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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.UserListGrid[source]

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

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

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[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)[source]

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

get_value(trans, grid, user)[source]
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)[source]

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

get_value(trans, grid, user)[source]
title = 'Users'
model_class

alias of galaxy.model.User

template = '/admin/user/grid.mako'
default_sort_key = 'email'
columns = [<galaxy.webapps.galaxy.controllers.admin.EmailColumn object>, <galaxy.webapps.galaxy.controllers.admin.UserNameColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.ExternalColumn object>, <galaxy.webapps.galaxy.controllers.admin.LastLoginColumn object>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object>, <galaxy.webapps.galaxy.controllers.admin.TimeCreatedColumn object>, <galaxy.webapps.galaxy.controllers.admin.ActivatedColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]
num_rows_per_page = 50
preserve_state = False
use_paging = True
get_current_item(trans, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.admin.RoleListGrid[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)[source]

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

get_value(trans, grid, role)[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)[source]

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

get_value(trans, grid, role)[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)[source]

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

get_value(trans, grid, role)[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)[source]

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

get_value(trans, grid, role)[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)[source]

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

get_value(trans, grid, role)[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)[source]

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

get_value(trans, grid, role)[source]
title = 'Roles'
model_class

alias of galaxy.model.Role

template = '/admin/dataset_security/role/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.admin.TypeColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]
num_rows_per_page = 50
preserve_state = False
use_paging = True
apply_query_filter(trans, query, **kwargs)[source]
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)[source]

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

get_value(trans, grid, group)[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)[source]

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

get_value(trans, grid, group)[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)[source]

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

get_value(trans, grid, group)[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)[source]

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

get_value(trans, grid, group)[source]
title = 'Groups'
model_class

alias of galaxy.model.Group

template = '/admin/dataset_security/group/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.RolesColumn object>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]
num_rows_per_page = 50
preserve_state = False
use_paging = True
class galaxy.webapps.galaxy.controllers.admin.QuotaListGrid[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)[source]

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

get_value(trans, grid, quota)[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)[source]

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

get_value(trans, grid, quota)[source]
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)[source]

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

get_value(trans, grid, quota)[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)[source]

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

get_value(trans, grid, quota)[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)[source]

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

get_value(trans, grid, quota)[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)[source]

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

get_value(trans, grid, quota)[source]
title = 'Quotas'
model_class

alias of galaxy.model.Quota

template = '/admin/quota/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.galaxy.controllers.admin.NameColumn object>, <galaxy.webapps.galaxy.controllers.admin.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.admin.AmountColumn object>, <galaxy.webapps.galaxy.controllers.admin.UsersColumn object>, <galaxy.webapps.galaxy.controllers.admin.GroupsColumn object>, <galaxy.webapps.galaxy.controllers.admin.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]
num_rows_per_page = 50
preserve_state = False
use_paging = True
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)[source]

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

get_value(trans, grid, tool_version)[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)[source]

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

get_value(trans, grid, tool_version)[source]
title = 'Tool versions'
model_class

alias of galaxy.model.tool_shed_install.ToolVersion

template = '/admin/tool_version/grid.mako'
default_sort_key = 'tool_id'
columns = [<galaxy.webapps.galaxy.controllers.admin.ToolIdColumn object>, <galaxy.webapps.galaxy.controllers.admin.ToolVersionsColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = []
operations = []
standard_filters = []
default_filter = {}
num_rows_per_page = 50
preserve_state = False
use_paging = True
build_initial_query(trans, **kwd)[source]
class galaxy.webapps.galaxy.controllers.admin.AdminGalaxy(app)[source]

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

user_list_grid = <galaxy.webapps.galaxy.controllers.admin.UserListGrid object>
role_list_grid = <galaxy.webapps.galaxy.controllers.admin.RoleListGrid object>
group_list_grid = <galaxy.webapps.galaxy.controllers.admin.GroupListGrid object>
quota_list_grid = <galaxy.webapps.galaxy.controllers.admin.QuotaListGrid object>
tool_version_list_grid = <galaxy.webapps.galaxy.controllers.admin.ToolVersionListGrid object>
delete_operation = <galaxy.web.framework.helpers.grids.GridOperation object>
undelete_operation = <galaxy.web.framework.helpers.grids.GridOperation object>
purge_operation = <galaxy.web.framework.helpers.grids.GridOperation object>
quotas(trans, *args, **kwargs)[source]
create_quota(trans, *args, **kwargs)[source]
rename_quota(trans, *args, **kwargs)[source]
manage_users_and_groups_for_quota(trans, *args, **kwargs)[source]
edit_quota(trans, *args, **kwargs)[source]
set_quota_default(trans, *args, **kwargs)[source]
unset_quota_default(trans, *args, **kwargs)[source]
mark_quota_deleted(trans, *args, **kwargs)[source]
undelete_quota(trans, *args, **kwargs)[source]
purge_quota(trans, *args, **kwargs)[source]
impersonate(trans, *args, **kwargs)[source]
check_for_tool_dependencies(trans, migration_stage)[source]
review_tool_migration_stages(trans, *args, **kwargs)[source]
tool_errors(trans, *args, **kwargs)[source]
view_datatypes_registry(trans, *args, **kwargs)[source]
view_tool_data_tables(trans, *args, **kwargs)[source]
display_applications(trans, *args, **kwargs)[source]
reload_display_application(trans, *args, **kwargs)[source]
recalculate_user_disk_usage(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.admin_toolshed module

class galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed(app)[source]

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

installed_repository_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.InstalledRepositoryGrid object>
repository_installation_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.RepositoryInstallationGrid object>
tool_dependency_grid = <tool_shed.galaxy_install.grids.admin_toolshed_grids.ToolDependencyGrid object>
activate_repository(trans, *args, **kwargs)[source]

Activate a repository that was deactivated but not uninstalled.

browse_repository(trans, *args, **kwargs)[source]
browse_repositories(trans, *args, **kwargs)[source]
browse_tool_dependency(trans, *args, **kwargs)[source]
browse_tool_shed(trans, *args, **kwargs)[source]
browse_toolsheds(trans, *args, **kwargs)[source]
browse_tool_sheds(trans, *args, **kwargs)[source]
check_for_updates(trans, *args, **kwargs)[source]

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

deactivate_or_uninstall_repository(trans, *args, **kwargs)[source]

