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 .arvdocker import arv_docker_get_image
from . import done
-from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields, make_builder
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')
def update_pipeline_component(self, r):
pass
+ def _required_env(self):
+ env = {}
+ env["HOME"] = self.outdir
+ env["TMPDIR"] = self.tmpdir
+ return env
+
def run(self, runtimeContext):
# ArvadosCommandTool subclasses from cwltool.CommandLineTool,
# which calls makeJobRunner() to get a new ArvadosContainer
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": {},
- }
+ if runtimeContext.submit_request_uuid:
+ container_request = self.arvrunner.api.container_requests().get(
+ uuid=runtimeContext.submit_request_uuid
+ ).execute(num_retries=self.arvrunner.num_retries)
+ else:
+ container_request = {}
+
+ container_request["command"] = self.command_line
+ container_request["name"] = self.name
+ container_request["output_path"] = self.outdir
+ container_request["cwd"] = self.outdir
+ container_request["priority"] = runtimeContext.priority
+ container_request["state"] = "Committed"
+ container_request.setdefault("properties", {})
+
runtime_constraints = {}
if runtimeContext.project_uuid:
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 or ".", 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:
+ with vwd.open(dst, "w") as n:
n.write(p.resolved)
def keepemptydirs(p):
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 + "/"
"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)
+ runtimeContext.project_uuid,
+ runtimeContext.force_docker_pull,
+ runtimeContext.tmp_outdir_prefix)
network_req, _ = self.get_requirement("NetworkAccess")
if network_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.arvrunner.api._rootDesc["revision"] >= "20210628":
+ storage_class_req, _ = self.get_requirement("http://arvados.org/cwl#OutputStorageClass")
+ if storage_class_req and storage_class_req.get("intermediateStorageClass"):
+ container_request["output_storage_classes"] = aslist(storage_class_req["intermediateStorageClass"])
+ else:
+ container_request["output_storage_classes"] = runtimeContext.intermediate_storage_classes.strip().split(",")
+
if self.timelimit is not None and self.timelimit > 0:
scheduling_parameters["max_run_time"] = self.timelimit
enable_reuse = reuse_req["enableReuse"]
container_request["use_existing"] = enable_reuse
+ properties_req, _ = self.get_requirement("http://arvados.org/cwl#ProcessProperties")
+ if properties_req:
+ for pr in properties_req["processProperties"]:
+ container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+
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)
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))
+ except Exception as 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):
if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
+ properties_req, _ = self.embedded_tool.get_requirement("http://arvados.org/cwl#ProcessProperties")
+ if properties_req:
+ builder = make_builder(self.job_order, self.embedded_tool.hints, self.embedded_tool.requirements, runtimeContext, self.embedded_tool.metadata)
+ for pr in properties_req["processProperties"]:
+ container_req["properties"][pr["propertyName"]] = builder.do_eval(pr["propertyValue"])
# --local means execute the workflow instead of submitting a container request
# --api=containers means use the containers API
"--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 runtimeContext.debug:
command.append("--debug")
- if runtimeContext.storage_classes != "default":
+ if runtimeContext.storage_classes != "default" and runtimeContext.storage_classes:
command.append("--storage-classes=" + runtimeContext.storage_classes)
+ if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
+ command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
+
if self.on_error:
command.append("--on-error=" + self.on_error)
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(