Update tests related to make_output_collection

[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 b04fb190e963e965524679bb4473767820e8b849..d53ec5c7f8590430ee623701724bcc4757e8b04e 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -146,6 +146,8 @@ class ArvadosContainer(JobBase):
                     mounts[targetdir]["path"] = path
             prevdir = targetdir + "/"
 
+        intermediate_collection_info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
+
         with Perf(metrics, "generatefiles %s" % self.name):
             if self.generatefiles["listing"]:
                 vwd = arvados.collection.Collection(api_client=self.arvrunner.api,
@@ -197,12 +199,11 @@ class ArvadosContainer(JobBase):
 
                 if not runtimeContext.current_container:
                     runtimeContext.current_container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger)
-                info = arvados_cwl.util.get_intermediate_collection_info(self.name, runtimeContext.current_container, runtimeContext.intermediate_output_ttl)
-                vwd.save_new(name=info["name"],
+                vwd.save_new(name=intermediate_collection_info["name"],
                              owner_uuid=runtimeContext.project_uuid,
                              ensure_unique_name=True,
-                             trash_at=info["trash_at"],
-                             properties=info["properties"])
+                             trash_at=intermediate_collection_info["trash_at"],
+                             properties=intermediate_collection_info["properties"])
 
                 prev = None
                 for f, p in sorteditems:
@@ -247,7 +248,8 @@ class ArvadosContainer(JobBase):
                                                                     runtimeContext.project_uuid,
                                                                     runtimeContext.force_docker_pull,
                                                                     runtimeContext.tmp_outdir_prefix,
-                                                                    runtimeContext.match_local_docker)
+                                                                    runtimeContext.match_local_docker,
+                                                                    runtimeContext.copy_deps)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -340,6 +342,16 @@ class ArvadosContainer(JobBase):
             for pr in properties_req["processProperties"]:
                 container_request["properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
 
+        output_properties_req, _ = self.get_requirement("http://arvados.org/cwl#OutputCollectionProperties")
+        if output_properties_req:
+            if self.arvrunner.api._rootDesc["revision"] >= "20220510":
+                container_request["output_properties"] = {}
+                for pr in output_properties_req["outputProperties"]:
+                    container_request["output_properties"][pr["propertyName"]] = self.builder.do_eval(pr["propertyValue"])
+            else:
+                logger.warning("%s API server is too old to support setting properties on output collections.",
+                               self.arvrunner.label(self))
+
         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)
@@ -394,7 +406,7 @@ class ArvadosContainer(JobBase):
                     processStatus = "permanentFail"
 
                 if rcode == 137:
-                    logger.warning("%s This container was killed on the compute instance.  The most common reason is that it attempted to allocate too much RAM and was targeted by the Out Of Memory (OOM) killer.  Try resubmitting with a higher 'ramMin'.",
+                    logger.warning("%s Container may have been killed for using too much RAM.  Try resubmitting with a higher 'ramMin'.",
                                  self.arvrunner.label(self))
             else:
                 processStatus = "permanentFail"
@@ -465,7 +477,7 @@ class RunnerContainer(Runner):
             "cwd": "/var/spool/cwl",
             "priority": self.priority,
             "state": "Committed",
-            "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image),
+            "container_image": arvados_jobs_image(self.arvrunner, self.jobs_image, runtimeContext),
             "mounts": {
                 "/var/lib/cwl/cwl.input.json": {
                     "kind": "json",
@@ -500,7 +512,7 @@ class RunnerContainer(Runner):
                 "portable_data_hash": "%s" % workflowcollection
             }
         else:
-            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
+            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext)
             workflowpath = "/var/lib/cwl/workflow.json#main"
             container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
                 "kind": "json",
@@ -550,17 +562,17 @@ class RunnerContainer(Runner):
         if runtimeContext.intermediate_storage_classes != "default" and runtimeContext.intermediate_storage_classes:
             command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
 
-        if self.on_error:
+        if runtimeContext.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 runtimeContext.intermediate_output_ttl:
+            command.append("--intermediate-output-ttl=%d" % runtimeContext.intermediate_output_ttl)
 
-        if self.arvrunner.trash_intermediate:
+        if runtimeContext.trash_intermediate:
             command.append("--trash-intermediate")
 
-        if self.arvrunner.project_uuid:
-            command.append("--project-uuid="+self.arvrunner.project_uuid)
+        if runtimeContext.project_uuid:
+            command.append("--project-uuid="+runtimeContext.project_uuid)
 
         if self.enable_dev:
             command.append("--enable-dev")
@@ -581,8 +593,8 @@ class RunnerContainer(Runner):
     def run(self, runtimeContext):
         runtimeContext.keepprefix = "keep:"
         job_spec = self.arvados_job_spec(runtimeContext)
-        if self.arvrunner.project_uuid:
-            job_spec["owner_uuid"] = self.arvrunner.project_uuid
+        if runtimeContext.project_uuid:
+            job_spec["owner_uuid"] = runtimeContext.project_uuid
 
         extra_submit_params = {}
         if runtimeContext.submit_runner_cluster: