From 8b81031bf86ed5fbb412dcfd8fa0fe3dd3457279 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Mon, 3 Nov 2014 22:10:39 +0800
Subject: [PATCH] Disabling tests for Lsf706 specific functionality.

---
 .../examples/ExampleUnifiedGenotyperQueueTest.scala    |  2 +-
 .../queue/pipeline/examples/HelloWorldQueueTest.scala  |  6 +++---
 .../broadinstitute/gatk/queue/pipeline/QueueTest.scala |  4 ++--
 .../gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java     | 10 +++++-----
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala
index c4e81047f..d49bee6a5 100644
--- a/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala
+++ b/protected/gatk-queue-extensions-distribution/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala
@@ -91,7 +91,7 @@ class ExampleUnifiedGenotyperQueueTest {
       " -R " + BaseTest.hg18Reference,
       " -I " + BaseTest.validationDataLocation + "OV-0930.normal.chunk.bam",
       " -L " + intervalsPath).mkString
-    spec.jobRunners = Seq("Lsf706")
+    spec.jobRunners = Seq("GridEngine")
     QueueTest.executeTest(spec)
   }
 
diff --git a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
index 093050aa9..cef77f961 100644
--- a/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
+++ b/public/gatk-queue-extensions-public/src/test/scala/org/broadinstitute/gatk/queue/pipeline/examples/HelloWorldQueueTest.scala
@@ -68,7 +68,7 @@ class HelloWorldQueueTest {
     QueueTest.executeTest(spec)
   }
 
-  @Test(timeOut=36000000)
+  @Test(enabled=false, timeOut=36000000)
   def testHelloWorldWithLsfResource() {
     val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfResource"
@@ -78,7 +78,7 @@ class HelloWorldQueueTest {
     QueueTest.executeTest(spec)
   }
 
-  @Test(timeOut=36000000)
+  @Test(enabled=false, timeOut=36000000)
   def testHelloWorldWithLsfResourceAndMemoryLimit() {
     val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfResourceAndMemoryLimit"
@@ -88,7 +88,7 @@ class HelloWorldQueueTest {
     QueueTest.executeTest(spec)
   }
 
-  @Test(timeOut=36000000)
+  @Test(enabled=false, timeOut=36000000)
   def testHelloWorldWithLsfEnvironment() {
     val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfEnvironment"
diff --git a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
index 5cd25eb0c..024fcb6f1 100644
--- a/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
+++ b/public/gatk-queue/src/test/scala/org/broadinstitute/gatk/queue/pipeline/QueueTest.scala
@@ -53,12 +53,12 @@ object QueueTest extends BaseTest with Logging {
   /**
    * 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.
    */
-  final val defaultJobRunners = Seq("Lsf706", "GridEngine")
+  final val defaultJobRunners = Seq("GridEngine")
 
   /**
    * Returns the top level output path to this test.
diff --git a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
index 4af2bf7c7..e9df412e7 100644
--- a/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
+++ b/public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/jna/lsf/v7_0_6/LibBatQueueTest.java
@@ -42,19 +42,19 @@ import java.io.File;
  * Really unit tests, but these tests will only run on systems with LSF set up.
  */
 public class LibBatQueueTest extends BaseTest {
-    @BeforeClass
+    @BeforeClass(enabled=false)
     public void initLibBat() {
         Assert.assertFalse(LibBat.lsb_init("LibBatQueueTest") < 0, LibBat.lsb_sperror("lsb_init() failed"));
     }
 
-    @Test
+    @Test(enabled=false)
     public void testClusterName() {
         String clusterName = LibLsf.ls_getclustername();
         System.out.println("Cluster name: " + clusterName);
         Assert.assertNotNull(clusterName);
     }
 
-    @Test
+    @Test(enabled=false)
     public void testReadConfEnv() {
         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);
     }
 
-    @Test
+    @Test(enabled=false)
     public void testReadQueueLimits() {
         String queue = "hour";
         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);
     }
 
-    @Test
+    @Test(enabled=false)
     public void testSubmitEcho() throws Exception {
         if ( ! queueTestRunModeIsSet ) {
             throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode");