def uninstall_repository(self, trans, id=None, **kwd):
"""
DELETE /api/tool_shed_repositories/id
DELETE /api/tool_shed_repositories/
:param id: encoded repository id. Either id or name, owner, changeset_revision and tool_shed_url need to be supplied
:param kwd:
'remove_from_disk': Remove repository from disk or deactivate repository. Defaults to `True` (= remove repository from disk).
'name': Repository name
'owner': Repository owner
'changeset_revision': Changeset revision to uninstall
'tool_shed_url': Tool Shed URL
"""
remove_from_disk = util.asbool(kwd.get('remove_from_disk', True))
if id:
try:
repository = get_tool_shed_repository_by_id(self.app, id)
except ValueError:
raise HTTPBadRequest(
detail="No repository with id '%s' found" % id)
else:
tsr_arguments = [
'name', 'owner', 'changeset_revision', 'tool_shed_url'
]
try:
tsr_arguments = {key: kwd[key] for key in tsr_arguments}
except KeyError as e:
raise HTTPBadRequest(detail="Missing required parameter '%s'" %
e.args[0])
repository = get_installed_repository(
app=self.app,
tool_shed=tsr_arguments['tool_shed_url'],
name=tsr_arguments['name'],
owner=tsr_arguments['owner'],
changeset_revision=tsr_arguments['changeset_revision'])
if not repository:
raise HTTPBadRequest(detail="Repository not found")
irm = InstalledRepositoryManager(app=self.app)
errors = irm.uninstall_repository(repository=repository,
remove_from_disk=remove_from_disk)
if not errors:
action = 'removed' if remove_from_disk else 'deactivated'
return {
'message':
f'The repository named {repository.name} has been {action}.'
}
else:
raise Exception(
f'Attempting to uninstall tool dependencies for repository named {repository.name} resulted in errors: {errors}'
)
def show(self, trans, id, **kwd):
"""
GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}
Display a dictionary containing information about a specified tool_shed_repository.
.. code-block::
{
id: (string) Galaxy ID
status: (string) Installation status
name: (string) Repository name
deleted: (bool) Repository deleted
ctx_rev: (int) Changeset revision number (0, 1, 2...)
error_message: (string) Installation error message
installed_changeset_revision: (string) Initially installed changeset revision. Used to construct path to repository within Galaxies filesystem. Does not change if a repository is updated.
tool_shed: (string) Repository toolshed hostname
dist_to_shed: (bool)
url: (string) API url of repository
uninstalled: (bool) Tool has been uninstalled
owner: (string) Repository owner within toolshed
changeset_revision: (string) Changeset revision of repository
include_datatypes: (bool) Repository includes installed datatypes
tool_shed_status: (dict) See https://github.com/galaxyproject/galaxy/issues/10453
latest_installable_revision: (string) Most recent version available on toolshed
revision_update: (string)
revision_upgrade: (string)
repository_deprecated: (string) Repository has been depreciated
}
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
tool_shed_repository = get_tool_shed_repository_by_id(self.app, id)
if tool_shed_repository is None:
log.debug(
"Unable to locate tool_shed_repository record for id %s." %
(str(id)))
return {}
tool_shed_repository_dict = tool_shed_repository.as_dict(
value_mapper=self.__get_value_mapper(trans, tool_shed_repository))
tool_shed_repository_dict['url'] = url_for(
controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id(tool_shed_repository.id))
return tool_shed_repository_dict
def show(self, trans, id, **kwd):
"""
GET /api/tool_shed_repositories/{encoded_tool_shed_repsository_id}
Display a dictionary containing information about a specified tool_shed_repository.
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
tool_shed_repository = get_tool_shed_repository_by_id(self.app, id)
if tool_shed_repository is None:
log.debug(
"Unable to locate tool_shed_repository record for id %s." %
(str(id)))
return {}
tool_shed_repository_dict = tool_shed_repository.as_dict(
value_mapper=self.__get_value_mapper(trans, tool_shed_repository))
tool_shed_repository_dict['url'] = url_for(
controller='tool_shed_repositories',
action='show',
id=trans.security.encode_id(tool_shed_repository.id))
return tool_shed_repository_dict