Fix CWL tests refs #18238

[arvados.git] / sdk / cwl / arvados_cwl / arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c6e4577d03bcd8d36af869d8b6ec63cc2531bc47..ae3c6688955301141f0af3405787c9f831fb58b7 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -28,7 +28,7 @@ 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
@@ -57,6 +57,12 @@ class ArvadosContainer(JobBase):
     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
@@ -234,8 +240,6 @@ class ArvadosContainer(JobBase):
                                 "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:"+__version__}
 
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
@@ -279,11 +283,13 @@ class ArvadosContainer(JobBase):
         if self.output_ttl < 0:
             raise WorkflowException("Invalid value %d for output_ttl, cannot be less than zero" % container_request["output_ttl"])
 
-        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.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
@@ -483,7 +489,7 @@ class RunnerContainer(Runner):
         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_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+                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
@@ -514,10 +520,10 @@ class RunnerContainer(Runner):
         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":
+        if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 
         if self.on_error: