10088: Updated cwltool deduplicates dependencies to avoid creating separate

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index b11ca548176b64d68c6953b26e93813053ceada6..7bfdba8b80e48d9cb24d7054933b428aa3729764 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -24,6 +24,7 @@ from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
 from .arvtool import ArvadosCommandTool
 from .fsaccess import CollectionFsAccess
 from .arvworkflow import make_workflow
+from .perf import Perf
 
 from cwltool.process import shortname, UnsupportedRequirement
 from cwltool.pathmapper import adjustFileObjs
@@ -97,7 +98,8 @@ class ArvCwlRunner(object):
                         self.cond.acquire()
                         j = self.processes[uuid]
                         logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
-                        j.done(event["properties"]["new_attributes"])
+                        with Perf(logger, "done %s" % j.name):
+                            j.done(event["properties"]["new_attributes"])
                         self.cond.notify()
                     finally:
                         self.cond.release()
@@ -162,6 +164,9 @@ class ArvCwlRunner(object):
             logger.setLevel(logging.WARN)
             logging.getLogger('arvados.arv-run').setLevel(logging.WARN)
 
+        if self.debug:
+            logger.setLevel(logging.DEBUG)
+
         useruuid = self.api.users().current().execute()["uuid"]
         self.project_uuid = kwargs.get("project_uuid") if kwargs.get("project_uuid") else useruuid
         self.pipeline = None
@@ -177,7 +182,6 @@ class ArvCwlRunner(object):
         if kwargs.get("create_workflow") or kwargs.get("update_workflow"):
             return make_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
 
-        self.debug = kwargs.get("debug")
         self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
 
         kwargs["make_fs_access"] = make_fs_access
@@ -244,7 +248,8 @@ class ArvCwlRunner(object):
 
             for runnable in jobiter:
                 if runnable:
-                    runnable.run(**kwargs)
+                    with Perf(logger, "run"):
+                        runnable.run(**kwargs)
                 else:
                     if self.processes:
                         self.cond.wait(1)
@@ -329,7 +334,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=True, dest="enable_reuse",
                         help="")
 
-    parser.add_argument("--project-uuid", type=str, help="Project that will own the workflow jobs, if not provided, will go to home project.")
+    parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
                         default=False)
@@ -341,7 +346,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=True, dest="submit")
     exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")
     exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow.")
-    exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow.")
+    exgroup.add_argument("--update-workflow", type=str, metavar="UUID", help="Update existing Arvados workflow with uuid.")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",