Rework conditions for running Kubernetes staging tests.

lib/galaxy_test/driver/integration_util.py

@@ -15,6 +15,8 @@
 from .driver_util import GalaxyTestDriver
 
 NO_APP_MESSAGE = "test_case._app called though no Galaxy has been configured."
+# Following should be for Homebrew Rabbitmq and Docker on Mac "amqp://guest:guest@localhost:5672//"
+AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", None)
 
 
 def _identity(func):
@@ -28,6 +30,12 @@ def skip_if_jenkins(cls):
     return cls
 
 
+def skip_unless_amqp():
+    if AMQP_URL is not None:
+        return _identity
+    return pytest.mark.skip("AMQP_URL is not set, required for this test.")
+
+
 def skip_unless_executable(executable):
     if which(executable):
         return _identity

test/integration/test_kubernetes_staging.py

@@ -15,14 +15,19 @@
 import string
 import tempfile
 
+from galaxy.jobs.runners.util.pykube_util import (
+    Job,
+    pykube_client_from_dict,
+)
 from galaxy_test.base.populators import skip_without_tool
 from galaxy_test.driver import integration_util
 from .test_containerized_jobs import EXTENDED_TIMEOUT, MulledJobTestCases
 from .test_job_environments import BaseJobEnvironmentIntegrationTestCase
+from .test_local_job_cancellation import CancelsJob
 
 TOOL_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'tools'))
-AMQP_URL = os.environ.get("GALAXY_TEST_AMQP_URL", "amqp://guest:guest@localhost:5672//")
 GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST = os.environ.get("GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST", "host.docker.internal")
+AMQP_URL = integration_util.AMQP_URL
 
 
 CONTAINERIZED_TEMPLATE = """
@@ -32,7 +37,6 @@
     workers: 1
   pulsar_k8s:
     load: galaxy.jobs.runners.pulsar:PulsarKubernetesJobRunner
-    galaxy_url: ${infrastructure_url}
     amqp_url: ${amqp_url}
 
 execution:
@@ -63,7 +67,6 @@
     workers: 1
   pulsar_k8s:
     load: galaxy.jobs.runners.pulsar:PulsarKubernetesJobRunner
-    galaxy_url: ${infrastructure_url}
     amqp_url: ${amqp_url}
 
 execution:
@@ -87,35 +90,33 @@
 
 def job_config(template_str, jobs_directory):
     job_conf_template = string.Template(template_str)
-    port = os.environ.get('GALAXY_TEST_PORT')
-    assert port
-    infrastructure_url = "http://%s:%s" % (GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST, port)
     container_amqp_url = to_infrastructure_uri(AMQP_URL)
     job_conf_str = job_conf_template.substitute(jobs_directory=jobs_directory,
                                                 tool_directory=TOOL_DIR,
                                                 k8s_config_path=integration_util.k8s_config_path(),
                                                 amqp_url=AMQP_URL,
                                                 container_amqp_url=container_amqp_url,
-                                                infrastructure_url=infrastructure_url,
                                                 )
     with tempfile.NamedTemporaryFile(suffix="_kubernetes_integration_job_conf.yml", mode="w", delete=False) as job_conf:
         job_conf.write(job_conf_str)
     return job_conf.name
 
 
 @integration_util.skip_unless_kubernetes()
-@integration_util.skip_unless_fixed_port()
+@integration_util.skip_unless_amqp()
 class BaseKubernetesStagingTest(BaseJobEnvironmentIntegrationTestCase, MulledJobTestCases):
+    # Test leverages $UWSGI_PORT in job code, need to set this up.
+    require_uwsgi = True
 
     def setUp(self):
-        super(KubernetesStagingContainerIntegrationTestCase, self).setUp()
+        super(BaseKubernetesStagingTest, self).setUp()
         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())
-        super(KubernetesStagingContainerIntegrationTestCase, cls).setUpClass()
+        super(BaseKubernetesStagingTest, cls).setUpClass()
 
 
 class KubernetesStagingContainerIntegrationTestCase(BaseKubernetesStagingTest):
@@ -128,6 +129,7 @@ def handle_galaxy_config_kwds(cls, config):
         config["default_job_shell"] = '/bin/sh'
         # Disable local tool dependency resolution.
         config["tool_dependency_dir"] = "none"
+        set_infrastucture_url(config)
 
     @skip_without_tool("job_environment_default")
     def test_job_environment(self):
@@ -149,6 +151,7 @@ def handle_galaxy_config_kwds(cls, config):
         # Disable tool dependency resolution.
         config["tool_dependency_dir"] = "none"
         config["enable_beta_mulled_containers"] = "true"
+        set_infrastucture_url(config)
 
     def test_mulled_simple(self):
         self.dataset_populator.run_tool("mulled_example_simple", {}, self.history_id)
@@ -157,6 +160,11 @@ def test_mulled_simple(self):
         assert "0.7.15-r1140" in output
 
 
+def set_infrastucture_url(config):
+    infrastructure_url = "http://%s:$UWSGI_PORT" % GALAXY_TEST_KUBERNETES_INFRASTRUCTURE_HOST
+    config["galaxy_infrastructure_url"] = infrastructure_url
+
+
 def to_infrastructure_uri(uri):
     # remap MQ or file server URI hostnames for in-container versions, this is sloppy
     # should actually parse the URI and rebuild with correct host