.webapps.galaxy.controllers.external_services.ExternalServiceController(app)

Bases: galaxy.web.base.controller.BaseUIController

access_action(trans, *args, **kwargs)

forms Module

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

Bases: galaxy.web.base.controller.BaseUIController

browse_form_definitions(trans, *args, **kwargs)

build_form_definition_field_widgets(trans, layout_grids, field_index, field, form_type)

This method returns a list of widgets which describes a form definition field. This includes the field label, helptext, type, selectfield options, required/optional & layout

create_form_definition(trans, *args, **kwargs)

delete_form_definition(trans, *args, **kwargs)

edit_form_definition(trans, *args, **kwargs)

This callback method is for handling form editing. The value of response_redirect should be an URL that is defined by the caller. This allows for redirecting as desired when the form changes have been saved. For an example of how this works, see the edit_template() method in the base controller.

empty_field = {'visible': True, 'helptext': '', 'name': '', 'default': '', 'layout': 'none', 'selectlist': [], 'required': False, 'type': 'TextField', 'label': ''}

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

get_current_form(trans, **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

get_saved_form(form_definition)

This retrieves the saved form and returns a dictionary containing the name, desc, type, layout & fields of the form

save_form_definition(trans, form_definition_current_id=None, **kwd)

This method saves the current form

show_editable_form_definition(trans, form_definition, current_form, message='', status='done', response_redirect=None, **kwd)

Displays the form and any of the changes made to it in edit mode. In this method all the widgets are build for all name, description and all the fields of a form definition.

undelete_form_definition(trans, *args, **kwargs)

view_latest_form_definition(trans, *args, **kwargs)

Displays the layout of the latest version of the form definition

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, inbound=False)

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

get_value(trans, grid, form)

class FormsGrid.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, inbound=False)

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

get_value(trans, grid, form)

class FormsGrid.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, inbound=False)

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

get_value(trans, grid, form)

FormsGrid.build_initial_query(trans, **kwargs)

FormsGrid.columns = [<galaxy.webapps.galaxy.controllers.forms.NameColumn object at 0x7f85ccf5cd50>, <galaxy.webapps.galaxy.controllers.forms.DescriptionColumn object at 0x7f85ccf5cd10>, <galaxy.webapps.galaxy.controllers.forms.TypeColumn object at 0x7f85ccf5ca10>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85ccf5c810>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85ccf5cf50>]

FormsGrid.default_filter = {'deleted': 'False'}

FormsGrid.default_sort_key = '-create_time'

FormsGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85ccec72d0>]

FormsGrid.model_class

alias of FormDefinitionCurrent

FormsGrid.num_rows_per_page = 50

FormsGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ccf5ca50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ccf5c910>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ccec7290>]

FormsGrid.preserve_state = True

FormsGrid.template = 'admin/forms/grid.mako'

FormsGrid.title = 'Forms'

FormsGrid.use_paging = True

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, inbound=False)

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

HistoryAllPublishedGrid.apply_query_filter(trans, query, **kwargs)

HistoryAllPublishedGrid.build_initial_query(trans, **kwargs)

HistoryAllPublishedGrid.columns = [<galaxy.webapps.galaxy.controllers.history.NameURLColumn object at 0x7f85cbfb0650>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f85cbe78790>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f85cbe78810>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f85cbe78850>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f85cbe78890>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f85cbe788d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cbfb0590>]

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

HistoryAllPublishedGrid.default_sort_key = 'update_time'

HistoryAllPublishedGrid.model_class

alias of History

HistoryAllPublishedGrid.num_rows_per_page = 50

HistoryAllPublishedGrid.operations = []

HistoryAllPublishedGrid.title = 'Published Histories'

HistoryAllPublishedGrid.use_async = True

HistoryAllPublishedGrid.use_paging = True

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

citations(trans)

copy(trans, *args, **kwargs)

Copy one or more histories

create_new_current(trans, *args, **kwargs)

current_history_json(trans, *args, **kwargs)

delete_current(trans, purge=False)

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

delete_hidden_datasets(trans)

This method deletes all hidden datasets in the current history.

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).

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

Export a history to an archive.

get_item(trans, id)

get_name_and_link_async(trans, *args, **kwargs)

Returns history’s name and link.

history_data(trans, history)

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

Import another user’s history via a shared URL

import_archive(trans, *args, **kwargs)

Import a history from a file archive.

index(trans)

list(trans, *args, **kwargs)

List all available histories

list_as_xml(trans)

XML history list for functional tests

list_published(trans, **kwargs)

list_shared(trans, *args, **kwargs)

List histories shared with current user by others

name_autocomplete_data(trans, q=None, limit=None, timestamp=None)

Return autocomplete data for history names

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

purge_deleted_datasets(trans)

rate_async(trans, *args, **kwargs)

Rate a history asynchronously and return updated community data.

rename(trans, *args, **kwargs)

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, *args, **kwargs)

Set history’s importable attribute and slug.

set_as_current(trans, *args, **kwargs)

share(trans, *args, **kwargs)

share_restricted(trans, *args, **kwargs)

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

sharing(trans, *args, **kwargs)

Handle history sharing.

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

structure(trans, id=None, **kwargs)

switch_to_history(trans, *args, **kwargs)

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

Unhide the datasets in the active history – this does not require a logged in user.

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')

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

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, inbound=False)

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

get_value(trans, grid, history)

class HistoryListGrid.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, inbound=False)

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

get_value(trans, grid, history)

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

class HistoryListGrid.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, inbound=False)

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

get_link(trans, grid, history)

HistoryListGrid.apply_query_filter(trans, query, **kwargs)

HistoryListGrid.columns = [<galaxy.webapps.galaxy.controllers.history.HistoryListNameColumn object at 0x7f85cbfb02d0>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object at 0x7f85cbfb0110>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cbfb04d0>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cbe78190>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbf9ce90>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbe781d0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbe78210>, <galaxy.webapps.galaxy.controllers.history.DeletedColumn object at 0x7f85cbe78250>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cbfb0550>]

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

HistoryListGrid.default_sort_key = '-update_time'

HistoryListGrid.get_current_item(trans, **kwargs)

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

HistoryListGrid.model_class

alias of History

HistoryListGrid.num_rows_per_page = 50

HistoryListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78290>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe782d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78310>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78350>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78390>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe783d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78410>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78450>]

HistoryListGrid.preserve_state = False

HistoryListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cbe78490>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cbe784d0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cbe78510>]

HistoryListGrid.template = '/history/grid.mako'

HistoryListGrid.title = 'Saved Histories'

HistoryListGrid.use_async = True

HistoryListGrid.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, inbound=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, inbound=False)

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

get_value(trans, grid, history)

class SharedHistoryListGrid.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, inbound=False)

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

get_value(trans, grid, history)

SharedHistoryListGrid.apply_query_filter(trans, query, **kwargs)

SharedHistoryListGrid.build_initial_query(trans, **kwargs)

SharedHistoryListGrid.columns = [<galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbe78590>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object at 0x7f85cbe785d0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbe78610>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cbe78650>, <galaxy.webapps.galaxy.controllers.history.SharedByColumn object at 0x7f85cbe78690>]

SharedHistoryListGrid.default_filter = {}

SharedHistoryListGrid.default_sort_key = '-update_time'

SharedHistoryListGrid.model_class

alias of History

SharedHistoryListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe786d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78710>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cbe78750>]

SharedHistoryListGrid.standard_filters = []

SharedHistoryListGrid.title = 'Histories shared with you by others'

library Module

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

Bases: galaxy.web.base.controller.BaseUIController

browse_libraries(trans, **kwd)

index(trans, **kwd)

library_list_grid = <galaxy.webapps.galaxy.controllers.library.LibraryListGrid object>

list(trans, **kwd)

class galaxy.webapps.galaxy.controllers.library.LibraryListGrid

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, inbound=False)

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

get_value(trans, grid, library)

class LibraryListGrid.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, inbound=False)

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

get_value(trans, grid, library)

LibraryListGrid.apply_query_filter(trans, query, **kwd)

LibraryListGrid.build_initial_query(trans, **kwargs)

LibraryListGrid.columns = [<galaxy.webapps.galaxy.controllers.library.NameColumn object at 0x7f85db92e210>, <galaxy.webapps.galaxy.controllers.library.DescriptionColumn object at 0x7f85ccc52310>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85ccc52650>]

LibraryListGrid.default_filter = {'deleted': 'False', 'description': 'All', 'purged': 'False', 'name': 'All'}

LibraryListGrid.default_sort_key = 'name'

LibraryListGrid.model_class

alias of Library

LibraryListGrid.num_rows_per_page = 50

LibraryListGrid.preserve_state = False

LibraryListGrid.standard_filters = []

LibraryListGrid.template = '/library/grid.mako'

