def arvExecutor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
tool.visit(self.check_writable)
if kwargs.get("quiet"):
logger.setLevel(logging.WARN)
logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
useruuid = self.api.users().current().execute()["uuid"]
self.project_uuid = kwargs.get("project_uuid") if kwargs.get(
"project_uuid") else useruuid
self.pipeline = None
make_fs_access = kwargs.get("make_fs_access") or partial(
CollectionFsAccess, api_client=self.api)
self.fs_access = make_fs_access(kwargs["basedir"])
if kwargs.get("create_template"):
tmpl = RunnerTemplate(self, tool, job_order,
kwargs.get("enable_reuse"))
tmpl.save()
# cwltool.main will write our return value to stdout.
return tmpl.uuid
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
kwargs["on_error"] = "continue"
kwargs["compute_checksum"] = kwargs.get("compute_checksum")
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
kwargs["docker_outdir"] = "/var/spool/cwl"
kwargs["tmpdir"] = "/tmp"
kwargs["docker_tmpdir"] = "/tmp"
elif self.work_api == "jobs":
kwargs["outdir"] = "$(task.outdir)"
kwargs["docker_outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
runnerjob = None
if kwargs.get("submit"):
if self.work_api == "containers":
if tool.tool["class"] == "CommandLineTool":
runnerjob = tool.job(job_order, self.output_callback,
**kwargs).next()
else:
runnerjob = RunnerContainer(self, tool, job_order,
kwargs.get("enable_reuse"))
else:
runnerjob = RunnerJob(self, tool, job_order,
kwargs.get("enable_reuse"))
if not kwargs.get(
"submit"
) and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid": self.project_uuid,
"name": shortname(tool.tool["id"]),
"components": {},
"state": "RunningOnClient"
}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
if runnerjob and not kwargs.get("wait"):
runnerjob.run()
return runnerjob.uuid
self.poll_api = arvados.api('v1')
self.polling_thread = threading.Thread(target=self.poll_states)
self.polling_thread.start()
if runnerjob:
jobiter = iter((runnerjob, ))
else:
if "cwl_runner_job" in kwargs:
self.uuid = kwargs.get("cwl_runner_job").get('uuid')
jobiter = tool.job(job_order, self.output_callback, **kwargs)
try:
self.cond.acquire()
# Will continue to hold the lock for the duration of this code
# except when in cond.wait(), at which point on_message can update
# job state and process output callbacks.
for runnable in jobiter:
if runnable:
runnable.run(**kwargs)
else:
if self.processes:
self.cond.wait(1)
else:
logger.error(
"Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs."
)
break
while self.processes:
self.cond.wait(1)
except UnsupportedRequirement:
raise
except:
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
logger.error(
"Caught unhandled exception, marking pipeline as failed. Error was: %s",
sys.exc_info()[1],
exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
self.api.pipeline_instances().update(
uuid=self.pipeline["uuid"], body={
"state": "Failed"
}).execute(num_retries=self.num_retries)
if runnerjob and runnerjob.uuid and self.work_api == "containers":
self.api.container_requests().update(
uuid=runnerjob.uuid, body={
"priority": "0"
}).execute(num_retries=self.num_retries)
finally:
self.cond.release()
self.stop_polling.set()
self.polling_thread.join()
if self.final_status == "UnsupportedRequirement":
raise UnsupportedRequirement("Check log for details.")
if self.final_status != "success":
raise WorkflowException("Workflow failed.")
if self.final_output is None:
raise WorkflowException("Workflow did not return a result.")
if kwargs.get("compute_checksum"):
adjustFileObjs(self.final_output,
partial(compute_checksums, self.fs_access))
return self.final_output
def run(self,
runtimeContext, # type: RuntimeContext
tmpdir_lock=None # type: Optional[threading.Lock]
): # type: (...) -> None
log.debug(
"[job %s] self.__dict__ in run() ----------------------",
self.name
)
log.debug(pformat(self.__dict__))
if not self.successCodes:
self.successCodes = [0]
task = self.create_task_msg()
log.info(
"[job %s] CREATED TASK MSG----------------------",
self.name
)
log.info(pformat(task))
try:
self.id = self.client.create_task(task)
log.info(
"[job %s] SUBMITTED TASK ----------------------",
self.name
)
log.info("[job %s] task id: %s ", self.name, self.id)
except Exception as e:
log.error(
"[job %s] Failed to submit task to TES service:\n%s",
self.name, e
)
raise WorkflowException(e)
max_tries = 10
current_try = 1
self.exit_code = None
while not self.is_done():
delay = 1.5 * current_try**2
time.sleep(
random.randint(
round(
delay -
0.5 *
delay),
round(
delay +
0.5 *
delay)))
try:
task = self.client.get_task(self.id, "MINIMAL")
self.state = task.state
log.debug(
"[job %s] POLLING %s, result: %s", self.name,
pformat(self.id), task.state
)
except Exception as e:
log.error("[job %s] POLLING ERROR %s", self.name, e)
if current_try <= max_tries:
current_try += 1
continue
else:
log.error("[job %s] MAX POLLING RETRIES EXCEEDED",
self.name)
break
try:
process_status = None
if self.state != "COMPLETE" \
and self.exit_code not in self.successCodes:
process_status = "permanentFail"
log.error("[job %s] job error:\n%s", self.name, self.state)
remote_cwl_output_json = False
if self.remote_storage_url:
remote_fs_access = runtimeContext.make_fs_access(
self.remote_storage_url)
remote_cwl_output_json = remote_fs_access.exists(
remote_fs_access.join(
self.remote_storage_url, "cwl.output.json"))
if self.remote_storage_url:
original_outdir = self.builder.outdir
if not remote_cwl_output_json:
self.builder.outdir = self.remote_storage_url
outputs = self.collect_outputs(self.remote_storage_url,
self.exit_code)
self.builder.outdir = original_outdir
else:
outputs = self.collect_outputs(self.outdir, self.exit_code)
cleaned_outputs = {}
for k, v in outputs.items():
if isinstance(k, bytes):
k = k.decode("utf8")
if isinstance(v, bytes):
v = v.decode("utf8")
cleaned_outputs[k] = v
self.outputs = cleaned_outputs
if not process_status:
process_status = "success"
except (WorkflowException, Exception) as err:
log.error("[job %s] job error:\n%s", self.name, err)
if log.isEnabledFor(logging.DEBUG):
log.exception(err)
process_status = "permanentFail"
finally:
if self.outputs is None:
self.outputs = {}
with self.runtime_context.workflow_eval_lock:
self.output_callback(self.outputs, process_status)
log.info(
"[job %s] OUTPUTS ------------------",
self.name
)
log.info(pformat(self.outputs))
self.cleanup(self.runtime_context.rm_tmpdir)
return
def run(self, runtimeContext): # noqa: C901
"""Run a job."""
self._setup(runtimeContext)
env = self.environment
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
vars_to_preserve = runtimeContext.preserve_environment
if runtimeContext.preserve_entire_environment:
vars_to_preserve = os.environ
if vars_to_preserve is not None:
for key, value in os.environ.items():
if key in vars_to_preserve and key not in env:
env[key] = value
env["HOME"] = self.builder.outdir
env["TMPDIR"] = self.tmpdir
if "PATH" not in env:
env["PATH"] = os.environ["PATH"]
if "SYSTEMROOT" not in env and "SYSTEMROOT" in os.environ:
env["SYSTEMROOT"] = os.environ["SYSTEMROOT"]
try:
stage_files(self.pathmapper, ignore_writable=True, symlink=False)
if getattr(self, "generatemapper", ""):
stage_files(
self.generatemapper,
ignore_writable=self.inplace_update,
symlink=False,
)
relink_initialworkdir(
self.generatemapper,
self.outdir,
self.builder.outdir,
inplace_update=self.inplace_update,
)
except OSError:
# cwltool/process.py, line 239, in stage_files
# shutil.copytree(p.resolved, p.target)
pass
self.add_volumes(self.pathmapper)
if getattr(self, "generatemapper", ""):
self.add_volumes(self.generatemapper)
# useful for debugging
log.debug(f"[job {self.name}] self.__dict__ in run() ---------------")
log.debug(pformat(self.__dict__))
task = self.create_task_msg(
runtimeContext.working_dir, runtimeContext.workflow_uuid
)
log.info(f"[job {self.name}] CREATED TASK MSG----------------------")
log.info(pformat(task))
try:
# task_id = job_id received from job-controller
task_id = runtimeContext.pipeline.service.submit(**task)
task_id = str(task_id["job_id"])
running_jobs = {"total": 1, "job_ids": [task_id]}
runtimeContext.publisher.publish_workflow_status(
runtimeContext.workflow_uuid,
1,
message={"progress": {"running": running_jobs,}},
)
log.info(f"[job {self.name}] SUBMITTED TASK --------------------")
log.info(f"[job {self.name}] task id: {task_id} ")
self.task_name_map[self.name] = task_id
operation = runtimeContext.pipeline.service.check_status(task_id)
except Exception as e:
log.error(
f"[job {self.name}] " f"Failed to submit task to job controller:\n{e}"
)
raise WorkflowException(e)
def callback(rcode):
try:
outputs = self.collect_outputs(self.outdir, rcode=rcode)
cleaned_outputs = {}
for k, v in outputs.items():
if isinstance(k, bytes):
k = k.decode("utf8")
if isinstance(v, bytes):
v = v.decode("utf8")
cleaned_outputs[k] = v
self.outputs = cleaned_outputs
self.output_callback(self.outputs, "success")
except WorkflowException as e:
log.error(f"[job {self.name}] workflow job error:\n{e}")
self.output_callback({}, "permanentFail")
except Exception as e:
log.error(f"[job {self.name}] job error:\n{e}")
self.output_callback({}, "permanentFail")
finally:
if self.outputs is not None:
log.info(f"[job {self.name}] OUTPUTS ------------------")
log.info(pformat(self.outputs))
self.cleanup(runtimeContext.rm_tmpdir)
poll = ReanaPipelinePoll(
workflow_uuid=runtimeContext.workflow_uuid,
task_id=self.task_name_map.get(self.name),
jobname=self.name,
service=runtimeContext.pipeline.service,
operation=operation,
callback=callback,
publisher=runtimeContext.publisher,
)
runtimeContext.pipeline.add_thread(poll)
poll.start()
def arv_executor(self,
updated_tool,
job_order,
runtimeContext,
logger=None):
self.debug = runtimeContext.debug
workbench1 = self.api.config()["Services"]["Workbench1"]["ExternalURL"]
workbench2 = self.api.config()["Services"]["Workbench2"]["ExternalURL"]
controller = self.api.config()["Services"]["Controller"]["ExternalURL"]
logger.info("Using cluster %s (%s)",
self.api.config()["ClusterID"], workbench2 or workbench1
or controller)
updated_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))
default_storage_classes = ",".join([
k for k, v in self.api.config().get("StorageClasses", {
"default": {
"Default": True
}
}).items() if v.get("Default") is True
])
if runtimeContext.storage_classes == "default":
runtimeContext.storage_classes = default_storage_classes
if runtimeContext.intermediate_storage_classes == "default":
runtimeContext.intermediate_storage_classes = default_storage_classes
if not runtimeContext.name:
runtimeContext.name = self.name = updated_tool.tool.get(
"label") or updated_tool.metadata.get(
"label") or os.path.basename(updated_tool.tool["id"])
# Upload local file references in the job order.
job_order = upload_job_order(self, "%s input" % runtimeContext.name,
updated_tool, job_order)
# the last clause means: if it is a command line tool, and we
# are going to wait for the result, and always_submit_runner
# is false, then we don't submit a runner process.
submitting = (runtimeContext.update_workflow
or runtimeContext.create_workflow or
(runtimeContext.submit
and not (updated_tool.tool["class"] == "CommandLineTool"
and runtimeContext.wait
and not runtimeContext.always_submit_runner)))
loadingContext = self.loadingContext.copy()
loadingContext.do_validate = False
if submitting:
loadingContext.do_update = False
# Document may have been auto-updated. Reload the original
# document with updating disabled because we want to
# submit the document with its original CWL version, not
# the auto-updated one.
tool = load_tool(updated_tool.tool["id"], loadingContext)
else:
tool = updated_tool
# 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":
uuid = 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,
submit_runner_image=runtimeContext.submit_runner_image)
self.stdout.write(uuid + "\n")
return (None, "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 submitting:
tool = RunnerContainer(
self,
updated_tool,
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)
else:
runtimeContext.runnerjob = tool.tool["id"]
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)
self.stdout.write(runnerjob.uuid + "\n")
return (None, "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)
if workbench2 or workbench1:
logger.info("Output at %scollections/%s", workbench2
or workbench1, 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 = ""
storage_class_req, _ = tool.get_requirement(
"http://arvados.org/cwl#OutputStorageClass")
if storage_class_req and storage_class_req.get(
"finalStorageClass"):
storage_classes = aslist(
storage_class_req["finalStorageClass"])
else:
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 run(self, runtimeContext):
# ArvadosCommandTool subclasses from cwltool.CommandLineTool,
# which calls makeJobRunner() to get a new ArvadosContainer
# object. The fields that define execution such as
# command_line, environment, etc are set on the
# ArvadosContainer object by CommandLineTool.job() before
# run() is called.
runtimeContext = self.job_runtime
container_request = {
"command": self.command_line,
"name": self.name,
"output_path": self.outdir,
"cwd": self.outdir,
"priority": runtimeContext.priority,
"state": "Committed",
"properties": {},
}
runtime_constraints = {}
if runtimeContext.project_uuid:
container_request["owner_uuid"] = runtimeContext.project_uuid
if self.arvrunner.secret_store.has_secret(self.command_line):
raise WorkflowException(
"Secret material leaked on command line, only file literals may contain secrets"
)
if self.arvrunner.secret_store.has_secret(self.environment):
raise WorkflowException(
"Secret material leaked in environment, only file literals may contain secrets"
)
resources = self.builder.resources
if resources is not None:
runtime_constraints["vcpus"] = math.ceil(resources.get("cores", 1))
runtime_constraints["ram"] = math.ceil(
resources.get("ram") * 2**20)
mounts = {
self.outdir: {
"kind": "tmp",
"capacity": math.ceil(resources.get("outdirSize", 0) * 2**20)
},
self.tmpdir: {
"kind": "tmp",
"capacity": math.ceil(resources.get("tmpdirSize", 0) * 2**20)
}
}
secret_mounts = {}
scheduling_parameters = {}
rf = [
self.pathmapper.mapper(f) for f in self.pathmapper.referenced_files
]
rf.sort(key=lambda k: k.resolved)
prevdir = None
for resolved, target, tp, stg in rf:
if not stg:
continue
if prevdir and target.startswith(prevdir):
continue
if tp == "Directory":
targetdir = target
else:
targetdir = os.path.dirname(target)
sp = resolved.split("/", 1)
pdh = sp[0][5:] # remove "keep:"
mounts[targetdir] = {
"kind": "collection",
"portable_data_hash": pdh
}
if pdh in self.pathmapper.pdh_to_uuid:
mounts[targetdir]["uuid"] = self.pathmapper.pdh_to_uuid[pdh]
if len(sp) == 2:
if tp == "Directory":
path = sp[1]
else:
path = os.path.dirname(sp[1])
if path and path != "/":
mounts[targetdir]["path"] = path
prevdir = targetdir + "/"
with Perf(metrics, "generatefiles %s" % self.name):
if self.generatefiles["listing"]:
vwd = arvados.collection.Collection(
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
generatemapper = NoFollowPathMapper(
self.generatefiles["listing"], "", "", separateDirs=False)
sorteditems = sorted(generatemapper.items(),
key=lambda n: n[1].target)
logger.debug("generatemapper is %s", sorteditems)
with Perf(metrics, "createfiles %s" % self.name):
for f, p in sorteditems:
if not p.target:
pass
elif p.type in ("File", "Directory", "WritableFile",
"WritableDirectory"):
if p.resolved.startswith("_:"):
vwd.mkdirs(p.target)
else:
source, path = self.arvrunner.fs_access.get_collection(
p.resolved)
vwd.copy(path or ".",
p.target,
source_collection=source)
elif p.type == "CreateFile":
if self.arvrunner.secret_store.has_secret(
p.resolved):
secret_mounts[
"%s/%s" % (self.outdir, p.target)] = {
"kind":
"text",
"content":
self.arvrunner.secret_store.retrieve(
p.resolved)
}
else:
with vwd.open(p.target, "w") as n:
n.write(p.resolved)
def keepemptydirs(p):
if isinstance(p, arvados.collection.RichCollectionBase):
if len(p) == 0:
p.open(".keep", "w").close()
else:
for c in p:
keepemptydirs(p[c])
keepemptydirs(vwd)
if not runtimeContext.current_container:
runtimeContext.current_container = arvados_cwl.util.get_current_container(
self.arvrunner.api, self.arvrunner.num_retries, logger)
info = arvados_cwl.util.get_intermediate_collection_info(
self.name, runtimeContext.current_container,
runtimeContext.intermediate_output_ttl)
vwd.save_new(name=info["name"],
owner_uuid=runtimeContext.project_uuid,
ensure_unique_name=True,
trash_at=info["trash_at"],
properties=info["properties"])
prev = None
for f, p in sorteditems:
if (not p.target or self.arvrunner.secret_store.has_secret(
p.resolved) or
(prev is not None and p.target.startswith(prev))):
continue
mountpoint = "%s/%s" % (self.outdir, p.target)
mounts[mountpoint] = {
"kind": "collection",
"portable_data_hash": vwd.portable_data_hash(),
"path": p.target
}
if p.type.startswith("Writable"):
mounts[mountpoint]["writable"] = True
prev = p.target + "/"
container_request["environment"] = {
"TMPDIR": self.tmpdir,
"HOME": self.outdir
}
if self.environment:
container_request["environment"].update(self.environment)
if self.stdin:
sp = self.stdin[6:].split("/", 1)
mounts["stdin"] = {
"kind": "collection",
"portable_data_hash": sp[0],
"path": sp[1]
}
if self.stderr:
mounts["stderr"] = {
"kind": "file",
"path": "%s/%s" % (self.outdir, self.stderr)
}
if self.stdout:
mounts["stdout"] = {
"kind": "file",
"path": "%s/%s" % (self.outdir, self.stdout)
}
(docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
if not docker_req:
docker_req = {"dockerImageId": "arvados/jobs"}
container_request["container_image"] = arv_docker_get_image(
self.arvrunner.api, docker_req, runtimeContext.pull_image,
runtimeContext.project_uuid)
network_req, _ = self.get_requirement("NetworkAccess")
if network_req:
runtime_constraints["API"] = network_req["networkAccess"]
api_req, _ = self.get_requirement(
"http://arvados.org/cwl#APIRequirement")
if api_req:
runtime_constraints["API"] = True
runtime_req, _ = self.get_requirement(
"http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
runtime_constraints["keep_cache_ram"] = math.ceil(
runtime_req["keep_cache"] * 2**20)
if "outputDirType" in runtime_req:
if runtime_req["outputDirType"] == "local_output_dir":
