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>

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)

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 0x7f92ec719d90>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f92ec7194d0>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object at 0x7f92ec719590>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f92ec719050>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ec719450>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ec7191d0>]

GroupListGrid.default_sort_key = 'name'

GroupListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92ec7195d0>]

GroupListGrid.model_class

alias of Group

GroupListGrid.num_rows_per_page = 50

GroupListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719550>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719390>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719cd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719e90>]

GroupListGrid.preserve_state = False

GroupListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec719850>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec7198d0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec7193d0>]

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 0x7f92ec719110>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object at 0x7f92ec719d10>, <galaxy.webapps.galaxy.controllers.admin.AmountColumn object at 0x7f92ec719610>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f92ec719350>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f92ec719a50>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f92ec719290>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ec719b90>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ec719690>]

QuotaListGrid.default_sort_key = 'name'

QuotaListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92ec719e50>]

QuotaListGrid.model_class

alias of Quota

QuotaListGrid.num_rows_per_page = 50

QuotaListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719bd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719a90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719c90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719dd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719e10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719310>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719210>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719f90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ec719ed0>]

QuotaListGrid.preserve_state = False

QuotaListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec7192d0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec719410>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec719f50>]

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 0x7f92eb356590>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object at 0x7f92eb3564d0>, <galaxy.webapps.galaxy.controllers.admin.TypeColumn object at 0x7f92eb356210>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f92eb356c10>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object at 0x7f92eb356650>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f92eb356ad0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92eb356510>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92eb356050>]

RoleListGrid.default_sort_key = 'name'

RoleListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92eb356790>]

RoleListGrid.model_class

alias of Role

RoleListGrid.num_rows_per_page = 50

RoleListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356110>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356410>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356a10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356250>]

RoleListGrid.preserve_state = False

RoleListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb356910>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb356190>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ec719790>]

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 0x7f92ec719b10>, <galaxy.webapps.galaxy.controllers.admin.ToolVersionsColumn object at 0x7f92f4557650>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ec719490>]

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 0x7f92eb356390>, <galaxy.webapps.galaxy.controllers.admin.UserNameColumn object at 0x7f92eb356350>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object at 0x7f92eb3566d0>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object at 0x7f92eb356b90>, <galaxy.webapps.galaxy.controllers.admin.ExternalColumn object at 0x7f92eb3562d0>, <galaxy.webapps.galaxy.controllers.admin.LastLoginColumn object at 0x7f92eb356b10>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object at 0x7f92eb3563d0>, <galaxy.webapps.galaxy.controllers.admin.TimeCreatedColumn object at 0x7f92eb356810>, <galaxy.webapps.galaxy.controllers.admin.ActivatedColumn object at 0x7f92eb356150>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92eb356490>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92eb356290>]

UserListGrid.default_sort_key = 'email'

UserListGrid.get_current_item(trans, **kwargs)

UserListGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92eb3561d0>]

UserListGrid.model_class

alias of User

UserListGrid.num_rows_per_page = 50

UserListGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356690>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eb356710>]

UserListGrid.preserve_state = False

UserListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb356a50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb356bd0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb3565d0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92eb3560d0>]

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.

install_tool_shed_repositories(trans, *args, **kwargs)

Install specified tool shed repositories.

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.web.base.controller.UsesHistoryMixin, galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin, 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 0x7f92e5732c50>, <galaxy.webapps.galaxy.controllers.dataset.HistoryColumn object at 0x7f92e56b1350>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e56b12d0>, <galaxy.webapps.galaxy.controllers.dataset.StatusColumn object at 0x7f92e56b1390>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e56b13d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e56b1410>]

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 0x7f92e56b1450>]

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 0x7f92e5966e90>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92ea61ded0>, <galaxy.webapps.galaxy.controllers.external_service.ExternalServiceTypeColumn object at 0x7f92ea61df90>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92ea61d890>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ea61dc10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ea61dfd0>]

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

ExternalServiceGrid.default_sort_key = '-create_time'

ExternalServiceGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92ea61d1d0>, <galaxy.web.framework.helpers.grids.GridAction object at 0x7f92ea61da10>]

ExternalServiceGrid.model_class

alias of ExternalService

ExternalServiceGrid.num_rows_per_page = 50

ExternalServiceGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ea61d950>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ea61d210>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ea61d250>]

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 0x7f92f34b9890>, <galaxy.webapps.galaxy.controllers.forms.DescriptionColumn object at 0x7f92f34b9c10>, <galaxy.webapps.galaxy.controllers.forms.TypeColumn object at 0x7f92f34b96d0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92f34b9d10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92f34b9110>]

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

FormsGrid.default_sort_key = '-create_time'

FormsGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92f34b9650>]

FormsGrid.model_class

alias of FormDefinitionCurrent

FormsGrid.num_rows_per_page = 50

FormsGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92f34b9b10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92f34b95d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92f34b91d0>]

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 0x7f92e53651d0>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f92e5365210>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f92e5365290>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f92e53652d0>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f92e5365310>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f92e5365350>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e5365390>]

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.UsesHistoryMixin, galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin, 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_item_content_async(trans, id)

Returns item content in HTML format.

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, galaxy.web.base.controller.UsesHistoryMixin

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 0x7f92e5150250>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object at 0x7f92e5b93ad0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e5b93b90>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e5b93c10>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e5b93c50>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e5b93c90>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e5b93cd0>, <galaxy.webapps.galaxy.controllers.history.DeletedColumn object at 0x7f92e5b93d10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e5b93d50>]

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 0x7f92e5b93d90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93dd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93e10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93e50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93e90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93ed0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93f10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5b93f50>]

HistoryListGrid.preserve_state = False

HistoryListGrid.standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92e5b93f90>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92e5b93fd0>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92e5365050>]

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 0x7f92e5150310>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object at 0x7f92e9227f10>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e5365090>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e53650d0>, <galaxy.webapps.galaxy.controllers.history.SharedByColumn object at 0x7f92e5365110>]

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 0x7f92e51505d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5365150>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e5365190>]

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 0x7f92e5150350>, <galaxy.webapps.galaxy.controllers.library.DescriptionColumn object at 0x7f92e9b2eb50>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e9b2e690>]

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 0x7f92ea7cf310>, <galaxy.webapps.galaxy.controllers.library_admin.DescriptionColumn object at 0x7f92ea7cf690>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92ea7cf510>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92ea7cf090>, <galaxy.webapps.galaxy.controllers.library_admin.StatusColumn object at 0x7f92ea7cf8d0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ea7cf910>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ea7cfb10>]

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 0x7f92ea7cf150>]

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 0x7f92ea7cf290>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ea7cff50>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ea7cf410>, <galaxy.web.framework.helpers.grids.GridColumnFilter object at 0x7f92ea7cff90>]

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 0x7f92e49e4710>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e9b2ec10>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a8b350>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92e4a8b390>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a8b3d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b410>]

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 0x7f92e4aee710>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e4a8b190>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a8b210>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92e4a8b250>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a8b290>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b2d0>]

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 0x7f92e49e4590>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f92e49e4610>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f92e4a8b050>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f92e4a8b090>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f92e4a8b0d0>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f92e4a8b110>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b150>]

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.UsesHistoryMixin, 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 0x7f92e49e4510>, <galaxy.webapps.galaxy.controllers.page.URLColumn object at 0x7f92e4a9e150>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f92e49e45d0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e4a9ed50>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a9ed90>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a9edd0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4aee790>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a9ee10>]

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 0x7f92e4a9ee50>]

PageListGrid.model_class

alias of Page

PageListGrid.operations = [<galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation object at 0x7f92e4a9ee90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e4a9eed0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e4a9ef10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e4a9ef50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e4a9ef90>]

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 0x7f92e4a8b5d0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e4a8b610>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a8b690>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92e4a8b6d0>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a8b710>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b750>]

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 0x7f92e4a8b790>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e4a8b7d0>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e4a8b810>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a8b890>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a8b8d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b910>]

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 0x7f92e49e4850>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92e4a8b450>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e4a8b4d0>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92e4a8b510>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92e4a8b550>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e4a8b590>]

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 0x7f92e3421310>, <galaxy.webapps.galaxy.controllers.request_type.DescriptionColumn object at 0x7f92e34213d0>, <galaxy.webapps.galaxy.controllers.request_type.RequestFormColumn object at 0x7f92e3421410>, <galaxy.webapps.galaxy.controllers.request_type.SampleFormColumn object at 0x7f92e34214d0>, <galaxy.webapps.galaxy.controllers.request_type.ExternalServiceColumn object at 0x7f92e3421650>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92e34216d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e3421750>]

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

RequestTypeGrid.default_sort_key = '-create_time'

RequestTypeGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92e3421a90>]

RequestTypeGrid.model_class

alias of RequestType

RequestTypeGrid.num_rows_per_page = 50

RequestTypeGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e34217d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3421850>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3421890>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3421950>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3421990>]

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 0x7f92ea61d910>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e31061d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3106710>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3106690>]

