mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_20.09' into dev
This commit is contained in:
mvdbeek
@@ -96,10 +96,11 @@ class ItemGrabber:
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HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION,
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HANDLER_ASSIGNMENT_METHODS.DB_SKIP_LOCKED,
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}
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try:
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return [m for m in handler_assignment_methods if m in grabbable_methods][0]
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except IndexError:
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return
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if handler_assignment_methods:
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try:
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return [m for m in handler_assignment_methods if m in grabbable_methods][0]
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except IndexError:
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return
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def grab_unhandled_items(self):
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"""
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@@ -6,7 +6,6 @@ import logging
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import math
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import os
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import re
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from time import sleep
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import yaml
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@@ -20,11 +19,12 @@ from galaxy.jobs.runners.util.pykube_util import (
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DEFAULT_JOB_API_VERSION,
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ensure_pykube,
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find_job_object_by_name,
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find_pod_object_by_name,
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galaxy_instance_id,
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Job,
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job_object_dict,
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Pod,
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produce_unique_k8s_job_name,
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produce_k8s_job_prefix,
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pull_policy,
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pykube_client_from_dict,
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stop_job,
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@@ -88,7 +88,10 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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self.setup_volumes()
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def setup_volumes(self):
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volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(','))
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if self.runner_params.get('k8s_persistent_volume_claims'):
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volume_claims = dict(volume.split(":") for volume in self.runner_params['k8s_persistent_volume_claims'].split(','))
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else:
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volume_claims = {}
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mountable_volumes = [{'name': claim_name, 'persistentVolumeClaim': {'claimName': claim_name}} for claim_name in volume_claims]
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self.runner_params['k8s_mountable_volumes'] = mountable_volumes
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volume_mounts = [{'name': claim_name, 'mountPath': mount_path} for claim_name, mount_path in volume_claims.items()]
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@@ -120,45 +123,21 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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return
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# Construction of the Kubernetes Job object follows: http://kubernetes.io/docs/user-guide/persistent-volumes/
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k8s_job_name = self.__produce_unique_k8s_job_name(job_wrapper.get_id_tag())
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k8s_job_prefix = self.__produce_k8s_job_prefix()
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k8s_job_obj = job_object_dict(
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self.runner_params,
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k8s_job_name,
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k8s_job_prefix,
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self.__get_k8s_job_spec(ajs)
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)
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# Checks if job exists and is trusted, or if it needs re-creation.
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job = Job(self._pykube_api, k8s_job_obj)
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job_exists = job.exists()
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if job_exists and not self._galaxy_instance_id:
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# if galaxy instance id is not set, then we don't trust matching jobs and we simply delete and
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# re-create the job
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log.debug("Matching job exists, but Job is not trusted, so it will be deleted and a new one created.")
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job.delete()
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elapsed_seconds = 0
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while job.exists():
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sleep(3)
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elapsed_seconds += 3
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if elapsed_seconds > self.runner_params['k8s_timeout_seconds_job_deletion']:
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log.debug(
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"Timed out before k8s could delete existing untrusted job %s, not queuing associated Galaxy job."
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% k8s_job_name)
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return
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log.debug("Waiting for job to be deleted " + k8s_job_name)
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Job(self._pykube_api, k8s_job_obj).create()
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elif job_exists and self._galaxy_instance_id:
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# The job exists and we trust the identifier.
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log.debug("Matching job exists, but Job is trusted, so we simply use the existing one for " + k8s_job_name)
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# We simply leave the k8s job to be handled later on by check_watched_item().
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else:
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# Creates the Kubernetes Job if it doesn't exist.
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job.create()
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job.create()
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job_id = job.metadata['name']
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# define job attributes in the AsyncronousJobState for follow-up
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ajs.job_id = k8s_job_name
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ajs.job_id = job_id
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# store runner information for tracking if Galaxy restarts
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job_wrapper.set_external_id(k8s_job_name)
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job_wrapper.set_external_id(job_id)
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self.monitor_queue.put(ajs)
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def __get_pull_policy(self):
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@@ -206,10 +185,9 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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"""Parse the ID of the Galaxy instance from runner params."""
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return galaxy_instance_id(self.runner_params)
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def __produce_unique_k8s_job_name(self, galaxy_internal_job_id):
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# wrapper.get_id_tag() instead of job_id for compatibility with TaskWrappers.
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def __produce_k8s_job_prefix(self):
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instance_id = self._galaxy_instance_id or ''
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return produce_unique_k8s_job_name(app_prefix='gxy', instance_id=instance_id, job_id=galaxy_internal_job_id)
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return produce_k8s_job_prefix(app_prefix='gxy', instance_id=instance_id)
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def __get_k8s_job_spec(self, ajs):
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"""Creates the k8s Job spec. For a Job spec, the only requirement is to have a .spec.template.
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@@ -227,7 +205,21 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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(see pod selector) and an appropriate restart policy."""
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k8s_spec_template = {
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"metadata": {
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"labels": {"app": self.__produce_unique_k8s_job_name(ajs.job_wrapper.get_id_tag())[:-5]}
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"labels": {
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"app.kubernetes.io/name": ajs.job_wrapper.tool.old_id,
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"app.kubernetes.io/instance": self.__produce_k8s_job_prefix(),
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"app.kubernetes.io/version": ajs.job_wrapper.tool.version,
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"app.kubernetes.io/component": "tool",
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"app.kubernetes.io/part-of": "galaxy",
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"app.kubernetes.io/managed-by": "galaxy",
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"app.galaxyproject.org/job_id": ajs.job_wrapper.get_id_tag(),
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"app.galaxyproject.org/instance": self._galaxy_instance_id or "",
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"app.galaxyproject.org/handler": self.app.config.server_name,
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"app.galaxyproject.org/destination": ajs.job_wrapper.job_destination.id,
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},
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"annotations": {
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"app.galaxyproject.org/tool_id": ajs.job_wrapper.tool.id,
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}
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},
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"spec": {
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"volumes": self.runner_params['k8s_mountable_volumes'],
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@@ -401,8 +393,8 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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def check_watched_item(self, job_state):
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"""Checks the state of a job already submitted on k8s. Job state is an AsynchronousJobState"""
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jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id,
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namespace=self.runner_params['k8s_namespace'])
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jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
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if len(jobs.response['items']) == 1:
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job = Job(self._pykube_api, jobs.response['items'][0])
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job_destination = job_state.job_wrapper.job_destination
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@@ -506,8 +498,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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||||
marks the job for resubmission (resubmit logic is part of destinations).
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"""
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||||
pods = Pod.objects(self._pykube_api).filter(selector="app=%s" % job_state.job_id,
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namespace=self.runner_params['k8s_namespace'])
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pods = find_pod_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
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if not pods.response['items']:
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return False
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@@ -522,17 +513,16 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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"""Attempts to delete a dispatched job to the k8s cluster"""
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job = job_wrapper.get_job()
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try:
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name = job.job_runner_external_id
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namespace = self.runner_params['k8s_namespace']
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job_to_delete = find_job_object_by_name(self._pykube_api, name, namespace)
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if job_to_delete:
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self.__cleanup_k8s_job(job_to_delete)
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job_to_delete = find_job_object_by_name(self._pykube_api, job.get_job_runner_external_id(), self.runner_params['k8s_namespace'])
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if job_to_delete and len(job_to_delete.response['items']) > 0:
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k8s_job = Job(self._pykube_api, job_to_delete.response['items'][0])
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self.__cleanup_k8s_job(k8s_job)
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# TODO assert whether job parallelism == 0
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# assert not job_to_delete.exists(), "Could not delete job,"+job.job_runner_external_id+" it still exists"
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log.debug(f"({job.id}/{job.job_runner_external_id}) Terminated at user's request")
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except Exception as e:
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log.exception("({}/{}) User killed running job, but error encountered during termination: {}".format(
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job.id, job.job_runner_external_id, e))
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job.id, job.get_job_runner_external_id(), e))
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def recover(self, job, job_wrapper):
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"""Recovers jobs stuck in the queued/running state when Galaxy started"""
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@@ -561,8 +551,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
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||||
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||||
def finish_job(self, job_state):
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super().finish_job(job_state)
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jobs = Job.objects(self._pykube_api).filter(selector="app=" + job_state.job_id,
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namespace=self.runner_params['k8s_namespace'])
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jobs = find_job_object_by_name(self._pykube_api, job_state.job_id, self.runner_params['k8s_namespace'])
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if len(jobs.response['items']) != 1:
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log.warning("More than one job matches selector. Possible configuration error"
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" in job id '%s'", job_state.job_id)
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||||
@@ -2,7 +2,6 @@
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||||
import logging
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||||
import os
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||||
import re
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||||
import uuid
|
||||
|
||||
try:
|
||||
from pykube.config import KubeConfig
|
||||
@@ -46,18 +45,9 @@ def pykube_client_from_dict(params):
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return pykube_client
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|
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|
||||
def produce_unique_k8s_job_name(app_prefix=None, instance_id=None, job_id=None):
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if job_id is None:
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job_id = str(uuid.uuid4())
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job_name = ""
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if app_prefix:
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job_name += "%s-" % app_prefix
|
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|
||||
if instance_id and len(instance_id) > 0:
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||||
job_name += "%s-" % instance_id
|
||||
|
||||
return "{}{}-{}".format(job_name, job_id, uuid.uuid4())[-63:]
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def produce_k8s_job_prefix(app_prefix=None, instance_id=None):
|
||||
job_name_elems = [app_prefix or "", instance_id or ""]
|
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return '-'.join(elem for elem in job_name_elems if elem)
|
||||
|
||||
|
||||
def pull_policy(params):
|
||||
@@ -69,23 +59,13 @@ def pull_policy(params):
|
||||
|
||||
|
||||
def find_job_object_by_name(pykube_api, job_name, namespace=None):
|
||||
return _find_object_by_name(Job, pykube_api, job_name, namespace=namespace)
|
||||
if not job_name:
|
||||
raise ValueError("job name must not be empty")
|
||||
return Job.objects(pykube_api).filter(field_selector={"metadata.name": job_name}, namespace=namespace)
|
||||
|
||||
|
||||
def find_pod_object_by_name(pykube_api, pod_name, namespace=None):
|
||||
return _find_object_by_name(Pod, pykube_api, pod_name, namespace=namespace)
|
||||
|
||||
|
||||
def _find_object_by_name(clazz, pykube_api, object_name, namespace=None):
|
||||
filter_kwd = dict(selector="app=%s" % object_name)
|
||||
if namespace is not None:
|
||||
filter_kwd["namespace"] = namespace
|
||||
|
||||
objs = clazz.objects(pykube_api).filter(**filter_kwd)
|
||||
obj = None
|
||||
if len(objs.response['items']) > 0:
|
||||
obj = clazz(pykube_api, objs.response['items'][0])
|
||||
return obj
|
||||
def find_pod_object_by_name(pykube_api, job_name, namespace=None):
|
||||
return Pod.objects(pykube_api).filter(selector="job-name=" + job_name, namespace=namespace)
|
||||
|
||||
|
||||
def stop_job(job, cleanup="always"):
|
||||
@@ -106,16 +86,13 @@ def stop_job(job, cleanup="always"):
|
||||
job.api.raise_for_status(r)
|
||||
|
||||
|
||||
def job_object_dict(params, job_name, spec):
|
||||
def job_object_dict(params, job_prefix, spec):
|
||||
k8s_job_obj = {
|
||||
"apiVersion": params.get('k8s_job_api_version', DEFAULT_JOB_API_VERSION),
|
||||
"kind": "Job",
|
||||
"metadata": {
|
||||
# metadata.name is the name of the pod resource created, and must be unique
|
||||
# http://kubernetes.io/docs/user-guide/configuring-containers/
|
||||
"name": job_name,
|
||||
"generateName": job_prefix + "-",
|
||||
"namespace": params.get('k8s_namespace', DEFAULT_NAMESPACE),
|
||||
"labels": {"app": job_name}
|
||||
},
|
||||
"spec": spec,
|
||||
}
|
||||
@@ -152,7 +129,7 @@ __all__ = (
|
||||
"Job",
|
||||
"job_object_dict",
|
||||
"Pod",
|
||||
"produce_unique_k8s_job_name",
|
||||
"produce_k8s_job_prefix",
|
||||
"pull_policy",
|
||||
"pykube_client_from_dict",
|
||||
"stop_job",
|
||||
|
||||
@@ -548,7 +548,7 @@ class WeblessApplicationStack(ApplicationStack):
|
||||
for m in remove_methods:
|
||||
try:
|
||||
job_config.handler_assignment_methods.remove(m)
|
||||
log.debug("%s: Removed '%s' from handler assignment methods due to use of mules", conf_class_name, m)
|
||||
log.debug("%s: Removed '%s' from handler assignment methods due to use of --attach-to-pool", conf_class_name, m)
|
||||
except ValueError:
|
||||
pass
|
||||
if add_method not in job_config.handler_assignment_methods:
|
||||
|
||||
@@ -267,19 +267,18 @@ class WorkflowRequestMonitor(Monitors):
|
||||
self.workflow_scheduling_manager = workflow_scheduling_manager
|
||||
self._init_monitor_thread(name="WorkflowRequestMonitor.monitor_thread", target=self.__monitor, config=app.config)
|
||||
self.invocation_grabber = None
|
||||
if self.workflow_scheduling_manager.handler_assignment_methods_configured:
|
||||
self_handler_tags = set(self.app.job_config.self_handler_tags)
|
||||
self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id)
|
||||
handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods)
|
||||
if handler_assignment_method:
|
||||
self.invocation_grabber = ItemGrabber(
|
||||
app=app,
|
||||
grab_type='WorkflowInvocation',
|
||||
handler_assignment_method=handler_assignment_method,
|
||||
max_grab=self.workflow_scheduling_manager.handler_max_grab,
|
||||
self_handler_tags=self_handler_tags,
|
||||
handler_tags=self_handler_tags,
|
||||
)
|
||||
self_handler_tags = set(self.app.job_config.self_handler_tags)
|
||||
self_handler_tags.add(self.workflow_scheduling_manager.default_handler_id)
|
||||
handler_assignment_method = ItemGrabber.get_grabbable_handler_assignment_method(self.workflow_scheduling_manager.handler_assignment_methods)
|
||||
if handler_assignment_method:
|
||||
self.invocation_grabber = ItemGrabber(
|
||||
app=app,
|
||||
grab_type='WorkflowInvocation',
|
||||
handler_assignment_method=handler_assignment_method,
|
||||
max_grab=self.workflow_scheduling_manager.handler_max_grab,
|
||||
self_handler_tags=self_handler_tags,
|
||||
handler_tags=self_handler_tags,
|
||||
)
|
||||
|
||||
def __monitor(self):
|
||||
to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-app"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-auth"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-data"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-job-execution"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-job-metrics"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-objectstore"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-selenium"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,7 +6,14 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.1.0.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
* Initial import from dev branch of Galaxy during 20.01 development cycle.