# Currently the default behavior.
pass
elif runtime_req["outputDirType"] == "keep_output_dir":
mounts[self.outdir] = {
"kind": "collection",
"writable": True
}
partition_req, _ = self.get_requirement(
"http://arvados.org/cwl#PartitionRequirement")
if partition_req:
scheduling_parameters["partitions"] = aslist(
partition_req["partition"])
intermediate_output_req, _ = self.get_requirement(
"http://arvados.org/cwl#IntermediateOutput")
if intermediate_output_req:
self.output_ttl = intermediate_output_req["outputTTL"]
else:
self.output_ttl = self.arvrunner.intermediate_output_ttl
if self.output_ttl < 0:
raise WorkflowException(
"Invalid value %d for output_ttl, cannot be less than zero" %
container_request["output_ttl"])
if self.timelimit is not None and self.timelimit > 0:
scheduling_parameters["max_run_time"] = self.timelimit
extra_submit_params = {}
if runtimeContext.submit_runner_cluster:
extra_submit_params[
"cluster_id"] = runtimeContext.submit_runner_cluster
container_request["output_name"] = "Output for step %s" % (self.name)
container_request["output_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["secret_mounts"] = secret_mounts
container_request["runtime_constraints"] = runtime_constraints
container_request["scheduling_parameters"] = scheduling_parameters
enable_reuse = runtimeContext.enable_reuse
if enable_reuse:
reuse_req, _ = self.get_requirement("WorkReuse")
if reuse_req:
enable_reuse = reuse_req["enableReuse"]
reuse_req, _ = self.get_requirement(
"http://arvados.org/cwl#ReuseRequirement")
if reuse_req:
enable_reuse = reuse_req["enableReuse"]
container_request["use_existing"] = enable_reuse
if runtimeContext.runnerjob.startswith("arvwf:"):
wfuuid = runtimeContext.runnerjob[6:runtimeContext.runnerjob.
index("#")]
wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(
num_retries=self.arvrunner.num_retries)
if container_request["name"] == "main":
container_request["name"] = wfrecord["name"]
container_request["properties"]["template_uuid"] = wfuuid
self.output_callback = self.arvrunner.get_wrapped_callback(
self.output_callback)
try:
if runtimeContext.submit_request_uuid:
response = self.arvrunner.api.container_requests().update(
uuid=runtimeContext.submit_request_uuid,
body=container_request,
**extra_submit_params).execute(
num_retries=self.arvrunner.num_retries)
else:
response = self.arvrunner.api.container_requests().create(
body=container_request, **extra_submit_params).execute(
num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
self.arvrunner.process_submitted(self)
if response["state"] == "Final":
logger.info("%s reused container %s",
self.arvrunner.label(self),
response["container_uuid"])
else:
logger.info("%s %s state is %s", self.arvrunner.label(self),
response["uuid"], response["state"])
except Exception:
logger.exception("%s got an error", self.arvrunner.label(self))
self.output_callback({}, "permanentFail")
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 direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
merged_map = upload_workflow_deps(self, tool)
# Reload tool object which may have been updated by
# upload_workflow_deps
# Don't validate this time because it will just print redundant errors.
loadingContext = self.loadingContext.copy()
loadingContext.loader = tool.doc_loader
loadingContext.avsc_names = tool.doc_schema
loadingContext.metadata = tool.metadata
loadingContext.do_validate = False
tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
loadingContext)
# Upload local file references in the job order.
job_order = upload_job_order(self, "%s input" % runtimeContext.name,
tool, job_order)
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 == "jobs":
tmpl = RunnerTemplate(
self,
tool,
job_order,
runtimeContext.enable_reuse,
uuid=existing_uuid,
submit_runner_ram=runtimeContext.submit_runner_ram,
name=runtimeContext.name,
merged_map=merged_map,
loadingContext=loadingContext)
tmpl.save()
# cwltool.main will write our return value to stdout.
return (tmpl.uuid, "success")
elif 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.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"
elif self.work_api == "jobs":
if runtimeContext.priority != DEFAULT_PRIORITY:
raise Exception("--priority not implemented for jobs API.")
runtimeContext.outdir = "$(task.outdir)"
runtimeContext.docker_outdir = "$(task.outdir)"
runtimeContext.tmpdir = "$(task.tmpdir)"
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)
elif self.work_api == "jobs":
tool = RunnerJob(
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,
merged_map=merged_map)
elif runtimeContext.cwl_runner_job is None and self.work_api == "jobs":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid":
self.project_uuid,
"name":
runtimeContext.name if runtimeContext.
name else shortname(tool.tool["id"]),
"components": {},
"state":
"RunningOnClient"
}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
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 = jobiter.next()
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")
else:
logger.error(
"Execution failed:\n%s",
sys.exc_info()[1],
exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
self.api.pipeline_instances().update(
uuid=self.pipeline["uuid"], body={
"state": "Failed"
}).execute(num_retries=self.num_retries)
if runtimeContext.submit and isinstance(tool, Runner):
runnerjob = tool
if runnerjob.uuid and self.work_api == "containers":
self.api.container_requests().update(
uuid=runnerjob.uuid, body={
"priority": "0"
}).execute(num_retries=self.num_retries)
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 collect_output(
self,
schema, # type: Dict[Text, Any]
builder, # type: Builder
outdir, # type: Text
fs_access, # type: StdFsAccess
compute_checksum=True # type: bool
):
# type: (...) -> Optional[Union[Dict[Text, Any], List[Union[Dict[Text, Any], Text]]]]
"""
Collect outputs from the step :term:`Process` following its execution.
.. note:
When :term:`CWL` runner tries to forward ``step(i) outputs -> step(i+1) inputs``
using :meth:`collect_outputs`, it expects exact ``outputBindings`` locations to be matched.
In other words, a definition like ``outputBindings: {glob: outputs/*.txt}`` will generate results located
in ``step(i)`` as ``"<tmp-workdir>/outputs/file.txt"`` and ``step(i+1)`` will look explicitly
in ``"<tmp-workdir>/outputs`` using the ``glob`` pattern. Because each of our :term:`Process` in
the workflow are distinct/remote entities, each one stages its outputs at different URL locations,
not sharing the same *root directory*. When we stage intermediate results locally, the sub-dirs are lost.
Therefore, they act like individual :term:`CWL` runner calls where the *final results* are moved back
to the local directory for convenient access, but our *local directory* is the URL WPS-outputs location.
To let :term:`CWL` :term:`Workflow` inter-steps mapping work as intended, we must remap the locations
ignoring any nested dirs where the modified *outputBindings* definition will be able to match as if each
step :term:`Process` outputs were generated locally.
"""
result = [] # type: List[Any]
empty_and_optional = False
debug = LOGGER.isEnabledFor(logging.DEBUG)
if "outputBinding" in schema:
binding = schema["outputBinding"]
globpatterns = [] # type: List[Text]
revmap = partial(command_line_tool.revmap_file, builder, outdir)
if "glob" in binding:
with SourceLine(binding, "glob", WorkflowException, debug):
for glob in aslist(binding["glob"]):
glob = builder.do_eval(glob)
if glob:
globpatterns.extend(aslist(glob))
# rebase glob pattern as applicable (see note)
for glob in list(globpatterns):
if not any(
glob.startswith(part)
for part in [".", "/", "~"]) and "/" in glob:
glob = builder.do_eval(glob.split("/")[-1])
if glob:
globpatterns.extend(aslist(glob))
for glob in globpatterns:
if glob.startswith(outdir):
glob = glob[len(outdir) + 1:]
elif glob == ".":
glob = outdir
elif glob.startswith("/"):
raise WorkflowException(
"glob patterns must not start with '/'")
try:
prefix = fs_access.glob(outdir)
key = cmp_to_key(
cast(Callable[[Text, Text], int],
locale.strcoll))
# In case of stdout.log or stderr.log file not created
if "stdout" in self.tool and "stderr" in self.tool \
and glob in (self.tool["stdout"], self.tool["stderr"]):
filepath = Path(fs_access.join(outdir, glob))
if not filepath.is_file():
Path(filepath).touch()
result.extend([{
"location":
g,
"path":
fs_access.join(builder.outdir,
g[len(prefix[0]) + 1:]),
"basename":
os.path.basename(g),
"nameroot":
os.path.splitext(os.path.basename(g))[0],
"nameext":
os.path.splitext(os.path.basename(g))[1],
"class":
"File" if fs_access.isfile(g) else "Directory"
} for g in sorted(fs_access.glob(
fs_access.join(outdir, glob)),
key=key)])
except (OSError, IOError) as exc:
LOGGER.warning(Text(exc))
except Exception:
LOGGER.exception("Unexpected error from fs_access")
raise
for files in result:
rfile = files.copy()
# TODO This function raise an exception and seems to be related to docker (which is not used here)
# revmap(rfile)
if files["class"] == "Directory":
load_listing = builder.loadListing or (
binding and binding.get("loadListing"))
if load_listing and load_listing != "no_listing":
get_listing(fs_access, files,
(load_listing == "deep_listing"))
else:
with fs_access.open(rfile["location"], "rb") as f:
contents = b""
if binding.get("loadContents") or compute_checksum:
contents = f.read(CONTENT_LIMIT)
if binding.get("loadContents"):
files["contents"] = contents.decode("utf-8")
if compute_checksum:
checksum = hashlib.sha1() # nosec: B303
while contents != b"":
checksum.update(contents)
contents = f.read(1024 * 1024)
files[
"checksum"] = f"sha1${checksum.hexdigest()}"
f.seek(0, 2)
file_size = f.tell()
files["size"] = file_size
optional = False
single = False
if isinstance(schema["type"], list):
if "null" in schema["type"]:
optional = True
if "File" in schema["type"] or "Directory" in schema["type"]:
single = True
elif schema["type"] == "File" or schema["type"] == "Directory":
single = True
if "outputEval" in binding:
with SourceLine(binding, "outputEval", WorkflowException,
debug):
result = builder.do_eval(binding["outputEval"],
context=result)
if single:
if not result and not optional:
with SourceLine(binding, "glob", WorkflowException, debug):
raise WorkflowException(
f"Did not find output file with glob pattern: '{globpatterns}'"
)
elif not result and optional:
pass
elif isinstance(result, list):
if len(result) > 1:
raise WorkflowException(
"Multiple matches for output item that is a single file."
)
result = result[0]
if "secondaryFiles" in schema:
with SourceLine(schema, "secondaryFiles", WorkflowException,
debug):
for primary in aslist(result):
if isinstance(primary, dict):
primary.setdefault("secondaryFiles", [])
pathprefix = primary["path"][0:primary["path"].
rindex("/") + 1]
for file in aslist(schema["secondaryFiles"]):
if isinstance(
file,
dict) or "$(" in file or "${" in file:
sfpath = builder.do_eval(file,
context=primary)
subst = False
else:
sfpath = file
subst = True
for sfitem in aslist(sfpath):
if isinstance(sfitem, str):
if subst:
sfitem = {
"path":
substitute(
primary["path"], sfitem)
}
else:
sfitem = {
"path": pathprefix + sfitem
}
if "path" in sfitem and "location" not in sfitem:
revmap(sfitem)
if fs_access.isfile(sfitem["location"]):
sfitem["class"] = "File"
primary["secondaryFiles"].append(
sfitem)
elif fs_access.isdir(sfitem["location"]):
sfitem["class"] = "Directory"
primary["secondaryFiles"].append(
sfitem)
if "format" in schema:
for primary in aslist(result):
primary["format"] = builder.do_eval(schema["format"],
context=primary)
# Ensure files point to local references outside of the run environment
# TODO: Again removing revmap....
# adjustFileObjs(result, revmap)
if not result and optional:
return None
if not empty_and_optional and isinstance(
schema["type"], dict) and schema["type"]["type"] == "record":
out = {}
for f in schema["type"]["fields"]:
out[shortname(
f["name"])] = self.collect_output( # type: ignore
f,
builder,
outdir,
fs_access,
compute_checksum=compute_checksum)
return out
return result
def add_volumes(self, pathmapper, mounts, secret_store=None):
# type: (PathMapper, List[Text], SecretStore) -> None
host_outdir = self.outdir
container_outdir = self.builder.outdir
for src, vol in pathmapper.items():
if not vol.staged:
continue
host_outdir_tgt = None # type: Optional[Text]
if vol.target.startswith(container_outdir+"/"):
host_outdir_tgt = os.path.join(
host_outdir, vol.target[len(container_outdir)+1:])
if vol.type in ("File", "Directory"):
if not vol.resolved.startswith("_:"):
mounts.append(u"%s:%s" % (
docker_windows_path_adjust(vol.resolved),
docker_windows_path_adjust(vol.target)))
elif vol.type == "WritableFile":
if self.inplace_update:
mounts.append(u"%s:%s" % (
docker_windows_path_adjust(vol.resolved),
docker_windows_path_adjust(vol.target)))
else:
if host_outdir_tgt:
shutil.copy(vol.resolved, host_outdir_tgt)
ensure_writable(host_outdir_tgt)
else:
raise WorkflowException(
"Unable to compute host_outdir_tgt for "
"WriteableFile.")
elif vol.type == "WritableDirectory":
if vol.resolved.startswith("_:"):
if host_outdir_tgt:
os.makedirs(host_outdir_tgt, 0o0755)
else:
raise WorkflowException(
"Unable to compute host_outdir_tgt for "
"WritableDirectory.")
else:
if self.inplace_update:
mounts.append(u"%s:%s" % (
docker_windows_path_adjust(vol.resolved),
docker_windows_path_adjust(vol.target)))
else:
if host_outdir_tgt:
shutil.copytree(vol.resolved, host_outdir_tgt)
ensure_writable(host_outdir_tgt)
else:
raise WorkflowException(
"Unable to compute host_outdir_tgt for "
"WritableDirectory.")
elif vol.type == "CreateFile":
if secret_store:
contents = secret_store.retrieve(vol.resolved)
else:
contents = vol.resolved
if host_outdir_tgt:
with open(host_outdir_tgt, "wb") as f:
f.write(contents.encode("utf-8"))
else:
fd, createtmp = tempfile.mkstemp(dir=self.tmpdir)
with os.fdopen(fd, "wb") as f:
f.write(contents.encode("utf-8"))
mounts.append(u"%s:%s" % (
docker_windows_path_adjust(createtmp),
docker_windows_path_adjust(vol.target)))
return mounts
def executor(self, tool, job_order, **kwargs):
final_output = []
final_status = []
def output_callback(out, status):
final_status.append(status)
final_output.append(out)
if "basedir" not in kwargs:
raise WorkflowException("Must provide 'basedir' in kwargs")
output_dirs = set()
if kwargs.get("outdir"):
finaloutdir = os.path.abspath(kwargs.get("outdir"))
else:
finaloutdir = None
if kwargs.get("tmp_outdir_prefix"):
kwargs["outdir"] = tempfile.mkdtemp(
prefix=kwargs["tmp_outdir_prefix"]
)
else:
kwargs["outdir"] = tempfile.mkdtemp()
output_dirs.add(kwargs["outdir"])
kwargs["mutation_manager"] = MutationManager()
jobReqs = None
if "cwl:requirements" in job_order:
jobReqs = job_order["cwl:requirements"]
elif ("cwl:defaults" in tool.metadata and
"cwl:requirements" in tool.metadata["cwl:defaults"]):
jobReqs = tool.metadata["cwl:defaults"]["cwl:requirements"]
if jobReqs:
for req in jobReqs:
tool.requirements.append(req)
if kwargs.get("default_container"):
tool.requirements.insert(0, {
"class": "DockerRequirement",
"dockerPull": kwargs["default_container"]
})
jobs = tool.job(job_order, output_callback, **kwargs)
try:
for runnable in jobs:
if runnable:
builder = kwargs.get("builder", None)
if builder is not None:
runnable.builder = builder
if runnable.outdir:
output_dirs.add(runnable.outdir)
runnable.run(**kwargs)
else:
time.sleep(1)
except WorkflowException as e:
raise e
except Exception as e:
log.error('Workflow error')
raise WorkflowException(unicode(e))
self.wait()
log.info('All processes have joined')
if final_output and final_output[0] and finaloutdir:
final_output[0] = relocateOutputs(
final_output[0], finaloutdir,
output_dirs, kwargs.get("move_outputs"),
kwargs["make_fs_access"](""))
if kwargs.get("rm_tmpdir"):
cleanIntermediate(output_dirs)
if final_output and final_status:
return (final_output[0], final_status[0])
else:
return (None, "permanentFail")
def make_workflow_exception(msg):
name = shortname(port["id"])
return WorkflowException(
f"Error collecting output for parameter '{name}':\n{msg}"
)
def arv_docker_get_image(api_client, dockerRequirement, pull_image,
project_uuid, force_pull, tmp_outdir_prefix,
match_local_docker):
"""Check if a Docker image is available in Keep, if not, upload it using arv-keepdocker."""
