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Disabling tests for Lsf706 specific functionality.

This commit is contained in:
Khalid Shakir 2014-11-03 22:10:39 +08:00
parent f93b5b2c39
commit 8b81031bf8
4 changed files with 11 additions and 11 deletions
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2
protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala
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@ -91,7 +91,7 @@ class ExampleUnifiedGenotyperQueueTest {
" -R " + BaseTest.hg18Reference, " -R " + BaseTest.hg18Reference,
" -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam", " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam",
" -L " + intervalsPath).mkString " -L " + intervalsPath).mkString
spec.jobRunners = Seq("Lsf706") spec.jobRunners = Seq("GridEngine")
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }

6
public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
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@ -68,7 +68,7 @@ class HelloWorldQueueTest {
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }
@Test(timeOut=36000000) @Test(enabled=false, timeOut=36000000)
def testHelloWorldWithLsfResource() { def testHelloWorldWithLsfResource() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "HelloWorldWithLsfResource" spec.name = "HelloWorldWithLsfResource"
@ -78,7 +78,7 @@ class HelloWorldQueueTest {
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }
@Test(timeOut=36000000) @Test(enabled=false, timeOut=36000000)
def testHelloWorldWithLsfResourceAndMemoryLimit() { def testHelloWorldWithLsfResourceAndMemoryLimit() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "HelloWorldWithLsfResourceAndMemoryLimit" spec.name = "HelloWorldWithLsfResourceAndMemoryLimit"
@ -88,7 +88,7 @@ class HelloWorldQueueTest {
QueueTest.executeTest(spec) QueueTest.executeTest(spec)
} }
@Test(timeOut=36000000) @Test(enabled=false, timeOut=36000000)
def testHelloWorldWithLsfEnvironment() { def testHelloWorldWithLsfEnvironment() {
val spec = new QueueTestSpec val spec = new QueueTestSpec
spec.name = "HelloWorldWithLsfEnvironment" spec.name = "HelloWorldWithLsfEnvironment"

4
public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
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@ -53,12 +53,12 @@ object QueueTest extends BaseTest with Logging {
/** /**
* All the job runners configured to run QueueTests at The Broad. * All the job runners configured to run QueueTests at The Broad.
*/ */
final val allJobRunners = Seq("Lsf706", "GridEngine", "Shell") final val allJobRunners = Seq("GridEngine", "Shell")
/** /**
* The default job runners to run. * The default job runners to run.
*/ */
final val defaultJobRunners = Seq("Lsf706", "GridEngine") final val defaultJobRunners = Seq("GridEngine")
/** /**
* Returns the top level output path to this test. * Returns the top level output path to this test.

10
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
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@ -42,19 +42,19 @@ import java.io.File;
* Really unit tests, but these tests will only run on systems with LSF set up. * Really unit tests, but these tests will only run on systems with LSF set up.
*/ */
public class LibBatQueueTest extends BaseTest { public class LibBatQueueTest extends BaseTest {
@BeforeClass @BeforeClass(enabled=false)
public void initLibBat() { public void initLibBat() {
Assert.assertFalse(LibBat.lsb_init("LibBatQueueTest") < 0, LibBat.lsb_sperror("lsb_init() failed")); Assert.assertFalse(LibBat.lsb_init("LibBatQueueTest") < 0, LibBat.lsb_sperror("lsb_init() failed"));
} }
@Test @Test(enabled=false)
public void testClusterName() { public void testClusterName() {
String clusterName = LibLsf.ls_getclustername(); String clusterName = LibLsf.ls_getclustername();
System.out.println("Cluster name: " + clusterName); System.out.println("Cluster name: " + clusterName);
Assert.assertNotNull(clusterName); Assert.assertNotNull(clusterName);
} }
@Test @Test(enabled=false)
public void testReadConfEnv() { public void testReadConfEnv() {
LibLsf.config_param[] configParams = (LibLsf.config_param[]) new LibLsf.config_param().toArray(4); LibLsf.config_param[] configParams = (LibLsf.config_param[]) new LibLsf.config_param().toArray(4);
@ -77,7 +77,7 @@ public class LibBatQueueTest extends BaseTest {
Assert.assertNull(configParams[3].paramValue); Assert.assertNull(configParams[3].paramValue);
} }
@Test @Test(enabled=false)
public void testReadQueueLimits() { public void testReadQueueLimits() {
String queue = "hour"; String queue = "hour";
StringArray queues = new StringArray(new String[] {queue}); StringArray queues = new StringArray(new String[] {queue});
@ -92,7 +92,7 @@ public class LibBatQueueTest extends BaseTest {
Assert.assertTrue(runLimit > 0, "LSF run limit is not greater than zero: " + runLimit); Assert.assertTrue(runLimit > 0, "LSF run limit is not greater than zero: " + runLimit);
} }
@Test @Test(enabled=false)
public void testSubmitEcho() throws Exception { public void testSubmitEcho() throws Exception {
if ( ! queueTestRunModeIsSet ) { if ( ! queueTestRunModeIsSet ) {
throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode"); throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode");