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Override some k8s runner params with destination params #10520

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Jan 7, 2021
Merged

Override some k8s runner params with destination params #10520

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20 changes: 18 additions & 2 deletions lib/galaxy/jobs/runners/kubernetes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,10 @@ def queue_job(self, job_wrapper):
job_wrapper.set_external_id(job_id)
self.monitor_queue.put(ajs)

def __get_overridable_params(self, job_wrapper, param_key):
dest_params = self.__get_destination_params(job_wrapper)
return dest_params.get(param_key, self.runner_params[param_key])

def __get_pull_policy(self):
return pull_policy(self.runner_params)

Expand Down Expand Up @@ -227,8 +231,10 @@ def __get_k8s_job_spec_template(self, ajs):
"containers": self.__get_k8s_containers(ajs),
"priorityClassName": self.runner_params['k8s_pod_priority_class'],
"tolerations": yaml.safe_load(self.runner_params['k8s_tolerations'] or "[]"),
"affinity": yaml.safe_load(self.runner_params['k8s_affinity'] or "{}"),
"nodeSelector": yaml.safe_load(self.runner_params['k8s_node_selector'] or "{}")
"affinity": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper,
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Are these things something we could test in https://github.com/mvdbeek/galaxy/blob/4842e0dbb9203209edcccfc72675c9b90e7b8b2d/test/integration/test_kubernetes_runner.py#L93 ? Set to some value that would prevent running the job and then override it in the destination ?

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Yeh I could try adding some tests

'k8s_affinity') or "{}"),
"nodeSelector": yaml.safe_load(self.__get_overridable_params(ajs.job_wrapper,
'k8s_node_selector') or "{}")
}
}
# TODO include other relevant elements that people might want to use from
Expand Down Expand Up @@ -391,6 +397,16 @@ def __get_k8s_container_name(self, job_wrapper):
return cleaned_id
return "job-container"

def __get_destination_params(self, job_wrapper):
"""Obtains allowable runner param overrides from the destination"""
job_destination = job_wrapper.job_destination
OVERRIDABLE_PARAMS = ["k8s_node_selector", "k8s_affinity"]
new_params = {}
for each_param in OVERRIDABLE_PARAMS:
if each_param in job_destination.params:
new_params[each_param] = job_destination.params[each_param]
return new_params

def check_watched_item(self, job_state):
"""Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState"""
jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
Expand Down