LibraryListGrid.title = 'Data Libraries'

LibraryListGrid.use_paging = True

library_admin Module

class galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin(app)

Bases: galaxy.web.base.controller.BaseUIController

browse_libraries(trans, *args, **kwargs)

create_library(trans, *args, **kwargs)

delete_library(trans, *args, **kwargs)

library_list_grid = <galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid object>

purge_library(trans, *args, **kwargs)

undelete_library(trans, *args, **kwargs)

class galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid

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, inbound=False)

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

get_value(trans, grid, library)

class LibraryListGrid.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, inbound=False)

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

get_value(trans, grid, library)

class LibraryListGrid.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, inbound=False)

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

get_value(trans, grid, library)

LibraryListGrid.columns = [<galaxy.webapps.galaxy.controllers.library_admin.NameColumn object at 0x7f85cc125dd0>, <galaxy.webapps.galaxy.controllers.library_admin.DescriptionColumn object at 0x7f85cc125d50>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc125ed0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc125e50>, <galaxy.webapps.galaxy.controllers.library_admin.StatusColumn object at 0x7f85cc125d10>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85cc125cd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cc125e10>]

LibraryListGrid.default_filter = {'deleted': 'False', 'description': 'All', 'purged': 'False', 'name': 'All'}

LibraryListGrid.default_sort_key = 'name'

LibraryListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85cc125690>]

LibraryListGrid.model_class

alias of Library

LibraryListGrid.num_rows_per_page = 50

LibraryListGrid.preserve_state = False

LibraryListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cc125610>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cc125590>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cc125510>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f85cc125850>]

LibraryListGrid.template = '/admin/library/grid.mako'

LibraryListGrid.title = 'Data Libraries'

LibraryListGrid.use_paging = True

library_common Module

class galaxy.webapps.galaxy.controllers.library_common.LibraryCommon(app)

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

act_on_multiple_datasets(trans, cntrller, library_id=None, ldda_ids='', **kwd)

add_history_datasets_to_library(trans, cntrller, library_id, folder_id, hda_ids='', **kwd)

browse_library(trans, cntrller='library', **kwd)

create_folder(trans, cntrller, parent_id, library_id, **kwd)

delete_library_item(trans, cntrller, library_id, item_id, item_type, **kwd)

download_dataset_from_folder(trans, cntrller, id, library_id=None, **kwd)

Catches the dataset id and displays file contents as directed

folder_info(trans, cntrller, id, library_id, **kwd)

folder_permissions(trans, cntrller, id, library_id, **kwd)

get_path_paste_uploaded_datasets(trans, cntrller, params, library_bunch, response_code, message)

get_server_dir_uploaded_datasets(trans, cntrller, params, full_dir, import_dir_desc, library_bunch, response_code, message)

import_datasets_to_histories(trans, cntrller, library_id='', folder_id='', ldda_ids='', target_history_id='', target_history_ids='', new_history_name='', **kwd)

ldda_edit_info(trans, cntrller, library_id, folder_id, id, **kwd)

ldda_info(trans, cntrller, library_id, folder_id, id, **kwd)

ldda_permissions(trans, cntrller, library_id, folder_id, id, **kwd)

library_dataset_info(trans, cntrller, id, library_id, **kwd)

library_dataset_permissions(trans, cntrller, id, library_id, **kwd)

library_info(trans, cntrller, **kwd)

library_item_updates(trans, *args, **kwargs)

library_permissions(trans, cntrller, **kwd)

make_library_item_public(trans, cntrller, library_id, item_type, id, **kwd)

make_library_uploaded_dataset(trans, cntrller, params, name, path, type, library_bunch, in_folder=None)

manage_template_inheritance(trans, cntrller, item_type, library_id, folder_id=None, ldda_id=None, **kwd)

move_library_item(trans, cntrller, item_type, item_id, source_library_id='', make_target_current=True, **kwd)

undelete_library_item(trans, cntrller, library_id, item_id, item_type, **kwd)

upload_dataset(trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd)

upload_library_dataset(trans, cntrller, library_id, folder_id, **kwd)

galaxy.webapps.galaxy.controllers.library_common.activatable_folders(trans, folder)

galaxy.webapps.galaxy.controllers.library_common.activatable_folders_and_library_datasets(trans, folder)

galaxy.webapps.galaxy.controllers.library_common.active_folders(trans, folder)

galaxy.webapps.galaxy.controllers.library_common.active_folders_and_library_datasets(trans, folder)

galaxy.webapps.galaxy.controllers.library_common.branch_deleted(folder)

galaxy.webapps.galaxy.controllers.library_common.datasets_for_lddas(trans, lddas)

Given a list of LDDAs, return a list of Datasets for them.

galaxy.webapps.galaxy.controllers.library_common.get_comptypes(trans)

galaxy.webapps.galaxy.controllers.library_common.get_containing_library_from_library_dataset(trans, library_dataset)

Given a library_dataset, get the containing library

galaxy.webapps.galaxy.controllers.library_common.get_sorted_accessible_library_items(trans, cntrller, items, sort_attr)

galaxy.webapps.galaxy.controllers.library_common.lucene_search(trans, cntrller, search_term, search_url, **kwd)

Return display of results from a full-text lucene search of data libraries.

galaxy.webapps.galaxy.controllers.library_common.map_library_datasets_to_lddas(trans, lib_datasets)

Given a list of LibraryDatasets, return a map from the LibraryDatasets to their LDDAs. If an LDDA does not exist for a LibraryDataset, then there will be no entry in the return hash.

galaxy.webapps.galaxy.controllers.library_common.sort_by_attr(seq, attr)

Sort the sequence of objects by object’s attribute Arguments: seq - the list or any sequence (including immutable one) of objects to sort. attr - the name of attribute to sort by

galaxy.webapps.galaxy.controllers.library_common.whoosh_search(trans, cntrller, search_term, **kwd)

Return display of results from a full-text whoosh search of data libraries.

mobile Module

class galaxy.webapps.galaxy.controllers.mobile.Mobile(app)

Bases: galaxy.web.base.controller.BaseUIController

dataset_detail(trans, id)

dataset_peek(trans, id)

history_detail(trans, id)

history_list(trans)

index(trans, **kwargs)

settings(trans, email=None, password=None)

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.NameColumn object at 0x7f85cb9fd6d0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cb9fda50>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cb9fdad0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85cb9fdb10>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cb9fdb50>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cb9fdb90>]

model_class

alias of 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.NameColumn object at 0x7f85cc64c790>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cc640110>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc640150>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85cc640190>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cc6400d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cc01de90>]

model_class

alias of 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, inbound=False)

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

get_value(trans, grid, item)

ItemSelectionGrid.apply_query_filter(trans, query, **kwargs)

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

ItemSelectionGrid.default_sort_key = '-update_time'

ItemSelectionGrid.num_rows_per_page = 10

ItemSelectionGrid.show_item_checkboxes = True

ItemSelectionGrid.template = '/page/select_items_grid.mako'

ItemSelectionGrid.use_async = True

ItemSelectionGrid.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 at 0x7f85cc640c10>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f85cc64c610>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f85cc640610>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f85cc640910>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f85cc640050>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f85cc64c5d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cc640090>]

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

default_sort_key = 'update_time'

model_class

alias of Page

title = 'Published Pages'

use_async = True

use_panels = True

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

create(trans, *args, **kwargs)

Create a new page

display(trans, *args, **kwargs)

display_by_username_and_slug(trans, username, slug)

Display page based on a username and slug.

edit(trans, *args, **kwargs)

Edit a page’s attributes.

edit_content(trans, *args, **kwargs)

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, *args, **kwargs)

Returns page’s name and link.

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

Get a page from the database by id.

list(trans, *args, **kwargs)

List user’s pages.

list_datasets_for_selection(trans, *args, **kwargs)

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

list_histories_for_selection(trans, *args, **kwargs)

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

list_pages_for_selection(trans, *args, **kwargs)

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

list_published(trans, *args, **kwargs)

list_visualizations_for_selection(trans, *args, **kwargs)

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

list_workflows_for_selection(trans, *args, **kwargs)

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

rate_async(trans, *args, **kwargs)

Rate a page asynchronously and return updated community data.

save(trans, *args, **kwargs)

set_accessible_async(trans, *args, **kwargs)

Set page’s importable attribute and slug.

share(trans, *args, **kwargs)

Handle sharing with an individual user.

sharing(trans, *args, **kwargs)

Handle page sharing.

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, inbound=False)

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

get_value(trans, grid, item)

PageListGrid.apply_query_filter(trans, query, **kwargs)

PageListGrid.columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85cc64cb50>, <galaxy.webapps.galaxy.controllers.page.URLColumn object at 0x7f85cc64cad0>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f85cc64c310>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cc64c150>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cc64c350>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc64c490>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cc640c50>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cc640dd0>]

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

PageListGrid.default_sort_key = '-update_time'

PageListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85cc640d50>]

PageListGrid.model_class

alias of Page

PageListGrid.operations = [<galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation object at 0x7f85cc640d10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cc64c710>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cc640cd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cc6403d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85cc6404d0>]

PageListGrid.title = 'Pages'

PageListGrid.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 at 0x7f85cc64c550>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cb9fdf90>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cb9fd910>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85cb9fde10>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cb9fdcd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cb9fdd10>]

model_class

alias of 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 at 0x7f85cb9fdd50>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85cb9fded0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cb9fd650>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cb9fd750>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cb9fd790>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cb9fd7d0>]

model_class

alias of 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.NameColumn object at 0x7f85cc64c510>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85cb9fdbd0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85cb9fdc50>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85cb9fdd90>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f85cb9fdf10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85cb9fdf50>]

model_class

alias of StoredWorkflow

title = 'Saved Workflows'

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

request_type Module

class galaxy.webapps.galaxy.controllers.request_type.RequestType(app)

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

browse_request_types(trans, *args, **kwargs)

create_request_type(trans, *args, **kwargs)

delete_request_type(trans, *args, **kwargs)

edit_request_type(trans, *args, **kwargs)

request_type_grid = <galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid object>

request_type_permissions(trans, *args, **kwargs)

undelete_request_type(trans, *args, **kwargs)

view_editable_request_type(trans, *args, **kwargs)

view_form_definition(trans, *args, **kwargs)

view_request_type(trans, *args, **kwargs)

class galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid

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, inbound=False)

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

get_value(trans, grid, request_type)

class RequestTypeGrid.ExternalServiceColumn(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, inbound=False)

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

get_value(trans, grid, request_type)

class RequestTypeGrid.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, inbound=False)

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

get_value(trans, grid, request_type)

class RequestTypeGrid.RequestFormColumn(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, inbound=False)

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

get_value(trans, grid, request_type)

class RequestTypeGrid.SampleFormColumn(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, inbound=False)

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

get_value(trans, grid, request_type)

RequestTypeGrid.columns = [<galaxy.webapps.galaxy.controllers.request_type.NameColumn object at 0x7f85cc64c6d0>, <galaxy.webapps.galaxy.controllers.request_type.DescriptionColumn object at 0x7f85ca6b15d0>, <galaxy.webapps.galaxy.controllers.request_type.RequestFormColumn object at 0x7f85ca6b1610>, <galaxy.webapps.galaxy.controllers.request_type.SampleFormColumn object at 0x7f85ca6b1650>, <galaxy.webapps.galaxy.controllers.request_type.ExternalServiceColumn object at 0x7f85ca6b1690>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85ca6b16d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85ca6b1710>]

RequestTypeGrid.default_filter = {'deleted': 'False'}

RequestTypeGrid.default_sort_key = '-create_time'

RequestTypeGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85ca6b18d0>]

RequestTypeGrid.model_class

alias of RequestType

RequestTypeGrid.num_rows_per_page = 50

RequestTypeGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca6b1790>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca6b17d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca6b1810>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca6b1850>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca6b1890>]

RequestTypeGrid.preserve_state = True

RequestTypeGrid.template = 'admin/request_type/grid.mako'

RequestTypeGrid.title = 'Request Types'

RequestTypeGrid.use_paging = True

requests Module

class galaxy.webapps.galaxy.controllers.requests.Requests(app)

Bases: galaxy.web.base.controller.BaseUIController

browse_requests(trans, **kwd)

find_samples_index(trans, *args, **kwargs)

index(trans, *args, **kwargs)

request_grid = <galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid object>

class galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid

Bases: galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid

apply_query_filter(trans, query, **kwd)

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

operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7450>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca24b310>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca24b5d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85ca24b350>]

requests_admin Module

class galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid

Bases: galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid

class UserColumn(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, inbound=False)

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

get_value(trans, grid, request)

AdminRequestsGrid.col = <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>

AdminRequestsGrid.columns = [<galaxy.webapps.galaxy.controllers.requests_common.NameColumn object at 0x7f85db921050>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object at 0x7f85dc5e7c90>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object at 0x7f85dc5e77d0>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object at 0x7f85dc5e7590>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85dc5e7490>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85dc5e7c10>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object at 0x7f85dc5e73d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dc5e74d0>, <galaxy.webapps.galaxy.controllers.requests_admin.UserColumn object at 0x7f85dd2755d0>]

AdminRequestsGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f85dbf86f90>]

AdminRequestsGrid.operation = <galaxy.web.framework.helpers.grids.GridOperation object>

AdminRequestsGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7450>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dd275810>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dd275f10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dd275e50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dbf86510>]

class galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid

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

class ExternalServiceColumn(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, inbound=False)

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

get_value(trans, grid, sample_dataset)

class DataTransferGrid.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, inbound=False)

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

get_value(trans, grid, sample_dataset)

class DataTransferGrid.SizeColumn(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, inbound=False)

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

get_value(trans, grid, sample_dataset)

class DataTransferGrid.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, inbound=False)

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

get_value(trans, grid, sample_dataset)

DataTransferGrid.apply_query_filter(trans, query, **kwd)

DataTransferGrid.columns = [<galaxy.webapps.galaxy.controllers.requests_admin.NameColumn object at 0x7f85dbf86e90>, <galaxy.webapps.galaxy.controllers.requests_admin.SizeColumn object at 0x7f85dbf86550>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85dbf86610>, <galaxy.webapps.galaxy.controllers.requests_admin.ExternalServiceColumn object at 0x7f85dbf86b90>, <galaxy.webapps.galaxy.controllers.requests_admin.StatusColumn object at 0x7f85dbf86410>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dbf86c90>]

DataTransferGrid.default_sort_key = '-create_time'

DataTransferGrid.model_class

alias of SampleDataset

DataTransferGrid.num_rows_per_page = 50

DataTransferGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dbf869d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dbf86a10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dbf86210>]

DataTransferGrid.preserve_state = True

DataTransferGrid.template = 'admin/requests/sample_datasets_grid.mako'

DataTransferGrid.title = 'Sample Datasets'

DataTransferGrid.use_paging = False

class galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin(app)

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

browse_requests(trans, *args, **kwargs)

datatx_grid = <galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid object>

get_file_details(trans, *args, **kwargs)

index(trans, *args, **kwargs)

initiate_data_transfer(trans, *args, **kwargs)

manage_datasets(trans, *args, **kwargs)

open_folder(trans, *args, **kwargs)

reject_request(trans, *args, **kwargs)

rename_datasets(trans, *args, **kwargs)

request_grid = <galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid object>

select_datasets_to_transfer(trans, *args, **kwargs)

update_sample_dataset_status(trans, cntrller, sample_dataset_ids, new_status, error_msg=None)

galaxy.webapps.galaxy.controllers.requests_admin.build_rename_datasets_for_sample_select_field(trans, sample_dataset, selected_value='none')

requests_common Module

class galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon(app)

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

add_sample(trans, *args, **kwargs)

add_samples(trans, *args, **kwargs)

create_request(trans, *args, **kwargs)

dataset_transfer_status_updates(trans, *args, **kwargs)

delete_request(trans, *args, **kwargs)

delete_sample(trans, *args, **kwargs)

edit_basic_request_info(trans, *args, **kwargs)

edit_email_settings(trans, *args, **kwargs)

Allow for changing the email notification settings where email is sent to a list of users whenever the request state changes to one selected for notification.

edit_samples(trans, *args, **kwargs)

find_samples(trans, *args, **kwargs)

sample_datasets_updates(trans, *args, **kwargs)

sample_state_updates(trans, *args, **kwargs)

submit_request(trans, *args, **kwargs)

undelete_request(trans, *args, **kwargs)

update_request_state(trans, *args, **kwargs)

update_sample_state(trans, cntrller, sample_ids, new_state, comment=None)

view_request(trans, *args, **kwargs)

view_request_history(trans, *args, **kwargs)

view_sample(trans, *args, **kwargs)

view_sample_datasets(trans, *args, **kwargs)

view_sample_history(trans, *args, **kwargs)

class galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid

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, inbound=False)

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

get_value(trans, grid, request)

class RequestsGrid.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, inbound=False)

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

get_value(trans, grid, request)

class RequestsGrid.SamplesColumn(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, inbound=False)

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

get_value(trans, grid, request)

class RequestsGrid.StateColumn(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, inbound=False)

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

filter(trans, user, query, column_filter)

Modify query to filter request by state.

get_value(trans, grid, request)

class RequestsGrid.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, inbound=False)

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

get_value(trans, grid, request)

RequestsGrid.columns = [<galaxy.webapps.galaxy.controllers.requests_common.NameColumn object at 0x7f85db921050>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object at 0x7f85dc5e7c90>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object at 0x7f85dc5e77d0>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object at 0x7f85dc5e7590>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85dc5e7490>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f85dc5e7c10>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object at 0x7f85dc5e73d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85dc5e74d0>]

RequestsGrid.default_filter = {'deleted': 'False', 'state': 'All'}

RequestsGrid.default_sort_key = '-update_time'

RequestsGrid.model_class

alias of Request

RequestsGrid.num_rows_per_page = 50

RequestsGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85dc5e7450>]

RequestsGrid.template = 'requests/grid.mako'

RequestsGrid.title = 'Sequencing Requests'

RequestsGrid.use_paging = True

galaxy.webapps.galaxy.controllers.requests_common.invalid_id_redirect(trans, cntrller, obj_id, item='sequencing request', action='browse_requests')

root Module

Contains the main interface in the Universe class

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

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

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

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

clear_history(trans)

Clears the history for a user.

dataset_make_primary(trans, id=None)

Copies a dataset and makes primary.

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

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

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.

display_child(trans, parent_id=None, designation=None, tofile=None, toext='.txt')

Returns child data directly into the browser, based upon parent_id and designation.

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).

history(trans, as_xml=False, show_deleted=None, show_hidden=None, **kwd)

Display the current history in its own page or as xml.

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_as_xml(trans, show_deleted=None, show_hidden=None)

history_delete(trans, id)

Backward compatibility with check_galaxy script.

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_options(trans)

Displays a list of history related actions.

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

Sets the permissions on a history.

index(trans, id=None, tool_id=None, mode=None, workflow_id=None, m_c=None, m_a=None, **kwd)

Called on the root url to display the main Galaxy page.

peek(trans, id=None)

Returns a ‘peek’ at the data.

tool_help(trans, id)

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

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.

welcome(trans)

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

add_tag_async(trans, *args, **kwargs)

Add tag to an item.

get_tagging_elt_async(trans, *args, **kwargs)

Returns HTML for editing an item’s tags.

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.

tool_runner Module

Upload class

class galaxy.webapps.galaxy.controllers.tool_runner.AddFrameData

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

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, from_noframe=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.

upload_async_create(trans, *args, **kwargs)

Precreate datasets for asynchronous uploading.

upload_async_message(trans, **kwd)

ucsc_proxy Module

Contains the UCSC proxy

class galaxy.webapps.galaxy.controllers.ucsc_proxy.UCSCProxy(app)

Bases: galaxy.web.base.controller.BaseUIController

create_display(store)

Creates a more meaningulf display name

index(trans, init=False, **kwd)

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.CreatesUsersMixin, galaxy.web.base.controller.CreatesApiKeysMixin

activate(trans, **kwd)

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

api_keys(trans, *args, **kwargs)

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

Provides a form with which one can change their password. If token is provided, don’t require current password.

create(trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd)

dbkeys(trans, *args, **kwargs)

Handle custom builds.

delete_address(trans, *args, **kwargs)

edit_address(trans, *args, **kwargs)

edit_info(trans, cntrller, **kwd)

Edit user information = username, email or password.

edit_toolbox_filters(trans, *args, **kwargs)

edit_username(trans, *args, **kwargs)

get_activation_token(trans, email)

Check for the activation token. Create new activation token and store it in the database if no token found.

get_most_recently_used_tool_async(trans, *args, **kwargs)

Returns information about the most recently used tool.

index(trans, cntrller, **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.

log_user_action_async(trans, action, context, params)

Log a user action asynchronously. If user is not logged in, do nothing.

login(trans, refresh_frames=[], **kwd)

Handle Galaxy Log in

logout(trans, logout_all=False)

manage_addresses(trans, **kwd)

manage_user_info(trans, cntrller, **kwd)

Manage a user’s login, password, public username, type, addresses, etc.

new_address(trans, *args, **kwargs)

openid_associate(trans, cntrller='user', **kwd)

Associates a user with an OpenID log in

openid_auth(trans, **kwd)

Handles user request to access an OpenID provider

openid_disassociate(trans, *args, **kwargs)

Disassociates a user with an OpenID

openid_manage(trans, *args, **kwargs)

Manage OpenIDs for user

openid_process(trans, **kwd)

Handle’s response from OpenID Providers

prepare_activation_link(trans, email)

Prepare the account activation link for the user.

proceed_login(trans, user, redirect)

Function processes user login. It is called in case all the login requirements are valid.

resend_verification(trans)

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

resend_verification_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.