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)[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

find_tools_in_tool_shed(trans, *args, **kwargs)[source]
find_workflows_in_tool_shed(trans, *args, **kwargs)[source]
generate_workflow_image(trans, *args, **kwargs)[source]

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

get_file_contents(trans, *args, **kwargs)[source]
get_tool_dependencies(trans, *args, **kwargs)[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, *args, **kwargs)[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.

import_workflow(trans, *args, **kwargs)[source]

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

initiate_tool_dependency_installation(trans, *args, **kwargs)[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, *args, **kwargs)[source]

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

install_tool_dependencies_with_update(trans, *args, **kwargs)[source]

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

manage_repositories(trans, *args, **kwargs)[source]
manage_repository(trans, *args, **kwargs)[source]
manage_repository_tool_dependencies(trans, *args, **kwargs)[source]
manage_tool_dependencies(trans, *args, **kwargs)[source]
monitor_repository_installation(trans, *args, **kwargs)[source]
open_folder(trans, *args, **kwargs)[source]
prepare_for_install(trans, *args, **kwargs)[source]
purge_repository(trans, *args, **kwargs)[source]

Purge a “white ghost” repository from the database.

reinstall_repository(trans, *args, **kwargs)[source]

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)[source]

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)[source]

Repair specified tool shed repositories.

repository_installation_status_updates(trans, *args, **kwargs)[source]
reselect_tool_panel_section(trans, *args, **kwargs)[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.

reset_metadata_on_selected_installed_repositories(trans, *args, **kwargs)[source]
reset_repository_metadata(trans, *args, **kwargs)[source]

Reset all metadata on a single installed tool shed repository.

reset_to_install(trans, *args, **kwargs)[source]

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

set_tool_versions(trans, *args, **kwargs)[source]

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_status_updates(trans, *args, **kwargs)[source]
uninstall_tool_dependencies(trans, *args, **kwargs)[source]
update_to_changeset_revision(trans, *args, **kwargs)[source]

Update a cloned repository to the latest revision possible.

update_tool_shed_status_for_installed_repository(trans, *args, **kwargs)[source]
view_tool_metadata(trans, *args, **kwargs)[source]
view_workflow(trans, *args, **kwargs)[source]

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

galaxy.webapps.galaxy.controllers.async module

Upload class

class galaxy.webapps.galaxy.controllers.async.ASync(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

default(trans, tool_id=None, data_id=None, data_secret=None, **kwd)[source]

Catches the tool id and redirects as needed

index(trans, tool_id=None, data_secret=None, **kwd)[source]

Manages ascynchronous connections

galaxy.webapps.galaxy.controllers.biostar module

Controller for integration with the Biostar application

class galaxy.webapps.galaxy.controllers.biostar.BiostarController(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

Provides integration with Biostar through external authentication, see: http://liondb.com/help/x/

biostar_redirect(trans, payload=None, biostar_action=None)[source]

Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and optional information about a specific tool.

biostar_tool_tag_redirect(trans, tool_id=None)[source]

Generate a redirect to a Biostar site using tag for tool.

biostar_question_redirect(trans, payload=None)[source]

Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool.

biostar_tool_question_redirect(trans, tool_id=None)[source]

Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool.

biostar_tool_bug_report(trans, hda=None, email=None, message=None)[source]

Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool error.

biostar_logout(trans)[source]

Log out of biostar

galaxy.webapps.galaxy.controllers.data_manager module

class galaxy.webapps.galaxy.controllers.data_manager.DataManager(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

index(trans, **kwd)[source]
manage_data_manager(trans, **kwd)[source]
view_job(trans, **kwd)[source]
manage_data_table(trans, **kwd)[source]
reload_tool_data_tables(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.dataset module

class galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid[source]

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

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

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

get_value(trans, grid, hda)[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)[source]

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

get_value(trans, grid, hda)[source]
get_accepted_filters()[source]

Returns a list of accepted filters for this column.

title = 'Saved Datasets'
model_class

alias of galaxy.model.HistoryDatasetAssociation

template = '/dataset/grid.mako'
default_sort_key = '-update_time'
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.dataset.HistoryColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.webapps.galaxy.controllers.dataset.StatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = []
default_filter = {'deleted': 'False', 'name': 'All', 'tags': 'All'}
preserve_state = False
use_async = True
use_paging = True
num_rows_per_page = 50
build_initial_query(trans, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.dataset.DatasetInterface(app)[source]

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

stored_list_grid = <galaxy.webapps.galaxy.controllers.dataset.HistoryDatasetAssociationListGrid object>
__init__(app)[source]
errors(trans, id)[source]
stdout(trans, dataset_id=None, **kwargs)[source]
stderr(trans, dataset_id=None, **kwargs)[source]
exit_code(trans, dataset_id=None, **kwargs)[source]
report_error(trans, id, email='', message='', **kwd)[source]
default(trans, dataset_id=None, **kwd)[source]
get_metadata_file(trans, hda_id, metadata_name)[source]

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

transfer_status(trans, *args, **kwargs)[source]

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

display(trans, dataset_id=None, preview=False, filename=None, to_ext=None, offset=None, ck_size=None, **kwd)[source]
edit(trans, dataset_id=None, filename=None, hid=None, **kwd)[source]

Allows user to modify parameters of an HDA.

list(trans, *args, **kwargs)[source]

List all available datasets

imp(trans, dataset_id=None, **kwd)[source]

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

Returns dataset’s name and link.

get_embed_html_async(trans, id)[source]

Returns HTML for embedding a dataset in a page.

set_accessible_async(trans, *args, **kwargs)[source]

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

rate_async(trans, *args, **kwargs)[source]

Rate a dataset asynchronously and return updated community data.

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_item_content_async(trans, id)[source]

Returns item content in HTML format.

annotate_async(trans, id, new_annotation=None, **kwargs)[source]
get_annotation_async(trans, id)[source]
display_at(trans, dataset_id, filename=None, **kwd)[source]

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

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

Access to external display applications

delete(trans, dataset_id, filename, show_deleted_on_refresh=False)[source]
delete_async(trans, dataset_id, filename)[source]
undelete(trans, dataset_id, filename)[source]
undelete_async(trans, dataset_id, filename)[source]
unhide(trans, dataset_id, filename)[source]
purge(trans, dataset_id, filename, show_deleted_on_refresh=False)[source]
purge_async(trans, dataset_id, filename)[source]
show_params(trans, dataset_id=None, from_noframe=None, **kwd)[source]

Show the parameters used for the job associated with an HDA

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

galaxy.webapps.galaxy.controllers.error module

class galaxy.webapps.galaxy.controllers.error.Error(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

index(trans)[source]

galaxy.webapps.galaxy.controllers.external_service module

class galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid[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)[source]

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

get_value(trans, grid, external_service)[source]
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, target=None)[source]

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

get_value(trans, grid, external_service)[source]
title = 'External Services'
template = 'admin/external_service/grid.mako'
model_class

alias of galaxy.model.ExternalService

default_sort_key = '-create_time'
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = {'deleted': 'False'}
columns = [<galaxy.webapps.galaxy.controllers.external_service.NameColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.external_service.ExternalServiceTypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>, <galaxy.web.framework.helpers.grids.GridAction object>]
class galaxy.webapps.galaxy.controllers.external_service.ExternalService(app)[source]

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

external_service_grid = <galaxy.webapps.galaxy.controllers.external_service.ExternalServiceGrid object>
browse_external_services(trans, *args, **kwargs)[source]
create_external_service(trans, *args, **kwargs)[source]
view_external_service(trans, *args, **kwargs)[source]
edit_external_service(trans, *args, **kwargs)[source]
edit_external_service_form_definition(trans, *args, **kwargs)[source]
update_external_service_form_definition(trans, *args, **kwargs)[source]
delete_external_service(trans, *args, **kwargs)[source]
undelete_external_service(trans, *args, **kwargs)[source]
reload_external_service_types(trans, *args, **kwargs)[source]
get_external_service_type(trans, external_service_type_id, action='browse_external_services')[source]

galaxy.webapps.galaxy.controllers.external_services module

class galaxy.webapps.galaxy.controllers.external_services.ExternalServiceController(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

access_action(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.forms module

class galaxy.webapps.galaxy.controllers.forms.FormsGrid[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)[source]

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

get_value(trans, grid, form)[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)[source]

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

get_value(trans, grid, form)[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)[source]

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

get_value(trans, grid, form)[source]
title = 'Forms'
template = 'admin/forms/grid.mako'
model_class

alias of galaxy.model.FormDefinitionCurrent

default_sort_key = '-create_time'
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = {'deleted': 'False'}
columns = [<galaxy.webapps.galaxy.controllers.forms.NameColumn object>, <galaxy.webapps.galaxy.controllers.forms.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.forms.TypeColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
build_initial_query(trans, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.forms.Forms(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

empty_field = {'default': '', 'helptext': '', 'label': '', 'layout': 'none', 'name': '', 'required': False, 'selectlist': [], 'type': 'TextField', 'visible': True}
forms_grid = <galaxy.webapps.galaxy.controllers.forms.FormsGrid object>
browse_form_definitions(trans, *args, **kwargs)[source]
view_latest_form_definition(trans, *args, **kwargs)[source]

Displays the layout of the latest version of the form definition

create_form_definition(trans, *args, **kwargs)[source]
edit_form_definition(trans, *args, **kwargs)[source]

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.

get_saved_form(form_definition)[source]

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

get_current_form(trans, **kwd)[source]

This method gets all the unsaved user-entered form details and returns a dictionary containing the name, desc, type, layout & fields of the form

save_form_definition(trans, form_definition_current_id=None, **kwd)[source]

This method saves the current form

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

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.

delete_form_definition(trans, *args, **kwargs)[source]
undelete_form_definition(trans, *args, **kwargs)[source]
build_form_definition_field_widgets(trans, layout_grids, field_index, field, form_type)[source]

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

galaxy.webapps.galaxy.controllers.history module

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

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

get_value(trans, grid, history)[source]
class galaxy.webapps.galaxy.controllers.history.HistoryListGrid[source]

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

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

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

get_value(trans, grid, history)[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)[source]

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

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)[source]

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

get_value(trans, grid, history)[source]
sort(trans, query, ascending, column_name=None)[source]
title = 'Saved Histories'
model_class

alias of galaxy.model.History

template = '/history/grid.mako'
default_sort_key = '-update_time'
columns = [<galaxy.webapps.galaxy.controllers.history.HistoryListNameColumn object>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
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>]
standard_filters = [<galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>, <galaxy.web.framework.helpers.grids.GridColumnFilter object>]
default_filter = {'deleted': 'False', 'name': 'All', 'sharing': 'All', 'tags': 'All'}
num_rows_per_page = 10
preserve_state = False
use_async = True
use_paging = True
info_text = 'Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.'
get_current_item(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid[source]

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

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

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

get_value(trans, grid, history)[source]
class SharedByColumn(label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, nowrap=False, filterable=None, sortable=True, label_id_prefix=None, target=None)[source]

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

get_value(trans, grid, history)[source]
title = 'Histories shared with you by others'
model_class

alias of galaxy.model.History

template = '/history/shared_grid.mako'
default_sort_key = '-update_time'
default_filter = {}
columns = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.DatasetsByStateColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.history.SharedByColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
standard_filters = []
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
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)[source]

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

title = 'Published Histories'
model_class

alias of galaxy.model.History

default_sort_key = 'update_time'
default_filter = {'public_url': 'All', 'tags': 'All', 'username': 'All'}
use_paging = True
num_rows_per_page = 50
use_async = True
columns = [<galaxy.webapps.galaxy.controllers.history.NameURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = []
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.history.HistoryController(app)[source]

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

__init__(app)[source]
index(trans)[source]
list_as_xml(trans)[source]

XML history list for functional tests

stored_list_grid = <galaxy.webapps.galaxy.controllers.history.HistoryListGrid object>
shared_list_grid = <galaxy.webapps.galaxy.controllers.history.SharedHistoryListGrid object>
published_list_grid = <galaxy.webapps.galaxy.controllers.history.HistoryAllPublishedGrid object>
list_published(trans, **kwargs)[source]
list(trans, *args, **kwargs)[source]

List all available histories

list_shared(trans, *args, **kwargs)[source]

List histories shared with current user by others

citations(trans)[source]
as_xml(trans, id=None, show_deleted=None, show_hidden=None)[source]

Return a history in xml format.

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).

structure(trans, id=None, **kwargs)[source]
view(trans, id=None, show_deleted=False, show_hidden=False, use_panels=True)[source]

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

view_multiple(trans, *args, **kwargs)[source]
display_by_username_and_slug(trans, username, slug)[source]

Display history based on a username and slug.

sharing(trans, *args, **kwargs)[source]

Handle history sharing.

share(trans, *args, **kwargs)[source]
adjust_hidden(trans, id=None, **kwd)[source]

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

share_restricted(trans, *args, **kwargs)[source]
purge_deleted_datasets(trans)[source]
delete(trans, id, purge=False)[source]

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

resume_paused_jobs(trans, current=False, ids=None)[source]

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

rate_async(trans, *args, **kwargs)[source]

Rate a history asynchronously and return updated community data.

import_archive(trans, *args, **kwargs)[source]

Import a history from a file archive.

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

Export a history to an archive.

Returns history’s name and link.

set_accessible_async(trans, *args, **kwargs)[source]

Set history’s importable attribute and slug.

rename(trans, *args, **kwargs)[source]
switch_to_history(trans, *args, **kwargs)[source]

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

get_item(trans, id)[source]
history_data(trans, history)[source]

Return the given history in a serialized, dictionary form.

set_as_current(trans, *args, **kwargs)[source]

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

current_history_json(trans, *args, **kwargs)[source]

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

create_new_current(trans, *args, **kwargs)[source]

Create a new, current history for the current user

galaxy.webapps.galaxy.controllers.library module

class galaxy.webapps.galaxy.controllers.library.LibraryListGrid[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)[source]

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

get_value(trans, grid, library)[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)[source]

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

get_value(trans, grid, library)[source]
title = 'Data Libraries'
model_class

alias of galaxy.model.Library

template = '/library/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.galaxy.controllers.library.NameColumn object>, <galaxy.webapps.galaxy.controllers.library.DescriptionColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
standard_filters = []
default_filter = {'deleted': 'False', 'description': 'All', 'name': 'All', 'purged': 'False'}
num_rows_per_page = 50
preserve_state = False
use_paging = True
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwd)[source]
class galaxy.webapps.galaxy.controllers.library.Library(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

library_list_grid = <galaxy.webapps.galaxy.controllers.library.LibraryListGrid object>
list(trans, **kwd)[source]
index(trans, *args, **kwargs)[source]
browse_libraries(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.library_admin module

class galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid[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)[source]

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

get_value(trans, grid, library)[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)[source]

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

get_value(trans, grid, library)[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)[source]

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

get_value(trans, grid, library)[source]
title = 'Data Libraries'
model_class

alias of galaxy.model.Library

template = '/admin/library/grid.mako'
default_sort_key = 'name'
columns = [<galaxy.webapps.galaxy.controllers.library_admin.NameColumn object>, <galaxy.webapps.galaxy.controllers.library_admin.DescriptionColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.library_admin.StatusColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
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>]
default_filter = {'deleted': 'False', 'description': 'All', 'name': 'All', 'purged': 'False'}
num_rows_per_page = 50
preserve_state = False
use_paging = True
class galaxy.webapps.galaxy.controllers.library_admin.LibraryAdmin(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

library_list_grid = <galaxy.webapps.galaxy.controllers.library_admin.LibraryListGrid object>
browse_libraries(trans, *args, **kwargs)[source]
create_library(trans, *args, **kwargs)[source]
delete_library(trans, *args, **kwargs)[source]
undelete_library(trans, *args, **kwargs)[source]
purge_library(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.library_common module

class galaxy.webapps.galaxy.controllers.library_common.LibraryCommon(app)[source]

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

library_item_updates(trans, *args, **kwargs)[source]
browse_library(trans, *args, **kwargs)[source]
library_info(trans, *args, **kwargs)[source]
library_permissions(trans, *args, **kwargs)[source]
create_folder(trans, cntrller, parent_id, library_id, **kwd)[source]
folder_info(trans, *args, **kwargs)[source]
folder_permissions(trans, *args, **kwargs)[source]
ldda_edit_info(trans, *args, **kwargs)[source]
ldda_info(trans, *args, **kwargs)[source]
ldda_permissions(trans, *args, **kwargs)[source]
upload_library_dataset(trans, cntrller, library_id, folder_id, **kwd)[source]
upload_dataset(trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd)[source]
make_library_uploaded_dataset(trans, cntrller, params, name, path, type, library_bunch, in_folder=None)[source]
get_server_dir_uploaded_datasets(trans, cntrller, params, full_dir, import_dir_desc, library_bunch, response_code, message)[source]
get_path_paste_uploaded_datasets(trans, cntrller, params, library_bunch, response_code, message)[source]
add_history_datasets_to_library(trans, *args, **kwargs)[source]
download_dataset_from_folder(trans, *args, **kwargs)[source]

Catches the dataset id and displays file contents as directed

library_dataset_info(trans, *args, **kwargs)[source]
library_dataset_permissions(trans, *args, **kwargs)[source]
make_library_item_public(trans, *args, **kwargs)[source]
act_on_multiple_datasets(trans, *args, **kwargs)[source]
import_datasets_to_histories(trans, *args, **kwargs)[source]
manage_template_inheritance(trans, *args, **kwargs)[source]
move_library_item(trans, *args, **kwargs)[source]
delete_library_item(trans, *args, **kwargs)[source]
undelete_library_item(trans, *args, **kwargs)[source]
galaxy.webapps.galaxy.controllers.library_common.active_folders(trans, folder)[source]
galaxy.webapps.galaxy.controllers.library_common.activatable_folders(trans, folder)[source]
galaxy.webapps.galaxy.controllers.library_common.map_library_datasets_to_lddas(trans, lib_datasets)[source]

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.datasets_for_lddas(trans, lddas)[source]

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

galaxy.webapps.galaxy.controllers.library_common.active_folders_and_library_datasets(trans, folder)[source]
galaxy.webapps.galaxy.controllers.library_common.activatable_folders_and_library_datasets(trans, folder)[source]
galaxy.webapps.galaxy.controllers.library_common.branch_deleted(folder)[source]
galaxy.webapps.galaxy.controllers.library_common.get_containing_library_from_library_dataset(trans, library_dataset)[source]

Given a library_dataset, get the containing library

galaxy.webapps.galaxy.controllers.library_common.get_comptypes(trans)[source]
galaxy.webapps.galaxy.controllers.library_common.get_sorted_accessible_library_items(trans, cntrller, items, sort_attr)[source]
galaxy.webapps.galaxy.controllers.library_common.sort_by_attr(seq, attr)[source]

