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test_kubernetes_runner.py
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test_kubernetes_runner.py
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"""Integration tests for the Kubernetes runner."""
# Tested on docker for mac 18.06.1-ce-mac73 using the default kubernetes setup,
# also works on minikube
import collections
import json
import os
import string
import subprocess
import tempfile
import time
import pytest
from galaxy.util import unicodify
from galaxy_test.base.populators import (
DatasetPopulator,
skip_without_tool,
)
from galaxy_test.driver import integration_util
from .test_containerized_jobs import MulledJobTestCases
from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
PERSISTENT_VOLUME_NAME = 'pv-galaxy-integration-test'
PERSISTENT_VOLUME_CLAIM_NAME = 'galaxy-pvc-integration-test'
Config = collections.namedtuple('ConfigTuple', 'path')
TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'tools'))
class KubeSetupConfigTuple(Config):
def setup(self):
subprocess.check_call(['kubectl', 'create', '-f', self.path])
def teardown(self):
subprocess.check_call(['kubectl', 'delete', '-f', self.path])
def persistent_volume(path, persistent_volume_name):
volume_yaml = string.Template("""
kind: PersistentVolume
apiVersion: v1
metadata:
name: $persistent_volume_name
labels:
type: local
spec:
capacity:
storage: 5Gi
accessModes:
- ReadWriteMany
persistentVolumeReclaimPolicy: Retain
storageClassName: manual
local:
path: $path
nodeAffinity:
required:
nodeSelectorTerms:
- matchExpressions:
- key: app
operator: NotIn
values:
- 'i-do-not-exist'
""").substitute(path=path,
persistent_volume_name=persistent_volume_name)
with tempfile.NamedTemporaryFile(suffix="_persistent_volume.yml", mode="w", delete=False) as volume:
volume.write(volume_yaml)
return KubeSetupConfigTuple(path=volume.name)
def persistent_volume_claim(persistent_volume_name, persistent_volum_claim_name):
peristent_volume_claim_yaml = string.Template("""
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
name: $persistent_volume_claim_name
spec:
accessModes:
- ReadWriteMany
volumeName: $persistent_volume_name
resources:
requests:
storage: 2Gi
storageClassName: manual
""").substitute(persistent_volume_name=persistent_volume_name,
persistent_volume_claim_name=persistent_volum_claim_name)
with tempfile.NamedTemporaryFile(suffix="_persistent_volume_claim.yml", mode="w", delete=False) as volume_claim:
volume_claim.write(peristent_volume_claim_yaml)
return KubeSetupConfigTuple(path=volume_claim.name)
def job_config(jobs_directory):
job_conf_template = string.Template("""<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
<plugin id="k8s" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
<param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
<param id="k8s_config_path">$k8s_config_path</param>
<param id="k8s_galaxy_instance_id">gx-short-id</param>
<param id="k8s_run_as_user_id">$$uid</param>
</plugin>
<plugin id="k8s_walltime_short" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
<param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
<param id="k8s_config_path">$k8s_config_path</param>
<param id="k8s_galaxy_instance_id">gx-short-id</param>
<param id="k8s_walltime_limit">10</param>
<param id="k8s_run_as_user_id">$$uid</param>
</plugin>
<plugin id="k8s_no_cleanup" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
<param id="k8s_persistent_volume_claims">jobs-directory-claim:$jobs_directory,tool-directory-claim:$tool_directory</param>
<param id="k8s_config_path">$k8s_config_path</param>
<param id="k8s_galaxy_instance_id">gx-short-id</param>
<param id="k8s_cleanup_job">never</param>
<param id="k8s_run_as_user_id">$$uid</param>
</plugin>
</plugins>
<destinations default="k8s_destination">
<destination id="k8s_destination" runner="k8s">
<param id="limits_cpu">1.1</param>
<param id="limits_memory">10M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="k8s_destination_walltime_short" runner="k8s_walltime_short">
<param id="limits_cpu">1.1</param>
<param id="limits_memory">10M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="k8s_destination_no_cleanup" runner="k8s_no_cleanup">
<param id="limits_cpu">1.1</param>
<param id="limits_memory">10M</param>
<param id="docker_enabled">true</param>
<param id="docker_default_container_id">busybox:ubuntu-14.04</param>
<env id="SOME_ENV_VAR">42</env>
</destination>
<destination id="local_dest" runner="local">
</destination>
</destinations>
<tools>
<tool id="upload1" destination="local_dest"/>
<tool id="create_2" destination="k8s_destination_walltime_short"/>
<tool id="galaxy_slots_and_memory" destination="k8s_destination_no_cleanup"/>
</tools>
</job_conf>
""")
job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
tool_directory=TOOL_DIR,
k8s_config_path=integration_util.k8s_config_path(),
)
with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.xml", mode="w", delete=False) as job_conf:
job_conf.write(job_conf_str)
return Config(job_conf.name)
class KubernetesDatasetPopulator(DatasetPopulator):
def wait_for_history(self, *args, **kwargs):
try:
super(KubernetesDatasetPopulator, self).wait_for_history(*args, **kwargs)
except AssertionError:
print("Kubernetes status:\n %s" % unicodify(subprocess.check_output(['kubectl', 'describe', 'nodes'])))
raise
@integration_util.skip_unless_kubernetes()
class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
def setUp(self):
super(BaseKubernetesIntegrationTestCase, self).setUp()
self.dataset_populator = KubernetesDatasetPopulator(self.galaxy_interactor)
self.history_id = self.dataset_populator.new_history()
@classmethod
def setUpClass(cls):
# realpath for docker deployed in a VM on Mac, also done in driver_util.
cls.jobs_directory = os.path.realpath(tempfile.mkdtemp())
cls.volumes = [
[cls.jobs_directory, 'jobs-directory-volume', 'jobs-directory-claim'],
[TOOL_DIR, 'tool-directory-volume', 'tool-directory-claim'],
]
cls.persistent_volumes = []
cls.persistent_volume_claims = []
for (path, volume, claim) in cls.volumes:
volume_obj = persistent_volume(path, volume)
volume_obj.setup()
cls.persistent_volumes.append(volume_obj)
claim_obj = persistent_volume_claim(volume, claim)
claim_obj.setup()
cls.persistent_volume_claims.append(claim_obj)
cls.job_config = job_config(jobs_directory=cls.jobs_directory)
super(BaseKubernetesIntegrationTestCase, cls).setUpClass()
@classmethod
def tearDownClass(cls):
for claim in cls.persistent_volume_claims:
claim.teardown()
for volume in cls.persistent_volumes:
volume.teardown()
super(BaseKubernetesIntegrationTestCase, cls).tearDownClass()
@classmethod
def handle_galaxy_config_kwds(cls, config):
# TODO: implement metadata setting as separate job, as service or side-car
config['retry_metadata_internally'] = True
config["jobs_directory"] = cls.jobs_directory
config["file_path"] = cls.jobs_directory
config["job_config_file"] = cls.job_config.path
config["default_job_shell"] = '/bin/sh'
# Disable tool dependency resolution.
config["tool_dependency_dir"] = "none"
@skip_without_tool("job_environment_default")
def test_job_environment(self):
job_env = self._run_and_get_environment_properties()
assert job_env.some_env == '42'
@staticmethod
def _wait_for_external_state(sa_session, job, expected):
# Not checking the state here allows the change from queued to running to overwrite
# the change from queued to deleted_new in the API thread - this is a problem because
# the job will still run. See issue https://github.com/galaxyproject/galaxy/issues/4960.
max_tries = 60
while max_tries > 0 and job.job_runner_external_id is None or job.state != expected:
sa_session.refresh(job)
time.sleep(1)
max_tries -= 1
@skip_without_tool('cat_data_and_sleep')
def test_kill_process(self):
with self.dataset_populator.test_history() as history_id:
hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
running_inputs = {
"input1": {"src": "hda", "id": hda1["id"]},
"sleep_time": 240,
}
running_response = self.dataset_populator.run_tool(
"cat_data_and_sleep",
running_inputs,
history_id,
assert_ok=False,
).json()
job_dict = running_response["jobs"][0]
app = self._app
sa_session = app.model.context.current
job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
assert not job.finished
external_id = job.job_runner_external_id
output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
status = json.loads(output)
assert status['status']['active'] == 1
delete_response = self.dataset_populator.cancel_job(job_dict["id"])
assert delete_response.json() is True
# Wait for job to be cancelled in kubernetes
time.sleep(2)
# The default job config removes jobs, didn't find a better way to check that the job doesn't exist anymore
with pytest.raises(subprocess.CalledProcessError) as excinfo:
subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json'], stderr=subprocess.STDOUT)
assert "not found" in unicodify(excinfo.value.output)
@skip_without_tool('cat_data_and_sleep')
def test_external_job_delete(self):
with self.dataset_populator.test_history() as history_id:
hda1 = self.dataset_populator.new_dataset(history_id, content="1 2 3")
running_inputs = {
"input1": {"src": "hda", "id": hda1["id"]},
"sleep_time": 240,
}
running_response = self.dataset_populator.run_tool(
"cat_data_and_sleep",
running_inputs,
history_id,
assert_ok=False,
)
job_dict = running_response.json()["jobs"][0]
app = self._app
sa_session = app.model.context.current
job = sa_session.query(app.model.Job).get(app.security.decode_id(job_dict["id"]))
self._wait_for_external_state(sa_session, job, app.model.Job.states.RUNNING)
external_id = job.job_runner_external_id
output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
status = json.loads(output)
assert status['status']['active'] == 1
output = unicodify(subprocess.check_output(['kubectl', 'delete', 'job', external_id, '-o', 'name']))
assert 'job.batch/%s' % external_id in output
result = self.dataset_populator.wait_for_tool_run(run_response=running_response, history_id=history_id,
assert_ok=False).json()
details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
assert details['state'] == app.model.Job.states.ERROR, details
@skip_without_tool('job_properties')
def test_exit_code_127(self):
inputs = {
'failbool': True
}
running_response = self.dataset_populator.run_tool(
"job_properties",
inputs,
self.history_id,
assert_ok=False,
)
result = self.dataset_populator.wait_for_tool_run(run_response=running_response, history_id=self.history_id, assert_ok=False).json()
details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
assert details['state'] == 'error', details
assert details['stdout'].strip() == 'The bool is not true', details
assert details['stderr'].strip() == 'The bool is very not true', details
assert details['exit_code'] == 127, details
@skip_without_tool('Count1')
def test_python_dep(self):
with self.dataset_populator.test_history() as history_id:
hda1 = self.dataset_populator.new_dataset(history_id, content="1\t2\t3", file_type='tabular', wait=True)
self.dataset_populator.run_tool(
'Count1',
{'input': {"src": "hda", "id": hda1["id"]},
'column': [1]},
self.history_id,
assert_ok=True,
)
@skip_without_tool('galaxy_slots_and_memory')
def test_slots_and_memory(self):
running_response = self.dataset_populator.run_tool(
'galaxy_slots_and_memory',
{},
self.history_id,
assert_ok=True
)
dataset_content = self.dataset_populator.get_history_dataset_content(self.history_id, hid=1).strip()
CPU = '2'
MEM = '10'
MEM_PER_SLOT = '5'
assert [CPU, MEM, MEM_PER_SLOT] == dataset_content.split('\n'), dataset_content
# Tool is mapped to destination without cleanup, make sure job still exists in kubernetes API
job_dict = running_response["jobs"][0]
job = self.galaxy_interactor.get("jobs/%s" % job_dict['id'], admin=True).json()
external_id = job['external_id']
output = unicodify(subprocess.check_output(['kubectl', 'get', 'job', external_id, '-o', 'json']))
status = json.loads(output)
assert 'active' not in status['status']
@skip_without_tool('create_2')
def test_walltime_limit(self):
running_response = self.dataset_populator.run_tool(
'create_2',
{'sleep_time': 60},
self.history_id,
assert_ok=False
)
result = self.dataset_populator.wait_for_tool_run(run_response=running_response,
history_id=self.history_id,
assert_ok=False).json()
details = self.dataset_populator.get_job_details(result['jobs'][0]['id'], full=True).json()
assert details['state'] == 'error'
hda_details = self.dataset_populator.get_history_dataset_details(self.history_id, assert_ok=False)
assert hda_details['misc_info'] == 'Job was active longer than specified deadline'