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 0x7f92f11abf50>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object at 0x7f92f11ab190>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object at 0x7f92eb39a9d0>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object at 0x7f92eb39a190>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92ea61d790>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ea61d7d0>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object at 0x7f92ea61d190>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ea61de50>, <galaxy.webapps.galaxy.controllers.requests_admin.UserColumn object at 0x7f92e3106450>]

AdminRequestsGrid.global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92e2fb3dd0>]

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

AdminRequestsGrid.operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92ea61d910>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2fb3c90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2fb3d10>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2fb3d50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2fb3d90>]

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 0x7f92e2fb3e10>, <galaxy.webapps.galaxy.controllers.requests_admin.SizeColumn object at 0x7f92e2fb3e50>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e2fb3e90>, <galaxy.webapps.galaxy.controllers.requests_admin.ExternalServiceColumn object at 0x7f92e2fb3ed0>, <galaxy.webapps.galaxy.controllers.requests_admin.StatusColumn object at 0x7f92e2fb3f10>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e2fb3f50>]

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 0x7f92e2fb3f90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2fb3fd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e2f78050>]

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 0x7f92f11abf50>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object at 0x7f92f11ab190>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object at 0x7f92eb39a9d0>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object at 0x7f92eb39a190>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92ea61d790>, <galaxy.web.framework.helpers.grids.DeletedColumn object at 0x7f92ea61d7d0>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object at 0x7f92ea61d190>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92ea61de50>]

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 0x7f92ea61d910>]

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.web.base.controller.UsesHistoryMixin, galaxy.web.base.controller.UsesHistoryDatasetAssociationMixin, 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)

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 the new password.

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 0x7f92e3e0b110>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e362e1d0>]

default_filter = {'openid': 'All'}

default_sort_key = '-create_time'

model_class

alias of UserOpenID

operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e362e2d0>]

template = '/user/openid_manage.mako'

title = 'OpenIDs linked to your account'

use_panels = False

visualization Module

class galaxy.webapps.galaxy.controllers.visualization.DbKeyColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, inbound=False)

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

Column for filtering by and displaying dataset dbkey.

filter(trans, user, query, dbkey)

Filter by dbkey.

class galaxy.webapps.galaxy.controllers.visualization.DbKeyPlaceholderColumn(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

Placeholder to keep track of dbkey.

filter(trans, user, query, dbkey)

class galaxy.webapps.galaxy.controllers.visualization.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

Column for filtering by history id.

filter(trans, user, query, history_id)

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

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

apply_query_filter(trans, query, **kwargs)

available_tracks = None

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e8e5d390>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5dc90>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5de10>, <galaxy.webapps.galaxy.controllers.visualization.HistoryColumn object at 0x7f92e8e5da90>, <galaxy.webapps.galaxy.controllers.visualization.DbKeyColumn object at 0x7f92e8e5d3d0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e8e5d090>]

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

default_sort_key = '-hid'

get_current_item(trans, **kwargs)

Current item for grid is the history being queried. This is a bit of hack since current_item typically means the current item in the grid.

model_class

alias of HistoryDatasetAssociation

template = 'tracks/history_datasets_select_grid.mako'

title = 'Add Datasets'

use_async = True

use_paging = False

class galaxy.webapps.galaxy.controllers.visualization.HistorySelectionGrid

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

Grid enables user to select a history, which is then used to display datasets from the history.

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.webapps.galaxy.controllers.visualization.NameColumn object at 0x7f92f528e490>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e3e0b050>, <galaxy.webapps.galaxy.controllers.visualization.DbKeyPlaceholderColumn object at 0x7f92e8e5d910>]

datasets_action = 'list_history_datasets'

datasets_param = 'f-history'

default_sort_key = '-update_time'

model_class

alias of History

num_rows_per_page = 10

template = '/tracks/history_select_grid.mako'

title = 'Add Track: Select History'

use_async = True

use_paging = True

class galaxy.webapps.galaxy.controllers.visualization.LibrarySelectionGrid

Bases: galaxy.webapps.galaxy.controllers.library.LibraryListGrid

Grid enables user to select a Library, which is then used to display datasets from the history.

columns = [<galaxy.webapps.galaxy.controllers.visualization.NameColumn object at 0x7f92e8e5d150>]

datasets_action = 'list_library_datasets'

datasets_param = 'f-library'

model_class

alias of Library

num_rows_per_page = 10

template = '/tracks/history_select_grid.mako'

title = 'Add Track: Select Library'

use_async = True

use_paging = True

class galaxy.webapps.galaxy.controllers.visualization.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_link(trans, grid, history)

get_value(trans, grid, history)

class galaxy.webapps.galaxy.controllers.visualization.OpenObject

Bases: dict

A dict that allows assignment and attribute retrieval using the dot operator.

