def copy_object(self, ref, target_ws_id, target_ws_name, target_name,
src_info):
"""
Copies an object from one workspace to another.
"""
if not target_ws_id and not target_ws_name:
raise ValueError("Neither target workspace id nor name is defined")
if not src_info:
src_info_tuple = self.ws.get_object_info_new({
'objects': [{
'ref': ref
}],
'includeMetadata':
0
})[0]
src_info = ServiceUtils.object_info_to_object(src_info_tuple)
if not target_name:
target_name = src_info['name']
obj_info_tuple = self.ws.copy_object({
'from': {
'ref': ref
},
'to': {
'wsid': target_ws_id,
'workspace': target_ws_name,
'name': target_name
}
})
obj_info = ServiceUtils.object_info_to_object(obj_info_tuple)
return {'info': obj_info}
def _completeNewNarrative(self, workspaceId, objectId, importData,
is_temporary, title, num_cells):
"""
'Completes' the new narrative by updating workspace metadata with the required fields and
copying in data from the importData list of references.
"""
new_meta = {
'narrative': str(objectId),
'is_temporary': is_temporary,
'searchtags': 'narrative',
'cell_count': str(num_cells)
}
if is_temporary == 'false' and title is not None:
new_meta['narrative_nice_name'] = title
self.ws.alter_workspace_metadata({
'wsi': {
'id': workspaceId
},
'new': new_meta
})
# copy_to_narrative:
if importData:
objectsToCopy = [{'ref': x} for x in importData]
infoList = self.ws.get_object_info_new({
'objects': objectsToCopy,
'includeMetadata': 0
})
for item in infoList:
objectInfo = ServiceUtils.object_info_to_object(item)
self.copy_object(objectInfo['ref'], workspaceId, None, None,
objectInfo)
return self.ws.get_workspace_info({'id': workspaceId})
def _create_temp_narrative(self, cells, parameters, importData,
includeIntroCell, title):
# Migration to python of JavaScript class from https://github.com/kbase/kbase-ui/blob/4d31151d13de0278765a69b2b09f3bcf0e832409/src/client/modules/plugins/narrativemanager/modules/narrativeManager.js#L414
narr_id = int(round(time.time() * 1000))
workspaceName = self.user_id + ':narrative_' + str(narr_id)
narrativeName = "Narrative." + str(narr_id)
ws = self.ws
ws_info = ws.create_workspace({
'workspace': workspaceName,
'description': ''
})
[narrativeObject, metadataExternal
] = self._fetchNarrativeObjects(workspaceName, cells, parameters,
includeIntroCell, title)
is_temporary = 'true'
if title is not None and title != 'Untitled':
is_temporary = 'false'
metadataExternal['is_temporary'] = is_temporary
objectInfo = ws.save_objects({
'workspace':
workspaceName,
'objects': [{
'type':
'KBaseNarrative.Narrative',
'data':
narrativeObject,
'name':
narrativeName,
'meta':
metadataExternal,
'provenance': [{
'script':
'NarrativeManager.py',
'description':
'Created new ' + 'Workspace/Narrative bundle.'
}],
'hidden':
0
}]
})[0]
objectInfo = ServiceUtils.object_info_to_object(objectInfo)
ws_info = self._completeNewNarrative(ws_info[0], objectInfo['id'],
importData, is_temporary, title,
len(narrativeObject['cells']))
return {
'workspaceInfo': ServiceUtils.workspace_info_to_object(ws_info),
'narrativeInfo': objectInfo
}
def find_report_from_object(self, upa):
#TODO:
# 1. make sure upa's real.
# first, fetch object references (without data)
ref_list = self.ws_client.list_referencing_objects([{"ref": upa}])[0]
# scan it for a report.
# if we find at least one, return them
# if we find 0, test if it's a copy, and search upstream.
if len(ref_list):
report_upas = list()
for ref_info in ref_list:
if "KBaseReport.Report" in ref_info[2]:
report_upas.append(
ServiceUtils.object_info_to_object(ref_info)['ref'])
if len(report_upas):
return self.build_output(upa, report_upas)
else:
return self.find_report_from_copy_source(upa)
else:
return self.find_report_from_copy_source(upa)