[ARVADOS] updated: e33f8c3fe2bd7b9d4d4f63540d38cd9732b7f854

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py      | 5 +----
 sdk/cwl/arvados_cwl/arvcontainer.py  | 5 ++---
 sdk/cwl/arvados_cwl/arvjob.py        | 3 +--
 sdk/cwl/arvados_cwl/crunch_script.py | 2 +-
 4 files changed, 5 insertions(+), 10 deletions(-)

       via  e33f8c3fe2bd7b9d4d4f63540d38cd9732b7f854 (commit)
       via  74e9a4dd2edc0b17d08d9b5ac8c7293dd9e93503 (commit)
      from  5f8e65c488277b3f259f791d1cd17361bd67009d (commit)

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commit e33f8c3fe2bd7b9d4d4f63540d38cd9732b7f854
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Jan 5 11:17:57 2017 -0500

    10793: Move output_callback to finally block to ensure it is always called.

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 30c163d..0c6fc75 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -173,10 +173,9 @@ class ArvadosContainer(object):
             processStatus = "permanentFail"
         except Exception as e:
             logger.exception("%s while getting output object: %s", self.arvrunner.label(self), e)
-            self.output_callback({}, "permanentFail")
-        else:
-            self.output_callback(outputs, processStatus)
+            processStatus = "permanentFail"
         finally:
+            self.output_callback(outputs, processStatus)
             if record["uuid"] in self.arvrunner.processes:
                 del self.arvrunner.processes[record["uuid"]]
 
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 08374a4..11ef653 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -223,9 +223,8 @@ class ArvadosJob(object):
                 logger.error("Unexpected output type %s '%s'", type(outputs), outputs)
                 outputs = {}
                 processStatus = "permanentFail"
-
-            self.output_callback(outputs, processStatus)
         finally:
+            self.output_callback(outputs, processStatus)
             if record["uuid"] in self.arvrunner.processes:
                 del self.arvrunner.processes[record["uuid"]]
 

commit 74e9a4dd2edc0b17d08d9b5ac8c7293dd9e93503
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Thu Jan 5 10:45:30 2017 -0500

    10793: Return output, status tuple from executor.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 850aa88..4288c16 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -482,14 +482,11 @@ class ArvCwlRunner(object):
             self.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.output_tags, self.final_output)
             self.set_crunch_output()
 
-        if self.final_status != "success":
-            raise WorkflowException("Workflow failed.")
-
         if kwargs.get("compute_checksum"):
             adjustDirObjs(self.final_output, partial(getListing, self.fs_access))
             adjustFileObjs(self.final_output, partial(compute_checksums, self.fs_access))
 
-        return self.final_output
+        return (self.final_output, self.final_status)
 
 
 def versionstring():
diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 71c65bc..1c7f570 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -99,7 +99,7 @@ def run():
         args.basedir = os.getcwd()
         args.name = None
         args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
-        outputObj = runner.arv_executor(t, job_order_object, **vars(args))
+        runner.arv_executor(t, job_order_object, **vars(args))
     except Exception as e:
         if isinstance(e, WorkflowException):
             logging.info("Workflow error %s", e)

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