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

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

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

galaxy.webapps.galaxy.controllers.mobile module

class galaxy.webapps.galaxy.controllers.mobile.Mobile(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

index(trans, **kwargs)[source]
history_list(trans)[source]
history_detail(trans, id)[source]
dataset_detail(trans, id)[source]
dataset_peek(trans, id)[source]
settings(trans, email=None, password=None)[source]

galaxy.webapps.galaxy.controllers.page module

galaxy.webapps.galaxy.controllers.page.format_bool(b)[source]
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)[source]

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

get_value(trans, grid, item)[source]
use_panels = True
title = 'Pages'
model_class

alias of galaxy.model.Page

default_filter = {'published': 'All', 'sharing': 'All', 'tags': 'All', 'title': 'All'}
default_sort_key = '-update_time'
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.page.URLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.DisplayByUsernameAndSlugGridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.page.PageAllPublishedGrid[source]

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

use_panels = True
use_async = True
title = 'Published Pages'
model_class

alias of galaxy.model.Page

default_sort_key = 'update_time'
default_filter = {'title': 'All', 'username': 'All'}
columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
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)[source]

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

get_value(trans, grid, item)[source]
show_item_checkboxes = True
template = '/page/select_items_grid.mako'
default_filter = {'deleted': 'False', 'sharing': 'All'}
default_sort_key = '-update_time'
use_async = True
use_paging = True
num_rows_per_page = 10
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.page.HistorySelectionGrid[source]

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

Grid for selecting histories.

title = 'Saved Histories'
model_class

alias of galaxy.model.History

columns = [<galaxy.webapps.galaxy.controllers.page.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.page.HistoryDatasetAssociationSelectionGrid[source]

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

Grid for selecting HDAs.

title = 'Saved Datasets'
model_class

alias of galaxy.model.HistoryDatasetAssociation

columns = [<galaxy.webapps.galaxy.controllers.page.NameColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.page.WorkflowSelectionGrid[source]

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

Grid for selecting workflows.

title = 'Saved Workflows'
model_class

alias of galaxy.model.StoredWorkflow

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

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

Grid for selecting pages.

title = 'Saved Pages'
model_class

alias of galaxy.model.Page

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
class galaxy.webapps.galaxy.controllers.page.VisualizationSelectionGrid[source]

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

Grid for selecting visualizations.

title = 'Saved Visualizations'
model_class

alias of galaxy.model.Visualization

columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
class galaxy.webapps.galaxy.controllers.page.PageController(app)[source]

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

__init__(app)[source]
list(trans, *args, **kwargs)[source]

List user’s pages.

list_published(trans, *args, **kwargs)[source]
create(trans, *args, **kwargs)[source]

Create a new page

edit(trans, *args, **kwargs)[source]

Edit a page’s attributes.

edit_content(trans, *args, **kwargs)[source]

Render the main page editor interface.

sharing(trans, *args, **kwargs)[source]

Handle page sharing.

share(trans, *args, **kwargs)[source]

Handle sharing with an individual user.

save(trans, *args, **kwargs)[source]
display(trans, *args, **kwargs)[source]
display_by_username_and_slug(trans, username, slug)[source]

Display page based on a username and slug.

set_accessible_async(trans, *args, **kwargs)[source]

Set page’s importable attribute and slug.

rate_async(trans, *args, **kwargs)[source]

Rate a page asynchronously and return updated community data.

get_embed_html_async(trans, id)[source]

Returns HTML for embedding a workflow in a page.

Returns page’s name and link.

list_histories_for_selection(trans, *args, **kwargs)[source]

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

list_workflows_for_selection(trans, *args, **kwargs)[source]

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

list_visualizations_for_selection(trans, *args, **kwargs)[source]

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

list_pages_for_selection(trans, *args, **kwargs)[source]

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

list_datasets_for_selection(trans, *args, **kwargs)[source]

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

get_editor_iframe(trans)[source]

Returns the document for the page editor’s iframe.

get_page(trans, id, check_ownership=True, check_accessible=False)[source]

Get a page from the database by id.

get_item(trans, id)[source]

galaxy.webapps.galaxy.controllers.request_type module

class galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid[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)[source]

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

get_value(trans, grid, request_type)[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)[source]

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

get_value(trans, grid, request_type)[source]
class 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, target=None)[source]

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

get_value(trans, grid, request_type)[source]
class 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, target=None)[source]

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

get_value(trans, grid, request_type)[source]
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, target=None)[source]

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

get_value(trans, grid, request_type)[source]
title = 'Request Types'
template = 'admin/request_type/grid.mako'
model_class

alias of galaxy.model.RequestType

default_sort_key = '-create_time'
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = {'deleted': 'False'}
columns = [<galaxy.webapps.galaxy.controllers.request_type.NameColumn object>, <galaxy.webapps.galaxy.controllers.request_type.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.request_type.RequestFormColumn object>, <galaxy.webapps.galaxy.controllers.request_type.SampleFormColumn object>, <galaxy.webapps.galaxy.controllers.request_type.ExternalServiceColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
class galaxy.webapps.galaxy.controllers.request_type.RequestType(app)[source]

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

request_type_grid = <galaxy.webapps.galaxy.controllers.request_type.RequestTypeGrid object>
browse_request_types(trans, *args, **kwargs)[source]
create_request_type(trans, *args, **kwargs)[source]
view_editable_request_type(trans, *args, **kwargs)[source]
edit_request_type(trans, *args, **kwargs)[source]
view_request_type(trans, *args, **kwargs)[source]
delete_request_type(trans, *args, **kwargs)[source]
undelete_request_type(trans, *args, **kwargs)[source]
request_type_permissions(trans, *args, **kwargs)[source]
view_form_definition(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.requests module

class galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid[source]

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

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>]
apply_query_filter(trans, query, **kwd)[source]
operation = <galaxy.web.framework.helpers.grids.GridOperation object>
class galaxy.webapps.galaxy.controllers.requests.Requests(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

request_grid = <galaxy.webapps.galaxy.controllers.requests.UserRequestsGrid object>
index(trans, *args, **kwargs)[source]
find_samples_index(trans, *args, **kwargs)[source]
browse_requests(trans, **kwd)[source]

galaxy.webapps.galaxy.controllers.requests_admin module

class galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid[source]

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, target=None)[source]

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

get_value(trans, grid, request)[source]
columns = [<galaxy.webapps.galaxy.controllers.requests_common.NameColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>, <galaxy.webapps.galaxy.controllers.requests_admin.UserColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
col = <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>
operation = <galaxy.web.framework.helpers.grids.GridOperation object>
class galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid[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)[source]

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

get_value(trans, grid, sample_dataset)[source]
class 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, target=None)[source]

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

get_value(trans, grid, sample_dataset)[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)[source]

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

get_value(trans, grid, sample_dataset)[source]
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, target=None)[source]

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

get_value(trans, grid, sample_dataset)[source]
title = 'Sample Datasets'
template = 'admin/requests/sample_datasets_grid.mako'
model_class

alias of galaxy.model.SampleDataset

default_sort_key = '-create_time'
num_rows_per_page = 50
preserve_state = True
use_paging = False
columns = [<galaxy.webapps.galaxy.controllers.requests_admin.NameColumn object>, <galaxy.webapps.galaxy.controllers.requests_admin.SizeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.requests_admin.ExternalServiceColumn object>, <galaxy.webapps.galaxy.controllers.requests_admin.StatusColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
apply_query_filter(trans, query, **kwd)[source]
class galaxy.webapps.galaxy.controllers.requests_admin.RequestsAdmin(app)[source]

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

request_grid = <galaxy.webapps.galaxy.controllers.requests_admin.AdminRequestsGrid object>
datatx_grid = <galaxy.webapps.galaxy.controllers.requests_admin.DataTransferGrid object>
index(trans, *args, **kwargs)[source]
browse_requests(trans, *args, **kwargs)[source]
reject_request(trans, *args, **kwargs)[source]
manage_datasets(trans, *args, **kwargs)[source]
rename_datasets(trans, *args, **kwargs)[source]
initiate_data_transfer(trans, *args, **kwargs)[source]
update_sample_dataset_status(trans, cntrller, sample_dataset_ids, new_status, error_msg=None)[source]
galaxy.webapps.galaxy.controllers.requests_admin.build_rename_datasets_for_sample_select_field(trans, sample_dataset, selected_value='none')[source]

galaxy.webapps.galaxy.controllers.requests_common module

class galaxy.webapps.galaxy.controllers.requests_common.RequestsGrid[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)[source]

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

get_value(trans, grid, request)[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)[source]

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

get_value(trans, grid, request)[source]
class 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, target=None)[source]

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

get_value(trans, grid, request)[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)[source]

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

get_value(trans, grid, request)[source]
class 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, target=None)[source]

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

get_value(trans, grid, request)[source]
filter(trans, user, query, column_filter)[source]

Modify query to filter request by state.

title = 'Sequencing Requests'
template = 'requests/grid.mako'
model_class

alias of galaxy.model.Request

default_sort_key = '-update_time'
num_rows_per_page = 50
use_paging = True
default_filter = {'deleted': 'False', 'state': 'All'}
columns = [<galaxy.webapps.galaxy.controllers.requests_common.NameColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.DescriptionColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.SamplesColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.TypeColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.DeletedColumn object>, <galaxy.webapps.galaxy.controllers.requests_common.StateColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>]
class galaxy.webapps.galaxy.controllers.requests_common.RequestsCommon(app)[source]

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

sample_state_updates(trans, *args, **kwargs)[source]
sample_datasets_updates(trans, *args, **kwargs)[source]
dataset_transfer_status_updates(trans, *args, **kwargs)[source]
create_request(trans, *args, **kwargs)[source]
view_request(trans, *args, **kwargs)[source]
edit_basic_request_info(trans, *args, **kwargs)[source]
submit_request(trans, *args, **kwargs)[source]
edit_samples(trans, *args, **kwargs)[source]
update_sample_state(trans, cntrller, sample_ids, new_state, comment=None)[source]
delete_request(trans, *args, **kwargs)[source]
undelete_request(trans, *args, **kwargs)[source]
view_request_history(trans, *args, **kwargs)[source]
edit_email_settings(trans, *args, **kwargs)[source]

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.

update_request_state(trans, *args, **kwargs)[source]
find_samples(trans, *args, **kwargs)[source]
view_sample_history(trans, *args, **kwargs)[source]
add_samples(trans, *args, **kwargs)[source]
add_sample(trans, *args, **kwargs)[source]
view_sample(trans, *args, **kwargs)[source]
delete_sample(trans, *args, **kwargs)[source]
view_sample_datasets(trans, *args, **kwargs)[source]
galaxy.webapps.galaxy.controllers.requests_common.invalid_id_redirect(trans, cntrller, obj_id, item='sequencing request', action='browse_requests')[source]

galaxy.webapps.galaxy.controllers.root module

Contains the main interface in the Universe class

class galaxy.webapps.galaxy.controllers.root.RootController(app)[source]

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

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

__init__(app)[source]
default(trans, target1=None, target2=None, **kwd)[source]

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

client(trans, **kwd)[source]

Endpoint for clientside routes. Currently a passthrough to index (minus kwargs) though we can differentiate it more in the future. Should not be used with url_for – see (https://github.com/galaxyproject/galaxy/issues/1878) for why.

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’).

login(trans, redirect=None, **kwd)[source]

User login path for client-side.

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

Data are returned in JSON format.

tool_help(trans, id)[source]

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

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

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_child(trans, parent_id=None, designation=None, tofile=None, toext='.txt')[source]

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

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_delete(trans, id)[source]

Backward compatibility with check_galaxy script.

clear_history(trans)[source]

Clears the history for a user.

history_import(trans, id=None, confirm=False, **kwd)[source]
history_new(trans, name=None)[source]

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

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

Adds a POSTed file to a History.

history_set_default_permissions(trans, id=None, **kwd)[source]

Sets the permissions on a history.

dataset_make_primary(trans, id=None)[source]

Copies a dataset and makes primary.

welcome(trans)[source]
bucket_proxy(trans, bucket=None, **kwd)[source]
echo(trans, **kwd)[source]

Echos parameters (debugging).

echo_json(trans, *args, **kwargs)[source]

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)[source]

Raises an exception (debugging).

generate_json_error(trans, *args, **kwargs)[source]

Raises an exception (debugging).

galaxy.webapps.galaxy.controllers.search module

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

get_tagging_elt_async(trans, *args, **kwargs)[source]

Returns HTML for editing an item’s tags.

add_tag_async(trans, *args, **kwargs)[source]

Add tag to an item.

remove_tag_async(trans, *args, **kwargs)[source]

Remove tag from an item.

retag_async(trans, *args, **kwargs)[source]

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

tag_autocomplete_data(trans, *args, **kwargs)[source]

Get autocomplete data for an item’s tags.

galaxy.webapps.galaxy.controllers.tool_runner module

Controller handles external tool related requests

class galaxy.webapps.galaxy.controllers.tool_runner.ToolRunner(app)[source]

Bases: galaxy.web.base.controller.BaseUIController

biomart(trans, tool_id='biomart', **kwd)[source]

Catches the tool id and redirects as needed

hapmapmart(trans, tool_id='hapmapmart', **kwd)[source]

Catches the tool id and redirects as needed

default(trans, tool_id=None, **kwd)[source]

Catches the tool id and redirects as needed

index(trans, tool_id=None, from_noframe=None, **kwd)[source]
rerun(trans, id=None, job_id=None, **kwd)[source]

Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in.

data_source_redirect(trans, tool_id=None)[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

redirect(trans, redirect_url=None, **kwd)[source]

galaxy.webapps.galaxy.controllers.user module

Contains the user interface in the Universe class

class galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid[source]

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

use_panels = False
title = 'OpenIDs linked to your account'
model_class

alias of galaxy.model.UserOpenID

template = '/user/openid_manage.mako'
default_filter = {'openid': 'All'}
default_sort_key = '-create_time'
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>]
build_initial_query(trans, **kwd)[source]
class galaxy.webapps.galaxy.controllers.user.User(app)[source]

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

user_openid_grid = <galaxy.webapps.galaxy.controllers.user.UserOpenIDGrid object>
installed_len_files = None
openid_auth(trans, **kwd)[source]

Handles user request to access an OpenID provider

openid_process(trans, **kwd)[source]

Handle’s response from OpenID Providers

openid_associate(trans, cntrller='user', **kwd)[source]

Associates a user with an OpenID log in

openid_disassociate(trans, *args, **kwargs)[source]

Disassociates a user with an OpenID

openid_manage(trans, *args, **kwargs)[source]

Manage OpenIDs for user

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

Handle Galaxy Log in

proceed_login(trans, user, redirect)[source]

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

resend_verification(trans)[source]

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)[source]

Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link.

is_outside_grace_period(trans, create_time)[source]

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

logout(trans, logout_all=False)[source]
create(trans, cntrller='user', redirect_url='', refresh_frames=[], **kwd)[source]
send_verification_email(trans, email, username)[source]

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

Prepare the account activation link for the user.

get_activation_token(trans, email)[source]

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

activate(trans, **kwd)[source]

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

reset_password(trans, email=None, **kwd)[source]

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

get_most_recently_used_tool_async(trans, *args, **kwargs)[source]

Returns information about the most recently used tool.

set_user_pref_async(trans, pref_name, pref_value)[source]

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

log_user_action_async(trans, action, context, params)[source]

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

change_password(trans, token=None, **kwd)[source]

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

NOTE: This endpoint has been temporarily returned to the user controller, and will go away once there is a suitable replacement.

edit_info(trans, *args, **kwargs)[source]

TEMPORARY ENDPOINT - added back to support admin-level user info editing prior to adminjs. This is code that was prematurely removed from the user controller when the user-side editing functionality was replaced.

The method manage_user_info, which follows this, should also be removed at that time.

Edit user information = username, email or password.

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

index(trans, *args, **kwargs)[source]
admin_api_keys(trans, *args, **kwargs)[source]
all_users(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.visualization module

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, target=None)[source]

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

get_value(trans, grid, history)[source]
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, target=None)[source]

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

Placeholder to keep track of dbkey.

filter(trans, user, query, dbkey)[source]
class galaxy.webapps.galaxy.controllers.visualization.HistorySelectionGrid[source]

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

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

title = 'Add Track: Select History'
model_class

alias of galaxy.model.History

template = '/tracks/history_select_grid.mako'
default_sort_key = '-update_time'
datasets_action = 'list_history_datasets'
datasets_param = 'f-history'
columns = [<galaxy.webapps.galaxy.controllers.visualization.NameColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.webapps.galaxy.controllers.visualization.DbKeyPlaceholderColumn object>]
num_rows_per_page = 10
use_async = True
use_paging = True
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.visualization.LibrarySelectionGrid[source]

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

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

title = 'Add Track: Select Library'
template = '/tracks/history_select_grid.mako'
model_class

alias of galaxy.model.Library

datasets_action = 'list_library_datasets'
datasets_param = 'f-library'
columns = [<galaxy.webapps.galaxy.controllers.visualization.NameColumn object>]
num_rows_per_page = 10
use_async = True
use_paging = True
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, target=None)[source]

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

Column for filtering by and displaying dataset dbkey.

filter(trans, user, query, dbkey)[source]

Filter by 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, target=None)[source]

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

Column for filtering by history id.

filter(trans, user, query, history_id)[source]
class galaxy.webapps.galaxy.controllers.visualization.HistoryDatasetsSelectionGrid[source]

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

available_tracks = None
title = 'Add Datasets'
template = 'tracks/history_datasets_select_grid.mako'
model_class

alias of galaxy.model.HistoryDatasetAssociation

default_filter = {'deleted': 'False', 'shared': 'All'}
default_sort_key = '-hid'
use_async = True
use_paging = False
columns = [<galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.webapps.galaxy.controllers.visualization.HistoryColumn object>, <galaxy.webapps.galaxy.controllers.visualization.DbKeyColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
get_current_item(trans, **kwargs)[source]

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.

build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.visualization.TracksterSelectionGrid[source]

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

title = 'Insert into visualization'
template = '/tracks/add_to_viz.mako'
model_class

alias of galaxy.model.Visualization

default_sort_key = '-update_time'
use_async = True
use_paging = False
show_item_checkboxes = True
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>]
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.visualization.VisualizationListGrid[source]

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

get_url_args(item)[source]

Returns dictionary used to create item link.

get_display_name(trans, item)[source]
title = 'Saved Visualizations'
model_class

alias of galaxy.model.Visualization

default_sort_key = '-update_time'
default_filter = {'deleted': 'False', 'sharing': 'All', 'tags': 'All', 'title': 'All'}
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.web.framework.helpers.grids.SharingStatusColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
global_actions = [<galaxy.web.framework.helpers.grids.GridAction object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.visualization.VisualizationAllPublishedGrid[source]

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

use_panels = True
use_async = True
title = 'Published Visualizations'
model_class

alias of galaxy.model.Visualization

default_sort_key = 'update_time'
default_filter = {'title': 'All', 'username': 'All'}
columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.visualization.VisualizationController(app)[source]

