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)