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Source code for tool_shed.galaxy_install.grids.admin_toolshed_grids
import logging
from galaxy import util
from galaxy.model import tool_shed_install
from galaxy.web import url_for
from galaxy.web.framework.helpers import grids, iff
from tool_shed.util import repository_util
log = logging.getLogger(__name__)
[docs]def generate_deprecated_repository_img_str(include_mouse_over=False):
if include_mouse_over:
deprecated_tip_str = 'class="icon-button" title="This repository is deprecated in the Tool Shed"'
else:
deprecated_tip_str = ''
return f"<img src=\"{url_for('/static')}/images/icon_error_sml.gif\" {deprecated_tip_str}/>"
[docs]def generate_includes_workflows_img_str(include_mouse_over=False):
if include_mouse_over:
deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"'
else:
deprecated_tip_str = ''
return f"<img src=\"{url_for('/static')}/images/fugue/gear.png\" {deprecated_tip_str}/>"
[docs]def generate_latest_revision_img_str(include_mouse_over=False):
if include_mouse_over:
latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"'
else:
latest_revision_tip_str = ''
return f"<img src=\"{url_for('/static')}/style/ok_small.png\" {latest_revision_tip_str}/>"
[docs]def generate_revision_updates_img_str(include_mouse_over=False):
if include_mouse_over:
revision_updates_tip_str = 'class="icon-button" title="Updates are available in the Tool Shed for this revision"'
else:
revision_updates_tip_str = ''
return f"<img src=\"{url_for('/static')}/images/icon_warning_sml.gif\" {revision_updates_tip_str}/>"
[docs]def generate_revision_upgrades_img_str(include_mouse_over=False):
if include_mouse_over:
revision_upgrades_tip_str = 'class="icon-button" title="A newer installable revision is available for this repository"'
else:
revision_upgrades_tip_str = ''
return f"<img src=\"{url_for('/static')}/images/up.gif\" {revision_upgrades_tip_str}/>"
[docs]def generate_unknown_img_str(include_mouse_over=False):
if include_mouse_over:
unknown_tip_str = 'class="icon-button" title="Unable to get information from the Tool Shed"'
else:
unknown_tip_str = ''
return f"<img src=\"{url_for('/static')}/style/question-octagon-frame.png\" {unknown_tip_str}/>"
[docs]class InstalledRepositoryGrid(grids.Grid):
[docs] class ToolShedStatusColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
if tool_shed_repository.tool_shed_status:
tool_shed_status_str = ''
if tool_shed_repository.is_deprecated_in_tool_shed:
tool_shed_status_str += generate_deprecated_repository_img_str(include_mouse_over=True)
if tool_shed_repository.is_latest_installable_revision:
tool_shed_status_str += generate_latest_revision_img_str(include_mouse_over=True)
if tool_shed_repository.revision_update_available:
tool_shed_status_str += generate_revision_updates_img_str(include_mouse_over=True)
if tool_shed_repository.upgrade_available:
tool_shed_status_str += generate_revision_upgrades_img_str(include_mouse_over=True)
if tool_shed_repository.includes_workflows:
tool_shed_status_str += generate_includes_workflows_img_str(include_mouse_over=True)
else:
tool_shed_status_str = generate_unknown_img_str(include_mouse_over=True)
return tool_shed_status_str
[docs] class NameColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.name)
[docs] class DescriptionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return util.unicodify(tool_shed_repository.description)
[docs] class OwnerColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.owner)
[docs] class RevisionColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.changeset_revision)
[docs] class StatusColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return repository_util.get_tool_shed_repository_status_label(trans.app, tool_shed_repository)
[docs] class ToolShedColumn(grids.TextColumn):
[docs] def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.tool_shed
[docs] class DeletedColumn(grids.DeletedColumn):
[docs] def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = {"Active": "False", "Deactivated or uninstalled": "True", "All": "All"}
accepted_filters = []
for label, val in accepted_filter_labels_and_vals.items():
args = {self.key: val}
accepted_filters.append(grids.GridColumnFilter(label, args))
return accepted_filters
# Grid definition
title = "Installed tool shed repositories"
model_class = tool_shed_install.ToolShedRepository
default_sort_key = "name"
columns = [
ToolShedStatusColumn(label=""),
NameColumn(label="Name",
key="name",
link=(lambda item: iff(item.status in [tool_shed_install.ToolShedRepository.installation_status.CLONING],
None,
dict(controller="admin_toolshed", action="manage_repository", id=item.id))),
target="center",
attach_popup=True),
DescriptionColumn(label="Description"),
OwnerColumn(label="Owner"),
RevisionColumn(label="Revision"),
StatusColumn(label="Installation Status",
filterable="advanced"),
ToolShedColumn(label="Tool shed"),
# Columns that are valid for filtering but are not visible.
DeletedColumn(label="Status",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [grids.GridOperation(label="Update tool shed status",
condition=(lambda item: not item.deleted),
allow_multiple=False),
grids.GridOperation(label="Get updates",
condition=(lambda item:
not item.deleted
and item.revision_update_available
and item.status not in [
tool_shed_install.ToolShedRepository.installation_status.ERROR,
tool_shed_install.ToolShedRepository.installation_status.NEW]),
allow_multiple=False,
target="center",
url_args=dict(controller='admin_toolshed',
action='check_for_updates')),
grids.GridOperation(label="Install latest revision",
condition=(lambda item: item.upgrade_available),
allow_multiple=False,
target="center",
url_args=dict(controller='admin_toolshed',
action='install_latest_repository_revision')),
grids.GridOperation(label="Install",
condition=(lambda item:
not item.deleted
and item.status == tool_shed_install.ToolShedRepository.installation_status.NEW),
allow_multiple=False,
target='center',
url_args=dict(controller='admin_toolshed',
action='manage_repository',
operation='install')),
grids.GridOperation(label="Deactivate or uninstall",
condition=(lambda item:
not item.deleted
and item.status != tool_shed_install.ToolShedRepository.installation_status.NEW),
allow_multiple=True,
target="center",
url_args=dict(controller='admin_toolshed',
action='deactivate_or_uninstall_repository')),
grids.GridOperation(label="Activate or reinstall",
condition=(lambda item: item.deleted),
allow_multiple=False,
target='center',
url_args=dict(controller='admin_toolshed',
action='restore_repository')),
grids.GridOperation(label="Purge",
condition=(lambda item: item.is_new),
allow_multiple=False,
target='center',
url_args=dict(controller='admin_toolshed',
action='purge_repository'))]
default_filter = dict(deleted="False")
num_rows_per_page = 50
use_paging = False
[docs] def build_initial_query(self, trans, **kwd):
return trans.install_model.context.query(self.model_class) \
.order_by(self.model_class.table.c.tool_shed,
self.model_class.table.c.name,
self.model_class.table.c.owner,
self.model_class.table.c.ctx_rev)
@property
def legend(self):
legend_str = f'{generate_revision_updates_img_str()} Updates are available in the Tool Shed for this revision<br/>'
legend_str += f'{generate_revision_upgrades_img_str()} A newer installable revision is available for this repository<br/>'
legend_str += f'{generate_latest_revision_img_str()} This is the latest installable revision of this repository<br/>'
legend_str += f'{generate_deprecated_repository_img_str()} This repository is deprecated in the Tool Shed<br/>'
legend_str += f'{generate_includes_workflows_img_str()} This repository contains exported workflows<br/>'
legend_str += f'{generate_unknown_img_str()} Unable to get information from the Tool Shed<br/>'
return legend_str