+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
import logging
import json
import os
+import urllib
+import time
+import datetime
+import ciso8601
import ruamel.yaml as yaml
from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
from cwltool.utils import aslist
import arvados.collection
from .arvdocker import arv_docker_get_image
from . import done
-from .runner import Runner, arvados_jobs_image
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location
from .fsaccess import CollectionFetcher
+from .pathmapper import NoFollowPathMapper, trim_listing
+from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
+metrics = logging.getLogger('arvados.cwl-runner.metrics')
class ArvadosContainer(object):
"""Submit and manage a Crunch container request for executing a CWL CommandLineTool."""
"cwd": self.outdir,
"priority": 1,
"state": "Committed",
- "properties": {}
+ "properties": {},
}
runtime_constraints = {}
+
+ resources = self.builder.resources
+ if resources is not None:
+ runtime_constraints["vcpus"] = resources.get("cores", 1)
+ runtime_constraints["ram"] = resources.get("ram") * 2**20
+
mounts = {
self.outdir: {
- "kind": "tmp"
+ "kind": "tmp",
+ "capacity": resources.get("outdirSize", 0) * 2**20
+ },
+ self.tmpdir: {
+ "kind": "tmp",
+ "capacity": resources.get("tmpdirSize", 0) * 2**20
}
}
scheduling_parameters = {}
- dirs = set()
- for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if tp == "Directory" and '/' not in p[6:]:
- mounts[p] = {
- "kind": "collection",
- "portable_data_hash": p[6:]
- }
- dirs.add(p[6:])
- for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if p[6:].split("/")[0] not in dirs:
- mounts[p] = {
- "kind": "collection",
- "portable_data_hash": p[6:]
- }
-
- if self.generatefiles["listing"]:
- raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
+ 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 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], "", "",
+ separateDirs=False)
+
+ with Perf(metrics, "createfiles %s" % self.name):
+ for f, p in generatemapper.items():
+ if not p.target:
+ pass
+ elif p.type in ("File", "Directory"):
+ source, path = self.arvrunner.fs_access.get_collection(p.resolved)
+ vwd.copy(path, p.target, source_collection=source)
+ elif p.type == "CreateFile":
+ with vwd.open(p.target, "w") as n:
+ n.write(p.resolved.encode("utf-8"))
+
+ with Perf(metrics, "generatefiles.save_new %s" % self.name):
+ vwd.save_new()
+
+ for f, p in generatemapper.items():
+ if not p.target:
+ continue
+ mountpoint = "%s/%s" % (self.outdir, p.target)
+ mounts[mountpoint] = {"kind": "collection",
+ "portable_data_hash": vwd.portable_data_hash(),
+ "path": p.target}
container_request["environment"] = {"TMPDIR": self.tmpdir, "HOME": self.outdir}
if self.environment:
container_request["environment"].update(self.environment)
if self.stdin:
- raise UnsupportedRequirement("Stdin redirection currently not suppported")
+ sp = self.stdin[6:].split("/", 1)
+ mounts["stdin"] = {"kind": "collection",
+ "portable_data_hash": sp[0],
+ "path": sp[1]}
if self.stderr:
- raise UnsupportedRequirement("Stderr redirection currently not suppported")
+ mounts["stderr"] = {"kind": "file",
+ "path": "%s/%s" % (self.outdir, self.stderr)}
if self.stdout:
mounts["stdout"] = {"kind": "file",
(docker_req, docker_is_req) = get_feature(self, "DockerRequirement")
if not docker_req:
- docker_req = {"dockerImageId": arvados_jobs_image(self.arvrunner)}
+ docker_req = {"dockerImageId": "arvados/jobs"}
container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
docker_req,
pull_image,
self.arvrunner.project_uuid)
- resources = self.builder.resources
- if resources is not None:
- runtime_constraints["vcpus"] = resources.get("cores", 1)
- runtime_constraints["ram"] = resources.get("ram") * 2**20
-
api_req, _ = get_feature(self, "http://arvados.org/cwl#APIRequirement")
if api_req:
runtime_constraints["API"] = True
runtime_req, _ = get_feature(self, "http://arvados.org/cwl#RuntimeConstraints")
if runtime_req:
if "keep_cache" in runtime_req:
- runtime_constraints["keep_cache_ram"] = runtime_req["keep_cache"]
+ runtime_constraints["keep_cache_ram"] = 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, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
if partition_req:
scheduling_parameters["partitions"] = aslist(partition_req["partition"])
+ intermediate_output_req, _ = get_feature(self, "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 WorkflowError("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
+
+ container_request["output_ttl"] = self.output_ttl
container_request["mounts"] = mounts
container_request["runtime_constraints"] = runtime_constraints
- container_request["use_existing"] = kwargs.get("enable_reuse", True)
container_request["scheduling_parameters"] = scheduling_parameters
+ enable_reuse = kwargs.get("enable_reuse", True)
+ if enable_reuse:
+ reuse_req, _ = get_feature(self, "http://arvados.org/cwl#ReuseRequirement")
+ if reuse_req:
+ enable_reuse = reuse_req["enableReuse"]
+ container_request["use_existing"] = enable_reuse
+
if kwargs.get("runnerjob", "").startswith("arvwf:"):
wfuuid = kwargs["runnerjob"][6:kwargs["runnerjob"].index("#")]
wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
self.uuid = response["uuid"]
self.arvrunner.processes[self.uuid] = self
- logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-
if response["state"] == "Final":
+ logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
self.done(response)
+ 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)))
self.output_callback({}, "permanentFail")
def done(self, record):
+ outputs = {}
try:
container = self.arvrunner.api.containers().get(
uuid=record["container_uuid"]
num_retries=self.arvrunner.num_retries)
done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
- outputs = {}
+ 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)
+ 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 ""
+ logger.info("%s Intermediate output %s (%s) will be trashed%s%s%s." % (
+ self.arvrunner.label(self), record["output_uuid"], container["output"], aftertime, orpart, oncomplete))
+ self.arvrunner.add_intermediate_output(record["output_uuid"])
+
if container["output"]:
outputs = done.done_outputs(self, container, "/tmp", self.outdir, "/keep")
except WorkflowException as e:
processStatus = "permanentFail"
except Exception as e:
logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
- self.output_callback({}, "permanentFail")
- else:
- self.output_callback(outputs, processStatus)
+ processStatus = "permanentFail"
finally:
+ self.output_callback(outputs, processStatus)
if record["uuid"] in self.arvrunner.processes:
del self.arvrunner.processes[record["uuid"]]
the +body+ argument to container_requests().create().
"""
- workflowmapper = super(RunnerContainer, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
+ adjustDirObjs(self.job_order, trim_listing)
+ adjustFileObjs(self.job_order, trim_anonymous_location)
+ adjustDirObjs(self.job_order, trim_anonymous_location)
container_req = {
"owner_uuid": self.arvrunner.project_uuid,
"cwd": "/var/spool/cwl",
"priority": 1,
"state": "Committed",
- "container_image": arvados_jobs_image(self.arvrunner),
+ "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
"mounts": {
"/var/lib/cwl/cwl.input.json": {
"kind": "json",
"properties": {}
}
- workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
- if workflowcollection.startswith("keep:"):
- workflowcollection = workflowcollection[5:workflowcollection.index('/')]
- workflowname = os.path.basename(self.tool.tool["id"])
+ if self.tool.tool.get("id", "").startswith("keep:"):
+ sp = self.tool.tool["id"].split('/')
+ workflowcollection = sp[0][5:]
+ workflowname = "/".join(sp[1:])
workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
container_req["mounts"]["/var/lib/cwl/workflow"] = {
"kind": "collection",
"portable_data_hash": "%s" % workflowcollection
- }
- elif workflowcollection.startswith("arvwf:"):
+ }
+ else:
+ packed = packed_workflow(self.arvrunner, self.tool)
workflowpath = "/var/lib/cwl/workflow.json#main"
- wfuuid = workflowcollection[6:workflowcollection.index("#")]
- wfrecord = self.arvrunner.api.workflows().get(uuid=wfuuid).execute(num_retries=self.arvrunner.num_retries)
- wfobj = yaml.safe_load(wfrecord["definition"])
- if container_req["name"].startswith("arvwf:"):
- container_req["name"] = wfrecord["name"]
container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
"kind": "json",
- "json": wfobj
+ "content": packed
}
- container_req["properties"]["template_uuid"] = wfuuid
+ if self.tool.tool.get("id", "").startswith("arvwf:"):
+ container_req["properties"]["template_uuid"] = self.tool.tool["id"][6:33]
command = ["arvados-cwl-runner", "--local", "--api=containers", "--no-log-timestamps"]
if self.output_name:
else:
command.append("--disable-reuse")
+ if self.on_error:
+ command.append("--on-error=" + self.on_error)
+
+ if self.intermediate_output_ttl:
+ command.append("--intermediate-output-ttl=%d" % self.intermediate_output_ttl)
+
+ if self.arvrunner.trash_intermediate:
+ command.append("--trash-intermediate")
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
projects / arvados.git / blobdiff