X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/f170c5a75f22a6db11ca93eed5b0dfc9c65c4270..876b9e64d1364770486552060222f5f6b1b5e2ea:/sdk/cwl/arvados_cwl/arvcontainer.py

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index c9170c51b7..ae3c668895 100644
--- 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
@@ -67,15 +73,21 @@ class ArvadosContainer(JobBase):
 
         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:
@@ -228,8 +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,
@@ -273,11 +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
@@ -303,6 +315,11 @@ class ArvadosContainer(JobBase):
                 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)
@@ -468,6 +485,11 @@ class RunnerContainer(Runner):
             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
@@ -498,10 +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: