Rename existing PipelineTests to QueueTests to prepare for upcoming push of new pipeline tests

-These tests are really integration tests for Queue rather than generalized
 pipeline tests, so it makes sense to call them QueueTests.

-Rename test classes and maven build targets, and update shell scripts
 to reflect new naming.

ant-bridge.sh

@@ -103,14 +103,14 @@ for arg in "${@}" ; do
             mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
             mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
 
-        # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
+        # TODO: This runs only the queue tests (full, non-dry run), but not the commit tests for Queue.
         elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
             mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo}"
             mvn_args="${mvn_args} -Dsting.packagetests.enabled=true"
-            mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
+            mvn_args="${mvn_args} -Dsting.packagequeuetests.skipped=false"
-            mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
+            mvn_args="${mvn_args} -Dsting.queuetests.run=true"
 
         elif [[ "${arg}" == "committests" ]] ; then
             mvn_args="verify -Dsting.committests.skipped=false"
@@ -130,11 +130,11 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "knowledgebasetest" ]] ; then
             mvn_args="verify -Dsting.knowledgebasetests.skipped=false"
 
-        elif [[ "${arg}" == "pipelinetest" ]] ; then
+        elif [[ "${arg}" == "queuetest" ]] ; then
-            mvn_args="verify -Dsting.pipelinetests.skipped=false"
+            mvn_args="verify -Dsting.queuetests.skipped=false"
 
-        elif [[ "${arg}" == "pipelinetestrun" ]] ; then
+        elif [[ "${arg}" == "queuetestrun" ]] ; then
-            mvn_args="verify -Dsting.pipelinetests.skipped=false -Dsting.pipelinetests.run=true"
+            mvn_args="verify -Dsting.queuetests.skipped=false -Dsting.queuetests.run=true"
 
         elif [[ "${arg}" == "fasttest" ]] ; then
             mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true"

pom.xml

@@ -48,7 +48,7 @@
         <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
         <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
-        <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
+        <sting.packagequeuetests.skipped>${sting.packagecommittests.skipped}</sting.packagequeuetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
         <sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
 
@@ -62,7 +62,7 @@
         <sting.serialcommittests.skipped>true</sting.serialcommittests.skipped>
         <sting.serialunittests.skipped>${sting.serialcommittests.skipped}</sting.serialunittests.skipped>
         <sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
-        <sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
+        <sting.serialqueuetests.skipped>${sting.serialcommittests.skipped}</sting.serialqueuetests.skipped>
         <sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
         <sting.serialknowledgebasetests.skipped>true</sting.serialknowledgebasetests.skipped>
     </properties>
@@ -561,7 +561,7 @@
                             <sting.packagetests.artifactId>${sting.packagetests.artifactId}</sting.packagetests.artifactId>
                             <sting.packagetests.testClasses>${project.build.testOutputDirectory}</sting.packagetests.testClasses>
                             <sting.packagetests.basedir>${project.basedir}</sting.packagetests.basedir>
-                            <sting.pipelinetests.run>${sting.pipelinetests.run}</sting.pipelinetests.run>
+                            <sting.queuetests.run>${sting.queuetests.run}</sting.queuetests.run>
                             <maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
                             <maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
                         </properties>
@@ -613,7 +613,7 @@
                             </configuration>
                         </execution>
                         <execution>
-                            <id>package-pipelinetests</id>
+                            <id>package-queuetests</id>
                             <goals>
                                 <goal>integration-test</goal>
                                 <goal>verify</goal>
@@ -622,11 +622,11 @@
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
-                                <reportsDirectory>${project.build.directory}/invoker-reports/pipeline/${it.test}</reportsDirectory>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/queuetest/${it.test}</reportsDirectory>
-                                <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
+                                <skipInvocation>${sting.packagequeuetests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
+                                    <sting.packagequeuetests.skipped>${sting.packagequeuetests.skipped}</sting.packagequeuetests.skipped>
                                 </properties>
                             </configuration>
                         </execution>

protected/gatk-protected/pom.xml

@@ -99,7 +99,7 @@
                         <id>package-knowledgebasetests</id>
                     </execution>
                     <execution>
-                        <id>package-pipelinetests</id>
+                        <id>package-queuetests</id>
                     </execution>
                 </executions>
             </plugin>

public/gatk-framework/pom.xml

@@ -86,7 +86,7 @@
                         <id>package-knowledgebasetests</id>
                     </execution>
                     <execution>
-                        <id>package-pipelinetests</id>
+                        <id>package-queuetests</id>
                     </execution>
                 </executions>
             </plugin>

public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java

@@ -135,7 +135,7 @@ public abstract class BaseTest {
     public final static String NA12878_PCRFREE = privateTestDir + "PCRFree.2x250.Illumina.20_10_11.bam";
     public final static String NA12878_WEx = privateTestDir + "CEUTrio.HiSeq.WEx.b37_decoy.NA12878.20_10_11mb.bam";
 
-    public static final boolean pipelineTestRunModeIsSet = System.getProperty("pipeline.run", "").equals("run");
+    public static final boolean queueTestRunModeIsSet = System.getProperty("queuetest.run", "").equals("true");
 
     /** before the class starts up */
     static {

public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionQueueTest.java

@@ -35,7 +35,7 @@ import org.testng.annotations.Test;
 import java.io.File;
 import java.util.*;
 
-public class JnaSessionPipelineTest extends BaseTest {
+public class JnaSessionQueueTest extends BaseTest {
     private String implementation = null;
     private static final SessionFactory factory = new JnaSessionFactory();
 
@@ -52,15 +52,15 @@ public class JnaSessionPipelineTest extends BaseTest {
 
     @Test(dependsOnMethods = { "testDrmaa" })
     public void testSubmitEcho() throws Exception {
-        if ( ! pipelineTestRunModeIsSet ) {
+        if ( ! queueTestRunModeIsSet ) {
-            throw new SkipException("Skipping testSubmitEcho because we are in pipeline test dry run mode");
+            throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode");
         }
 
         if (implementation.contains("LSF")) {
             System.err.println("    ***********************************************************");
             System.err.println("   *************************************************************");
             System.err.println("   ****                                                     ****");
-            System.err.println("  ****  Skipping JnaSessionPipelineTest.testSubmitEcho()     ****");
+            System.err.println("  ****  Skipping JnaSessionQueueTest.testSubmitEcho()        ****");
             System.err.println("  ****      Are you using the dotkit .combined_LSF_SGE?      ****");
             System.err.println("   ****                                                     ****");
             System.err.println("   *************************************************************");
@@ -68,7 +68,7 @@ public class JnaSessionPipelineTest extends BaseTest {
             throw new SkipException("Skipping testSubmitEcho because correct DRMAA implementation not found");
         }
 
-        File outFile = tryCreateNetworkTempFile("JnaSessionPipelineTest.out");
+        File outFile = tryCreateNetworkTempFile("JnaSessionQueueTest.out");
         Session session = factory.getSession();
         session.init(null);
         try {

public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaQueueTest.java

@@ -41,7 +41,7 @@ import java.io.File;
 import java.util.Arrays;
 import java.util.List;
 
-public class LibDrmaaPipelineTest extends BaseTest {
+public class LibDrmaaQueueTest extends BaseTest {
     private String implementation = null;
 
     @Test
@@ -88,7 +88,7 @@ public class LibDrmaaPipelineTest extends BaseTest {
 
     @Test(dependsOnMethods = { "testDrmaa" })
     public void testSubmitEcho() throws Exception {
-        if ( ! pipelineTestRunModeIsSet ) {
+        if ( ! queueTestRunModeIsSet ) {
             throw new SkipException("Skipping testSubmitEcho because we are in pipeline test dry run mode");
         }
 
@@ -96,7 +96,7 @@ public class LibDrmaaPipelineTest extends BaseTest {
             System.err.println("    *********************************************************");
             System.err.println("   ***********************************************************");
             System.err.println("   ****                                                   ****");
-            System.err.println("  ****  Skipping LibDrmaaPipelineTest.testSubmitEcho()     ****");
+            System.err.println("  ****  Skipping LibDrmaaQueueTest.testSubmitEcho()        ****");
             System.err.println("  ****     Are you using the dotkit .combined_LSF_SGE?     ****");
             System.err.println("   ****                                                   ****");
             System.err.println("   ***********************************************************");
@@ -107,7 +107,7 @@ public class LibDrmaaPipelineTest extends BaseTest {
         Memory error = new Memory(LibDrmaa.DRMAA_ERROR_STRING_BUFFER);
         int errnum;
 
-        File outFile = tryCreateNetworkTempFile("LibDrmaaPipelineTest.out");
+    File outFile = tryCreateNetworkTempFile("LibDrmaaQueueTest.out");
 
         errnum = LibDrmaa.drmaa_init(null, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN);
 

public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatQueueTest.java

@@ -39,12 +39,12 @@ import org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.*;
 import java.io.File;
 
 /**
- * Really unit tests, but these test will only run on systems with LSF setup.
+ * Really unit tests, but these tests will only run on systems with LSF set up.
  */
-public class LibBatPipelineTest extends BaseTest {
+public class LibBatQueueTest extends BaseTest {
     @BeforeClass
     public void initLibBat() {
-        Assert.assertFalse(LibBat.lsb_init("LibBatPipelineTest") < 0, LibBat.lsb_sperror("lsb_init() failed"));
+        Assert.assertFalse(LibBat.lsb_init("LibBatQueueTest") < 0, LibBat.lsb_sperror("lsb_init() failed"));
     }
 
     @Test
@@ -94,19 +94,19 @@ public class LibBatPipelineTest extends BaseTest {
 
     @Test
     public void testSubmitEcho() throws Exception {
-        if ( ! pipelineTestRunModeIsSet ) {
+        if ( ! queueTestRunModeIsSet ) {
-            throw new SkipException("Skipping testSubmitEcho because we are in pipeline test dry run mode");
+            throw new SkipException("Skipping testSubmitEcho because we are in queue test dry run mode");
         }
 
         String queue = "hour";
-        File outFile = tryCreateNetworkTempFile("LibBatPipelineTest.out");
+        File outFile = tryCreateNetworkTempFile("LibBatQueueTest.out");
 
         submit req = new submit();
 
         for (int i = 0; i < LibLsf.LSF_RLIM_NLIMITS; i++)
             req.rLimits[i] = LibLsf.DEFAULT_RLIMIT;
 
-        req.projectName = "LibBatPipelineTest";
+        req.projectName = "LibBatQueueTest";
         req.options |= LibBat.SUB_PROJECT_NAME;
 
         req.queue = queue;

public/gatk-package/pom.xml

@@ -105,9 +105,9 @@
                         </configuration>
                     </execution>
                     <execution>
-                        <id>pipeline-tests</id>
+                        <id>queue-tests</id>
                         <configuration>
-                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <skip>${sting.serialqueuetests.skipped}</skip>
                             <dependenciesToScan>
                                 <scan>org.broadinstitute.sting:.*</scan>
                             </dependenciesToScan>

public/package-tests/pom.xml

@@ -21,7 +21,7 @@
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <sting.packageunittests.skipped>true</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
-        <sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
+        <sting.packagequeuetests.skipped>true</sting.packagequeuetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
         <sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
     </properties>
@@ -161,13 +161,13 @@
                                 </configuration>
                             </execution>
                             <execution>
-                                <id>pipeline-tests</id>
+                                <id>queue-tests</id>
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
-                                <!-- run pipeline dry run tests -->
+                                <!-- run queue dry run tests -->
                                 <configuration>
-                                    <skip>${sting.packagepipelinetests.skipped}</skip>
+                                    <skip>${sting.packagequeuetests.skipped}</skip>
                                 </configuration>
                             </execution>
                             <execution>

public/pom.xml

@@ -19,7 +19,7 @@
         <module>sting-utils</module>
         <module>gatk-framework</module>
         <module>gatk-package</module>
- <!--       <module>external-example</module>  -->
+        <!--       <module>external-example</module>  -->
         <!-- queue optionally enabled as profiles -->
     </modules>
 

public/queue-framework/pom.xml

@@ -198,7 +198,7 @@
                         <id>package-knowledgebasetests</id>
                     </execution>
                     <execution>
-                        <id>package-pipelinetests</id>
+                        <id>package-queuetests</id>
                     </execution>
                 </executions>
             </plugin>

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTest.scala

@@ -39,13 +39,13 @@ import org.broadinstitute.sting.gatk.report.GATKReport
 import org.apache.commons.io.FileUtils
 import org.apache.commons.io.filefilter.WildcardFileFilter
 
-object PipelineTest extends BaseTest with Logging {
+object QueueTest extends BaseTest with Logging {
 
   private val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/"
   private val md5DB = new MD5DB()
 
   /**
-   * All the job runners configured to run PipelineTests at The Broad.
+   * All the job runners configured to run QueueTests at The Broad.
    */
   final val allJobRunners = Seq("Lsf706", "GridEngine", "Shell")
 
@@ -56,15 +56,15 @@ object PipelineTest extends BaseTest with Logging {
 
   /**
    * Returns the top level output path to this test.
-   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @param testName The name of the test passed to QueueTest.executeTest()
    * @param jobRunner The name of the job manager to run the jobs.
    * @return the top level output path to this test.
    */
-  def testDir(testName: String, jobRunner: String) = "pipelinetests/%s/%s/".format(testName, jobRunner)
+  def testDir(testName: String, jobRunner: String) = "queuetests/%s/%s/".format(testName, jobRunner)
 
   /**
    * Returns the directory where relative output files will be written for this test.
-   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @param testName The name of the test passed to QueueTest.executeTest()
    * @param jobRunner The name of the job manager to run the jobs.
    * @return the directory where relative output files will be written for this test.
    */
@@ -72,44 +72,44 @@ object PipelineTest extends BaseTest with Logging {
 
   /**
    * Returns the directory where temp files will be written for this test.
-   * @param testName The name of the test passed to PipelineTest.executeTest()
+   * @param testName The name of the test passed to QueueTest.executeTest()
    * @param jobRunner The name of the job manager to run the jobs.
    * @return the directory where temp files will be written for this test.
    */
   private def tempDir(testName: String, jobRunner: String) = testDir(testName, jobRunner) + "temp/"
 
   /**
-   * Runs the pipelineTest.
+   * Runs the queueTest.
-   * @param pipelineTest test to run.
+   * @param queueTest test to run.
    */
-  def executeTest(pipelineTest: PipelineTestSpec) {
+  def executeTest(queueTest: QueueTestSpec) {
-    var jobRunners = pipelineTest.jobRunners
+    var jobRunners = queueTest.jobRunners
     if (jobRunners == null)
       jobRunners = defaultJobRunners
-    jobRunners.foreach(executeTest(pipelineTest, _))
+    jobRunners.foreach(executeTest(queueTest, _))
   }
 
   /**
-   * Runs the pipelineTest.
+   * Runs the queueTest.
-   * @param pipelineTest test to run.
+   * @param queueTest test to run.
    * @param jobRunner The name of the job manager to run the jobs.
    */
-  def executeTest(pipelineTest: PipelineTestSpec, jobRunner: String) {
+  def executeTest(queueTest: QueueTestSpec, jobRunner: String) {
     // Reset the order of functions added to the graph.
     QScript.resetAddOrder()
 
-    val name = pipelineTest.name
+    val name = queueTest.name
     if (name == null)
-      Assert.fail("PipelineTestSpec.name is null")
+      Assert.fail("QueueTestSpec.name is null")
     println(Utils.dupString('-', 80))
-    executeTest(name, pipelineTest.args, pipelineTest.jobQueue, pipelineTest.expectedException, jobRunner)
+    executeTest(name, queueTest.args, queueTest.jobQueue, queueTest.expectedException, jobRunner)
-    if (BaseTest.pipelineTestRunModeIsSet) {
+    if (BaseTest.queueTestRunModeIsSet) {
-      assertMatchingMD5s(name, pipelineTest.fileMD5s.map{case (file, md5) => new File(runDir(name, jobRunner), file) -> md5}, pipelineTest.parameterize)
+      assertMatchingMD5s(name, queueTest.fileMD5s.map{case (file, md5) => new File(runDir(name, jobRunner), file) -> md5}, queueTest.parameterize)
-      if (pipelineTest.evalSpec != null)
+      if (queueTest.evalSpec != null)
-        validateEval(name, pipelineTest.evalSpec, jobRunner)
+        validateEval(name, queueTest.evalSpec, jobRunner)
-      for (path <- pipelineTest.expectedFilePaths)
+      for (path <- queueTest.expectedFilePaths)
         assertPathExists(runDir(name, jobRunner), path)
-      for (path <- pipelineTest.unexpectedFilePaths)
+      for (path <- queueTest.unexpectedFilePaths)
         assertPathDoesNotExist(runDir(name, jobRunner), path)
       println("  => %s PASSED (%s)".format(name, jobRunner))
     }
@@ -128,7 +128,7 @@ object PipelineTest extends BaseTest with Logging {
       Assert.fail("%d of %d MD5s did not match".format(failed, fileMD5s.size))
   }
 
-  private def validateEval(name: String, evalSpec: PipelineTestEvalSpec, jobRunner: String) {
+  private def validateEval(name: String, evalSpec: QueueTestEvalSpec, jobRunner: String) {
     // write the report to the shared validation data location
     val formatter = new SimpleDateFormat("yyyy.MM.dd.HH.mm.ss")
     val reportLocation = "%s%s/%s/validation.%s.eval".format(validationReportsDataLocation, jobRunner, name, formatter.format(new Date))
@@ -176,7 +176,7 @@ object PipelineTest extends BaseTest with Logging {
     if (jobQueue != null)
       command = Utils.appendArray(command, "-jobQueue", jobQueue)
 
-    if (BaseTest.pipelineTestRunModeIsSet)
+    if (BaseTest.queueTestRunModeIsSet)
       command = Utils.appendArray(command, "-run")
 
     // run the executable

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestEvalSpec.scala

@@ -28,7 +28,7 @@ package org.broadinstitute.sting.queue.pipeline
 /**
  * Data validations to evaluate on a GATKReport.
  */
-class PipelineTestEvalSpec {
+class QueueTestEvalSpec {
   /** Eval modules to output. */
   var evalReport: String = _
 

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestSpec.scala

@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.queue.pipeline
 
-class PipelineTestSpec(var name: String = null) {
+class QueueTestSpec(var name: String = null) {
 
   /** The arguments to pass to the Queue test, ex: "-S scala/qscript/examples/HelloWorld.scala" */
   var args: String = _
@@ -40,7 +40,7 @@ class PipelineTestSpec(var name: String = null) {
   var fileMD5s = Map.empty[String, String]
 
   /** VariantEval validations to run on a VCF after the pipeline has completed. */
-  var evalSpec: PipelineTestEvalSpec = _
+  var evalSpec: QueueTestEvalSpec = _
 
   /** Expected exception from the test. */
   var expectedException: Class[_ <: Exception] = null

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociQueueTest.scala

@@ -26,14 +26,14 @@
 package org.broadinstitute.sting.queue.pipeline.examples
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExampleCountLociPipelineTest {
+class ExampleCountLociQueueTest {
   @Test(timeOut=36000000)
   def testCountLoci() {
     val testOut = "count.out"
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "countloci"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala",
@@ -41,6 +41,6 @@ class ExampleCountLociPipelineTest {
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -o " + testOut).mkString
     spec.fileMD5s += testOut -> "ade93df31a6150321c1067e749cae9be"
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsQueueTest.scala

@@ -26,18 +26,18 @@
 package org.broadinstitute.sting.queue.pipeline.examples
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExampleCountReadsPipelineTest {
+class ExampleCountReadsQueueTest {
   @Test(timeOut=36000000)
   def testCountReads() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "countreads"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala

@@ -50,34 +50,34 @@ package org.broadinstitute.sting.queue.pipeline.examples
  */
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExamplePrintReadsPipelineTest {
+class ExamplePrintReadsQueueTest {
   @Test(timeOut=36000000)
   def testDevNullOutput() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "devnulloutput"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -out /dev/null").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testCleanupBai() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "cleanupbai"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExamplePrintReads.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -out exampleOut.bam").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
     spec.unexpectedFilePaths :+= ".queue/scatterGather/ExamplePrintReads-1-sg/temp_1_of_1/exampleOut.bai"
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterQueueTest.scala

@@ -74,18 +74,18 @@ package org.broadinstitute.sting.queue.pipeline.examples
  */
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExampleReadFilterPipelineTest {
+class ExampleReadFilterQueueTest {
   @Test(timeOut=36000000)
   def testExampleReadFilter() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "examplereadfilter"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam").mkString
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala

@@ -26,22 +26,22 @@
 package org.broadinstitute.sting.queue.pipeline.examples
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExampleRetryMemoryLimitPipelineTest {
+class ExampleRetryMemoryLimitQueueTest {
 
   // This test is currently disabled due to unexplained intermittent failures (see GSA-943)
   @Test(timeOut=36000000,enabled = false)
   def testRetryMemoryLimit() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "RetryMemoryLimit"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleRetryMemoryLimit.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -retry 1").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala

@@ -26,13 +26,13 @@
 package org.broadinstitute.sting.queue.pipeline.examples
 
 import org.testng.annotations.{DataProvider, Test}
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 import org.broadinstitute.sting.BaseTest
 
-class ExampleUnifiedGenotyperPipelineTest {
+class ExampleUnifiedGenotyperQueueTest {
   @Test(timeOut=36000000)
   def testUnifiedGenotyper() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "unifiedgenotyper"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
@@ -40,8 +40,8 @@ class ExampleUnifiedGenotyperPipelineTest {
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -filter QD",
       " -filterExpression 'QD < 2.0'").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @DataProvider(name = "ugIntervals")
@@ -54,7 +54,7 @@ class ExampleUnifiedGenotyperPipelineTest {
 
   @Test(dataProvider = "ugIntervals", timeOut=36000000)
   def testUnifiedGenotyperWithIntervals(intervalsName: String, intervalsPath: String) {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "unifiedgenotyper_with_" + intervalsName
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
@@ -62,20 +62,20 @@ class ExampleUnifiedGenotyperPipelineTest {
       " -R " + BaseTest.hg18Reference,
       " -L " + intervalsPath).mkString
     spec.jobRunners = Seq("Lsf706")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testUnifiedGenotyperNoGCOpt() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "unifiedgenotyper_no_gc_opt"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -noGCOpt").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @DataProvider(name="resMemReqParams")
@@ -83,7 +83,7 @@ class ExampleUnifiedGenotyperPipelineTest {
 
   @Test(dataProvider = "resMemReqParams", timeOut=36000000)
   def testUnifiedGenotyperResMemReqParam(reqParam: String) {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "unifiedgenotyper_" + reqParam
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
@@ -91,21 +91,21 @@ class ExampleUnifiedGenotyperPipelineTest {
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -resMemReqParam " + reqParam).mkString
     spec.jobRunners = Seq("GridEngine")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testUnifiedGenotyperLogDirectory() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "unifiedgenotyper_with_log_directory"
     spec.args = Array(
       " -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala",
       " -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
       " -I " + BaseTest.publicTestDir + "exampleBAM.bam",
       " -logDir exampleUGLogDir").mkString
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
     spec.expectedFilePaths :+= "exampleUGLogDir/exampleBAM.unfiltered.vcf.out"
     spec.expectedFilePaths :+= "exampleUGLogDir/exampleBAM.unfiltered.eval.out"
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldQueueTest.scala

@@ -26,127 +26,127 @@
 package org.broadinstitute.sting.queue.pipeline.examples
 
 import org.testng.annotations.Test
-import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
+import org.broadinstitute.sting.queue.pipeline.{QueueTest, QueueTestSpec}
 
-class HelloWorldPipelineTest {
+class HelloWorldQueueTest {
   @Test(timeOut=36000000)
   def testHelloWorld() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorld"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithRunName() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithRunName"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -runName HelloWorld"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithMemoryLimit() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldMemoryLimit"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -memLimit 1.25"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithPriority() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithPriority"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -jobPriority 100"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithLsfResource() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfResource"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -jobResReq rusage[iodine_io=1] -jobResReq select[swp>0] -jobResReq order[swp]"
     spec.jobRunners = Seq("Lsf706")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithLsfResourceAndMemoryLimit() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfResourceAndMemoryLimit"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -memLimit 1.25 -jobResReq rusage[iodine_io=1] -jobResReq select[swp>0] -jobResReq order[swp]"
     spec.jobRunners = Seq("Lsf706")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithLsfEnvironment() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLsfEnvironment"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -jobEnv tv"
     spec.jobRunners = Seq("Lsf706")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResource() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithGridEngineResource"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -jobResReq s_core=1000M"
     spec.jobRunners = Seq("GridEngine")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineResourceAndMemoryLimit() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithGridEngineResourceAndMemoryLimit"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -memLimit 1.25 -jobResReq s_core=1000M"
     spec.jobRunners = Seq("GridEngine")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithGridEngineEnvironment() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithGridEngineEnvironment"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -jobEnv \"make 1\""
     spec.jobRunners = Seq("GridEngine")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   // disabled because our DRMAA implementation doesn't support wallTime
   @Test(enabled=false, timeOut=36000000)
   def testHelloWorldWithWalltime() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithWalltime"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -wallTime 100"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 
   @Test(timeOut=36000000)
   def testHelloWorldWithLogDirectory() {
-    val spec = new PipelineTestSpec
+    val spec = new QueueTestSpec
     spec.name = "HelloWorldWithLogDirectory"
     spec.args = "-S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/HelloWorld.scala" +
       " -logDir pipelineLogDir"
-    spec.jobRunners = PipelineTest.allJobRunners
+    spec.jobRunners = QueueTest.allJobRunners
     spec.expectedFilePaths = Seq("pipelineLogDir/HelloWorld-1.out")
-    PipelineTest.executeTest(spec)
+    QueueTest.executeTest(spec)
   }
 }

public/queue-package/pom.xml

@@ -144,9 +144,9 @@
                         </configuration>
                     </execution>
                     <execution>
-                        <id>pipeline-tests</id>
+                        <id>queue-tests</id>
                         <configuration>
-                            <skip>${sting.serialpipelinetests.skipped}</skip>
+                            <skip>${sting.serialqueuetests.skipped}</skip>
                             <dependenciesToScan>
                                 <scan>org.broadinstitute.sting:.*</scan>
                             </dependenciesToScan>

public/sting-root/pom.xml

@@ -31,10 +31,10 @@
         <sting.committests.skipped>true</sting.committests.skipped>
         <sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
         <sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
-        <sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped>
+        <sting.queuetests.skipped>${sting.committests.skipped}</sting.queuetests.skipped>
         <sting.largescaletests.skipped>true</sting.largescaletests.skipped>
         <sting.knowledgebasetests.skipped>true</sting.knowledgebasetests.skipped>
-        <sting.pipelinetests.run>false</sting.pipelinetests.run>
+        <sting.queuetests.run>false</sting.queuetests.run>
         <scala.maxmemory>1g</scala.maxmemory>
         <test.maxmemory>4g</test.maxmemory>
         <java.gc.threads>4</java.gc.threads>
@@ -408,7 +408,7 @@
                             <clover.pertest.coverage>diff</clover.pertest.coverage>
                             <java.awt.headless>true</java.awt.headless>
                             <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
-                            <pipeline.run>${sting.pipelinetests.run}</pipeline.run>
+                            <queuetest.run>${sting.queuetests.run}</queuetest.run>
                             <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
                         </systemPropertyVariables>
                     </configuration>
@@ -431,19 +431,19 @@
                             </configuration>
                         </execution>
                         <execution>
-                            <id>pipeline-tests</id>
+                            <id>queue-tests</id>
                             <goals>
                                 <goal>integration-test</goal>
                                 <goal>verify</goal>
                             </goals>
-                            <!-- run pipeline dry run tests -->
+                            <!-- run queue dry run tests -->
                             <configuration>
-                                <!-- TODO: Re-enable pipeline tests by default? -->
+                                <!-- TODO: Re-enable queue tests by default? -->
-                                <skip>${sting.pipelinetests.skipped}</skip>
+                                <skip>${sting.queuetests.skipped}</skip>
-                                <reportsDirectory>${project.build.directory}/failsafe-reports/pipeline/${it.test}</reportsDirectory>
+                                <reportsDirectory>${project.build.directory}/failsafe-reports/queuetest/${it.test}</reportsDirectory>
-                                <summaryFile>${project.build.directory}/failsafe-reports/pipeline/failsafe-summary-${it.test}.xml</summaryFile>
+                                <summaryFile>${project.build.directory}/failsafe-reports/queuetest/failsafe-summary-${it.test}.xml</summaryFile>
                                 <includes>
-                                    <include>**/*PipelineTest.class</include>
+                                    <include>**/*QueueTest.class</include>
                                 </includes>
                             </configuration>
                         </execution>