Commit 3d21c2b2 authored by Keller Patrick's avatar Keller Patrick

Merged

parent 3646fa01
......@@ -487,6 +487,8 @@ class WorkflowWrapper(threading.Thread):
self.toilProcess.terminate()
wesDAO.update_Workflow(self.workflowDBID, state="CANCELED")
return
def callToilRunner(self):
"""
This method executes the workflow with the toil-cwl-runner in a sub process.
......@@ -498,17 +500,15 @@ class WorkflowWrapper(threading.Thread):
if not self.restart:
self.toilProcess = subprocess.Popen(self.toilRunnerArgsList, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=False)
else:
self.stopped = False
self.restart = False
self.toilProcess = None
self.toilProcess = subprocess.Popen(self.toilRunnerArgsListRestart, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=False)
self.stopped = False
for l in self.toilProcess.stdout:
self.workflowID = wesDAO.get_workflow_id(self.workflowDBID)["workflow_id"]
logfile.write(l.decode('utf-8'))
if not self.stopped:
wesParser.parse_log(self.logFilePath, wesDAO, self.workflowDBID)
def checkStatusOfJobs(self):
"""
This method is searching for all 'job' entries in the log written by the toil runner.
......
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