from cwltool.errors import WorkflowException
from cwltool.process import get_feature, UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFiles
+from cwltool.pathmapper import adjustFiles, 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_listing
from .fsaccess import CollectionFetcher
+from .pathmapper import NoFollowPathMapper
+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."""
dirs = set()
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if tp == "Directory" and '/' not in p[6:]:
+ pdh, p, tp = self.pathmapper.mapper(f)
+ if tp == "Directory" and '/' not in pdh:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh[5:]
}
- dirs.add(p[6:])
+ dirs.add(pdh)
+
for f in self.pathmapper.files():
- _, p, tp = self.pathmapper.mapper(f)
- if p[6:].split("/")[0] not in dirs:
+ res, p, tp = self.pathmapper.mapper(f)
+ pdh, path = res[5:].split("/", 1)
+ if pdh not in dirs:
mounts[p] = {
"kind": "collection",
- "portable_data_hash": p[6:]
+ "portable_data_hash": pdh
}
-
- if self.generatefiles["listing"]:
- raise UnsupportedRequirement("InitialWorkDirRequirement not supported with --api=containers")
+ if path:
+ mounts[p]["path"] = path
+
+ 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:
(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,
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
partition_req, _ = get_feature(self, "http://arvados.org/cwl#PartitionRequirement")
if partition_req:
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")
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)
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:
command.append("--output-name=" + self.output_name)
+ container_req["output_name"] = self.output_name
if self.output_tags:
command.append("--output-tags=" + self.output_tags)
+ if kwargs.get("debug"):
+ command.append("--debug")
+
if self.enable_reuse:
command.append("--enable-reuse")
else:
command.append("--disable-reuse")
+ if self.on_error:
+ command.append("--on-error=" + self.on_error)
+
command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
container_req["command"] = command
projects / arvados.git / blobdiff