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galaxy.webapps.galaxy.controllers package¶
Galaxy web controllers.
Submodules¶
galaxy.webapps.galaxy.controllers.admin module¶
-
class
galaxy.webapps.galaxy.controllers.admin.
AdminGalaxy
(app)[source]¶ Bases:
galaxy.webapps.base.controller.JSAppLauncher
-
activate_operation
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
delete_operation
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
group_list_grid
= <galaxy.webapps.galaxy.controllers.admin.GroupListGrid object>¶
-
impersonate_operation
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
manage_tool_dependencies
(trans, install_dependencies=False, uninstall_dependencies=False, remove_unused_dependencies=False, selected_tool_ids=None, selected_environments_to_uninstall=None, viewkey='View tool-centric dependencies')[source]¶
-
purge_operation
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
quota_list_grid
= <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid object>¶
-
resend_activation_email
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
role_list_grid
= <galaxy.webapps.galaxy.controllers.admin.RoleListGrid object>¶
-
tool_version_list_grid
= <galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid object>¶
-
undelete_operation
= <galaxy.web.framework.helpers.grids.GridOperation object>¶
-
user_list_grid
= <galaxy.webapps.galaxy.controllers.admin.UserListGrid object>¶
-
-
class
galaxy.webapps.galaxy.controllers.admin.
GroupListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
NameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
RolesColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
StatusColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
UsersColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.admin.GroupListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_sort_key
= 'name'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.Group
-
num_rows_per_page
= 50¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
standard_filters
= [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]¶
-
title
= 'Groups'¶
-
title_id
= 'groups-grid'¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.admin.
QuotaListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
AmountColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
DescriptionColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
GroupsColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
NameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
StatusColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
UsersColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.AmountColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_sort_key
= 'name'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.Quota
-
num_rows_per_page
= 50¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
standard_filters
= [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]¶
-
title
= 'Quotas'¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.admin.
RoleListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
DescriptionColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
GroupsColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
NameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
StatusColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
TypeColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
UsersColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.admin.RoleListGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.TypeColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.RoleListGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_sort_key
= 'name'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.Role
-
num_rows_per_page
= 50¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
standard_filters
= [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]¶
-
title
= 'Roles'¶
-
title_id
= 'roles-grid'¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.admin.
ToolVersionListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
ToolIdColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
ToolVersionsColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolIdColumn object>, <galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid.ToolVersionsColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_sort_key
= 'tool_id'¶
-
model_class
¶
-
num_rows_per_page
= 50¶
-
title
= 'Tool versions'¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.admin.
UserListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
ActivatedColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
DiskUsageColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
EmailColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
ExternalColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
GroupsColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
LastLoginColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
RolesColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
StatusColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
TimeCreatedColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
UserNameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.admin.UserListGrid.EmailColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.UserNameColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.LastLoginColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.DiskUsageColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.StatusColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.TimeCreatedColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.ActivatedColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserListGrid.ExternalColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.PurgedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'purged': 'False'}¶
-
default_sort_key
= 'email'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.User
-
num_rows_per_page
= 50¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
standard_filters
= [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]¶
-
title
= 'Users'¶
-
title_id
= 'users-grid'¶
-
use_default_filter
= True¶
-
use_paging
= True¶
-
class
-
galaxy.webapps.galaxy.controllers.admin.
get_group
(trans, id)[source]¶ Get a Group from the database by id.
-
galaxy.webapps.galaxy.controllers.admin.
get_quota
(trans, id)[source]¶ Get a Quota from the database by id.
galaxy.webapps.galaxy.controllers.admin_toolshed module¶
-
class
galaxy.webapps.galaxy.controllers.admin_toolshed.
AdminToolshed
(app)[source]¶ Bases:
galaxy.webapps.galaxy.controllers.admin.AdminGalaxy
-
activate_repository
(trans, **kwd)[source]¶ Activate a repository that was deactivated but not uninstalled.
-
display_image_in_repository
(trans, **kwd)[source]¶ Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. .. image:: https://raw.github.com/galaxy/some_image.png .. image:: $PATH_TO_IMAGES/some_image.png .. image:: /static/images/some_image.gif .. image:: some_image.jpg .. image:: /deep/some_image.png
-
get_tool_dependencies
(trans, repository_id, repository_name, repository_owner, changeset_revision)[source]¶ Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, owner and changeset revision. The received repository_id is the encoded id of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed.
-
get_updated_repository_information
(trans, repository_id, repository_name, repository_owner, changeset_revision)[source]¶ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an uninstalled tool shed repository.
-
initiate_tool_dependency_installation
(trans, tool_dependencies, **kwd)[source]¶ Install specified dependencies for repository tools. The received list of tool_dependencies are the database records for those dependencies defined in the tool_dependencies.xml file (contained in the repository) that should be installed. This allows for filtering out dependencies that have not been checked for installation on the ‘Manage tool dependencies’ page for an installed tool shed repository.
-
install_latest_repository_revision
(trans, **kwd)[source]¶ Install the latest installable revision of a repository that has been previously installed.
-
install_tool_dependencies_with_update
(trans, **kwd)[source]¶ Updating an installed tool shed repository where new tool dependencies but no new repository dependencies are included in the updated revision.
-
installed_repository_grid
= <tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid object>¶
-
reinstall_repository
(trans, **kwd)[source]¶ Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository and tool dependencies of the repository.
-
reselect_tool_panel_section
(trans, **kwd)[source]¶ 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.
-
galaxy.webapps.galaxy.controllers.async module¶
Upload class
-
class
galaxy.webapps.galaxy.controllers.async.
ASync
(app)[source]¶
galaxy.webapps.galaxy.controllers.authnz module¶
OAuth 2.0 and OpenID Connect Authentication and Authorization Controller.
-
class
galaxy.webapps.galaxy.controllers.authnz.
OIDC
(app)[source]¶ Bases:
galaxy.webapps.base.controller.JSAppLauncher
-
index
(trans, **kwargs)[source]¶ - GET /authnz/
- returns a list of third-party identities associated with the user.
Parameters: - trans (galaxy.webapps.base.webapp.GalaxyWebTransaction) – Galaxy web transaction.
- kwargs – empty dict
Return type: list of dicts
Returns: a list of third-party identities associated with the user account.
-
galaxy.webapps.galaxy.controllers.data_manager module¶
galaxy.webapps.galaxy.controllers.dataset module¶
-
class
galaxy.webapps.galaxy.controllers.dataset.
DatasetInterface
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.item_attrs.UsesItemRatings
,galaxy.webapps.base.controller.UsesExtendedMetadataMixin
-
copy_datasets
(trans, source_history=None, source_content_ids='', target_history_id=None, target_history_ids='', new_history_name='', do_copy=False, **kwd)[source]¶
-
display
(trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)[source]¶
-
display_application
(trans, dataset_id=None, user_id=None, app_name=None, link_name=None, app_action=None, action_param=None, action_param_extra=None, **kwds)[source]¶ Access to external display applications
-
display_at
(trans, dataset_id, filename=None, **kwd)[source]¶ 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)[source]¶ Display dataset by username and slug; because datasets do not yet have slugs, the slug is the dataset’s id.
-
get_edit
(trans, dataset_id=None, **kwd)[source]¶ Produces the input definitions available to modify dataset attributes
-
get_metadata_file
(trans, hda_id, metadata_name)[source]¶ Allows the downloading of metadata files associated with datasets (eg. bai index for bam files)
-
hda_deserializer
= GalaxyTypeDepends(_do_resolve)¶
-
hda_manager
= GalaxyTypeDepends(_do_resolve)¶
-
history_manager
= GalaxyTypeDepends(_do_resolve)¶
-
imp
(trans, dataset_id=None, **kwd)[source]¶ Import another user’s dataset via a shared URL; dataset is added to user’s current history.
-
rate_async
(trans, id, rating)[source]¶ Rate a dataset asynchronously and return updated community data.
-
set_accessible_async
(trans, id=None, accessible=False)[source]¶ Does nothing because datasets do not have an importable/accessible attribute. This method could potentially set another attribute.
-
galaxy.webapps.galaxy.controllers.error module¶
galaxy.webapps.galaxy.controllers.forms module¶
-
class
galaxy.webapps.galaxy.controllers.forms.
Forms
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
-
forms_grid
= <galaxy.webapps.galaxy.controllers.forms.FormsGrid object>¶
-
-
class
galaxy.webapps.galaxy.controllers.forms.
FormsGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
DescriptionColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
NameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
StatusColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
TypeColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.forms.FormsGrid.NameColumn object>, <galaxy.webapps.galaxy.controllers.forms.FormsGrid.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.forms.FormsGrid.TypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.forms.FormsGrid.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'deleted': 'False'}¶
-
default_sort_key
= '-update_time'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.FormDefinitionCurrent
-
num_rows_per_page
= 50¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
title
= 'Forms'¶
-
use_paging
= True¶
-
class
galaxy.webapps.galaxy.controllers.history module¶
-
class
galaxy.webapps.galaxy.controllers.history.
HistoryAllPublishedGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
NameURLColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶ Bases:
galaxy.web.framework.helpers.grids.PublicURLColumn
,galaxy.webapps.galaxy.controllers.history.NameColumn
-
columns
= [<galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid.NameURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'public_url': 'All', 'tags': 'All', 'username': 'All'}¶
-
default_sort_key
= 'update_time'¶
-
model_class
¶ alias of
galaxy.model.History
-
num_rows_per_page
= 50¶
-
title
= 'Published Histories'¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.history.
HistoryController
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.SharableMixin
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.item_attrs.UsesItemRatings
THIS METHOD IS A TEMPORARY ADDITION. It’ll allow us to fix the regression in history-wide actions, and will be removed in the first release after 17.01
-
as_xml
(trans, id=None, show_deleted=None, show_hidden=None)[source]¶ Return a history in xml format.
-
current_history_json
(trans)[source]¶ Return the current user’s current history in a serialized, dictionary form.
-
display_by_username_and_slug
(trans, username, slug)[source]¶ Display history based on a username and slug.
-
display_structured
(trans, id=None)[source]¶ Display a history as a nested structure showing the jobs and workflow invocations that created each dataset (if any).
-
history_export_view
= GalaxyTypeDepends(_do_resolve)¶
-
history_manager
= GalaxyTypeDepends(_do_resolve)¶
-
history_serializer
= GalaxyTypeDepends(_do_resolve)¶
List histories shared with current user by others
-
make_private
(trans, history_id=None, all_histories=False, **kwd)[source]¶ Sets the datasets within a history to private. Also sets the default permissions for the history to private, for future datasets.
-
published_list_grid
= <galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid object>¶
-
rate_async
(trans, id, rating)[source]¶ Rate a history asynchronously and return updated community data.
-
resume_paused_jobs
(trans, current=False, ids=None)[source]¶ Resume paused jobs the active history – this does not require a logged in user.
-
set_accessible_async
(trans, id=None, accessible=False)[source]¶ Set history’s importable attribute and slug.
-
slug_builder
= GalaxyTypeDepends(_do_resolve)¶
-
stored_list_grid
= <galaxy.webapps.galaxy.controllers.history.HistoryListGrid object>¶
-
switch_to_history
(trans, hist_id=None)[source]¶ Change the current user’s current history to one with hist_id.
-
class
galaxy.webapps.galaxy.controllers.history.
HistoryListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
DeletedColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
HistoryListNameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
ItemCountColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.webapps.galaxy.controllers.history.HistoryListGrid.HistoryListNameColumn object>, <galaxy.webapps.galaxy.controllers.history.HistoryListGrid.ItemCountColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.HistoryListGrid.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'deleted': 'False', 'name': 'All', 'sharing': 'All', 'tags': 'All'}¶
-
default_sort_key
= '-update_time'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
info_text
= 'Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.'¶
-
model_class
¶ alias of
galaxy.model.History
-
num_rows_per_page
= 15¶
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
standard_filters
= [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]¶
-
title
= 'Saved Histories'¶
-
use_paging
= True¶
-
class
galaxy.webapps.galaxy.controllers.interactive_environments module¶
API check for whether the current session’s interactive environment launch is ready
galaxy.webapps.galaxy.controllers.library module¶
galaxy.webapps.galaxy.controllers.openid module¶
galaxy.webapps.galaxy.controllers.page module¶
-
class
galaxy.webapps.galaxy.controllers.page.
HistoryDatasetAssociationSelectionGrid
[source]¶ Bases:
galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid
Grid for selecting HDAs.
-
columns
= [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
model_class
¶
-
title
= 'Saved Datasets'¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
HistorySelectionGrid
[source]¶ Bases:
galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid
Grid for selecting histories.
-
columns
= [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
model_class
¶ alias of
galaxy.model.History
-
title
= 'Saved Histories'¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
ItemSelectionGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
Base class for pages’ item selection grids.
-
class
NameColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
default_filter
= {'deleted': 'False', 'sharing': 'All'}¶
-
default_sort_key
= '-update_time'¶
-
num_rows_per_page
= 10¶
-
show_item_checkboxes
= True¶
-
use_paging
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.page.
PageAllPublishedGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
columns
= [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'title': 'All', 'username': 'All'}¶
-
default_sort_key
= 'update_time'¶
-
model_class
¶ alias of
galaxy.model.Page
-
title
= 'Published Pages'¶
-
use_panels
= True¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
PageController
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.SharableMixin
,galaxy.webapps.base.controller.UsesStoredWorkflowMixin
,galaxy.webapps.base.controller.UsesVisualizationMixin
,galaxy.model.item_attrs.UsesItemRatings
-
display_by_username_and_slug
(trans, username, slug)[source]¶ Display page based on a username and slug.
-
get_page
(trans, id, check_ownership=True, check_accessible=False)[source]¶ Get a page from the database by id.
-
hda_manager
= GalaxyTypeDepends(_do_resolve)¶
-
history_manager
= GalaxyTypeDepends(_do_resolve)¶
-
history_serializer
= GalaxyTypeDepends(_do_resolve)¶
-
list_datasets_for_selection
(trans, **kwargs)[source]¶ Returns HTML that enables a user to select one or more datasets.
-
list_histories_for_selection
(trans, **kwargs)[source]¶ Returns HTML that enables a user to select one or more histories.
-
list_pages_for_selection
(trans, **kwargs)[source]¶ Returns HTML that enables a user to select one or more pages.
-
list_visualizations_for_selection
(trans, **kwargs)[source]¶ Returns HTML that enables a user to select one or more visualizations.
-
list_workflows_for_selection
(trans, **kwargs)[source]¶ Returns HTML that enables a user to select one or more workflows.
-
page_manager
= GalaxyTypeDepends(_do_resolve)¶
-
rate_async
(trans, id, rating)[source]¶ Rate a page asynchronously and return updated community data.
-
set_accessible_async
(trans, id=None, accessible=False)[source]¶ Set page’s importable attribute and slug.
-
slug_builder
= GalaxyTypeDepends(_do_resolve)¶
-
workflow_manager
= GalaxyTypeDepends(_do_resolve)¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
PageListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
URLColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.page.PageListGrid.URLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'published': 'All', 'sharing': 'All', 'tags': 'All', 'title': 'All'}¶
-
default_sort_key
= '-update_time'¶
-
global_actions
= [<galaxy.web.framework.helpers.grids.GridAction object>]¶
-
model_class
¶ alias of
galaxy.model.Page
-
operations
= [<galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
-
title
= 'Pages'¶
-
use_panels
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.page.
PageSelectionGrid
[source]¶ Bases:
galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid
Grid for selecting pages.
