def setup(): shared.setup() global t_new, t_old, t_new_e, t_old_e, t_client_new, t_client_old, g_skip_shock g_skip_shock = not shared.services["shock_service_url"].startswith("http") t_new = AssemblyAPI(shared.services, shared.token, assembly_new) t_new_e = _Assembly(shared.services, shared.token, assembly_new) t_old = AssemblyAPI(shared.services, shared.token, assembly_old) t_old_e = _KBaseGenomes_ContigSet(shared.services, shared.token, assembly_old) t_client_new = AssemblyClientAPI(shared.services["assembly_service_url"], shared.token, assembly_new) t_client_old = AssemblyClientAPI(shared.services["assembly_service_url"], shared.token, assembly_old)
done = False while not done: results = ws.list_objects({ "workspaces": [fix_workspace], "type": "KBaseGenomeAnnotations.Assembly", "skip": skip, "limit": limit }) if len(results) == 0: done = True for x in results: count += 1 ac = AssemblyAPI(services, token, ref="{}/{}".format(fix_workspace, x[1])) handle_ref = ac.get_data()["fasta_handle_ref"] shock_node_id = None try: handle = hc.hids_to_handles([handle_ref])[0] shock_node_id = handle["id"] except Exception, e: print "Failed to retrieve handle {} from {}".format( handle_ref, services["handle_service_url"]) _log.exception(e) shock_node_id = handle_ref print "#" * 80 print x[1], shock_node_id