def test_run_e2e(self):
# hack to skip running the base Test class (which is the nose default behavior)
if self.__class__.__name__ in ('PbTestApp', 'PbTestScatterApp', 'PbTestGatherApp'):
return
if self.REQUIRES_PBCORE:
if not HAS_PBCORE:
self.assertTrue(True, pbcore_skip_msg("Skipping running e2e for {d}".format(d=self.DRIVER_EMIT)))
return
output_dir = get_temp_dir(suffix="rtc-test")
tmp_dir = get_temp_dir(suffix="rtc-temp")
log.debug("Driver {e}".format(e=self.DRIVER_EMIT))
log.debug("input files {i}".format(i=self.INPUT_FILES))
log.debug("running in {p}".format(p=output_dir))
output_tc = get_temp_file("-{n}-tool_contract.json".format(n=self.__class__.__name__), output_dir)
emit_tc_exe = "{e} > {o}".format(e=self.DRIVER_EMIT, o=output_tc)
rcode = subprocess.call([emit_tc_exe], shell=True)
self.assertEquals(rcode, 0, "Emitting tool contract failed for '{e}'".format(e=emit_tc_exe))
# sanity marshall-unmashalling
log.debug("Loading tool-contract from {p}".format(p=output_tc))
tc = load_tool_contract_from(output_tc)
log.info("Resolving tool contract to RTC")
rtc = self._to_rtc(tc, output_dir, tmp_dir)
output_json_rtc = get_temp_file("resolved_tool_contract.json", output_dir)
write_resolved_tool_contract(rtc, output_json_rtc)
# sanity
loaded_rtc = load_resolved_tool_contract_from(output_json_rtc)
self.assertIsInstance(loaded_rtc, ResolvedToolContract)
# Test Resolved options if specified.
for opt, resolved_value in self.RESOLVED_TASK_OPTIONS.iteritems():
self.assertTrue(opt in rtc.task.options, "Resolved option {x} not in RTC options.".format(x=opt))
# this needs to support polymorphic equals (i.e., almostEquals
if not isinstance(resolved_value, float):
emsg = "Resolved option {o} are not equal. Expected {a}, got {b}".format(o=opt, b=rtc.task.options[opt], a=resolved_value)
self.assertEquals(rtc.task.options[opt], resolved_value, emsg)
# Resolved NPROC
self.assertEquals(rtc.task.nproc, self.RESOLVED_NPROC)
log.info("running resolved contract {r}".format(r=output_json_rtc))
exe = "{d} {p}".format(p=output_json_rtc, d=self.DRIVER_RESOLVE)
log.info("Running exe '{e}'".format(e=exe))
rcode = subprocess.call([exe], shell=True)
self.assertEqual(rcode, 0, "Running from resolved tool contract failed from {e}".format(e=exe))
log.info("Successfully completed running e2e for {d}".format(d=self.DRIVER_EMIT))
self._test_outputs_exists(rtc)
self.run_after(rtc, output_dir)
def _w(args):
# FIXME.
setup_log(log, level=logging.DEBUG)
log.info("Registry {r}".format(r=registry))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {t.task.task_id:func for t, func in registry.rtc_runners.iteritems()}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
sys.stderr.write("ERROR. Unknown tool contract id {x}".format(x=rtc.task.task_id))
return -1
else:
exit_code = func(rtc)
log.info("Completed running {r} exitcode {e}".format(r=rtc, e=exit_code))
def _w(args):
started_at = time.time()
def run_time():
return time.time() - started_at
def exit_msg(rcode_):
return "Completed running {r} exitcode {e} in {t:.2f} sec.".format(
r=rtc, e=rcode_, t=run_time())
level = get_parsed_args_log_level(args)
setup_logger(None, level=level)
log.info("Loading pbcommand {v}".format(v=pbcommand.get_version()))
log.info("Registry {r}".format(r=registry))
log.info("Setting log-level to {d}".format(d=level))
log.debug("args {a}".format(a=args))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {
t.task.task_id: func
for t, func in registry.rtc_runners.iteritems()
}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
rcode = 1
log.error(
"Unknown tool contract id '{x}' Registered TC ids {i}".format(
x=rtc.task.task_id, i=id_funcs.keys()))
log.error(exit_msg(rcode))
return rcode
else:
log.info("Running id:{i} Resolved Tool Contract {r}".format(
r=rtc, i=rtc.task.task_id))
log.info("Runner func {f}".format(f=func))
exit_code = func(rtc)
if exit_code == 0:
log.info(exit_msg(exit_code))
else:
log.error(exit_msg(exit_code))
return exit_code
def _w(args):