-
columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
model_class
¶ alias of
galaxy.model.Page
-
title
= 'Saved Pages'¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
VisualizationSelectionGrid
[source]¶ Bases:
galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid
Grid for selecting visualizations.
-
columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
model_class
¶ alias of
galaxy.model.Visualization
-
title
= 'Saved Visualizations'¶
-
-
class
galaxy.webapps.galaxy.controllers.page.
WorkflowSelectionGrid
[source]¶ Bases:
galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid
Grid for selecting workflows.
-
columns
= [<galaxy.webapps.galaxy.controllers.page.ItemSelectionGrid.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
model_class
¶ alias of
galaxy.model.StoredWorkflow
-
title
= 'Saved Workflows'¶
-
galaxy.webapps.galaxy.controllers.root module¶
Contains the main interface in the Universe class
-
class
galaxy.webapps.galaxy.controllers.root.
RootController
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.JSAppLauncher
,galaxy.model.item_attrs.UsesAnnotations
Controller class that maps to the url root of Galaxy (i.e. ‘/’).
-
default
(trans, target1=None, target2=None, **kwd)[source]¶ Called on any url that does not match a controller method.
-
display_as
(trans, id=None, display_app=None, **kwd)[source]¶ Returns a file in a format that can successfully be displayed in display_app.
-
history_add_to
(trans, history_id=None, file_data=None, name='Data Added to History', info=None, ext='txt', dbkey='?', copy_access_from=None, **kwd)[source]¶ Adds a POSTed file to a History.
-
history_manager
= GalaxyTypeDepends(_do_resolve)¶
-
history_new
(trans, name=None)[source]¶ Create a new history with the given name and refresh the history panel.
-
history_serializer
= GalaxyTypeDepends(_do_resolve)¶
-
index
(trans, tool_id=None, workflow_id=None, history_id=None, m_c=None, m_a=None, **kwd)[source]¶ Root and entry point for client-side web app.
Parameters: - tool_id (str or None) – load center panel with given tool if not None
- workflow_id (encoded id or None) – load center panel with given workflow if not None
- history_id (encoded id or None) – switch current history to given history if not None
- m_c (str or None) – controller name (e.g. ‘user’)
- m_a (str or None) – controller method/action (e.g. ‘dbkeys’)
If m_c and m_a are present, the center panel will be loaded using the controller and action as a url: (e.g. ‘user/dbkeys’).
-
galaxy.webapps.galaxy.controllers.shed_tool_static module¶
-
class
galaxy.webapps.galaxy.controllers.shed_tool_static.
ShedToolStatic
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
-
index
(trans, shed, owner, repo, tool, version, image_file)[source]¶ Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. .. image:: https://raw.github.com/galaxy/some_image.png .. image:: $PATH_TO_IMAGES/some_image.png .. image:: /static/images/some_image.gif .. image:: some_image.jpg .. image:: /deep/some_image.png
-
galaxy.webapps.galaxy.controllers.tag module¶
Tags Controller: handles tagging/untagging of entities and provides autocomplete support.
-
class
galaxy.webapps.galaxy.controllers.tag.
TagsController
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.UsesTagsMixin
-
add_tag_async
(trans, item_id=None, item_class=None, new_tag=None, context=None)[source]¶ Add tag to an item.
-
get_tagging_elt_async
(trans, item_id, item_class, elt_context='')[source]¶ Returns HTML for editing an item’s tags.
-
remove_tag_async
(trans, item_id=None, item_class=None, tag_name=None, context=None)[source]¶ Remove tag from an item.
-
galaxy.webapps.galaxy.controllers.tool_runner module¶
Controller handles external tool related requests
-
class
galaxy.webapps.galaxy.controllers.tool_runner.
ToolRunner
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
-
data_source_redirect
(trans, tool_id=None)[source]¶ Redirects a user accessing a Data Source tool to its target action link. This method will subvert mix-mode content blocking in several browsers when accessing non-https data_source tools from an https galaxy server.
