parser.add_argument('--stderr', dest='stderr', help='Job stderr') parser.add_argument('--tool_id', dest='tool_id', help='Tool that was executed to produce the input dataset') parser.add_argument('--tool_parameters', dest='tool_parameters', help='Tool parameters that were set when producing the input dataset') parser.add_argument('--workflow_step_id', dest='workflow_step_id', default=None, help='Workflow step id') parser.add_argument('--user_email', dest='user_email', help='Current user email') args = parser.parse_args() payload = None statistics = [] datasets = [] # Generate the statistics and datasets. if args.inputs is None: payload = stats_util.get_base_json_dict(args.config_file, 'unknown', args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id) else: for input in args.inputs: file_path, hid, input_id, input_datatype, dbkey = input if payload is None: # Initialize the payload. payload = stats_util.get_base_json_dict(args.config_file, dbkey, args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id) statistics.append(stats_util.get_statistics(file_path, STATS)) datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype)) payload['statistics'] = statistics payload['datasets'] = datasets # Send the payload to PEGR. pegr_url = stats_util.get_pegr_url(args.config_file) response = stats_util.submit(args.config_file, payload) # Make sure all is well. stats_util.check_response(pegr_url, payload, response) # If all is well, store the results in the output. stats_util.store_results(args.output, pegr_url, payload, response)
payload = None statistics = [] datasets = [] # Generate the statistics and datasets. if args.input_gffs is None: payload = stats_util.get_base_json_dict(args.config_file, 'unknown', args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id) else: for input in args.input_gffs: file_path, hid, input_id, input_datatype, dbkey = input if payload is None: # Initialize the payload. payload = stats_util.get_base_json_dict(args.config_file, dbkey, args.history_id, args.history_name, args.stats_tool_id, args.stderr, args.tool_id, args.tool_parameters, args.user_email, args.workflow_step_id) statistics.append({}) datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype)) input_xmls = args.input_xmls or [] for input in input_xmls: file_path, hid, input_id, input_datatype, dbkey = input statistics.append({}) datasets.append(stats_util.get_datasets(args.config_file, input_id, input_datatype)) payload['statistics'] = statistics payload['datasets'] = datasets # Send the payload to PEGR. pegr_url = stats_util.get_pegr_url(args.config_file) response = stats_util.submit(args.config_file, payload) # Make sure all is well. stats_util.check_response(pegr_url, payload, response) # If all is well, store the results in the output. stats_util.store_results(args.output, pegr_url, payload, response)