import pkg_resources # part of setuptools
import Queue
import time
+import signal
+import thread
from cwltool.errors import WorkflowException
import cwltool.main
import arvados.config
from arvados.keep import KeepClient
from arvados.errors import ApiError
+import arvados.commands._util as arv_cmd
from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
-from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps, upload_dependencies
+from. runner import Runner, upload_docker, upload_job_order, upload_workflow_deps
from .arvtool import ArvadosCommandTool
from .arvworkflow import ArvadosWorkflow, upload_workflow
from .fsaccess import CollectionFsAccess, CollectionFetcher, collectionResolver, CollectionCache
self.workflow_eval_lock = threading.Condition(threading.RLock())
self.final_output = None
self.final_status = None
- self.uploaded = {}
self.num_retries = num_retries
self.uuid = None
self.stop_polling = threading.Event()
self.collection_cache = CollectionCache(self.api, self.keep_client, self.num_retries)
+ self.fetcher_constructor = partial(CollectionFetcher,
+ api_client=self.api,
+ fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
+ num_retries=self.num_retries)
+
self.work_api = None
expected_api = ["jobs", "containers"]
for api in expected_api:
def arv_make_tool(self, toolpath_object, **kwargs):
kwargs["work_api"] = self.work_api
- kwargs["fetcher_constructor"] = partial(CollectionFetcher,
- api_client=self.api,
- fs_access=CollectionFsAccess("", collection_cache=self.collection_cache),
- num_retries=self.num_retries)
+ kwargs["fetcher_constructor"] = self.fetcher_constructor
kwargs["resolver"] = partial(collectionResolver, self.api, num_retries=self.num_retries)
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
return ArvadosCommandTool(self, toolpath_object, **kwargs)
with self.workflow_eval_lock:
self.processes[container.uuid] = container
- def process_done(self, uuid):
+ def process_done(self, uuid, record):
with self.workflow_eval_lock:
- if uuid in self.processes:
- del self.processes[uuid]
+ j = self.processes[uuid]
+ logger.info("%s %s is %s", self.label(j), uuid, record["state"])
+ self.task_queue.add(partial(j.done, record))
+ del self.processes[uuid]
def wrapped_callback(self, cb, obj, st):
with self.workflow_eval_lock:
j.update_pipeline_component(event["properties"]["new_attributes"])
logger.info("%s %s is Running", self.label(j), uuid)
elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
- with self.workflow_eval_lock:
- j = self.processes[uuid]
- self.task_queue.add(partial(j.done, event["properties"]["new_attributes"]))
- logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
+ self.process_done(uuid, event["properties"]["new_attributes"])
def label(self, obj):
return "[%s %s]" % (self.work_api[0:-1], obj.name)
finally:
self.stop_polling.set()
- def get_uploaded(self):
- return self.uploaded.copy()
-
- def add_uploaded(self, src, pair):
- self.uploaded[src] = pair
-
def add_intermediate_output(self, uuid):
if uuid:
self.intermediate_output_collections.append(uuid)
self.api.collections().delete(uuid=i).execute(num_retries=self.num_retries)
except:
logger.warn("Failed to delete intermediate output: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
- if sys.exc_info()[0] is KeyboardInterrupt:
+ if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
break
def check_features(self, obj):
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 kwargs.get("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 kwargs.get("name"):
kwargs["name"] = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
except UnsupportedRequirement:
raise
except:
- if sys.exc_info()[0] is KeyboardInterrupt:
- logger.error("Interrupted, marking pipeline as failed")
+ if sys.exc_info()[0] is KeyboardInterrupt or sys.exc_info()[0] is SystemExit:
+ logger.error("Interrupted, workflow will be cancelled")
else:
logger.error("Execution failed: %s", sys.exc_info()[1], exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
default=None)
+ parser.add_argument("--submit-request-uuid", type=str,
+ default=None,
+ help="Update and commit supplied container request instead of creating a new one (containers API only).")
+
parser.add_argument("--name", type=str,
help="Name to use for workflow execution instance.",
default=None)
"http://arvados.org/cwl#ReuseRequirement"
])
-def main(args, stdout, stderr, api_client=None, keep_client=None):
+def exit_signal_handler(sigcode, frame):
+ logger.error("Caught signal {}, exiting.".format(sigcode))
+ sys.exit(-sigcode)
+
+def main(args, stdout, stderr, api_client=None, keep_client=None,
+ install_sig_handlers=True):
parser = arg_parser()
job_order_object = None
arvargs = parser.parse_args(args)
+ if install_sig_handlers:
+ arv_cmd.install_signal_handlers()
+
if arvargs.update_workflow:
if arvargs.update_workflow.find('-7fd4e-') == 5:
want_api = 'containers'
projects / arvados.git / blobdiff