Tested as working on Safari 7.0 and FireFox 26 Subverting did not work on Chrome 31
-
galaxy.webapps.galaxy.controllers.user module¶
Contains the user interface in the Universe class
-
class
galaxy.webapps.galaxy.controllers.user.
User
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.UsesFormDefinitionsMixin
,galaxy.webapps.base.controller.CreatesApiKeysMixin
-
activate
(trans, **kwd)[source]¶ Check whether token fits the user and then activate the user’s account.
-
change_password
(trans, payload=None, **kwd)[source]¶ Allows to change own password.
Parameters: payload (dict) – dictionary structure containing: * id: encoded user id * current: current user password * token: temporary token to change password (instead of id and current) * password: new password * confirm: new password (confirmation)
-
installed_len_files
= None¶
-
is_outside_grace_period
(trans, create_time)[source]¶ Function checks whether the user is outside the config-defined grace period for inactive accounts.
-
resend_activation_email
(trans, email, username)[source]¶ Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link.
-
resend_verification
(trans)[source]¶ Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.
-
reset_password
(trans, payload=None, **kwd)[source]¶ Reset the user’s password. Send an email with token that allows a password change.
-
user_manager
= GalaxyTypeDepends(_do_resolve)¶
-
galaxy.webapps.galaxy.controllers.userskeys module¶
Contains the user interface in the Universe class
-
class
galaxy.webapps.galaxy.controllers.userskeys.
User
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.UsesFormDefinitionsMixin
galaxy.webapps.galaxy.controllers.visualization module¶
-
class
galaxy.webapps.galaxy.controllers.visualization.
HistoryDatasetsSelectionGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
class
DbKeyColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
class
HistoryColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
-
available_tracks
= None¶
-
columns
= [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.HistoryColumn object>, <galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid.DbKeyColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'deleted': 'False', 'shared': 'All'}¶
-
default_sort_key
= '-hid'¶
-
model_class
¶
-
title
= 'Add Datasets'¶
-
class
-
class
galaxy.webapps.galaxy.controllers.visualization.
LibraryDatasetsSelectionGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
available_tracks
= None¶
-
columns
= [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'deleted': 'False'}¶
-
default_sort_key
= '-id'¶
-
model_class
¶
-
title
= 'Add Datasets'¶
-
-
class
galaxy.webapps.galaxy.controllers.visualization.
TracksterSelectionGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]¶
-
default_sort_key
= '-update_time'¶
-
model_class
¶ alias of
galaxy.model.Visualization
-
show_item_checkboxes
= True¶
-
title
= 'Insert into visualization'¶
-
use_paging
= False¶
-
-
class
galaxy.webapps.galaxy.controllers.visualization.
VisualizationAllPublishedGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
columns
= [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
-
default_filter
= {'title': 'All', 'username': 'All'}¶
-
default_sort_key
= 'update_time'¶
-
model_class
¶ alias of
galaxy.model.Visualization
-
title
= 'Published Visualizations'¶
-
use_panels
= True¶
-
-
class
galaxy.webapps.galaxy.controllers.visualization.
VisualizationController
(app: galaxy.structured_app.StructuredApp)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.SharableMixin
,galaxy.webapps.base.controller.UsesVisualizationMixin
,galaxy.model.item_attrs.UsesAnnotations
,galaxy.model.item_attrs.UsesItemRatings
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circster
(trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None)[source]¶ Display a circster visualization.
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display_by_username_and_slug
(trans, username, slug)[source]¶ Display visualization based on a username and slug.
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hda_manager
= GalaxyTypeDepends(_do_resolve)¶
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list_history_datasets
(trans, **kwargs)[source]¶ List a history’s datasets that can be added to a visualization.
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list_libraries
(trans, **kwargs)[source]¶ List all libraries that can be used for selecting datasets.
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list_library_datasets
(trans, **kwargs)[source]¶ List a library’s datasets that can be added to a visualization.
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rate_async
(trans, id, rating)[source]¶ Rate a visualization asynchronously and return updated community data.
