[ARVADOS] updated: 1.1.4-188-g32d79de

[Git user]

Summary of changes:
 sdk/cwl/arvados_cwl/__init__.py     | 11 +++++------
 sdk/cwl/arvados_cwl/arvcontainer.py |  3 ---
 sdk/cwl/arvados_cwl/arvjob.py       |  1 -
 sdk/cwl/arvados_cwl/runner.py       |  2 --
 4 files changed, 5 insertions(+), 12 deletions(-)

       via  32d79def3a400de6fbe4cd02a8c71643238d867d (commit)
      from  6e098e8fde75fcec7e5be1a4873029f394bd055a (commit)

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commit 32d79def3a400de6fbe4cd02a8c71643238d867d
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Thu May 3 15:48:16 2018 -0400

    13365: Further fixes to ensure output callback only happens once
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 8b31ece..b5c9195 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -157,10 +157,11 @@ class ArvCwlRunner(object):
         with self.workflow_eval_lock:
             self.processes[container.uuid] = container
 
-    def process_done(self, uuid):
+    def process_done(self, uuid, record):
         with self.workflow_eval_lock:
-            if uuid in self.processes:
-                del self.processes[uuid]
+            j = self.processes[uuid]
+            self.task_queue.add(partial(j.done, record))
+            del self.processes[uuid]
 
     def wrapped_callback(self, cb, obj, st):
         with self.workflow_eval_lock:
@@ -181,10 +182,8 @@ class ArvCwlRunner(object):
                         j.update_pipeline_component(event["properties"]["new_attributes"])
                         logger.info("%s %s is Running", self.label(j), uuid)
             elif event["properties"]["new_attributes"]["state"] in ("Complete", "Failed", "Cancelled", "Final"):
-                with self.workflow_eval_lock:
-                    j = self.processes[uuid]
-                self.task_queue.add(partial(j.done, event["properties"]["new_attributes"]))
                 logger.info("%s %s is %s", self.label(j), uuid, event["properties"]["new_attributes"]["state"])
+                self.process_done(uuid, event["properties"]["new_attributes"])
 
     def label(self, obj):
         return "[%s %s]" % (self.work_api[0:-1], obj.name)
diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 9588803..4e7811d 100644
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -316,7 +316,6 @@ class ArvadosContainer(object):
             processStatus = "permanentFail"
         finally:
             self.output_callback(outputs, processStatus)
-            self.arvrunner.process_done(record["uuid"])
 
 
 class RunnerContainer(Runner):
@@ -464,5 +463,3 @@ class RunnerContainer(Runner):
             self.arvrunner.output_callback({}, "permanentFail")
         else:
             super(RunnerContainer, self).done(container)
-        finally:
-            self.arvrunner.process_done(record["uuid"])
diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index 801be7d..04256c6 100644
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -264,7 +264,6 @@ class ArvadosJob(object):
                 processStatus = "permanentFail"
         finally:
             self.output_callback(outputs, processStatus)
-            self.arvrunner.process_done(record["uuid"])
 
 
 class RunnerJob(Runner):
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 6491933..8db3e61 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -431,5 +431,3 @@ class Runner(object):
             self.arvrunner.output_callback({}, "permanentFail")
         else:
             self.arvrunner.output_callback(outputs, processStatus)
-        finally:
-            self.arvrunner.process_done(record["uuid"])

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