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Prefer with open syntax within kubernetes.py

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This commit is contained in:
Luca Pireddu
2018-10-26 12:04:43 +02:00
parent e235343f76
commit cf02c98127
1 changed files with 20 additions and 23 deletions
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lib/galaxy/jobs/runners/kubernetes.py
+20 -23
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@@ -457,32 +457,29 @@ class KubernetesJobRunner(AsynchronousJobRunner):
elif len(jobs.response['items']) == 0:
# there is no job responding to this job_id, it is either lost or something happened.
log.error("No Jobs are available under expected selector app=" + job_state.job_id)
error_file = open(job_state.error_file, 'w')
error_file.write("No Kubernetes Jobs are available under expected selector app=" + job_state.job_id + "\n")
error_file.close()
with open(job_state.error_file, 'w') as error_file:
error_file.write("No Kubernetes Jobs are available under expected selector app=" + job_state.job_id + "\n")
self.mark_as_failed(job_state)
return job_state
else:
# there is more than one job associated to the expected unique job id used as selector.
log.error("There is more than one Kubernetes Job associated to job id " + job_state.job_id)
self.__produce_log_file(job_state)
error_file = open(job_state.error_file, 'w')
error_file.write("There is more than one Kubernetes Job associated to job id " + job_state.job_id + "\n")
error_file.close()
with open(job_state.error_file, 'w') as error_file:
error_file.write("There is more than one Kubernetes Job associated to job id " + job_state.job_id + "\n")
self.mark_as_failed(job_state)
return job_state
def _handle_job_failure(self, job, job_state, reason=None):
self.__produce_log_file(job_state)
error_file = open(job_state.error_file, 'w')
if reason == "OOM":
error_file.write("Job killed after running out of memory. Try with more memory.\n")
job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory."
job_state.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
else:
error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n")
job_state.fail_message = "More pods failed than allowed. See stdout for pods details."
error_file.close()
with open(job_state.error_file, 'w') as error_file:
if reason == "OOM":
error_file.write("Job killed after running out of memory. Try with more memory.\n")
job_state.fail_message = "Tool failed due to insufficient memory. Try with more memory."
job_state.runner_state = JobState.runner_states.MEMORY_LIMIT_REACHED
else:
error_file.write("Exceeded max number of Kubernetes pod retrials allowed for job\n")
job_state.fail_message = "More pods failed than allowed. See stdout for pods details."
job_state.running = False
self.mark_as_failed(job_state)
job.scale(replicas=0)
@@ -538,22 +535,22 @@ class KubernetesJobRunner(AsynchronousJobRunner):
def __produce_log_file(self, job_state):
pod_r = Pod.objects(self._pykube_api).filter(selector="app=" + job_state.job_id)
logs = ""
log_string = ""
for pod_obj in pod_r.response['items']:
try:
pod = Pod(self._pykube_api, pod_obj)
logs += "\n\n==== Pod " + pod.name + " log start ====\n\n"
logs += pod.logs(timestamps=True)
logs += "\n\n==== Pod " + pod.name + " log end ===="
log_string += "\n\n==== Pod " + pod.name + " log start ====\n\n"
log_string += pod.logs(timestamps=True)
log_string += "\n\n==== Pod " + pod.name + " log end ===="
except Exception as detail:
log.info("Could not write pod\'s " + pod_obj['metadata']['name'] +
" log file due to HTTPError " + str(detail))
log.info("Could not write log file for pod %s due to HTTPError %s",
detail, pod_obj['metadata']['name'])
if isinstance(log_string, text_type):
log_string = log_string.encode('utf8')
logs_file_path = job_state.output_file
try:
with open(logs_file_path, mode="w") as logs_file:
if isinstance(log_string, text_type):
log_string = log_string.encode('utf8')
logs_file.write(log_string)
except IOError as e:
log.error("Couldn't produce log files for %s", job_state.job_id)