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

__init__(app)[source]
list_libraries(trans, *args, **kwargs)[source]

List all libraries that can be used for selecting datasets.

list_library_datasets(trans, *args, **kwargs)[source]

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

list_histories(trans, *args, **kwargs)[source]

List all histories that can be used for selecting datasets.

list_current_history_datasets(trans, *args, **kwargs)[source]

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

list_history_datasets(trans, *args, **kwargs)[source]

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

list_datasets(trans, *args, **kwargs)[source]

List all datasets that can be added as tracks

list_tracks(trans, **kwargs)[source]
list_published(trans, *args, **kwargs)[source]
list(trans, *args, **kwargs)[source]
index(trans, *args, **kwargs)[source]

Lists user’s saved visualizations.

copy(trans, *args, **kwargs)[source]
set_accessible_async(trans, *args, **kwargs)[source]

Set visualization’s importable attribute and slug.

rate_async(trans, *args, **kwargs)[source]

Rate a visualization asynchronously and return updated community data.

imp(trans, *args, **kwargs)[source]

Import a visualization into user’s workspace.

sharing(trans, *args, **kwargs)[source]

Handle visualization sharing.

share(trans, *args, **kwargs)[source]

Handle sharing a visualization with a particular user.

display_by_username_and_slug(trans, username, slug)[source]

Display visualization based on a username and slug.

Returns visualization’s name and link.

get_item_content_async(trans, id)[source]

Returns item content in HTML format.

create(trans, *args, **kwargs)[source]

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

save(trans, *args, **kwargs)[source]

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

edit(trans, *args, **kwargs)[source]

Edit a visualization’s attributes.

render(trans, *args, **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}

saved(trans, *args, **kwargs)[source]

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

trackster(trans, *args, **kwargs)[source]

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

circster(trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None)[source]

Display a circster visualization.

sweepster(trans, id=None, hda_ldda=None, dataset_id=None, regions=None)[source]

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

get_item(trans, id)[source]
phyloviz(trans, id=None, dataset_id=None, tree_index=0, **kwargs)[source]
gie_list(trans, *args, **kwargs)[source]
bookmarks_from_dataset(trans, *args, **kwargs)[source]

galaxy.webapps.galaxy.controllers.workflow module

class galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid[source]

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

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

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

get_value(trans, grid, workflow)[source]
use_panels = True
title = 'Saved Workflows'
model_class

alias of galaxy.model.StoredWorkflow

default_filter = {'name': 'All', 'tags': 'All'}
default_sort_key = '-update_time'
columns = [<galaxy.web.framework.helpers.grids.TextColumn object>, <galaxy.web.framework.helpers.grids.IndividualTagsColumn object>, <galaxy.webapps.galaxy.controllers.workflow.StepsColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.GridColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid[source]

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

title = 'Published Workflows'
model_class

alias of galaxy.model.StoredWorkflow

default_sort_key = 'update_time'
default_filter = {'public_url': 'All', 'tags': 'All', 'username': 'All'}
use_async = True
columns = [<galaxy.web.framework.helpers.grids.PublicURLColumn object>, <galaxy.web.framework.helpers.grids.OwnerAnnotationColumn object>, <galaxy.web.framework.helpers.grids.OwnerColumn object>, <galaxy.web.framework.helpers.grids.CommunityRatingColumn object>, <galaxy.web.framework.helpers.grids.CommunityTagsColumn object>, <galaxy.web.framework.helpers.grids.ReverseSortColumn object>, <galaxy.web.framework.helpers.grids.MulticolFilterColumn object>]
operations = [<galaxy.web.framework.helpers.grids.GridOperation object>, <galaxy.web.framework.helpers.grids.GridOperation object>]
build_initial_query(trans, **kwargs)[source]
apply_query_filter(trans, query, **kwargs)[source]
class galaxy.webapps.galaxy.controllers.workflow.SingleTagContentsParser(target_tag)[source]

Bases: sgmllib.SGMLParser

__init__(target_tag)[source]
unknown_starttag(tag, attrs)[source]

Called for each start tag.

handle_data(text)[source]

Called for each block of plain text.

class galaxy.webapps.galaxy.controllers.workflow.WorkflowController(app)[source]

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

stored_list_grid = <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowListGrid object>
published_list_grid = <galaxy.webapps.galaxy.controllers.workflow.StoredWorkflowAllPublishedGrid object>
index(trans)[source]
list_grid(trans, *args, **kwargs)[source]

List user’s stored workflows.

list(trans, *args, **kwargs)[source]

Render workflow main page (management of existing workflows)

list_for_run(trans, *args, **kwargs)[source]

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

list_published(trans, **kwargs)[source]
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.

display_by_id(trans, id)[source]

Display workflow based on id.

get_item_content_async(trans, id)[source]

Returns item content in HTML format.

share(trans, *args, **kwargs)[source]
sharing(trans, *args, **kwargs)[source]

Handle workflow sharing.

imp(trans, *args, **kwargs)[source]

Imports a workflow shared by other users.

rename(trans, *args, **kwargs)[source]
rename_async(trans, *args, **kwargs)[source]
annotate_async(trans, *args, **kwargs)[source]
rate_async(trans, *args, **kwargs)[source]

Rate a workflow asynchronously and return updated community data.

set_accessible_async(trans, *args, **kwargs)[source]

Set workflow’s importable attribute and slug.

get_embed_html_async(trans, id)[source]

Returns HTML for embedding a workflow in a page.

Returns workflow’s name and link.

gen_image(trans, *args, **kwargs)[source]
copy(trans, *args, **kwargs)[source]
create(trans, *args, **kwargs)[source]

Create a new stored workflow with name workflow_name.

save_workflow_as(trans, *args, **kwargs)[source]

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

delete(trans, id=None)[source]

Mark a workflow as deleted

editor(trans, *args, **kwargs)[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.

load_workflow(trans, *args, **kwargs)[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.

export_to_myexp(trans, *args, **kwargs)[source]

Exports a workflow to myExperiment website.

for_direct_import(trans, *args, **kwargs)[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.

export_to_file(trans, *args, **kwargs)[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.

import_workflow(trans, cntrller='workflow', **kwd)[source]

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.

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]
run(trans, id, history_id=None, **kwargs)[source]
get_item(trans, id)[source]
tag_outputs(trans, id, **kwargs)[source]
configure_menu(trans, workflow_ids=None)[source]