import cwltool.workflow
import cwltool.main
from cwltool.process import shortname
+from cwltool.errors import WorkflowException
import threading
import cwltool.docker
import fnmatch
logger = logging.getLogger('arvados.cwl-runner')
logger.setLevel(logging.INFO)
-crunchrunner_pdh = "83db29f08544e1c319572a6bd971088a+140"
-crunchrunner_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/crunchrunner"
-certs_download = "https://cloud.curoverse.com/collections/download/qr1hi-4zz18-n3m1yxd0vx78jic/1i1u2qtq66k1atziv4ocfgsg5nu5tj11n4r6e0bhvjg03rix4m/ca-certificates.crt"
-
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: \$\(task\.keep\)=(.*)")
(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, 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)
try:
response = self.arvrunner.api.jobs().create(body={
"repository": "arvados",
"script_version": "master",
"minimum_script_version": "9e5b98e8f5f4727856b53447191f9c06e3da2ba6",
- "script_parameters": {"tasks": [script_parameters], "crunchrunner": crunchrunner_pdh+"/crunchrunner"},
+ "script_parameters": {"tasks": [script_parameters]},
"runtime_constraints": runtime_constraints
}, find_or_create=kwargs.get("enable_reuse", True)).execute(num_retries=self.arvrunner.num_retries)
tmpdir = None
outdir = None
keepdir = None
- for l in log.readlines():
+ 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 = keepre.match(l)
if g:
keepdir = g.group(1)
- if tmpdir and outdir and keepdir:
- break
+
+ 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)
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)
- try:
- self.api.collections().get(uuid=crunchrunner_pdh).execute()
- except arvados.errors.ApiError as e:
- import httplib2
- h = httplib2.Http(ca_certs=arvados.util.ca_certs_path())
- resp, content = h.request(crunchrunner_download, "GET")
- resp2, content2 = h.request(certs_download, "GET")
- with arvados.collection.Collection() as col:
- with col.open("crunchrunner", "w") as f:
- f.write(content)
- with col.open("ca-certificates.crt", "w") as f:
- f.write(content2)
-
- col.save_new("crunchrunner binary", ensure_unique_name=True)
-
+ self.debug = args.debug
self.fs_access = CollectionFsAccess(input_basedir)
kwargs["fs_access"] = self.fs_access
if sys.exc_info()[0] is KeyboardInterrupt:
logger.error("Interrupted, marking pipeline as failed")
else:
- logger.exception("Caught unhandled exception, marking pipeline as failed")
+ 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:
projects / arvados.git / blobdiff