14198: Bringing unit tests up to date WIP

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

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 940ae92e772afc9de7df30697e5ddaa60dda4887..189282ec281dd8c1966e6434bbc7221e9a557dce 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -18,6 +18,7 @@ from cwltool.job import JobBase
 
 from schema_salad.sourceline import SourceLine
 
+import arvados_cwl.util
 import ruamel.yaml as yaml
 
 import arvados.collection
@@ -76,7 +77,12 @@ class ArvadosJob(JobBase):
 
                 if vwd:
                     with Perf(metrics, "generatefiles.save_new %s" % self.name):
-                        vwd.save_new()
+                        info = get_intermediate_collection_info(self.name, None, runtimeContext.intermediate_output_ttl)
+                        vwd.save_new(name=info["name"],
+                                     owner_uuid=self.arvrunner.project_uuid,
+                                     ensure_unique_name=True,
+                                     trash_at=info["trash_at"],
+                                     properties=info["properties"])
 
                 for f, p in generatemapper.items():
                     if p.type == "File":
@@ -106,11 +112,14 @@ class ArvadosJob(JobBase):
 
         with Perf(metrics, "arv_docker_get_image %s" % self.name):
             (docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
-            if docker_req and runtimeContextuse_container is not False:
+            if docker_req and runtimeContext.use_container is not False:
                 if docker_req.get("dockerOutputDirectory"):
                     raise SourceLine(docker_req, "dockerOutputDirectory", UnsupportedRequirement).makeError(
                         "Option 'dockerOutputDirectory' of DockerRequirement not supported.")
-                runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api, docker_req, pull_image, self.arvrunner.project_uuid)
+                runtime_constraints["docker_image"] = arv_docker_get_image(self.arvrunner.api,
+                                                                           docker_req,
+                                                                           runtimeContext.pull_image,
+                                                                           self.arvrunner.project_uuid)
             else:
                 runtime_constraints["docker_image"] = "arvados/jobs"
 
@@ -252,7 +261,7 @@ class ArvadosJob(JobBase):
                                 dirs[g.group(1)] = g.group(2)
 
                     if processStatus == "permanentFail":
-                        done.logtail(logc, logger, "%s error log:" % self.arvrunner.label(self))
+                        done.logtail(logc, logger.error, "%s (%s) error log:" % (self.arvrunner.label(self), record["uuid"]), maxlen=40)
 
                     with Perf(metrics, "output collection %s" % self.name):
                         outputs = done.done(self, record, dirs["tmpdir"],
@@ -278,7 +287,7 @@ class ArvadosJob(JobBase):
 class RunnerJob(Runner):
     """Submit and manage a Crunch job that runs crunch_scripts/cwl-runner."""
 
-    def arvados_job_spec(self, runtimeContext):
+    def arvados_job_spec(self, debug=False):
         """Create an Arvados job specification for this workflow.
 
         The returned dict can be used to create a job (i.e., passed as
@@ -308,7 +317,7 @@ class RunnerJob(Runner):
         if self.on_error:
             self.job_order["arv:on_error"] = self.on_error
 
-        if runtimeContext.debug:
+        if debug:
             self.job_order["arv:debug"] = True
 
         return {
@@ -324,7 +333,7 @@ class RunnerJob(Runner):
         }
 
     def run(self, runtimeContext):
-        job_spec = self.arvados_job_spec(runtimeContext)
+        job_spec = self.arvados_job_spec(runtimeContext.debug)
 
         job_spec.setdefault("owner_uuid", self.arvrunner.project_uuid)