import arvados.events
import arvados.commands.keepdocker
import arvados.commands.run
+import arvados.collection
+import arvados.util
import cwltool.draft2tool
import cwltool.workflow
import cwltool.main
+from cwltool.process import shortname
+from cwltool.errors import WorkflowException
import threading
import cwltool.docker
import fnmatch
import logging
import re
import os
+import sys
from cwltool.process import get_feature
+from arvados.api import OrderedJsonModel
logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
-def arv_docker_get_image(api_client, dockerRequirement, pull_image):
+tmpdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.tmpdir\)=(.*)")
+outdirre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.outdir\)=(.*)")
+keepre = re.compile(r"^\S+ \S+ \d+ \d+ stderr \S+ \S+ crunchrunner: \$\(task\.keep\)=(.*)")
+
+
+def arv_docker_get_image(api_client, dockerRequirement, pull_image, project_uuid):
if "dockerImageId" not in dockerRequirement and "dockerPull" in dockerRequirement:
dockerRequirement["dockerImageId"] = dockerRequirement["dockerPull"]
if not images:
imageId = cwltool.docker.get_image(dockerRequirement, pull_image)
- args = [image_name]
+ args = ["--project-uuid="+project_uuid, image_name]
if image_tag:
args.append(image_tag)
+ logger.info("Uploading Docker image %s", ":".join(args[1:]))
arvados.commands.keepdocker.main(args)
return dockerRequirement["dockerImageId"]
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if docker_req and kwargs.get("use_container") is not False:
- runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image)
+ runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+ else:
+ runtime_constraints["docker_image"] = "arvados/jobs"
+
+ resources = self.builder.resources
+ if resources is not None:
+ runtime_constraints["min_cores_per_node"] = resources.get("cores", 1)
+ runtime_constraints["min_ram_mb_per_node"] = resources.get("ram")
+ runtime_constraints["min_scratch_mb_per_node"] = resources.get("tmpdirSize", 0) + resources.get("outdirSize", 0)
+
+ filters = [["repository", "=", "arvados"],
+ ["script", "=", "crunchrunner"],
+ ["script_version", "in git", "9e5b98e8f5f4727856b53447191f9c06e3da2ba6"]]
+ if not self.arvrunner.ignore_docker_for_reuse:
+ filters.append(["docker_image_locator", "in docker", runtime_constraints["docker_image"]])
try:
- response = self.arvrunner.api.jobs().create(body={
- "script": "crunchrunner",
- "repository": kwargs["repository"],
- "script_version": "master",
- "script_parameters": {"tasks": [script_parameters]},
- "runtime_constraints": runtime_constraints
- }, find_or_create=kwargs.get("enable_reuse", True)).execute()
+ response = self.arvrunner.api.jobs().create(
+ body={
+ "owner_uuid": self.arvrunner.project_uuid,
+ "script": "crunchrunner",
+ "repository": "arvados",
+ "script_version": "master",
+ "minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
+ "script_parameters": {"tasks": [script_parameters]},
+ "runtime_constraints": runtime_constraints
+ },
+ filters=filters,
+ find_or_create=kwargs.get("enable_reuse", True)
+ ).execute(num_retries=self.arvrunner.num_retries)
self.arvrunner.jobs[response["uuid"]] = self
- logger.info("Job %s is %s", response["uuid"], response["state"])
+ self.arvrunner.pipeline["components"][self.name] = {"job": response}
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
+ body={
+ "components": self.arvrunner.pipeline["components"]
+ }).execute(num_retries=self.arvrunner.num_retries)
+
+ logger.info("Job %s (%s) is %s", self.name, response["uuid"], response["state"])
if response["state"] in ("Complete", "Failed", "Cancelled"):
self.done(response)
logger.error("Got error %s" % str(e))
self.output_callback({}, "permanentFail")
+ def update_pipeline_component(self, record):
+ self.arvrunner.pipeline["components"][self.name] = {"job": record}
+ self.arvrunner.pipeline = self.arvrunner.api.pipeline_instances().update(uuid=self.arvrunner.pipeline["uuid"],
+ body={
+ "components": self.arvrunner.pipeline["components"]
+ }).execute(num_retries=self.arvrunner.num_retries)
def done(self, record):
+ try:
+ self.update_pipeline_component(record)
+ except:
+ pass
+
try:
if record["state"] == "Complete":
processStatus = "success"
try:
outputs = {}
- outputs = self.collect_outputs("keep:" + record["output"])
+ 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 exception while collecting job outputs:")
+ logger.exception("Got unknown exception while collecting job outputs:")
processStatus = "permanentFail"
self.output_callback(outputs, processStatus)
self._pathmap[src] = (src, "$(task.keep)/%s" % src[5:])
if src not in self._pathmap:
ab = cwltool.pathmapper.abspath(src, basedir)
- st = arvados.commands.run.statfile("", ab)
+ st = arvados.commands.run.statfile("", ab, fnPattern="$(task.keep)/%s/%s")
if kwargs.get("conformance_test"):
self._pathmap[src] = (src, ab)
elif isinstance(st, arvados.commands.run.UploadFile):
arvrunner.api,
dry_run=kwargs.get("dry_run"),
num_retries=3,
- fnPattern="$(task.keep)/%s/%s")
+ fnPattern="$(task.keep)/%s/%s",
+ project=arvrunner.project_uuid)
for src, ab, st in uploadfiles:
arvrunner.add_uploaded(src, (ab, st.fn))
self._pathmap[src] = (ab, st.fn)
+ self.keepdir = None
+
+ def reversemap(self, target):
+ if target.startswith("keep:"):
+ return (target, target)
+ elif self.keepdir and target.startswith(self.keepdir):
+ return (target, "keep:" + target[len(self.keepdir)+1:])
+ else:
+ return super(ArvPathMapper, self).reversemap(target)
class ArvadosCommandTool(cwltool.draft2tool.CommandLineTool):
