def test_tc_no_inputs(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
tc.task.input_file_types = []
def _run():
return tc.to_dict()
self.assertRaises(MalformedToolContractError, _run)
def test_01(self):
name = "dev_example_tool_contract.json"
p = get_data_file(name)
tc = load_tool_contract_from(p)
input_files = ["/tmp/file.txt"]
root_output_dir = "/tmp"
root_tmp_dir = root_output_dir
max_nproc = 2
rtc = resolve_tool_contract(tc, input_files, root_output_dir, root_tmp_dir, max_nproc, {})
log.info(pprint.pformat(rtc))
self.assertIsNotNone(rtc)
self.assertEqual(os.path.basename(rtc.task.output_files[0]),
"output.txt")
def test_01(self):
name = "dev_example_dev_txt_app_tool_contract.json"
p = get_data_file(name)
tc = load_tool_contract_from(p)
input_files = ["/tmp/file.txt"]
root_output_dir = "/tmp"
root_tmp_dir = root_output_dir
tmp_file = tempfile.NamedTemporaryFile().name
max_nproc = 2
tool_options = {}
rtc = resolve_tool_contract(tc, input_files, root_output_dir, root_tmp_dir, max_nproc, tool_options, False)
log.info(pprint.pformat(rtc))
self.assertIsNotNone(rtc)
self.assertEqual(os.path.basename(rtc.task.output_files[0]),
"output.txt")
# Validate Resolved Resource Types
log.debug("Resources {t}".format(t=rtc.task.resources))
self.assertEqual(len(rtc.task.tmpdir_resources), 1)
self.assertEqual(len(rtc.task.tmpfile_resources), 2)
def test_resolved_tool_contract_is_distributed(self):
workflow_options_json = os.path.join(self.job_dir, "workflow",
"options-workflow.json")
workflow_options = json.load(open(workflow_options_json))
distributed_mode = workflow_options["pbsmrtpipe.options.distributed_mode"]
tasks_dir = os.path.join(self.job_dir, "tasks")
for task_dir in os.listdir(tasks_dir):
if task_dir.startswith("."):
continue
tc_file = os.path.join(tasks_dir, task_dir, "tool-contract.json")
tc = load_tool_contract_from(tc_file)
rtc_file = os.path.join(tasks_dir, task_dir,
"resolved-tool-contract.json")
rtc = load_resolved_tool_contract_from(rtc_file)
if distributed_mode and tc.task.is_distributed:
self.assertTrue(rtc.task.is_distributed,
"Resolved tool contract {f} has unexpected is_distributed=False".format(f=rtc_file))
else:
self.assertFalse(rtc.task.is_distributed,
"Resolved tool contract {f} has unexpected is_distributed=True".format(f=rtc_file))
def _to_object(self, path):
log.debug("Loading from {p}".format(p=path))
return load_tool_contract_from(path)
def test_01(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
self.assertIsInstance(tc, ToolContract)
def tool_contract_to_meta_task_from_file(path):
"""Loads a tool contract from a path and converts it to a StaticMetaTask"""
tc = load_tool_contract_from(path)
# FIXME
max_chunks = 5
return tool_contract_to_meta_task(tc, max_chunks)
