Merge branch '17948-test-collection-tool' into main. Closes #17948

[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 fb23c2ccf73df514923f4fd0041814c6e8751833..c9170c51b732deee8f5a8bc383746c527ae5def7 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -21,8 +21,7 @@ import ruamel.yaml as yaml
 
 from cwltool.errors import WorkflowException
 from cwltool.process import UnsupportedRequirement, shortname
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.utils import aslist
+from cwltool.utils import aslist, adjustFileObjs, adjustDirObjs, visit_class
 from cwltool.job import JobBase
 
 import arvados.collection
@@ -235,7 +234,9 @@ class ArvadosContainer(JobBase):
         container_request["container_image"] = arv_docker_get_image(self.arvrunner.api,
                                                                     docker_req,
                                                                     runtimeContext.pull_image,
-                                                                    runtimeContext.project_uuid)
+                                                                    runtimeContext.project_uuid,
+                                                                    runtimeContext.force_docker_pull,
+                                                                    runtimeContext.tmp_outdir_prefix)
 
         network_req, _ = self.get_requirement("NetworkAccess")
         if network_req:
@@ -272,6 +273,12 @@ 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.timelimit is not None and self.timelimit > 0:
             scheduling_parameters["max_run_time"] = self.timelimit
 
@@ -325,8 +332,8 @@ class ArvadosContainer(JobBase):
                 logger.info("%s reused container %s", self.arvrunner.label(self), response["container_uuid"])
             else:
                 logger.info("%s %s state is %s", self.arvrunner.label(self), response["uuid"], response["state"])
-        except Exception:
-            logger.exception("%s got an error", self.arvrunner.label(self))
+        except Exception as e:
+            logger.exception("%s error submitting container\n%s", self.arvrunner.label(self), e)
             logger.debug("Container request was %s", container_request)
             self.output_callback({}, "permanentFail")
 
@@ -475,6 +482,7 @@ class RunnerContainer(Runner):
                    "--api=containers",
                    "--no-log-timestamps",
                    "--disable-validate",
+                   "--disable-color",
                    "--eval-timeout=%s" % self.arvrunner.eval_timeout,
                    "--thread-count=%s" % self.arvrunner.thread_count,
                    "--enable-reuse" if self.enable_reuse else "--disable-reuse",
@@ -493,6 +501,9 @@ class RunnerContainer(Runner):
         if runtimeContext.storage_classes != "default":
             command.append("--storage-classes=" + runtimeContext.storage_classes)
 
+        if runtimeContext.intermediate_storage_classes != "default":
+            command.append("--intermediate-storage-classes=" + runtimeContext.intermediate_storage_classes)
+
         if self.on_error:
             command.append("--on-error=" + self.on_error)
 
@@ -545,6 +556,17 @@ class RunnerContainer(Runner):
 
         logger.info("%s submitted container_request %s", self.arvrunner.label(self), response["uuid"])
 
+        workbench1 = self.arvrunner.api.config()["Services"]["Workbench1"]["ExternalURL"]
+        workbench2 = self.arvrunner.api.config()["Services"]["Workbench2"]["ExternalURL"]
+        url = ""
+        if workbench2:
+            url = "{}processes/{}".format(workbench2, response["uuid"])
+        elif workbench1:
+            url = "{}container_requests/{}".format(workbench1, response["uuid"])
+        if url:
+            logger.info("Monitor workflow progress at %s", url)
+
+
     def done(self, record):
         try:
             container = self.arvrunner.api.containers().get(