if "http://arvados.org/cwl#dockerCollectionPDH" in dockerRequirement:
return dockerRequirement["http://arvados.org/cwl#dockerCollectionPDH"]
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement = copy.deepcopy(dockerRequirement)
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
if hasattr(dockerRequirement, 'lc'):
dockerRequirement.lc.data[
"dockerImageId"] = dockerRequirement.lc.data["dockerPull"]
global cached_lookups
global cached_lookups_lock
with cached_lookups_lock:
if dockerRequirement["dockerImageId"] in cached_lookups:
return cached_lookups[dockerRequirement["dockerImageId"]]
with SourceLine(dockerRequirement, "dockerImageId", WorkflowException,
logger.isEnabledFor(logging.DEBUG)):
sp = dockerRequirement["dockerImageId"].split(":")
image_name = sp[0]
image_tag = sp[1] if len(sp) > 1 else "latest"
images = arvados.commands.keepdocker.list_images_in_arv(
api_client, 3, image_name=image_name, image_tag=image_tag)
if images and match_local_docker:
local_image_id = determine_image_id(
dockerRequirement["dockerImageId"])
if local_image_id:
# find it in the list
found = False
for i in images:
if i[1]["dockerhash"] == local_image_id:
found = True
images = [i]
break
if not found:
# force re-upload.
images = []
if not images:
# Fetch Docker image if necessary.
try:
result = cwltool.docker.DockerCommandLineJob.get_image(
dockerRequirement, pull_image, force_pull,
tmp_outdir_prefix)
if not result:
raise WorkflowException("Docker image '%s' not available" %
dockerRequirement["dockerImageId"])
except OSError as e:
raise WorkflowException(
"While trying to get Docker image '%s', failed to execute 'docker': %s"
% (dockerRequirement["dockerImageId"], e))
# Upload image to Arvados
args = []
if project_uuid:
args.append("--project-uuid=" + project_uuid)
args.append(image_name)
args.append(image_tag)
logger.info("Uploading Docker image %s:%s", image_name, image_tag)
try:
arvados.commands.put.api_client = api_client
arvados.commands.keepdocker.main(args,
stdout=sys.stderr,
install_sig_handlers=False,
api=api_client)
except SystemExit as e:
# If e.code is None or zero, then keepdocker exited normally and we can continue
if e.code:
raise WorkflowException("keepdocker exited with code %s" %
e.code)
images = arvados.commands.keepdocker.list_images_in_arv(
api_client, 3, image_name=image_name, image_tag=image_tag)
if not images:
raise WorkflowException("Could not find Docker image %s:%s" %
(image_name, image_tag))
pdh = api_client.collections().get(
uuid=images[0][0]).execute()["portable_data_hash"]
with cached_lookups_lock:
cached_lookups[dockerRequirement["dockerImageId"]] = pdh
return pdh
def setUp(self):
self.executor = ThreadPoolJobExecutor(1000, 2)
self.workflow_exception = WorkflowException('workflow exception')
self.logger = Mock()
def validate_cluster_target(arvrunner, runtimeContext):
if (runtimeContext.submit_runner_cluster and
runtimeContext.submit_runner_cluster not in arvrunner.api._rootDesc["remoteHosts"] and
runtimeContext.submit_runner_cluster != arvrunner.api._rootDesc["uuidPrefix"]):
raise WorkflowException("Unknown or invalid cluster id '%s' known remote clusters are %s" % (runtimeContext.submit_runner_cluster,
", ".join(list(arvrunner.api._rootDesc["remoteHosts"].keys()))))
def _parsl_execute(
self,
runtime, # type: List[Text]
env, # type: MutableMapping[Text, Text]
runtimeContext # type: RuntimeContext
): # type: (...) -> None
scr, _ = self.get_requirement("ShellCommandRequirement")
shouldquote = needs_shell_quoting_re.search # type: Callable[[Any], Any]
if scr:
shouldquote = lambda x: False
_logger.info(
u"[job %s] %s$ %s%s%s%s", self.name, self.outdir, " \\\n ".join([
shellescape.quote(Text(arg))
if shouldquote(Text(arg)) else Text(arg)
for arg in (runtime + self.command_line)
]), u' < %s' % self.stdin if self.stdin else '', u' > %s' %
os.path.join(self.outdir, self.stdout) if self.stdout else '',
u' 2> %s' %
os.path.join(self.outdir, self.stderr) if self.stderr else '')
if self.joborder and runtimeContext.research_obj:
job_order = self.joborder
assert runtimeContext.prov_obj
runtimeContext.prov_obj.used_artefacts(
job_order, runtimeContext.process_run_id,
runtimeContext.reference_locations, str(self.name))
outputs = {} # type: Dict[Text,Text]
try:
stdin_path = None
if self.stdin:
rmap = self.pathmapper.reversemap(self.stdin)
if not rmap:
raise WorkflowException("{} missing from pathmapper".format(
self.stdin))
else:
stdin_path = rmap[1]
stderr_path = None
if self.stderr:
abserr = os.path.join(self.outdir, self.stderr)
dnerr = os.path.dirname(abserr)
if dnerr and not os.path.exists(dnerr):
os.makedirs(dnerr)
stderr_path = abserr
stdout_path = None
if self.stdout:
absout = os.path.join(self.outdir, self.stdout)
dn = os.path.dirname(absout)
if dn and not os.path.exists(dn):
os.makedirs(dn)
stdout_path = absout
commands = [Text(x) for x in (runtime + self.command_line)]
if runtimeContext.secret_store:
commands = runtimeContext.secret_store.retrieve(commands)
env = runtimeContext.secret_store.retrieve(env)
job_script_contents = None # type: Optional[Text]
builder = getattr(self, "builder", None) # type: Builder
if builder is not None:
job_script_contents = builder.build_job_script(commands)
print("Running my own execution layer")
rcode = _job_popen(
commands,
stdin_path=stdin_path,
stdout_path=stdout_path,
stderr_path=stderr_path,
env=env,
cwd=self.outdir,
job_dir=tempfile.mkdtemp(prefix=getdefault(
runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)),
job_script_contents=job_script_contents,
timelimit=self.timelimit,
name=self.name)
if self.successCodes and rcode in self.successCodes:
processStatus = "success"
elif self.temporaryFailCodes and rcode in self.temporaryFailCodes:
processStatus = "temporaryFail"
elif self.permanentFailCodes and rcode in self.permanentFailCodes:
processStatus = "permanentFail"
elif rcode == 0:
processStatus = "success"
else:
processStatus = "permanentFail"
if self.generatefiles["listing"]:
assert self.generatemapper is not None
relink_initialworkdir(self.generatemapper,
self.outdir,
self.builder.outdir,
inplace_update=self.inplace_update)
outputs = self.collect_outputs(self.outdir)
outputs = bytes2str_in_dicts(outputs) # type: ignore
except OSError as e:
if e.errno == 2:
if runtime:
_logger.error(u"'%s' not found", runtime[0])
else:
_logger.error(u"'%s' not found", self.command_line[0])
else:
_logger.exception("Exception while running job")
processStatus = "permanentFail"
except WorkflowException as e:
_logger.error(u"[job %s] Job error:\n%s" % (self.name, e))
processStatus = "permanentFail"
except Exception as e:
_logger.exception("Exception while running job")
processStatus = "permanentFail"
if runtimeContext.research_obj and self.prov_obj and \
runtimeContext.process_run_id:
#creating entities for the outputs produced by each step (in the provenance document)
self.prov_obj.generate_output_prov(outputs,
runtimeContext.process_run_id,
str(self.name))
self.prov_obj.document.wasEndedBy(runtimeContext.process_run_id, None,
self.prov_obj.workflow_run_uri,
datetime.datetime.now())
if processStatus != "success":
_logger.warning(u"[job %s] completed %s", self.name, processStatus)
else:
_logger.info(u"[job %s] completed %s", self.name, processStatus)
if _logger.isEnabledFor(logging.DEBUG):
_logger.debug(u"[job %s] %s", self.name, json_dumps(outputs, indent=4))
if self.generatemapper and runtimeContext.secret_store:
# Delete any runtime-generated files containing secrets.
for f, p in self.generatemapper.items():
if p.type == "CreateFile":
if runtimeContext.secret_store.has_secret(p.resolved):
host_outdir = self.outdir
container_outdir = self.builder.outdir
host_outdir_tgt = p.target
if p.target.startswith(container_outdir + "/"):
host_outdir_tgt = os.path.join(
host_outdir, p.target[len(container_outdir) + 1:])
os.remove(host_outdir_tgt)
if runtimeContext.workflow_eval_lock is None:
raise WorkflowException(
"runtimeContext.workflow_eval_lock must not be None")
with runtimeContext.workflow_eval_lock:
self.output_callback(outputs, processStatus)
if self.stagedir and os.path.exists(self.stagedir):
_logger.debug(u"[job %s] Removing input staging directory %s",
self.name, self.stagedir)
shutil.rmtree(self.stagedir, True)
if runtimeContext.rm_tmpdir:
_logger.debug(u"[job %s] Removing temporary directory %s", self.name,
self.tmpdir)
shutil.rmtree(self.tmpdir, True)
def collect_output_ports(
self,
ports, # type: Set[Dict[Text, Any]]
builder, # type: Builder
outdir, # type: Text
compute_checksum=True, # type: bool
jobname="", # type: Text
readers=None # type: Dict[Text, Any]
): # type: (...) -> OutputPorts
ret = {} # type: OutputPorts
debug = LOGGER.isEnabledFor(logging.DEBUG)
try:
fs_access = builder.make_fs_access(outdir)
custom_output = fs_access.join(outdir, "cwl.output.json")
if fs_access.exists(custom_output):
with fs_access.open(custom_output, "r") as f:
ret = json.load(f)
if debug:
LOGGER.debug(u"Raw output from %s: %s", custom_output,
json.dumps(ret, indent=4))
else:
for i, port in enumerate(ports):
def make_workflow_exception(msg):
return WorkflowException(
u"Error collecting output for parameter '%s':\n%s"
% (shortname(port["id"]), msg))
with SourceLine(ports, i, make_workflow_exception, debug):
fragment = shortname(port["id"])
ret[fragment] = self.collect_output(
port,
builder,
outdir,
fs_access,
compute_checksum=compute_checksum)
if ret:
# revmap = partial(command_line_tool.revmap_file, builder, outdir)
adjustDirObjs(ret, trim_listing)
# TODO: Attempt to avoid a crash because the revmap fct is not functional
# (intend for a docker usage only?)
# visit_class(ret, ("File", "Directory"), cast(Callable[[Any], Any], revmap))
visit_class(ret, ("File", "Directory"),
command_line_tool.remove_path)
normalizeFilesDirs(ret)
visit_class(
ret, ("File", "Directory"),
partial(command_line_tool.check_valid_locations,
fs_access))
if compute_checksum:
adjustFileObjs(ret, partial(compute_checksums, fs_access))
validate.validate_ex(self.names.get_name("outputs_record_schema",
""),
ret,
strict=False,
logger=LOGGER)
if ret is not None and builder.mutation_manager is not None:
adjustFileObjs(ret, builder.mutation_manager.set_generation)
return ret if ret is not None else {}
except validate.ValidationException as exc:
raise WorkflowException(
"Error validating output record: {!s}\nIn:\n{}".format(
exc, json.dumps(ret, indent=4)))
finally:
if builder.mutation_manager and readers:
for reader in readers.values():
builder.mutation_manager.release_reader(jobname, reader)
def done(self, record):
try:
self.update_pipeline_component(record)
except:
pass
try:
if record["state"] == "Complete":
processStatus = "success"
else:
processStatus = "permanentFail"
try:
outputs = {}
if record["output"]:
logc = arvados.collection.Collection(record["log"])
log = logc.open(logc.keys()[0])
tmpdir = None
outdir = None
keepdir = None
for l in log:
# Determine the tmpdir, outdir and keepdir paths from
# the job run. Unfortunately, we can't take the first
# values we find (which are expected to be near the
# top) and stop scanning because if the node fails and
# the job restarts on a different node these values
# will different runs, and we need to know about the
# final run that actually produced output.
g = tmpdirre.match(l)
if g:
tmpdir = g.group(1)
g = outdirre.match(l)
if g:
outdir = g.group(1)
g = keepre.match(l)
if g:
keepdir = g.group(1)
colname = "Output %s of %s" % (record["output"][0:7],
self.name)
# check if collection already exists with same owner, name and content
collection_exists = self.arvrunner.api.collections().list(
filters=[[
"owner_uuid", "=", self.arvrunner.project_uuid
], ['portable_data_hash', '=', record["output"]],
["name", "=", colname]]).execute(
num_retries=self.arvrunner.num_retries)
if not collection_exists["items"]:
# Create a collection located in the same project as the
# pipeline with the contents of the output.
# First, get output record.
collections = self.arvrunner.api.collections().list(
limit=1,
filters=[[
'portable_data_hash', '=', record["output"]
]],
select=[
"manifest_text"
]).execute(num_retries=self.arvrunner.num_retries)
if not collections["items"]:
raise WorkflowException(
"Job output '%s' cannot be found on API server"
% (record["output"]))
# Create new collection in the parent project
# with the output contents.
self.arvrunner.api.collections().create(
body={
"owner_uuid":
self.arvrunner.project_uuid,
"name":
colname,
"portable_data_hash":
record["output"],
"manifest_text":
collections["items"][0]["manifest_text"]
},
ensure_unique_name=True).execute(
num_retries=self.arvrunner.num_retries)
self.builder.outdir = outdir
self.builder.pathmapper.keepdir = keepdir
outputs = self.collect_outputs("keep:" + record["output"])
except WorkflowException as e:
logger.error("Error while collecting job outputs:\n%s",
e,
exc_info=(e if self.arvrunner.debug else False))
processStatus = "permanentFail"
except Exception as e:
logger.exception(
"Got unknown exception while collecting job outputs:")
processStatus = "permanentFail"
self.output_callback(outputs, processStatus)
finally:
del self.arvrunner.jobs[record["uuid"]]
def make_workflow_exception(msg):
return WorkflowException(
u"Error collecting output for parameter '%s':\n%s"
% (shortname(port["id"]), msg))
def run(self, runtimeContext):
# type: (RuntimeContext) -> None
(docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
self.prov_obj = runtimeContext.prov_obj
img_id = None
env = cast(MutableMapping[Text, Text], os.environ)
user_space_docker_cmd = runtimeContext.user_space_docker_cmd
if docker_req and user_space_docker_cmd:
# For user-space docker implementations, a local image name or ID
# takes precedence over a network pull
if 'dockerImageId' in docker_req:
img_id = str(docker_req["dockerImageId"])
elif 'dockerPull' in docker_req:
img_id = str(docker_req["dockerPull"])
# else:
# raise WorkflowException(SourceLine(docker_req).makeError(
# "Docker image must be specified as 'dockerImageId' or "
# "'dockerPull' when using user space implementations of "
# "Docker"))
else:
try:
if docker_req and runtimeContext.use_container:
img_id = str(
self.get_from_requirements(
docker_req, True, runtimeContext.pull_image,
getdefault(runtimeContext.force_docker_pull, False),
getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)))
if img_id is None:
if self.builder.find_default_container:
default_container = self.builder.find_default_container()
if default_container:
img_id = str(default_container)
if docker_req and img_id is None and runtimeContext.use_container:
raise Exception("Docker image not available")
if self.prov_obj and img_id and runtimeContext.process_run_id:
# TODO: Integrate with record_container_id
container_agent = self.prov_obj.document.agent(
uuid.uuid4().urn,
{"prov:type": PROV["SoftwareAgent"],
"cwlprov:image": img_id,
"prov:label": "Container execution of image %s" % img_id})
# FIXME: img_id is not a sha256 id, it might just be "debian:8"
#img_entity = document.entity("nih:sha-256;%s" % img_id,
# {"prov:label": "Container image %s" % img_id} )
# The image is the plan for this activity-agent association
#document.wasAssociatedWith(process_run_ID, container_agent, img_entity)
self.prov_obj.document.wasAssociatedWith(
runtimeContext.process_run_id, container_agent)
except Exception as err:
container = "Shifter"
_logger.debug("%s error", container, exc_info=True)
if docker_is_req:
raise UnsupportedRequirement(
"%s is required to run this tool: %s" % (container, err))
else:
raise WorkflowException(
"{0} is not available for this tool, try "
"--no-container to disable {0}, or install "
"a user space Docker replacement like uDocker with "
"--user-space-docker-cmd.: {1}".format(container, err))
self._setup(runtimeContext)
stageFiles(self.pathmapper, ignoreWritable=True, symLink=True,
secret_store=runtimeContext.secret_store)
runtime = self.create_runtime(env, runtimeContext, img_id)
self._execute(runtime, env, runtimeContext)
def collect_output(
self,
schema, # type: Dict[Text, Any]
builder, # type: Builder
outdir, # type: Text
fs_access, # type: StdFsAccess
compute_checksum=True # type: bool
):
# type: (...) -> Optional[Union[Dict[Text, Any], List[Union[Dict[Text, Any], Text]]]]
result = [] # type: List[Any]
empty_and_optional = False
debug = LOGGER.isEnabledFor(logging.DEBUG)
if "outputBinding" in schema:
binding = schema["outputBinding"]
globpatterns = [] # type: List[Text]
revmap = partial(command_line_tool.revmap_file, builder, outdir)
if "glob" in binding:
with SourceLine(binding, "glob", WorkflowException, debug):
for glob in aslist(binding["glob"]):
glob = builder.do_eval(glob)
if glob:
globpatterns.extend(aslist(glob))
for glob in globpatterns:
if glob.startswith(outdir):
glob = glob[len(outdir) + 1:]
elif glob == ".":
glob = outdir
elif glob.startswith("/"):
raise WorkflowException(
"glob patterns must not start with '/'")
try:
prefix = fs_access.glob(outdir)
key = cmp_to_key(
cast(Callable[[Text, Text], int],
locale.strcoll))
# In case of stdout.log or stderr.log file not created
if "stdout" in self.tool and "stderr" in self.tool \
and glob in (self.tool["stdout"], self.tool["stderr"]):
filepath = Path(fs_access.join(outdir, glob))
if not filepath.is_file():
Path(filepath).touch()
result.extend([{
"location":
g,
"path":
fs_access.join(builder.outdir,
g[len(prefix[0]) + 1:]),
"basename":
os.path.basename(g),
"nameroot":
os.path.splitext(os.path.basename(g))[0],
"nameext":
os.path.splitext(os.path.basename(g))[1],
"class":
"File" if fs_access.isfile(g) else "Directory"
} for g in sorted(fs_access.glob(
fs_access.join(outdir, glob)),
key=key)])
except (OSError, IOError) as exc:
LOGGER.warning(Text(exc))
except Exception:
LOGGER.exception("Unexpected error from fs_access")
raise
for files in result:
rfile = files.copy()
# TODO This function raise an exception and seems to be related to docker (which is not used here)
# revmap(rfile)
if files["class"] == "Directory":
load_listing = builder.loadListing or (
binding and binding.get("loadListing"))
if load_listing and load_listing != "no_listing":
get_listing(fs_access, files,
(load_listing == "deep_listing"))
else:
with fs_access.open(rfile["location"], "rb") as f:
contents = b""
if binding.get("loadContents") or compute_checksum:
contents = f.read(CONTENT_LIMIT)
if binding.get("loadContents"):
files["contents"] = contents.decode("utf-8")
if compute_checksum:
checksum = hashlib.sha1() # nosec: B303
while contents != b"":
checksum.update(contents)
contents = f.read(1024 * 1024)
files[
"checksum"] = "sha1$%s" % checksum.hexdigest(
)
f.seek(0, 2)
file_size = f.tell()
files["size"] = file_size
optional = False
single = False
if isinstance(schema["type"], list):
if "null" in schema["type"]:
optional = True
if "File" in schema["type"] or "Directory" in schema["type"]:
single = True
elif schema["type"] == "File" or schema["type"] == "Directory":
single = True
if "outputEval" in binding:
with SourceLine(binding, "outputEval", WorkflowException,
debug):
result = builder.do_eval(binding["outputEval"],
context=result)
if single:
if not result and not optional:
with SourceLine(binding, "glob", WorkflowException, debug):
raise WorkflowException(
"Did not find output file with glob pattern: '{}'".
format(globpatterns))
elif not result and optional:
pass
elif isinstance(result, list):
if len(result) > 1:
raise WorkflowException(
"Multiple matches for output item that is a single file."
