Merge pull request #3319 from jmchilton/job_resubmission_refinement_0

Make it easier to use job re-submission conditions.

test/integration/resubmission_default_job_conf.xml

@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<!-- 
+    Slimmed down resubmission_job_conf.xml for testing default resubmission rules.
+-->
+<job_conf>
+    <plugins>
+        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/>
+        <plugin id="first_failure_runner" type="runner" load="integration.resubmission_runners:FailOnlyFirstJobRunner" workers="2">
+        </plugin>
+        <plugin id="dynamic" type="runner">
+            <param id="rules_module">integration.resubmission_rules</param>
+        </plugin>
+    </plugins>
+
+    <handlers>
+        <handler id="main"/>
+    </handlers>
+
+    <destinations default="initial_destination">
+        <destination id="initial_destination" runner="dynamic">
+            <param id="type">python</param>
+            <param id="function">initial_destination</param>
+        </destination>
+
+        <destination id="fail_first_try" runner="first_failure_runner">
+        </destination>
+
+        <!-- Upload destination. -->
+        <destination id="local" runner="local">
+        </destination>
+
+    </destinations>
+
+    <resources default="test">
+      <group id="upload"></group>
+      <group id="test">test_name,failure_state,initial_destination,run_for</group>
+    </resources>
+
+    <tools>
+        <tool id="upload1" destination="local" resources="upload" />
+    </tools>
+
+</job_conf>

test/integration/resubmission_runners.py

@@ -63,4 +63,24 @@ class AssertionJobRunner(LocalJobRunner):
         super(AssertionJobRunner, self).queue_job(job_wrapper)
 
 
+class FailOnlyFirstJobRunner(LocalJobRunner):
+    """Job runner that knows about test cases and checks final state assumptions."""
+
+    tests_seen = []
+
+    def queue_job(self, job_wrapper):
+        resource_parameters = job_wrapper.get_resource_parameters()
+        try:
+            test_name = resource_parameters["test_name"]
+        except KeyError:
+            job_wrapper.fail("Job resource parameter test_name not set as required for this job runner.")
+            return
+
+        if test_name in self.tests_seen:
+            super(FailOnlyFirstJobRunner, self).queue_job(job_wrapper)
+        else:
+            self.tests_seen.append(test_name)
+            self._fail_job_local(job_wrapper, "Failing first attempt")
+
+
 __all__ = ('FailsJobRunner', 'AssertionJobRunner')

test/integration/test_job_resubmission.py

@@ -6,10 +6,27 @@ from base import integration_util
 
 SCRIPT_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
 JOB_RESUBMISSION_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_job_conf.xml")
+JOB_RESUBMISSION_DEFAULT_JOB_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_default_job_conf.xml")
 JOB_RESUBMISSION_JOB_RESOURCES_CONFIG_FILE = os.path.join(SCRIPT_DIRECTORY, "resubmission_job_resource_parameters_conf.xml")
 
 
-class JobResubmissionIntegrationTestCase(integration_util.IntegrationTestCase):
+class _BaseResubmissionIntegerationTestCase(integration_util.IntegrationTestCase):
+    framework_tool_and_types = True
+
+    def _assert_job_passes(self, resource_parameters):
+        self._run_tool_test("simple_constructs", resource_parameters=resource_parameters)
+
+    def _assert_job_fails(self, resource_parameters):
+        exception_thrown = False
+        try:
+            self._run_tool_test("simple_constructs", resource_parameters=resource_parameters)
+        except Exception:
+            exception_thrown = True
+
+        assert exception_thrown
+
+
+class JobResubmissionIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
 
     framework_tool_and_types = True
 
@@ -85,14 +102,16 @@ class JobResubmissionIntegrationTestCase(integration_util.IntegrationTestCase):
                                                      "initial_destination": "resubmit_after_two_delays",
                                                      "failure_state": "unknown_error"})
 
-    def _assert_job_passes(self, resource_parameters):
-        self._run_tool_test("simple_constructs", resource_parameters=resource_parameters)
 
-    def _assert_job_fails(self, resource_parameters):
-        exception_thrown = False
-        try:
-            self._run_tool_test("simple_constructs", resource_parameters=resource_parameters)
-        except Exception:
-            exception_thrown = True
+class JobResubmissionDefaultIntegrationTestCase(_BaseResubmissionIntegerationTestCase):
 
-        assert exception_thrown
+    framework_tool_and_types = True
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        config["default_job_resubmission_condition"] = "attempt < 2"
+        config["job_config_file"] = JOB_RESUBMISSION_DEFAULT_JOB_CONFIG_FILE
+        config["job_resource_params_file"] = JOB_RESUBMISSION_JOB_RESOURCES_CONFIG_FILE
+
+    def test_default_resubmission(self):
+        self._assert_job_passes(resource_parameters={"test_name": "test_default_resubmission"})

test/unit/jobs/test_job_configuration.py

@@ -22,6 +22,7 @@ class JobConfXmlParserTestCase( unittest.TestCase ):
             use_tasked_jobs=False,
             job_resource_params_file="/tmp/fake_absent_path",
             config_dict={},
+            default_job_resubmission_condition="",
         )
         self.__write_config_from( SIMPLE_JOB_CONF )
         self.app = bunch.Bunch( config=self.config, job_metrics=MockJobMetrics() )