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render
(trans, visualization_name, embedded=None, **kwargs)[source]¶ 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}
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save
(trans, vis_json=None, type=None, id=None, title=None, dbkey=None, annotation=None)[source]¶ Save a visualization; if visualization does not have an ID, a new visualization is created. Returns JSON of visualization.
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saved
(trans, id=None, revision=None, type=None, config=None, title=None, **kwargs)[source]¶ Save (on POST) or load (on GET) a visualization then render.
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set_accessible_async
(trans, id=None, accessible=False)[source]¶ Set visualization’s importable attribute and slug.
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slug_builder
= GalaxyTypeDepends(_do_resolve)¶
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class
galaxy.webapps.galaxy.controllers.visualization.
VisualizationListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
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columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
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default_filter
= {'deleted': 'False', 'sharing': 'All', 'tags': 'All', 'title': 'All'}¶
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default_sort_key
= '-update_time'¶
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model_class
¶ alias of
galaxy.model.Visualization
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operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
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title
= 'Saved Visualizations'¶
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galaxy.webapps.galaxy.controllers.workflow module¶
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class
galaxy.webapps.galaxy.controllers.workflow.
SingleTagContentsParser
(target_tag)[source]¶ Bases:
html.parser.HTMLParser
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class
galaxy.webapps.galaxy.controllers.workflow.
StoredWorkflowAllPublishedGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
-
columns
= [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
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default_filter
= {'public_url': 'All', 'tags': 'All', 'username': 'All'}¶
-
default_sort_key
= 'update_time'¶
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model_class
¶ alias of
galaxy.model.StoredWorkflow
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num_rows_per_page
= 50¶
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operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
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title
= 'Published Workflows'¶
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use_paging
= True¶
-
-
class
galaxy.webapps.galaxy.controllers.workflow.
StoredWorkflowListGrid
[source]¶ Bases:
galaxy.web.framework.helpers.grids.Grid
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class
StepsColumn
(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None, delayed=False)[source]¶
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columns
= [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid.StepsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]¶
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default_filter
= {'name': 'All', 'tags': 'All'}¶
-
default_sort_key
= '-update_time'¶
-
model_class
¶ alias of
galaxy.model.StoredWorkflow
-
operations
= [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]¶
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title
= 'Saved Workflows'¶
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use_panels
= True¶
-
class
-
class
galaxy.webapps.galaxy.controllers.workflow.
WorkflowController
(app)[source]¶ Bases:
galaxy.webapps.base.controller.BaseUIController
,galaxy.webapps.base.controller.SharableMixin
,galaxy.webapps.base.controller.UsesStoredWorkflowMixin
,galaxy.model.item_attrs.UsesItemRatings
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build_from_current_history
(trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None)[source]¶
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display_by_username_and_slug
(trans, username, slug, format='html')[source]¶ Display workflow based on a username and slug. Format can be html, json, or json-download.
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editor
(trans, id=None, workflow_id=None, version=None)[source]¶ 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.
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export_to_file
(trans, id)[source]¶ 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.
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export_to_myexp
(trans, id, myexp_username, myexp_password)[source]¶ Exports a workflow to myExperiment website.
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for_direct_import
(trans, id)[source]¶ 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.
-
load_workflow
(trans, id, version=None)[source]¶ 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>¶
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rate_async
(trans, id, rating)[source]¶ Rate a workflow asynchronously and return updated community data.
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save_workflow_as
(trans, workflow_name, workflow_data, workflow_annotation='', from_tool_form=False)[source]¶ Creates a new workflow based on Save As command. It is a new workflow, but is created with workflow_data already present.
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set_accessible_async
(trans, id=None, accessible=False)[source]¶ Set workflow’s importable attribute and slug.
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set_public_username
(trans, id, username, **kwargs)[source]¶ Set user’s public username and delegate to sharing()
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slug_builder
= <galaxy.managers.sharable.SlugBuilder object>¶
-
stored_list_grid
= <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid object>¶
-