Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
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