def test_fetcher(self):
class TestFetcher(schema_salad.ref_resolver.Fetcher):
def __init__(self, a, b):
pass
def fetch_text(self, url): # type: (unicode) -> unicode
if url == "baz:bar/foo.cwl":
return """
cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
inputs: []
outputs: []
"""
else:
raise RuntimeError("Not foo.cwl")
def check_exists(self, url): # type: (unicode) -> bool
if url == "baz:bar/foo.cwl":
return True
else:
return False
def test_resolver(d, a):
return "baz:bar/" + a
load_tool("foo.cwl", defaultMakeTool, resolver=test_resolver, fetcher_constructor=TestFetcher)
self.assertEquals(0, main(["--print-pre", "--debug", "foo.cwl"], resolver=test_resolver, fetcher_constructor=TestFetcher))
def test_fetcher(self):
class TestFetcher(schema_salad.ref_resolver.Fetcher):
def __init__(self, a, b):
pass
def fetch_text(self, url): # type: (unicode) -> unicode
if url == "baz:bar/foo.cwl":
return """
cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
inputs: []
outputs: []
"""
else:
raise RuntimeError("Not foo.cwl, was %s" % url)
def check_exists(self, url): # type: (unicode) -> bool
if url == "baz:bar/foo.cwl":
return True
else:
return False
def urljoin(self, base, url):
urlsp = urllib.parse.urlsplit(url)
if urlsp.scheme:
return url
basesp = urllib.parse.urlsplit(base)
if basesp.scheme == "keep":
return base + "/" + url
return urllib.parse.urljoin(base, url)
def test_resolver(d, a):
if a.startswith("baz:bar/"):
return a
else:
return "baz:bar/" + a
loadingContext = LoadingContext({"construct_tool_object": default_make_tool,
"resolver": test_resolver,
"fetcher_constructor": TestFetcher})
load_tool("foo.cwl", loadingContext)
self.assertEquals(0, main(["--print-pre", "--debug", "foo.cwl"], loadingContext=loadingContext))
def test_get_subgraph():
loadingContext = LoadingContext({"construct_tool_object": default_make_tool})
wf = norm(Path(get_data("tests/subgraph/count-lines1-wf.cwl")).as_uri())
loadingContext.do_update = False
tool = load_tool(wf, loadingContext)
sg = norm(Path(get_data("tests/subgraph")).as_uri())
def clean(val):
if isinstance(val, string_types):
if val.startswith(sg):
return val[len(sg)+1:]
if isinstance(val, dict):
return {k: clean(v) for k,v in val.items()}
if isinstance(val, list):
return [clean(v) for v in val]
return val
for a in ("file1", "file2", "file3", "count_output",
"output3", "output4", "output5",
"step1", "step2", "step3", "step4", "step5"):
extracted = get_subgraph([wf+"#"+a], tool)
with open(get_data("tests/subgraph/extract_"+a+".json")) as f:
assert json.load(f) == clean(convert_to_dict(extracted))
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():
# 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 viewitems(job_order_object):
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
arvargs.collection_cache_size = None
runner = arvados_cwl.ArvCwlExecutor(
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 __load(location):
return load_tool(
location,
setup_loadingContext(LoadingContext(default_cwl_args),
RuntimeContext(default_cwl_args),
argparse.Namespace(**default_cwl_args)))
def arv_executor(self, tool, job_order, runtimeContext, logger=None):
self.debug = runtimeContext.debug
tool.visit(self.check_features)
self.project_uuid = runtimeContext.project_uuid
self.pipeline = None
self.fs_access = runtimeContext.make_fs_access(runtimeContext.basedir)
self.secret_store = runtimeContext.secret_store
self.trash_intermediate = runtimeContext.trash_intermediate
if self.trash_intermediate and self.work_api != "containers":
raise Exception(
"--trash-intermediate is only supported with --api=containers."
)
self.intermediate_output_ttl = runtimeContext.intermediate_output_ttl
if self.intermediate_output_ttl and self.work_api != "containers":
raise Exception(
"--intermediate-output-ttl is only supported with --api=containers."
)
if self.intermediate_output_ttl < 0:
raise Exception(
"Invalid value %d for --intermediate-output-ttl, cannot be less than zero"
% self.intermediate_output_ttl)
if runtimeContext.submit_request_uuid and self.work_api != "containers":
raise Exception(
"--submit-request-uuid requires containers API, but using '{}' api"
.format(self.work_api))
if not runtimeContext.name:
runtimeContext.name = self.name = tool.tool.get(
"label") or tool.metadata.get("label") or os.path.basename(
tool.tool["id"])
# Upload local file references in the job order.
job_order = upload_job_order(self, "%s input" % runtimeContext.name,
tool, job_order)
submitting = (runtimeContext.update_workflow
or runtimeContext.create_workflow or
(runtimeContext.submit
and not (tool.tool["class"] == "CommandLineTool"
and runtimeContext.wait
and not runtimeContext.always_submit_runner)))
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
loadingContext.do_update = False
if submitting:
# Document may have been auto-updated. Reload the original
# document with updating disabled because we want to
# submit the original document, not the auto-updated one.
tool = load_tool(tool.tool["id"], loadingContext)
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
merged_map = upload_workflow_deps(self, tool)
# Recreate process object (ArvadosWorkflow or
# ArvadosCommandTool) because tool document may have been
# updated by upload_workflow_deps in ways that modify
# inheritance of hints or requirements.
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
tool = load_tool(tool.tool, loadingContext)
existing_uuid = runtimeContext.update_workflow
if existing_uuid or runtimeContext.create_workflow:
# Create a pipeline template or workflow record and exit.
if self.work_api == "containers":
return (upload_workflow(
self,
tool,
job_order,
self.project_uuid,
uuid=existing_uuid,
submit_runner_ram=runtimeContext.submit_runner_ram,
name=runtimeContext.name,
merged_map=merged_map), "success")
self.apply_reqs(job_order, tool)
self.ignore_docker_for_reuse = runtimeContext.ignore_docker_for_reuse
self.eval_timeout = runtimeContext.eval_timeout
runtimeContext = runtimeContext.copy()
runtimeContext.use_container = True
runtimeContext.tmpdir_prefix = "tmp"
runtimeContext.work_api = self.work_api
if self.work_api == "containers":
if self.ignore_docker_for_reuse:
raise Exception(
"--ignore-docker-for-reuse not supported with containers API."
)
runtimeContext.outdir = "/var/spool/cwl"
runtimeContext.docker_outdir = "/var/spool/cwl"
runtimeContext.tmpdir = "/tmp"
runtimeContext.docker_tmpdir = "/tmp"
if runtimeContext.priority < 1 or runtimeContext.priority > 1000:
raise Exception("--priority must be in the range 1..1000.")
if self.should_estimate_cache_size:
visited = set()
estimated_size = [0]
def estimate_collection_cache(obj):
if obj.get("location", "").startswith("keep:"):
m = pdh_size.match(obj["location"][5:])
if m and m.group(1) not in visited:
visited.add(m.group(1))
estimated_size[0] += int(m.group(2))
visit_class(job_order, ("File", "Directory"),
estimate_collection_cache)
runtimeContext.collection_cache_size = max(
((estimated_size[0] * 192) // (1024 * 1024)) + 1, 256)
self.collection_cache.set_cap(
runtimeContext.collection_cache_size * 1024 * 1024)
logger.info("Using collection cache size %s MiB",
runtimeContext.collection_cache_size)
runnerjob = None
if runtimeContext.submit:
# Submit a runner job to run the workflow for us.
if self.work_api == "containers":
if tool.tool[
"class"] == "CommandLineTool" and runtimeContext.wait and (
not runtimeContext.always_submit_runner):
runtimeContext.runnerjob = tool.tool["id"]
else:
tool = RunnerContainer(
self,
tool,
loadingContext,
runtimeContext.enable_reuse,
self.output_name,
self.output_tags,
submit_runner_ram=runtimeContext.submit_runner_ram,
name=runtimeContext.name,
on_error=runtimeContext.on_error,
submit_runner_image=runtimeContext.submit_runner_image,
intermediate_output_ttl=runtimeContext.
intermediate_output_ttl,
merged_map=merged_map,
priority=runtimeContext.priority,
secret_store=self.secret_store,
collection_cache_size=runtimeContext.
collection_cache_size,
collection_cache_is_default=self.
should_estimate_cache_size)
if runtimeContext.cwl_runner_job is not None:
self.uuid = runtimeContext.cwl_runner_job.get('uuid')
jobiter = tool.job(job_order, self.output_callback, runtimeContext)
if runtimeContext.submit and not runtimeContext.wait:
runnerjob = next(jobiter)
runnerjob.run(runtimeContext)
return (runnerjob.uuid, "success")
current_container = arvados_cwl.util.get_current_container(
self.api, self.num_retries, logger)
if current_container:
logger.info("Running inside container %s",
current_container.get("uuid"))
self.poll_api = arvados.api('v1', timeout=runtimeContext.http_timeout)
self.polling_thread = threading.Thread(target=self.poll_states)
self.polling_thread.start()
self.task_queue = TaskQueue(self.workflow_eval_lock, self.thread_count)
try:
self.workflow_eval_lock.acquire()
# Holds the lock while this code runs and releases it when
# it is safe to do so in self.workflow_eval_lock.wait(),
# at which point on_message can update job state and
# process output callbacks.
loopperf = Perf(metrics, "jobiter")
loopperf.__enter__()
for runnable in jobiter:
loopperf.__exit__()
if self.stop_polling.is_set():
break
if self.task_queue.error is not None:
raise self.task_queue.error
if runnable:
with Perf(metrics, "run"):
self.start_run(runnable, runtimeContext)
else:
if (self.task_queue.in_flight + len(self.processes)) > 0:
self.workflow_eval_lock.wait(3)
else:
logger.error(
"Workflow is deadlocked, no runnable processes and not waiting on any pending processes."
)
break
if self.stop_polling.is_set():
break
loopperf.__enter__()
loopperf.__exit__()
while (self.task_queue.in_flight + len(self.processes)) > 0:
if self.task_queue.error is not None:
raise self.task_queue.error
self.workflow_eval_lock.wait(3)
except UnsupportedRequirement:
raise
except:
if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info(
)[0] is SystemExit:
logger.error("Interrupted, workflow will be cancelled")
elif isinstance(sys.exc_info()[1], WorkflowException):
logger.error(
"Workflow execution failed:\n%s",
sys.exc_info()[1],
exc_info=(sys.exc_info()[1] if self.debug else False))
else:
logger.exception("Workflow execution failed")
if self.pipeline:
self.api.pipeline_instances().update(
uuid=self.pipeline["uuid"], body={
"state": "Failed"
}).execute(num_retries=self.num_retries)
if self.work_api == "containers" and not current_container:
# Not running in a crunch container, so cancel any outstanding processes.
for p in self.processes:
try:
self.api.container_requests().update(
uuid=p, body={
"priority": "0"
}).execute(num_retries=self.num_retries)
except Exception:
pass
finally:
self.workflow_eval_lock.release()
self.task_queue.drain()
self.stop_polling.set()
self.polling_thread.join()
self.task_queue.join()
if self.final_status == "UnsupportedRequirement":
raise UnsupportedRequirement("Check log for details.")
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
if runtimeContext.submit and isinstance(tool, Runner):
logger.info("Final output collection %s", tool.final_output)
else:
if self.output_name is None:
self.output_name = "Output of %s" % (shortname(
tool.tool["id"]))
if self.output_tags is None:
self.output_tags = ""
storage_classes = runtimeContext.storage_classes.strip().split(",")
self.final_output, self.final_output_collection = self.make_output_collection(
self.output_name, storage_classes, self.output_tags,
self.final_output)
self.set_crunch_output()
if runtimeContext.compute_checksum:
adjustDirObjs(self.final_output,
partial(get_listing, self.fs_access))
adjustFileObjs(self.final_output,
partial(compute_checksums, self.fs_access))
if self.trash_intermediate and self.final_status == "success":
self.trash_intermediate_output()
return (self.final_output, self.final_status)
def load_cwl(cwl_file):
load.loaders = {}
loading_context = cwltool.context.LoadingContext(get_default_args())
loading_context.construct_tool_object = default_make_tool
loading_context.resolver = tool_resolver
return load.load_tool(cwl_file, loading_context)
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()
def read_config_from_cwl_file(cwl_file):
print_pref = "[read_cwl_file]:"
configs = {}
metadata = {
"doc": "",
"workflow_name": os.path.basename(cwl_file),
"workflow_path": os.path.abspath(cwl_file),
"workflow_type": "CWL"
}
# cwltool needs to be imported on demand since
# repeatedly calling functions on a document named
# with same name caused errors.
from cwltool.context import LoadingContext
from cwltool.load_tool import load_tool
from cwltool.workflow import default_make_tool
loadingContext = LoadingContext({"construct_tool_object": default_make_tool, "disable_js_validation": True})
try:
cwl_document = load_tool(cwl_file, loadingContext)
except AssertionError as e:
raise AssertionError( print_pref + "failed to read cwl file \"" + cwl_file + "\": does not exist or is invalid")
inp_records = cwl_document.inputs_record_schema["fields"]
if "doc" in cwl_document.tool:
metadata["doc"] = cwl_document.tool["doc"]
for inp_rec in inp_records:
name = clean_string( inp_rec["name"] )
is_array = False
null_allowed = False
null_items_allowed = False
default_value = [""]
allowed_selection = [""]
# read type:
try:
type_, null_allowed, is_array, null_items_allowed, allowed_selection = read_inp_rec_type_field(inp_rec["type"])
except Exception as e:
raise AssertionError( print_pref + "E: reading type of param \"{}\": {}".format(name, str(e)))
# get the default:
if "default" in inp_rec:
if is_basic_type_instance(inp_rec["default"]):
default_value = [clean_string(inp_rec["default"])]
else:
if is_array and isinstance(inp_rec["default"], list):
default_value = []
for entry in inp_rec["default"]:
if is_basic_type_instance(inp_rec["default"]):
default_value.append(clean_string(entry))
else:
print(print_pref + "W: invalid default value for parameter " + name +
": will be ignored", file=sys.stderr)
default_value = [""]
elif type_ == "File" and isinstance(inp_rec["default"], dict):
print(print_pref + "W: invalid default value for parameter " + name +
": defaults for File class are not supported yet; will be ignored", file=sys.stderr)
default_value = [""]
else:
print(print_pref + "W: invalid default value for parameter " + name +
": will be ignored", file=sys.stderr)
default_value = [""]
else:
default_value = [""]
# read secondary files:
if type_ == "File" and "secondaryFiles" in inp_rec:
if isinstance(inp_rec["secondaryFiles"], str):
secondary_files = [ inp_rec["secondaryFiles"] ]
elif isinstance(inp_rec["secondaryFiles"], CommentedMap) and \
"pattern" in inp_rec["secondaryFiles"].keys():
secondary_files = [ inp_rec["secondaryFiles"]["pattern"] ]
elif isinstance(inp_rec["secondaryFiles"], CommentedSeq) or isinstance(inp_rec["secondaryFiles"], list):
secondary_files = []
for sec_file in inp_rec["secondaryFiles"]:
if isinstance(sec_file, CommentedMap) and "pattern" in sec_file:
secondary_files.append(sec_file["pattern"])
elif isinstance(sec_file, str):
secondary_files.append(sec_file)
else:
raise AssertionError(print_pref + "E: invalid secondaryFiles field for parameter " + name)
else:
raise AssertionError( print_pref + "E: invalid secondaryFiles field for parameter " + name )
else:
secondary_files = [ "" ]
# read doc:
if "doc" in inp_rec:
doc = inp_rec["doc"]
else:
doc = ""
# assemble config parameters:
inp_configs = {
"type": type_,
"is_array": is_array,
"null_allowed": null_allowed,
"null_items_allowed": null_items_allowed,
"secondary_files": secondary_files,
"default_value": default_value,
"allowed_selection": allowed_selection,
"doc": doc
}
# add to configs dict:
configs[ name ] = inp_configs
return configs, metadata