def _check_get_expression_set_params(self, params):
if 'ref' not in params or params['ref'] is None:
raise ValueError('"ref" parameter field specifiying the expression set is required')
elif not util.check_reference(params['ref']):
raise ValueError('"ref" parameter must be a valid workspace reference')
if 'include_item_info' in params:
if params['include_item_info'] not in [0, 1]:
raise ValueError('"include_item_info" parameter field can only be set to 0 or 1')
obj_spec = util.build_ws_obj_selector(params.get('ref'),
params.get('ref_path_to_set', []))
info = self.workspace_client.get_object_info3({"objects": [obj_spec]})
return info["infos"][0][2], obj_spec
def _get_set_info(self, set_refs):
objects = []
for s in set_refs:
objects.append(
util.build_ws_obj_selector(s['ref'], s.get('path_to_set', [])))
if len(objects) > 0:
obj_info_list = self.ws.get_object_info_new({
'objects': objects,
'includeMetadata': 1
})
set_list = []
for o in obj_info_list:
set_list.append({'ref': self._build_obj_ref(o), 'info': o})
return set_list
def _populate_item_object_info(self, set, ref_path_to_set):
items = set['data']['items']
objects = []
for item in items:
ref_path_to_item = ref_path_to_set + [item['ref']]
objects.append(
util.build_ws_obj_selector(item['ref'], ref_path_to_item))
if len(objects) > 0:
obj_info_list = self.ws.get_object_info_new({
'objects': objects,
'includeMetadata': 1
})
for k in range(0, len(obj_info_list)):
items[k]['info'] = obj_info_list[k]
def get_set(self,
ref,
include_item_info=False,
ref_path_to_set=[],
include_set_item_ref_paths=False):
"""
Get a set object from the Workspace using the set_type provided (e.g. set_type=KBaseSets.ReadsSet)
"""
obj_selector = util.build_ws_obj_selector(ref, ref_path_to_set)
ws_data = self._get_set_from_ws(obj_selector)
if include_item_info:
self._populate_item_object_info(ws_data, ref_path_to_set)
if include_set_item_ref_paths:
set_items = ws_data['data']['items']
util.populate_item_object_ref_paths(set_items, obj_selector)
return ws_data