)
result = result[0]
if "secondaryFiles" in schema:
with SourceLine(schema, "secondaryFiles", WorkflowException,
debug):
for primary in aslist(result):
if isinstance(primary, dict):
primary.setdefault("secondaryFiles", [])
pathprefix = primary["path"][0:primary["path"].
rindex("/") + 1]
for file in aslist(schema["secondaryFiles"]):
if isinstance(
file,
dict) or "$(" in file or "${" in file:
sfpath = builder.do_eval(file,
context=primary)
subst = False
else:
sfpath = file
subst = True
for sfitem in aslist(sfpath):
if isinstance(sfitem, str):
if subst:
sfitem = {
"path":
substitute(
primary["path"], sfitem)
}
else:
sfitem = {
"path": pathprefix + sfitem
}
if "path" in sfitem and "location" not in sfitem:
revmap(sfitem)
if fs_access.isfile(sfitem["location"]):
sfitem["class"] = "File"
primary["secondaryFiles"].append(
sfitem)
elif fs_access.isdir(sfitem["location"]):
sfitem["class"] = "Directory"
primary["secondaryFiles"].append(
sfitem)
if "format" in schema:
for primary in aslist(result):
primary["format"] = builder.do_eval(schema["format"],
context=primary)
# Ensure files point to local references outside of the run environment
# TODO: Again removing revmap....
# adjustFileObjs(result, revmap)
if not result and optional:
return None
if not empty_and_optional and isinstance(
schema["type"], dict) and schema["type"]["type"] == "record":
out = {}
for f in schema["type"]["fields"]:
out[shortname(
f["name"])] = self.collect_output( # type: ignore
f,
builder,
outdir,
fs_access,
compute_checksum=compute_checksum)
return out
return result
def executor(self, tool, job_order, runtimeContext, **kwargs):
"""Executor method."""
final_output = []
final_status = []
def output_callback(out, processStatus):
final_status.append(processStatus)
final_output.append(out)
if not runtimeContext.basedir:
raise WorkflowException('`runtimeContext` should contain a '
'`basedir`')
output_dirs = set()
if runtimeContext.outdir:
finaloutdir = os.path.abspath(runtimeContext.outdir)
else:
finaloutdir = None
if runtimeContext.tmp_outdir_prefix:
runtimeContext.outdir = tempfile.mkdtemp(
prefix=runtimeContext.tmp_outdir_prefix)
else:
runtimeContext.outdir = tempfile.mkdtemp()
output_dirs.add(runtimeContext.outdir)
runtimeContext.mutation_manager = MutationManager()
jobReqs = None
if "cwl:requirements" in job_order:
jobReqs = job_order["cwl:requirements"]
elif ("cwl:defaults" in tool.metadata
and "cwl:requirements" in tool.metadata["cwl:defaults"]):
jobReqs = tool.metadata["cwl:defaults"]["cwl:requirements"]
if jobReqs:
for req in jobReqs:
tool.requirements.append(req)
if not runtimeContext.default_container:
runtimeContext.default_container = 'frolvlad/alpine-bash'
runtimeContext.docker_outdir = os.path.join(runtimeContext.working_dir,
"cwl/docker_outdir")
runtimeContext.docker_tmpdir = os.path.join(runtimeContext.working_dir,
"cwl/docker_tmpdir")
runtimeContext.docker_stagedir = os.path.join(
runtimeContext.working_dir, "cwl/docker_stagedir")
jobs = tool.job(job_order, output_callback, runtimeContext)
try:
for runnable in jobs:
if runnable:
if runtimeContext.builder:
runnable.builder = runtimeContext.builder
if runnable.outdir:
output_dirs.add(runnable.outdir)
runnable.run(runtimeContext)
else:
# log.error(
# "Workflow cannot make any more progress"
# )
# break
time.sleep(1)
except WorkflowException as e:
traceback.print_exc()
raise e
except Exception as e:
traceback.print_exc()
raise WorkflowException(str(e))
# wait for all processes to finish
self.wait()
if final_output and final_output[0] and finaloutdir:
final_output[0] = relocateOutputs(
final_output[0], finaloutdir, output_dirs,
runtimeContext.move_outputs, runtimeContext.make_fs_access(""))
if runtimeContext.rm_tmpdir:
cleanIntermediate(output_dirs)
if final_output and final_status:
return str(final_output[0]), str(final_status[0])
else:
return None, "permanentFail"
def execute(self, runtime, env, runtime_context): # noqa: E811
# type: (List[Text], MutableMapping[Text, Text], RuntimeContext) -> None
self.results = self.wps_process.execute(self.builder.job, self.outdir,
self.expected_outputs)
if self.joborder and runtime_context.research_obj:
job_order = self.joborder
assert runtime_context.prov_obj
assert runtime_context.process_run_id
runtime_context.prov_obj.used_artefacts(
job_order, runtime_context.process_run_id, str(self.name))
outputs = {} # type: Dict[Text, Text]
try:
rcode = 0
if self.successCodes:
process_status = "success"
elif self.temporaryFailCodes:
process_status = "temporaryFail"
elif self.permanentFailCodes:
process_status = "permanentFail"
elif rcode == 0:
process_status = "success"
else:
process_status = "permanentFail"
if self.generatefiles["listing"]:
assert self.generatemapper is not None
relink_initialworkdir(self.generatemapper,
self.outdir,
self.builder.outdir,
inplace_update=self.inplace_update)
outputs = self.collect_outputs(self.outdir)
outputs = bytes2str_in_dicts(outputs) # type: ignore
except OSError as exc:
if exc.errno == 2:
if runtime:
LOGGER.exception(u"'%s' not found", runtime[0])
else:
LOGGER.exception(u"'%s' not found", self.command_line[0])
else:
LOGGER.exception("Exception while running job")
process_status = "permanentFail"
except WorkflowException as err:
LOGGER.exception(u"[job %s] Job error:\n%s", self.name, err)
process_status = "permanentFail"
except Exception: # noqa: W0703 # nosec: B110
LOGGER.exception("Exception while running job")
process_status = "permanentFail"
if runtime_context.research_obj and self.prov_obj and \
runtime_context.process_run_id:
# creating entities for the outputs produced by each step (in the provenance document)
self.prov_obj.generate_output_prov(outputs,
runtime_context.process_run_id,
str(self.name))
self.prov_obj.document.wasEndedBy(runtime_context.process_run_id,
None,
self.prov_obj.workflow_run_uri,
now())
if process_status != "success":
LOGGER.warning(u"[job %s] completed %s", self.name, process_status)
else:
LOGGER.info(u"[job %s] completed %s", self.name, process_status)
if LOGGER.isEnabledFor(logging.DEBUG):
LOGGER.debug(u"[job %s] %s", self.name,
json.dumps(outputs, indent=4))
if self.generatemapper and runtime_context.secret_store:
# Delete any runtime-generated files containing secrets.
for _, path_item in self.generatemapper.items():
if path_item.type == "CreateFile":
if runtime_context.secret_store.has_secret(
path_item.resolved):
host_outdir = self.outdir
container_outdir = self.builder.outdir
host_outdir_tgt = path_item.target
if path_item.target.startswith(container_outdir + "/"):
host_outdir_tgt = os.path.join(
host_outdir,
path_item.target[len(container_outdir) + 1:])
os.remove(host_outdir_tgt)
if runtime_context.workflow_eval_lock is None:
raise WorkflowException(
"runtime_context.workflow_eval_lock must not be None")
with runtime_context.workflow_eval_lock:
self.output_callback(outputs, process_status)
if self.stagedir and os.path.exists(self.stagedir):
LOGGER.debug(u"[job %s] Removing input staging directory %s",
self.name, self.stagedir)
shutil.rmtree(self.stagedir, True)
if runtime_context.rm_tmpdir:
LOGGER.debug(u"[job %s] Removing temporary directory %s",
self.name, self.tmpdir)
shutil.rmtree(self.tmpdir, True)
def arv_executor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
tool.visit(self.check_features)
self.project_uuid = kwargs.get("project_uuid")
self.pipeline = None
make_fs_access = kwargs.get("make_fs_access") or partial(
CollectionFsAccess, collection_cache=self.collection_cache)
self.fs_access = make_fs_access(kwargs["basedir"])
self.trash_intermediate = kwargs["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 = kwargs["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 not kwargs.get("name"):
kwargs["name"] = self.name = tool.tool.get(
"label") or tool.metadata.get("label") or os.path.basename(
tool.tool["id"])
