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fix: job deletion propagation policy #64

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fix: job deletion propagation policy #64

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17 changes: 2 additions & 15 deletions snakemake_executor_plugin_kubernetes/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -592,24 +592,11 @@ def unregister_secret(self):
def safe_delete_job(self, jobid, ignore_not_found=True):
import kubernetes.client

body = kubernetes.client.V1DeleteOptions()
body = kubernetes.client.V1DeleteOptions(propagation_policy="Foreground")
self.logger.debug(f"Deleting job {jobid} in namespace {self.namespace}")
try:
# Usually, kubernetes should delete the pods automatically
# when the job is deleted, but in some cases, this does not
# happen, so we delete the pods manually.
pods = self.kubeapi.list_namespaced_pod(
namespace=self.namespace,
label_selector=f"job-name={jobid}",
)
for pod in pods.items:
self.logger.debug(f"Deleting pod {pod.metadata.name} for job {jobid}")
self.kubeapi.delete_namespaced_pod(
pod.metadata.name, self.namespace, body=body
)

self.batchapi.delete_namespaced_job(
jobid, self.namespace, propagation_policy="Foreground", body=body
jobid, self.namespace, body=body
)
except kubernetes.client.rest.ApiException as e:
if e.status == 404 and ignore_not_found:
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