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* Initial import from dev branch of Galaxy during 20.09 branch of Galaxy.
|
||||
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.1.0.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-test-api"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -1,2 +1 @@
|
||||
galaxy-test-driver
|
||||
|
||||
galaxy-test-base
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* Initial release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-test-base"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-test-driver"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,7 +6,13 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.1.0.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
* Initial import from dev branch of Galaxy during 20.01 development cycle.
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.1.0.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-test-selenium"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -1,4 +1,3 @@
|
||||
galaxy-data
|
||||
nose
|
||||
pytest
|
||||
galaxy-test-base
|
||||
|
||||
|
||||
|
||||
@@ -5,10 +5,17 @@ History
|
||||
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0.dev2
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.9.0.dev3'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-tool-util"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-03)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-util"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -6,11 +6,17 @@ History
|
||||
.. to_doc
|
||||
|
||||
---------------------
|
||||
20.5.1.dev0
|
||||
20.9.1.dev0
|
||||
---------------------
|
||||
|
||||
|
||||
|
||||
---------------------
|
||||
20.9.0 (2020-10-15)
|
||||
---------------------
|
||||
|
||||
* First release from the 20.09 branch of Galaxy.
|
||||
|
||||
---------------------
|
||||
20.5.0 (2020-07-04)
|
||||
---------------------
|
||||
|
||||
@@ -1,4 +1,6 @@
|
||||
__version__ = '20.5.1.dev0'
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
__version__ = '20.9.1.dev0'
|
||||
|
||||
PROJECT_NAME = "galaxy-web-framework"
|
||||
PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
|
||||
|
||||
@@ -42,6 +42,19 @@ WORKFLOW_HANDLER_JOB_CONFIG_TEMPLATE = string.Template("""
|
||||
</job_conf>
|
||||
""")
|
||||
|
||||
POOL_JOB_CONFIG_TEMPLATE = string.Template("""<job_conf>
|
||||
<plugins>
|
||||
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
|
||||
</plugins>
|
||||
<handlers $assign_with>
|
||||
</handlers>
|
||||
<destinations default="local">
|
||||
<destination id="local" runner="local">
|
||||
</destination>
|
||||
</destinations>
|
||||
</job_conf>
|
||||
""")
|
||||
|
||||
WORKFLOW_SCHEDULERS_CONFIG_TEMPLATE = string.Template("""
|
||||
<workflow_schedulers default="core">
|
||||
<core id="core" />
|
||||
@@ -220,6 +233,15 @@ class JobHandlerAsWorkflowHandlerWithDbSkipLocked(BaseWorkflowHandlerConfigurati
|
||||
assert self.is_app_workflow_scheduler
|
||||
|
||||
|
||||
class JobHandlerAsWorkflowHandlerWithDbSkipLockedAttachToPool(JobHandlerAsWorkflowHandlerWithDbSkipLocked):
|
||||
|
||||
@classmethod
|
||||
def handle_galaxy_config_kwds(cls, config):
|
||||
config["job_config_file"] = config_file(POOL_JOB_CONFIG_TEMPLATE, assign_with=cls.assign_with)
|
||||
config["server_name"] = "handler0"
|
||||
config["attach_to_pools"] = ["job-handlers"]
|
||||
|
||||
|
||||
class DefaultWorkflowHandlerIfJobHandlerOffTestCase(BaseWorkflowHandlerConfigurationTestCase):
|
||||
|
||||
@classmethod
|
||||
|
||||
Reference in New Issue
Block a user