def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
debug = False
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
if "arv:debug" in job_order_object:
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
api_client=runner.api,
fs_access=make_fs_access(""),
num_retries=runner.num_retries))
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = debug
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
args.priority = arvados_cwl.DEFAULT_PRIORITY
args.do_validate = True
args.disable_js_validation = False
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()),
output_name=output_name, output_tags=output_tags)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.arv_make_tool,
fetcher_constructor=functools.partial(CollectionFetcher,
api_client=runner.api,
fs_access=make_fs_access(""),
num_retries=runner.num_retries))
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = False
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def run():
# Timestamps are added by crunch-job, so don't print redundant timestamps.
arvados.log_handler.setFormatter(logging.Formatter('%(name)s %(levelname)s: %(message)s'))
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
toolpath = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object.pop("cwl:tool"))
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
if "location" in v:
v["location"] = keeppath(v["location"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
output_name = None
output_tags = None
enable_reuse = True
on_error = "continue"
debug = False
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
if "arv:on_error" in job_order_object:
on_error = job_order_object["arv:on_error"]
del job_order_object["arv:on_error"]
if "arv:debug" in job_order_object:
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
arvargs = argparse.Namespace()
arvargs.work_api = "jobs"
arvargs.output_name = output_name
arvargs.output_tags = output_tags
arvargs.thread_count = 1
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
arvargs=arvargs)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
t = load_tool(toolpath, runner.loadingContext)
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
args = ArvRuntimeContext(vars(arvargs))
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.submit = False
args.debug = debug
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.name = None
args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
args.make_fs_access = make_fs_access
args.trash_intermediate = False
args.intermediate_output_ttl = 0
args.priority = arvados_cwl.DEFAULT_PRIORITY
args.do_validate = True
args.disable_js_validation = False
args.tmp_outdir_prefix = "tmp"
runner.arv_executor(t, job_order_object, args, logger=logger)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash()
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress':1.0
}).execute()
def run():
# Print package versions
logger.info(arvados_cwl.versionstring())
api = arvados.api("v1")
arvados_cwl.add_arv_hints()
runner = None
try:
job_order_object = arvados.current_job()['script_parameters']
pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
def keeppath(v):
if pdh_path.match(v):
return "keep:%s" % v
else:
return v
def keeppathObj(v):
v["location"] = keeppath(v["location"])
job_order_object["cwl:tool"] = "file://%s/%s" % (
os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
for k, v in job_order_object.items():
if isinstance(
v,
basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
"location": "keep:%s" % v
}
adjustFileObjs(job_order_object, keeppathObj)
adjustDirObjs(job_order_object, keeppathObj)
normalizeFilesDirs(job_order_object)
adjustDirObjs(
job_order_object,
functools.partial(
getListing,
arvados_cwl.fsaccess.CollectionFsAccess("", api_client=api)))
output_name = None
output_tags = None
enable_reuse = True
if "arv:output_name" in job_order_object:
output_name = job_order_object["arv:output_name"]
del job_order_object["arv:output_name"]
if "arv:output_tags" in job_order_object:
output_tags = job_order_object["arv:output_tags"]
del job_order_object["arv:output_tags"]
if "arv:enable_reuse" in job_order_object:
enable_reuse = job_order_object["arv:enable_reuse"]
del job_order_object["arv:enable_reuse"]
runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api(
'v1', model=OrderedJsonModel()),
output_name=output_name,
output_tags=output_tags)
t = load_tool(job_order_object, runner.arv_make_tool)
args = argparse.Namespace()
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.submit = False
args.debug = True
args.quiet = False
args.ignore_docker_for_reuse = False
args.basedir = os.getcwd()
args.cwl_runner_job = {
"uuid": arvados.current_job()["uuid"],
"state": arvados.current_job()["state"]
}
outputObj = runner.arv_executor(t, job_order_object, **vars(args))
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
else:
logging.exception("Unhandled exception")
if runner and runner.final_output_collection:
outputCollection = runner.final_output_collection.portable_data_hash(
)
else:
outputCollection = None
api.job_tasks().update(uuid=arvados.current_task()['uuid'],
body={
'output': outputCollection,
'success': False,
'progress': 1.0
}).execute()