#
# SPDX-License-Identifier: Apache-2.0
+from future import standard_library
+standard_library.install_aliases()
+from builtins import str
+
import logging
import json
import os
-import urllib
+import urllib.request, urllib.parse, urllib.error
import time
import datetime
import ciso8601
from cwltool.errors import WorkflowException
from cwltool.process import UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.utils import aslist
+from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
from cwltool.job import JobBase
import arvados.collection
from .fsaccess import CollectionFetcher
from .pathmapper import NoFollowPathMapper, trim_listing
from .perf import Perf
+from ._version import __version__
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
"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]
generatemapper = NoFollowPathMapper(self.generatefiles["listing"], "", "",
separateDirs=False)
- sorteditems = sorted(generatemapper.items(), None, key=lambda n: n[1].target)
+ 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"):
+ continue
+
+ if p.target.startswith("/"):
+ dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
+ else:
+ dst = p.target
+
+ if p.type in ("File", "Directory", "WritableFile", "WritableDirectory"):
if p.resolved.startswith("_:"):
- vwd.mkdirs(p.target)
+ vwd.mkdirs(dst)
else:
source, path = self.arvrunner.fs_access.get_collection(p.resolved)
- vwd.copy(path, p.target, source_collection=source)
+ vwd.copy(path or ".", dst, source_collection=source)
elif p.type == "CreateFile":
if self.arvrunner.secret_store.has_secret(p.resolved):
- secret_mounts["%s/%s" % (self.outdir, p.target)] = {
+ mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
+ secret_mounts[mountpoint] = {
"kind": "text",
"content": self.arvrunner.secret_store.retrieve(p.resolved)
}
else:
- with vwd.open(p.target, "w") as n:
- n.write(p.resolved.encode("utf-8"))
+ with vwd.open(dst, "w") as n:
+ n.write(p.resolved)
def keepemptydirs(p):
if isinstance(p, arvados.collection.RichCollectionBase):
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)
+ if p.target.startswith("/"):
+ dst = p.target[len(self.outdir)+1:] if p.target.startswith(self.outdir+"/") else p.target[1:]
+ else:
+ dst = p.target
+ mountpoint = p.target if p.target.startswith("/") else os.path.join(self.outdir, p.target)
mounts[mountpoint] = {"kind": "collection",
"portable_data_hash": vwd.portable_data_hash(),
- "path": p.target}
+ "path": dst}
if p.type.startswith("Writable"):
mounts[mountpoint]["writable"] = True
prev = p.target + "/"
(docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
if not docker_req:
- docker_req = {"dockerImageId": "arvados/jobs"}
+ docker_req = {"dockerImageId": "arvados/jobs:"+__version__}
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
runtimeContext.pull_image,
- runtimeContext.project_uuid)
+ runtimeContext.project_uuid,
+ runtimeContext.force_docker_pull,
+ runtimeContext.tmp_outdir_prefix)
+
+ 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:
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:
+ if self.timelimit is not None and self.timelimit > 0:
scheduling_parameters["max_run_time"] = self.timelimit
extra_submit_params = {}
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"]
else:
logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
except Exception as e:
- logger.error("%s got error %s" % (self.arvrunner.label(self), str(e)))
+ logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
+ logger.debug("Container request was %s", container_request)
self.output_callback({}, "permanentFail")
def done(self, record):
else:
processStatus = "permanentFail"
- if processStatus == "permanentFail":
- logc = arvados.collection.CollectionReader(container["log"],
+ if processStatus == "permanentFail" and record["log_uuid"]:
+ logc = arvados.collection.CollectionReader(record["log_uuid"],
api_client=self.arvrunner.api,
keep_client=self.arvrunner.keep_client,
num_retries=self.arvrunner.num_retries)
if record["output_uuid"]:
if self.arvrunner.trash_intermediate or self.arvrunner.intermediate_output_ttl:
# Compute the trash time to avoid requesting the collection record.
- trash_at = ciso8601.parse_datetime_unaware(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
+ trash_at = ciso8601.parse_datetime_as_naive(record["modified_at"]) + datetime.timedelta(0, self.arvrunner.intermediate_output_ttl)
aftertime = " at %s" % trash_at.strftime("%Y-%m-%d %H:%M:%S UTC") if self.arvrunner.intermediate_output_ttl else ""
orpart = ", or" if self.arvrunner.trash_intermediate and self.arvrunner.intermediate_output_ttl else ""
oncomplete = " upon successful completion of the workflow" if self.arvrunner.trash_intermediate else ""
if container["output"]:
outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
except WorkflowException as e:
+ # Only include a stack trace if in debug mode.
+ # A stack trace may obfuscate more useful output about the workflow.
logger.error("%s unable to collect output from %s:\n%s",
self.arvrunner.label(self), container["output"], e, exc_info=(e if self.arvrunner.debug else False))
processStatus = "permanentFail"
- except Exception as e:
- logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
+ except Exception:
+ logger.exception("%s while getting output object:", self.arvrunner.label(self))
processStatus = "permanentFail"
finally:
self.output_callback(outputs, processStatus)
"ram": 1024*1024 * (math.ceil(self.submit_runner_ram) + math.ceil(self.collection_cache_size)),
"API": True
},
- "use_existing": self.enable_reuse,
+ "use_existing": False, # Never reuse the runner container - see #15497.
"properties": {}
}
"--api=containers",
"--no-log-timestamps",
"--disable-validate",
+ "--disable-color",
"--eval-timeout=%s" % self.arvrunner.eval_timeout,
"--thread-count=%s" % self.arvrunner.thread_count,
"--enable-reuse" if self.enable_reuse else "--disable-reuse",
if self.arvrunner.project_uuid:
command.append("--project-uuid="+self.arvrunner.project_uuid)
+ if self.enable_dev:
+ command.append("--enable-dev")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
extra_submit_params["cluster_id"] = runtimeContext.submit_runner_cluster
if runtimeContext.submit_request_uuid:
+ if "cluster_id" in extra_submit_params:
+ # Doesn't make sense for "update" and actually fails
+ del extra_submit_params["cluster_id"]
response = self.arvrunner.api.container_requests().update(
uuid=runtimeContext.submit_request_uuid,
body=job_spec,
logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
+ workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
+ workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
+ url = ""
+ if workbench2:
+ url = "{}processes/{}".format(workbench2, response["uuid"])
+ elif workbench1:
+ url = "{}container_requests/{}".format(workbench1, response["uuid"])
+ if url:
+ logger.info("Monitor workflow progress at %s", url)
+
+
def done(self, record):
try:
container = self.arvrunner.api.containers().get(
uuid=record["container_uuid"]
).execute(num_retries=self.arvrunner.num_retries)
- except Exception as e:
- logger.exception("%s while getting runner container: %s", self.arvrunner.label(self), e)
+ container["log"] = record["log_uuid"]
+ except Exception:
+ logger.exception("%s while getting runner container", self.arvrunner.label(self))
self.arvrunner.output_callback({}, "permanentFail")
else:
super(RunnerContainer, self).done(container)
projects / arvados.git / blobdiff