Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.

Fixed integration tests to wait on their own for the job to run instead of using SUB2_BSUB_BLOCK.
Updated VariantRecalibrationIntegrationTests MD5s which were knocked out of sync whele SUB2_BSUB_BLOCK was exiting in the middle of integration tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4840 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java

@@ -4477,7 +4477,7 @@ public class LibBat {
      */
     public static final int SUB2_MODIFY_CMD = 0x02;
 
-    /**
+    /**//* Removed access to SUB2_BSUB_BLOCK since it exits the process (including the JVM) with the exit code of the submitted job. -kshakir December 14, 2010
      * < Submit a job in a synchronous
      * mode so that submission does not return until the job terminates.
      * Note once this flag is set, the \ref lsb_submit will never return if
@@ -4486,7 +4486,7 @@ public class LibBat {
      * API call in the blocking mode and the parent process wait on the
      * child process (see wait() for details.
      */
-    public static final int SUB2_BSUB_BLOCK = 0x04;
+    //public static final int SUB2_BSUB_BLOCK = 0x04;
 
     /**
      * < Submit from NT.

java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -30,15 +30,15 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
 
     VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
             "4eeffa7a1965ce0c25c5edd0bae76290",  // in vcf
-            "7407987a0148284ed910e1858116dd8d",  // tranches
+            "a04e00d00c991d76900634376bc1a9d1",  // tranches
             "f34b36c1da8bcb080a584592d1f6dae7",  // recalVCF
-            "1296ebde7dd61c1c58c11b07b31fd61b"); // cut VCF
+            "ee07ff6c0ff6108e00b131ce3c7a7f65"); // cut VCF
 
     VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
             "8937a3ae7f176dacf47b8ee6c0023416",  // in vcf
-            "2896657b5c30bfd8e82e62e58d94ef4e",  // tranches
+            "8da48dec888c9d4e3c3c7ed7943c0c61",  // tranches
             "ae6a1e0874c966312e891b5a3c47b0e3",  // recalVCF
-            "5eed2030d513fae05e45468fa0bb1538"); // cut VCF
+            "3ac16abdc5bbd5148f0cf88e8a7af3c9"); // cut VCF
 
     @DataProvider(name = "VRTest")
     public Object[][] createData1() {

java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatIntegrationTest.java

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.jna.lsf.v7_0_6;
 
+import com.sun.jna.ptr.IntByReference;
 import org.apache.commons.io.FileUtils;
 import org.testng.Assert;
 import org.testng.annotations.Test;
@@ -36,15 +37,15 @@ import java.io.File;
  * Really a unit test, but this test will only run on systems with LSF setup.
  */
 public class LibBatIntegrationTest extends BaseTest {
-    @Test(enabled=false)
+    @Test
     public void testClusterName() {
         String clusterName = LibLsf.ls_getclustername();
         System.out.println("Cluster name: " + clusterName);
         Assert.assertNotNull(clusterName);
     }
 
-    @Test(enabled=false)
+    @Test
-    public void testSubmitEcho() {
+    public void testSubmitEcho() throws InterruptedException {
         String queue = "hour";
         File outFile = new File("LibBatIntegrationTest.out");
 
@@ -65,14 +66,41 @@ public class LibBatIntegrationTest extends BaseTest {
         req.options |= LibBat.SUB_OUT_FILE;
 
         req.command = "echo \"Hello world.\"";
-        req.options2 |= LibBat.SUB2_BSUB_BLOCK;
 
         submitReply reply = new submitReply();
         long jobId = LibBat.lsb_submit(req, reply);
 
         Assert.assertFalse(jobId < 0, LibBat.lsb_sperror("Error dispatching"));
+
+        System.out.println("Waiting for job to run: " + jobId);
+        int jobStatus = LibBat.JOB_STAT_PEND;
+        while (isSet(jobStatus, LibBat.JOB_STAT_PEND) || isSet(jobStatus, LibBat.JOB_STAT_RUN)) {
+            Thread.sleep(30 * 1000L);
+
+            int numJobs = LibBat.lsb_openjobinfo(jobId, null, null, null, null, LibBat.ALL_JOB);
+            try {
+                Assert.assertEquals(numJobs, 1);
+    
+                IntByReference more = new IntByReference();
+
+                jobInfoEnt jobInfo = LibBat.lsb_readjobinfo(more);
+                Assert.assertNotNull(jobInfo, "Job info is null");
+                Assert.assertEquals(more.getValue(), 0, "More job info results than expected");
+
+                jobStatus = jobInfo.status;
+            } finally {
+                LibBat.lsb_closejobinfo();
+            }
+        }
+        Assert.assertTrue(isSet(jobStatus, LibBat.JOB_STAT_DONE), String.format("Unexpected job status: 0x%02x", jobStatus));
+
         Assert.assertTrue(FileUtils.waitFor(outFile, 120), "File not found: " + outFile.getAbsolutePath());
         Assert.assertTrue(outFile.delete(), "Unable to delete " + outFile.getAbsolutePath());
         Assert.assertEquals(reply.queue, req.queue, "LSF reply queue does not match requested queue.");
+        System.out.println("Validating that we reached the end of the test without exit.");
+    }
+
+    private static boolean isSet(int value, int flag) {
+        return ((value & flag) == flag);
     }
 }