# Upload direct dependencies of workflow steps, get back mapping of files to keep references.
# Also uploads docker images.
override_tools = {}
upload_workflow_deps(self, tool, override_tools)
# Reload tool object which may have been updated by
# upload_workflow_deps
tool = self.arv_make_tool(tool.doc_loader.idx[tool.tool["id"]],
makeTool=self.arv_make_tool,
loader=tool.doc_loader,
avsc_names=tool.doc_schema,
metadata=tool.metadata,
override_tools=override_tools)
# Upload local file references in the job order.
job_order = upload_job_order(self, "%s input" % kwargs["name"], tool,
job_order)
existing_uuid = kwargs.get("update_workflow")
if existing_uuid or kwargs.get("create_workflow"):
# Create a pipeline template or workflow record and exit.
if self.work_api == "jobs":
tmpl = RunnerTemplate(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
uuid=existing_uuid,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs["name"])
tmpl.save()
# cwltool.main will write our return value to stdout.
return (tmpl.uuid, "success")
elif self.work_api == "containers":
return (upload_workflow(
self,
tool,
job_order,
self.project_uuid,
uuid=existing_uuid,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs["name"]), "success")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
kwargs["compute_checksum"] = kwargs.get("compute_checksum")
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
kwargs["docker_outdir"] = "/var/spool/cwl"
kwargs["tmpdir"] = "/tmp"
kwargs["docker_tmpdir"] = "/tmp"
elif self.work_api == "jobs":
kwargs["outdir"] = "$(task.outdir)"
kwargs["docker_outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
runnerjob = None
if kwargs.get("submit"):
# Submit a runner job to run the workflow for us.
if self.work_api == "containers":
if tool.tool["class"] == "CommandLineTool" and kwargs.get(
"wait"):
kwargs["runnerjob"] = tool.tool["id"]
runnerjob = tool.job(job_order, self.output_callback,
**kwargs).next()
else:
runnerjob = RunnerContainer(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
self.output_name,
self.output_tags,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"),
on_error=kwargs.get("on_error"),
submit_runner_image=kwargs.get("submit_runner_image"),
intermediate_output_ttl=kwargs.get(
"intermediate_output_ttl"))
elif self.work_api == "jobs":
runnerjob = RunnerJob(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
self.output_name,
self.output_tags,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"),
on_error=kwargs.get("on_error"),
submit_runner_image=kwargs.get("submit_runner_image"))
elif "cwl_runner_job" not in kwargs and self.work_api == "jobs":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid":
self.project_uuid,
"name":
kwargs["name"] if kwargs.
get("name") else shortname(tool.tool["id"]),
"components": {},
"state":
"RunningOnClient"
}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
if runnerjob and not kwargs.get("wait"):
runnerjob.run(wait=kwargs.get("wait"))
return (runnerjob.uuid, "success")
self.poll_api = arvados.api('v1')
self.polling_thread = threading.Thread(target=self.poll_states)
self.polling_thread.start()
if runnerjob:
jobiter = iter((runnerjob, ))
else:
if "cwl_runner_job" in kwargs:
self.uuid = kwargs.get("cwl_runner_job").get('uuid')
jobiter = tool.job(job_order, self.output_callback, **kwargs)
try:
self.cond.acquire()
# Will continue to hold the lock for the duration of this code
# except when in cond.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 runnable:
with Perf(metrics, "run"):
runnable.run(**kwargs)
else:
if self.processes:
self.cond.wait(1)
else:
logger.error(
"Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs."
)
break
loopperf.__enter__()
loopperf.__exit__()
while self.processes:
self.cond.wait(1)
except UnsupportedRequirement:
raise
except:
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
logger.error(
"Execution failed: %s",
sys.exc_info()[1],
exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
self.api.pipeline_instances().update(
uuid=self.pipeline["uuid"], body={
"state": "Failed"
}).execute(num_retries=self.num_retries)
if runnerjob and runnerjob.uuid and self.work_api == "containers":
self.api.container_requests().update(
uuid=runnerjob.uuid, body={
"priority": "0"
}).execute(num_retries=self.num_retries)
finally:
self.cond.release()
self.stop_polling.set()
self.polling_thread.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 kwargs.get("submit") and isinstance(runnerjob, Runner):
logger.info("Final output collection %s", runnerjob.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 = ""
self.final_output, self.final_output_collection = self.make_output_collection(
self.output_name, self.output_tags, self.final_output)
self.set_crunch_output()
if kwargs.get("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 arv_executor(self, tool, job_order, **kwargs):
self.debug = kwargs.get("debug")
tool.visit(self.check_writable)
self.project_uuid = kwargs.get("project_uuid")
self.pipeline = None
make_fs_access = kwargs.get("make_fs_access") or partial(
CollectionFsAccess,
api_client=self.api,
keep_client=self.keep_client)
self.fs_access = make_fs_access(kwargs["basedir"])
existing_uuid = kwargs.get("update_workflow")
if existing_uuid or kwargs.get("create_workflow"):
if self.work_api == "jobs":
tmpl = RunnerTemplate(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
uuid=existing_uuid,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"))
tmpl.save()
# cwltool.main will write our return value to stdout.
return tmpl.uuid
else:
return upload_workflow(
self,
tool,
job_order,
self.project_uuid,
uuid=existing_uuid,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"))
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
kwargs["make_fs_access"] = make_fs_access
kwargs["enable_reuse"] = kwargs.get("enable_reuse")
kwargs["use_container"] = True
kwargs["tmpdir_prefix"] = "tmp"
kwargs["on_error"] = "continue"
kwargs["compute_checksum"] = kwargs.get("compute_checksum")
if not kwargs["name"]:
del kwargs["name"]
if self.work_api == "containers":
kwargs["outdir"] = "/var/spool/cwl"
kwargs["docker_outdir"] = "/var/spool/cwl"
kwargs["tmpdir"] = "/tmp"
kwargs["docker_tmpdir"] = "/tmp"
elif self.work_api == "jobs":
kwargs["outdir"] = "$(task.outdir)"
kwargs["docker_outdir"] = "$(task.outdir)"
kwargs["tmpdir"] = "$(task.tmpdir)"
upload_instance(self, shortname(tool.tool["id"]), tool, job_order)
runnerjob = None
if kwargs.get("submit"):
if self.work_api == "containers":
if tool.tool["class"] == "CommandLineTool":
kwargs["runnerjob"] = tool.tool["id"]
runnerjob = tool.job(job_order, self.output_callback,
**kwargs).next()
else:
runnerjob = RunnerContainer(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
self.output_name,
self.output_tags,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"))
else:
runnerjob = RunnerJob(
self,
tool,
job_order,
kwargs.get("enable_reuse"),
self.output_name,
self.output_tags,
submit_runner_ram=kwargs.get("submit_runner_ram"),
name=kwargs.get("name"))
if not kwargs.get(
"submit"
) and "cwl_runner_job" not in kwargs and not self.work_api == "containers":
# Create pipeline for local run
self.pipeline = self.api.pipeline_instances().create(
body={
"owner_uuid":
self.project_uuid,
"name":
kwargs["name"] if kwargs.
get("name") else shortname(tool.tool["id"]),
"components": {},
"state":
"RunningOnClient"
}).execute(num_retries=self.num_retries)
logger.info("Pipeline instance %s", self.pipeline["uuid"])
if runnerjob and not kwargs.get("wait"):
runnerjob.run(wait=kwargs.get("wait"))
return runnerjob.uuid
self.poll_api = arvados.api('v1')
self.polling_thread = threading.Thread(target=self.poll_states)
self.polling_thread.start()
if runnerjob:
jobiter = iter((runnerjob, ))
else:
if "cwl_runner_job" in kwargs:
self.uuid = kwargs.get("cwl_runner_job").get('uuid')
jobiter = tool.job(job_order, self.output_callback, **kwargs)
try:
self.cond.acquire()
# Will continue to hold the lock for the duration of this code
# except when in cond.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 runnable:
with Perf(metrics, "run"):
runnable.run(**kwargs)
else:
if self.processes:
self.cond.wait(1)
else:
logger.error(
"Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs."
)
break
loopperf.__enter__()
loopperf.__exit__()
while self.processes:
self.cond.wait(1)
except UnsupportedRequirement:
raise
except:
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
logger.error(
"Execution failed: %s",
sys.exc_info()[1],
exc_info=(sys.exc_info()[1] if self.debug else False))
if self.pipeline:
self.api.pipeline_instances().update(
uuid=self.pipeline["uuid"], body={
"state": "Failed"
}).execute(num_retries=self.num_retries)
if runnerjob and runnerjob.uuid and self.work_api == "containers":
self.api.container_requests().update(
uuid=runnerjob.uuid, body={
"priority": "0"
}).execute(num_retries=self.num_retries)
finally:
self.cond.release()
self.stop_polling.set()
self.polling_thread.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 kwargs.get("submit") and isinstance(runnerjob, Runner):
logger.info("Final output collection %s", runnerjob.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 = ""
self.final_output, self.final_output_collection = self.make_output_collection(
self.output_name, self.output_tags, self.final_output)
self.set_crunch_output()
if self.final_status != "success":
raise WorkflowException("Workflow failed.")
if kwargs.get("compute_checksum"):
adjustDirObjs(self.final_output, partial(getListing,
self.fs_access))
adjustFileObjs(self.final_output,
partial(compute_checksums, self.fs_access))
return self.final_output