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

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

send_verification_email(trans, email, username)

Send the verification email containing the activation link to the user’s email.

set_default_permissions(trans, cntrller, **kwd)

Set the user’s default permissions for the new histories

set_user_pref_async(trans, pref_name, pref_value)

Set a user preference asynchronously. If user is not logged in, do nothing.

toolbox_filters(trans, *args, **kwargs)

Sets the user’s default filters for the toolbox. Toolbox filters are specified in galaxy.ini. The user can activate them and the choice is stored in user_preferences.

undelete_address(trans, *args, **kwargs)

user_openid_grid = <galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid object>

class galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid

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

build_initial_query(trans, **kwd)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85caf31490>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85ca05ed50>]

default_filter = {'openid': 'All'}

default_sort_key = '-create_time'

model_class

alias of UserOpenID

operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d141fe50>]

template = '/user/openid_manage.mako'

title = 'OpenIDs linked to your account'

use_panels = False

visualization Module

workflow Module

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

Bases: sgmllib.SGMLParser

handle_data(text)

Called for each block of plain text.

unknown_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 at 0x7f85d8e32dd0>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f85d8e32bd0>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f85d8e328d0>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f85d8e32710>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f85d8e32890>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f85d233d150>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85d233d7d0>]

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

default_sort_key = 'update_time'

model_class

alias of StoredWorkflow

operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d233dcd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d233d2d0>]

title = 'Published Workflows'

use_async = 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, inbound=False)

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

get_value(trans, grid, workflow)

StoredWorkflowListGrid.apply_query_filter(trans, query, **kwargs)

StoredWorkflowListGrid.columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f85d8e32510>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f85d8e32cd0>, <galaxy.webapps.galaxy.controllers.workflow.StepsColumn object at 0x7f85d8e32a10>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85d8e32590>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f85d8e32490>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f85d8e32810>]

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

StoredWorkflowListGrid.default_sort_key = '-update_time'

StoredWorkflowListGrid.model_class

alias of StoredWorkflow

StoredWorkflowListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32d90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32a90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32f10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32e10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32ed0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f85d8e32750>]

StoredWorkflowListGrid.title = 'Saved Workflows'

StoredWorkflowListGrid.use_panels = True

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

annotate_async(trans, *args, **kwargs)

build_from_current_history(trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None)

configure_menu(trans, workflow_ids=None)

copy(trans, *args, **kwargs)

create(trans, *args, **kwargs)

Create a new stored workflow with name workflow_name.

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, *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.

editor_form_post(trans, *args, **kwargs)

Accepts a tool state and incoming values, and generates a new tool form and some additional information, packed into a json dictionary. This is used for the form shown in the right pane when a node is selected.

export(trans, *args, **kwargs)

Handles download/export workflow command.

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.

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.

gen_image(trans, *args, **kwargs)

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, *args, **kwargs)

Returns workflow’s name and link.

get_new_module_info(trans, *args, **kwargs)

Get the info for a new instance of a module initialized with default parameters (any keyword arguments will be passed along to the module). Result includes data inputs and outputs, html representation of the initial form, and the initial tool state (with default values). This is called asynchronously whenever a new node is added.

imp(trans, *args, **kwargs)

Imports a workflow shared by other users.

import_workflow(trans, cntrller='workflow', **kwd)

Import a workflow by reading an url, uploading a file, opening and reading the contents of a local file, or receiving the textual representation of a workflow via http.

index(trans)

list(trans, *args, **kwargs)

Render workflow main page (management of existing workflows)

list_for_run(trans, *args, **kwargs)

Render workflow list for analysis view (just allows running workflow or switching to management view)

list_grid(trans, *args, **kwargs)

List user’s stored workflows.

list_published(trans, **kwargs)

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.

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

rate_async(trans, *args, **kwargs)

Rate a workflow asynchronously and return updated community data.

rename(trans, *args, **kwargs)

rename_async(trans, *args, **kwargs)

run(trans, id, history_id=None, hide_fixed_params=False, **kwargs)

save_workflow(trans, *args, **kwargs)

Save the workflow described by workflow_data with id id.

set_accessible_async(trans, *args, **kwargs)

Set workflow’s importable attribute and slug.

share(trans, *args, **kwargs)

sharing(trans, *args, **kwargs)

Handle workflow sharing.

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

tag_outputs(trans, id, **kwargs)