def __init__(self, arvrunner, toolpath_object, **kwargs):
- super(ArvadosCommandTool, self).__init__(toolpath_object, outdir="$(task.outdir)", tmpdir="$(task.tmpdir)", **kwargs)
+ super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
self.arvrunner = arvrunner
def makeJobRunner(self):
self.cond = threading.Condition(self.lock)
self.final_output = None
self.uploaded = {}
+ self.num_retries = 4
def arvMakeTool(self, toolpath_object, **kwargs):
if "class" in toolpath_object and toolpath_object["class"] == "CommandLineTool":
def output_callback(self, out, processStatus):
if processStatus == "success":
logger.info("Overall job status is %s", processStatus)
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Complete"}).execute(num_retries=self.num_retries)
+
else:
logger.warn("Overall job status is %s", processStatus)
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
self.final_output = out
+
def on_message(self, event):
if "object_uuid" in event:
- if event["object_uuid"] in self.jobs and event["event_type"] == "update":
- if event["properties"]["new_attributes"]["state"] == "Running" and self.jobs[event["object_uuid"]].running is False:
- logger.info("Job %s is Running", event["object_uuid"])
- with self.lock:
- self.jobs[event["object_uuid"]].running = True
- elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
- logger.info("Job %s is %s", event["object_uuid"], event["properties"]["new_attributes"]["state"])
- try:
- self.cond.acquire()
- self.jobs[event["object_uuid"]].done(event["properties"]["new_attributes"])
- self.cond.notify()
- finally:
- self.cond.release()
+ if event["object_uuid"] in self.jobs and event["event_type"] == "update":
+ if event["properties"]["new_attributes"]["state"] == "Running" and self.jobs[event["object_uuid"]].running is False:
+ uuid = event["object_uuid"]
+ with self.lock:
+ j = self.jobs[uuid]
+ logger.info("Job %s (%s) is Running", j.name, uuid)
+ j.running = True
+ j.update_pipeline_component(event["properties"]["new_attributes"])
+ elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled"):
+ uuid = event["object_uuid"]
+ try:
+ self.cond.acquire()
+ j = self.jobs[uuid]
+ logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
+ j.done(event["properties"]["new_attributes"])
+ self.cond.notify()
+ finally:
+ self.cond.release()
def get_uploaded(self):
return self.uploaded.copy()
def arvExecutor(self, tool, job_order, input_basedir, args, **kwargs):
events = arvados.events.subscribe(arvados.api('v1'), [["object_uuid", "is_a", "arvados#job"]], self.on_message)
+ self.debug = args.debug
+ self.ignore_docker_for_reuse = args.ignore_docker_for_reuse
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
kwargs["enable_reuse"] = args.enable_reuse
- kwargs["repository"] = args.repository
+
+ kwargs["outdir"] = "$(task.outdir)"
+ kwargs["tmpdir"] = "$(task.tmpdir)"
+
+ useruuid = self.api.users().current().execute()["uuid"]
+ self.project_uuid = args.project_uuid if args.project_uuid else useruuid
if kwargs.get("conformance_test"):
return cwltool.main.single_job_executor(tool, job_order, input_basedir, args, **kwargs)
else:
+ 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"])
+
jobiter = tool.job(job_order,
- input_basedir,
- self.output_callback,
- **kwargs)
+ input_basedir,
+ self.output_callback,
+ docker_outdir="$(task.outdir)",
+ **kwargs)
- for runnable in jobiter:
- if runnable:
- with self.lock:
+ 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.jobs:
- try:
- self.cond.acquire()
- self.cond.wait()
- finally:
- self.cond.release()
else:
- logger.error("Workflow cannot make any more progress.")
- break
+ if self.jobs:
+ self.cond.wait(1)
+ else:
+ logger.error("Workflow is deadlocked, no runnable jobs and not waiting on any pending jobs.")
+ break
- while self.jobs:
- try:
- self.cond.acquire()
- self.cond.wait()
- finally:
- self.cond.release()
+ while self.jobs:
+ self.cond.wait(1)
- events.close()
+ events.close()
- if self.final_output is None:
- raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+ if self.final_output is None:
+ raise cwltool.workflow.WorkflowException("Workflow did not return a result.")
+
+ # create final output collection
+ 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()[0], exc_info=(sys.exc_info()[1] if self.debug else False))
+ self.api.pipeline_instances().update(uuid=self.pipeline["uuid"],
+ body={"state": "Failed"}).execute(num_retries=self.num_retries)
+ finally:
+ self.cond.release()
return self.final_output
def main(args, stdout, stderr, api_client=None):
- runner = ArvCwlRunner(api_client=arvados.api('v1'))
args.insert(0, "--leave-outputs")
parser = cwltool.main.arg_parser()
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--enable-reuse", action="store_true",
- default=False, dest="enable_reuse",
+ default=True, dest="enable_reuse",
help="")
exgroup.add_argument("--disable-reuse", action="store_false",
- default=False, dest="enable_reuse",
+ default=True, dest="enable_reuse",
help="")
-
- parser.add_argument('--repository', type=str, default="peter/crunchrunner", help="Repository containing the 'crunchrunner' program.")
+ parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs")
+ parser.add_argument("--ignore-docker-for-reuse", action="store_true",
+ help="Ignore Docker image version when deciding whether to reuse past jobs.",
+ default=False)
+
+ try:
+ runner = ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
+ except Exception as e:
+ logger.error(e)
+ return 1
return cwltool.main.main(args, executor=runner.arvExecutor, makeTool=runner.arvMakeTool, parser=parser)