X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/1885991dd79a75034f7650cccef16ebe3fd71959..ba15fa5da21f4bafd3f90a8d259ea2aae764c77e:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 0b302b6280..e8e2a51131 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -1,20 +1,27 @@
+# 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 adjustFileObjs, adjustDirObjs
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
 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, packed_workflow, trim_anonymous_location
+from .runner import Runner, arvados_jobs_image, packed_workflow, trim_anonymous_location, remove_redundant_fields
 from .fsaccess import CollectionFetcher
 from .pathmapper import NoFollowPathMapper, trim_listing
 from .perf import Perf
@@ -42,7 +49,7 @@ class ArvadosContainer(object):
             "cwd": self.outdir,
             "priority": 1,
             "state": "Committed",
-            "properties": {}
+            "properties": {},
         }
         runtime_constraints = {}
 
@@ -169,11 +176,27 @@ class ArvadosContainer(object):
         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)
@@ -199,6 +222,7 @@ class ArvadosContainer(object):
             self.output_callback({}, "permanentFail")
 
     def done(self, record):
+        outputs = {}
         try:
             container = self.arvrunner.api.containers().get(
                 uuid=record["container_uuid"]
@@ -225,7 +249,17 @@ class ArvadosContainer(object):
                                                            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:
@@ -252,8 +286,8 @@ class RunnerContainer(Runner):
         """
 
         adjustDirObjs(self.job_order, trim_listing)
-        adjustFileObjs(self.job_order, trim_anonymous_location)
-        adjustDirObjs(self.job_order, trim_anonymous_location)
+        visit_class(self.job_order, ("File", "Directory"), trim_anonymous_location)
+        visit_class(self.job_order, ("File", "Directory"), remove_redundant_fields)
 
         container_req = {
             "owner_uuid": self.arvrunner.project_uuid,
@@ -282,6 +316,7 @@ class RunnerContainer(Runner):
                 "ram": 1024*1024 * self.submit_runner_ram,
                 "API": True
             },
+            "use_existing": self.enable_reuse,
             "properties": {}
         }
 
@@ -323,6 +358,15 @@ class RunnerContainer(Runner):
         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")
+
+        if self.arvrunner.project_uuid:
+            command.append("--project-uuid="+self.arvrunner.project_uuid)
+
         command.extend([workflowpath, "/var/lib/cwl/cwl.input.json"])
 
         container_req["command"] = command