# FIXME.
setup_log(log, level=logging.DEBUG)
log.info("Registry {r}".format(r=registry))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {
t.task.task_id: func
for t, func in registry.rtc_runners.iteritems()
}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
sys.stderr.write("ERROR. Unknown tool contract id {x}".format(
x=rtc.task.task_id))
return -1
else:
exit_code = func(rtc)
log.info("Completed running {r} exitcode {e}".format(r=rtc,
e=exit_code))
def _w(args):
default_level = logging.INFO
level = args.log_level if hasattr(args, 'log_level') else default_level
setup_log(log, level=level)
log.info("Loading pbcommand {v}".format(v=pbcommand.get_version()))
log.info("Registry {r}".format(r=registry))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {t.task.task_id:func for t, func in registry.rtc_runners.iteritems()}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
sys.stderr.write("ERROR. Unknown tool contract id {x}".format(x=rtc.task.task_id))
return -1
else:
log.info("Running id:{i} Resolved Tool Contract {r}".format(r=rtc, i=rtc.task.task_id))
log.info("Runner func {f}".format(f=func))
exit_code = func(rtc)
log.info("Completed running {r} exitcode {e}".format(r=rtc, e=exit_code))
return exit_code
def loadRtcs(cls):
cls.tasks_dir = op.join(cls.job_dir, "tasks")
cls.resolved_tool_contracts = []
cls.runnable_tasks = []
tasks_rpt = op.join(cls.job_dir, "workflow", "report-tasks.json")
rpt = load_report_from_json(tasks_rpt)
table = {t.id: t for t in rpt.tables}['tasks']
tasks = {c.id: c.values for c in table.columns}['task_id']
for task_id_str in tasks:
fields = task_id_str.split()
task_name = fields[1].split(":")[-1]
task_dir = op.join(cls.tasks_dir, task_name)
if not op.isdir(task_dir):
continue
task_id, job_id = task_name.split("-")
rtc_json = op.join(task_dir, "resolved-tool-contract.json")
if not op.isfile(rtc_json):
log.warn("Can't find %s" % rtc_json)
continue
rtc = load_resolved_tool_contract_from(rtc_json)
cls.resolved_tool_contracts.append(rtc)
rt_json = op.join(task_dir, "runnable-task.json")
rt = RunnableTask.from_manifest_json(rt_json)
cls.runnable_tasks.append(rt)
def _w(args):
started_at = time.time()
def run_time():
return time.time() - started_at
def exit_msg(rcode_):
return "Completed running {r} exitcode {e} in {t:.2f} sec.".format(r=rtc, e=rcode_, t=run_time())
level = get_parsed_args_log_level(args)
setup_logger(None, level=level)
log.info("Loading pbcommand {v}".format(v=pbcommand.get_version()))
log.info("Registry {r}".format(r=registry))
log.info("Setting log-level to {d}".format(d=level))
log.debug("args {a}".format(a=args))
log.info("loading RTC from {i}".format(i=args.rtc_path))
rtc = load_resolved_tool_contract_from(args.rtc_path)
id_funcs = {t.task.task_id: func for t, func in registry.rtc_runners.iteritems()}
func = id_funcs.get(rtc.task.task_id, None)
if func is None:
rcode = 1
log.error("Unknown tool contract id '{x}' Registered TC ids {i}".format(x=rtc.task.task_id, i=id_funcs.keys()))
log.error(exit_msg(rcode))
return rcode
else:
log.info("Running id:{i} Resolved Tool Contract {r}".format(r=rtc, i=rtc.task.task_id))
log.info("Runner func {f}".format(f=func))
exit_code = func(rtc)
if exit_code == 0:
log.info(exit_msg(exit_code))
else:
log.error(exit_msg(exit_code))
return exit_code
def test_validate_resolved_tool_contracts(self):
for path in _get_all_from(DATA_DIR, _filter_rtc):
f = _to_assertion(path, validate_rtc)
f(self)
self.assertIsInstance(load_resolved_tool_contract_from(path), ResolvedToolContract)
def test_run_e2e(self):
# hack to skip running the base Test class (which is the nose default behavior)
if self.__class__.__name__ in ('PbTestApp', 'PbTestScatterApp',
'PbTestGatherApp'):
return
if self.REQUIRES_PBCORE:
if not HAS_PBCORE:
self.assertTrue(
True,
pbcore_skip_msg("Skipping running e2e for {d}".format(
d=self.DRIVER_EMIT)))
return
output_dir = get_temp_dir(suffix="rtc-test")
tmp_dir = get_temp_dir(suffix="rtc-temp")
log.debug("Driver {e}".format(e=self.DRIVER_EMIT))
log.debug("input files {i}".format(i=self.INPUT_FILES))
log.debug("running in {p}".format(p=output_dir))
output_tc = get_temp_file(
"-{n}-tool_contract.json".format(n=self.__class__.__name__),
output_dir)
emit_tc_exe = "{e} > {o}".format(e=self.DRIVER_EMIT, o=output_tc)
rcode = subprocess.call([emit_tc_exe], shell=True)
self.assertEquals(
rcode, 0,
"Emitting tool contract failed for '{e}'".format(e=emit_tc_exe))
# sanity marshall-unmashalling
log.debug("Loading tool-contract from {p}".format(p=output_tc))
tc = load_tool_contract_from(output_tc)
log.info("Resolving tool contract to RTC")
rtc = self._to_rtc(tc, output_dir, tmp_dir)
output_json_rtc = get_temp_file("resolved_tool_contract.json",
output_dir)
write_resolved_tool_contract(rtc, output_json_rtc)
# sanity
loaded_rtc = load_resolved_tool_contract_from(output_json_rtc)
self.assertIsInstance(loaded_rtc, ResolvedToolContract)
# Test Resolved options if specified.
for opt, resolved_value in self.RESOLVED_TASK_OPTIONS.iteritems():
self.assertTrue(
opt in rtc.task.options,
"Resolved option {x} not in RTC options.".format(x=opt))
# this needs to support polymorphic equals (i.e., almostEquals
if not isinstance(resolved_value, float):
emsg = "Resolved option {o} are not equal. Expected {a}, got {b}".format(
o=opt, b=rtc.task.options[opt], a=resolved_value)
self.assertEquals(rtc.task.options[opt], resolved_value, emsg)
# Resolved NPROC
self.assertEquals(rtc.task.nproc, self.RESOLVED_NPROC)
self.assertEquals(rtc.task.is_distributed,
self.RESOLVED_IS_DISTRIBUTED)
log.info("running resolved contract {r}".format(r=output_json_rtc))
exe = "{d} {p}".format(p=output_json_rtc, d=self.DRIVER_RESOLVE)
log.info("Running exe '{e}'".format(e=exe))
with tempfile.TemporaryFile() as stdout:
rcode = subprocess.call([exe], shell=True, stdout=stdout)
self.assertEquals(
rcode, 0,
"Running from resolved tool contract failed from {x}".format(
x=exe))
log.info("Successfully completed running e2e for {d}".format(
d=self.DRIVER_EMIT))
self._test_outputs_exists(rtc)
self.run_after(rtc, output_dir)
def test_validate_resolved_tool_contracts(self):
for path in _get_all_from(DATA_DIR, _filter_rtc):
f = _to_assertion(path, validate_rtc)
f(self)
self.assertIsInstance(load_resolved_tool_contract_from(path),
ResolvedToolContract)
def test_validate_resolved_tool_contracts(self):
for path in walker(DATA_DIR_RTC, json_filter):
f = _to_assertion(path, validate_rtc)
f(self)
self.assertIsInstance(load_resolved_tool_contract_from(path), ResolvedToolContract)
def test_validate_resolved_tool_contracts(self):
for path in walker(DATA_DIR_RTC, json_filter):
f = _to_assertion(path, validate_rtc)
f(self)
self.assertIsInstance(load_resolved_tool_contract_from(path),
ResolvedToolContract)
