From 879d7c22b63733dfd5f9e1c6cbe368c97e06495d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 30 Oct 2018 16:29:36 +0100
Subject: [PATCH] Add basic kubernetes integration test

Currently times out becasue jobs aren't monitored succesfully.
---
 test/base/integration_util.py              |   4 +
 test/integration/test_kubernetes_runner.py | 132 +++++++++++++++++++++
 2 files changed, 136 insertions(+)
 create mode 100644 test/integration/test_kubernetes_runner.py

diff --git a/test/base/integration_util.py b/test/base/integration_util.py
index 185fb3c26cd7..ef84e639fd5c 100644
--- a/test/base/integration_util.py
+++ b/test/base/integration_util.py
@@ -37,6 +37,10 @@ def skip_unless_singularity():
     return skip_unless_executable("singularity")
 
 
+def skip_unless_kubernetes():
+    return skip_unless_executable("kubectl")
+
+
 class IntegrationTestCase(TestCase, UsesApiTestCaseMixin):
     """Unit test case with utilities for spinning up Galaxy."""
 
diff --git a/test/integration/test_kubernetes_runner.py b/test/integration/test_kubernetes_runner.py
new file mode 100644
index 000000000000..9ce1575d407e
--- /dev/null
+++ b/test/integration/test_kubernetes_runner.py
@@ -0,0 +1,132 @@
+"""Integration tests for the CLI shell plugins and runners."""
+import collections
+import os
+import string
+import subprocess
+import tempfile
+
+from base import integration_util  # noqa: I100,I202
+from base.populators import skip_without_tool
+from .test_job_environments import BaseJobEnvironmentIntegrationTestCase  # noqa: I201
+
+integration_util.skip_unless_kubernetes()
+
+PERSISTENT_VOLUME_NAME = 'pv-galaxy-integration-test'
+PERSISTENT_VOLUME_CLAIM_NAME = 'galaxy-pvc-integration-test'
+Config = collections.namedtuple('ConfigTuple', 'path')
+
+
+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):
+    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():
+    peristent_volume_claim_yaml = string.Template("""
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: $persistent_volume_claim_name
+spec:
+  accessModes:
+    - ReadWriteMany
+  volumeName: $persistent_volume_name
+  resources:
+    requests:
+      storage: 2Gi
+  storageClassName: manual
+""").substitute(persistent_volume_name=PERSISTENT_VOLUME_NAME,
+                persistent_volume_claim_name=PERSISTENT_VOLUME_CLAIM_NAME)
+    with tempfile.NamedTemporaryFile(suffix="_persistent_volume_claim.yml", mode="w", delete=False) as volume_claim:
+        volume_claim.write(peristent_volume_claim_yaml)
+    return KubeSetupConfigTuple(path=volume_claim.name)
+
+
+def job_config(path):
+    job_conf_template = string.Template("""<job_conf>
+    <plugins>
+        <plugin id="k8s" type="runner" load="galaxy.jobs.runners.kubernetes:KubernetesJobRunner">
+            <param id="k8s_persistent_volume_claim_name">galaxy-pvc-integration-test</param>
+            <param id="k8s_persistent_volume_claim_mount_path">$path</param>
+            <param id="k8s_config_path">$k8s_config_path</param>
+            <param id="k8s_galaxy_instance_id">gx-short-id</param>
+        </plugin>
+    </plugins>
+    <destinations default="k8s_destination">
+        <destination id="k8s_destination" runner="k8s">
+            <param id="docker_enabled">true</param>
+            <env id="SOME_ENV_VAR">42</env>
+        </destination>
+    </destinations>
+</job_conf>
+""")
+    job_conf_str = job_conf_template.substitute(path=path, k8s_config_path=os.environ.get('GALAXY_TEST_KUBE_CONFIG_PATH', '~/.kube/config'))
+    with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf", mode="w", delete=False) as job_conf:
+        job_conf.write(job_conf_str)
+    return Config(job_conf.name)
+
+
+class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.jobs_directory = tempfile.mkdtemp()
+        cls.persistent_volume = persistent_volume(path=cls.jobs_directory)
+        cls.persistent_volume.setup()
+        cls.persistent_volume_claim = persistent_volume_claim()
+        cls.persistent_volume_claim.setup()
+        cls.job_config = job_config(path=cls.jobs_directory)
+        super(BaseKubernetesIntegrationTestCase, cls).setUpClass()
+
+    @classmethod
+    def tearDownClass(cls):
+        cls.persistent_volume_claim.teardown()
+        cls.persistent_volume.teardown()
+        super(BaseKubernetesIntegrationTestCase, cls).tearDownClass()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config, ):
+        config["jobs_directory"] = cls.jobs_directory
+        config["file_path"] = cls.jobs_directory
+        config["job_config_file"] = cls.job_config.path
+
+    @skip_without_tool("job_environment_default")
+    def test_running_cli_job(self):
+        job_env = self._run_and_get_environment_properties()
+        assert job_env.some_env == '42'