import json
import os
import urllib
+import time
+import datetime
+import ciso8601
import ruamel.yaml as yaml
"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"
+ "kind": "tmp",
+ "capacity": resources.get("tmpdirSize", 0) * 2**20
}
}
scheduling_parameters = {}
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
if runtime_req:
if "keep_cache" in runtime_req:
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)
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:
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