If an attribute isn’t contained in the dict None is returned (no KeyError). JSON-serializable.

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

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

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5dcd0>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5d250>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92e8e5d490>]

default_sort_key = '-update_time'

model_class

alias of Visualization

show_item_checkboxes = True

template = '/tracks/add_to_viz.mako'

title = 'Insert into visualization'

use_async = True

use_paging = False

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

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

apply_query_filter(trans, query, **kwargs)

build_initial_query(trans, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object at 0x7f92e3e0b190>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f92e3155190>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f92e8e5d210>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f92e8e5d790>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f92e8e5d710>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f92e8e5dbd0>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92e8e5d850>]

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

default_sort_key = 'update_time'

model_class

alias of Visualization

title = 'Published Visualizations'

use_async = True

use_panels = True

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

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

bookmarks_from_dataset(trans, *args, **kwargs)

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

Display a circster visualization.

copy(trans, *args, **kwargs)

create(trans, *args, **kwargs)

Creates a new visualization or returns a form for creating visualization.

display_by_username_and_slug(trans, username, slug)

Display visualization based on a username and slug.

edit(trans, *args, **kwargs)

Edit a visualization’s attributes.

get_item(trans, id)

get_item_content_async(trans, id)

Returns item content in HTML format.

get_name_and_link_async(trans, *args, **kwargs)

Returns visualization’s name and link.

imp(trans, *args, **kwargs)

Import a visualization into user’s workspace.

index(trans, *args, **kwargs)

Lists user’s saved visualizations.

list(trans, *args, **kwargs)

list_current_history_datasets(trans, *args, **kwargs)

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

list_datasets(trans, *args, **kwargs)

List all datasets that can be added as tracks

list_histories(trans, *args, **kwargs)

List all histories that can be used for selecting datasets.

list_history_datasets(trans, *args, **kwargs)

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

list_libraries(trans, *args, **kwargs)

List all libraries that can be used for selecting datasets.

list_library_datasets(trans, *args, **kwargs)

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

list_published(trans, *args, **kwargs)

list_tracks(trans, **kwargs)

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

rate_async(trans, *args, **kwargs)

Rate a visualization asynchronously and return updated community data.

render(trans, *args, **kwargs)

Render the appropriate visualization template, parsing the kwargs into appropriate variables and resources (such as ORM models) based on this visualizations param data in visualizations_conf.xml.

URL: /visualization/show/{visualization_name}

save(trans, *args, **kwargs)

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

saved(trans, *args, **kwargs)

set_accessible_async(trans, *args, **kwargs)

Set visualization’s importable attribute and slug.

share(trans, *args, **kwargs)

Handle sharing a visualization with a particular user.

sharing(trans, *args, **kwargs)

Handle visualization sharing.

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

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

trackster(trans, *args, **kwargs)

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

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

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

apply_query_filter(trans, query, **kwargs)

columns = [<galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5d2d0>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92e8e5dc50>, <galaxy.web.framework.helpers.grids.TextColumn object at 0x7f92eafd3310>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92eafd3a10>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object at 0x7f92eafd3750>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92eafd3ed0>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92eafd3e90>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92eafd3a90>]

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

default_sort_key = '-update_time'

get_display_name(trans, item)

get_url_args(item)

Returns dictionary used to create item link.

global_actions = [<galaxy.web.framework.helpers.grids.GridAction object at 0x7f92eafd3dd0>]

model_class

alias of Visualization

operations = [<galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eafd3c90>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eafd3910>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eafd33d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eafd30d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3155310>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92e3155150>]

title = 'Saved Visualizations'

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 0x7f92eaf7ef90>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object at 0x7f92eaf7ef50>, <galaxy.web.framework.helpers.grids.OwnerColumn object at 0x7f92eaf7e2d0>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object at 0x7f92eaf7e950>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object at 0x7f92eaf7ee90>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object at 0x7f92eaf7e050>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92eaf7e610>]

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 0x7f92eaf7e4d0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7efd0>]

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 0x7f92eaf7ee50>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object at 0x7f92eaf7e490>, <galaxy.webapps.galaxy.controllers.workflow.StepsColumn object at 0x7f92eaf7e250>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92eaf7e210>, <galaxy.web.framework.helpers.grids.GridColumn object at 0x7f92eaf7e110>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object at 0x7f92eaf7e590>]

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 0x7f92eaf7eb50>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7e090>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7e290>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7ebd0>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7e510>, <galaxy.web.framework.helpers.grids.GridOperation object at 0x7f92eaf7e450>]

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.

edit_attributes(trans, *args, **kwargs)

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)