diff --git a/ant-bridge.sh b/ant-bridge.sh index 9f4713d7c..fe0549fa1 100755 --- a/ant-bridge.sh +++ b/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.pipelinetests.run=true" + mvn_args="${mvn_args} -Dsting.packagequeuetests.skipped=false" + mvn_args="${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 - mvn_args="verify -Dsting.pipelinetests.skipped=false" + elif [[ "${arg}" == "queuetest" ]] ; then + mvn_args="verify -Dsting.queuetests.skipped=false" - elif [[ "${arg}" == "pipelinetestrun" ]] ; then - mvn_args="verify -Dsting.pipelinetests.skipped=false -Dsting.pipelinetests.run=true" + elif [[ "${arg}" == "queuetestrun" ]] ; then + mvn_args="verify -Dsting.queuetests.skipped=false -Dsting.queuetests.run=true" elif [[ "${arg}" == "fasttest" ]] ; then mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true" diff --git a/pom.xml b/pom.xml index e713df56f..eb3ace24f 100644 --- a/pom.xml +++ b/pom.xml @@ -48,7 +48,7 @@ true ${sting.packagecommittests.skipped} ${sting.packagecommittests.skipped} - ${sting.packagecommittests.skipped} + ${sting.packagecommittests.skipped} true true @@ -62,7 +62,7 @@ true ${sting.serialcommittests.skipped} ${sting.serialcommittests.skipped} - ${sting.serialcommittests.skipped} + ${sting.serialcommittests.skipped} true true @@ -561,7 +561,7 @@ ${sting.packagetests.artifactId} ${project.build.testOutputDirectory} ${project.basedir} - ${sting.pipelinetests.run} + ${sting.queuetests.run} ${maven.surefire.debug} ${maven.failsafe.debug} @@ -613,7 +613,7 @@ - package-pipelinetests + package-queuetests integration-test verify @@ -622,11 +622,11 @@ verify - ${project.build.directory}/invoker-reports/pipeline/${it.test} - ${sting.packagepipelinetests.skipped} + ${project.build.directory}/invoker-reports/queuetest/${it.test} + ${sting.packagequeuetests.skipped} true - ${sting.packagepipelinetests.skipped} + ${sting.packagequeuetests.skipped} diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml index 509f984a3..3d60c1d61 100644 --- a/protected/gatk-protected/pom.xml +++ b/protected/gatk-protected/pom.xml @@ -99,7 +99,7 @@ package-knowledgebasetests - package-pipelinetests + package-queuetests diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml index 068c062a7..de7b1748e 100644 --- a/public/gatk-framework/pom.xml +++ b/public/gatk-framework/pom.xml @@ -86,7 +86,7 @@ package-knowledgebasetests - package-pipelinetests + package-queuetests diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java index e8aed7d50..809a6f1a1 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/BaseTest.java +++ b/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 { diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionQueueTest.java similarity index 95% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java rename to public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionQueueTest.java index 5a6a1b769..1562ab93e 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java +++ b/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 ) { - throw new SkipException("Skipping testSubmitEcho because we are in pipeline test dry run mode"); + if ( ! queueTestRunModeIsSet ) { + 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 { diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaQueueTest.java similarity index 97% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java rename to public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaQueueTest.java index 13bad765b..3d861f078 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java +++ b/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); diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatQueueTest.java similarity index 92% rename from public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java rename to public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatQueueTest.java index 4db600fc1..d7ac75695 100644 --- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java +++ b/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 ) { - throw new SkipException("Skipping testSubmitEcho because we are in pipeline test dry run mode"); + if ( ! queueTestRunModeIsSet ) { + 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; diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml index 6a8ce94af..606d9f030 100644 --- a/public/gatk-package/pom.xml +++ b/public/gatk-package/pom.xml @@ -105,9 +105,9 @@ - pipeline-tests + queue-tests - ${sting.serialpipelinetests.skipped} + ${sting.serialqueuetests.skipped} org.broadinstitute.sting:.* diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml index 38ef796ae..f53e7e02e 100644 --- a/public/package-tests/pom.xml +++ b/public/package-tests/pom.xml @@ -21,7 +21,7 @@ ${project.basedir}/../.. true true - true + true true true @@ -161,13 +161,13 @@ - pipeline-tests + queue-tests verify - + - ${sting.packagepipelinetests.skipped} + ${sting.packagequeuetests.skipped} diff --git a/public/pom.xml b/public/pom.xml index 0cf40a052..9a0a8b2d0 100644 --- a/public/pom.xml +++ b/public/pom.xml @@ -19,7 +19,7 @@ sting-utils gatk-framework gatk-package - + diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml index 40c1ad5f0..ece0478b7 100644 --- a/public/queue-framework/pom.xml +++ b/public/queue-framework/pom.xml @@ -198,7 +198,7 @@ package-knowledgebasetests - package-pipelinetests + package-queuetests diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTest.scala similarity index 85% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTest.scala index 2800ba2da..9c32a40be 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +++ b/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. - * @param pipelineTest test to run. + * Runs the queueTest. + * @param queueTest test to run. */ - def executeTest(pipelineTest: PipelineTestSpec) { - var jobRunners = pipelineTest.jobRunners + def executeTest(queueTest: QueueTestSpec) { + var jobRunners = queueTest.jobRunners if (jobRunners == null) jobRunners = defaultJobRunners - jobRunners.foreach(executeTest(pipelineTest, _)) + jobRunners.foreach(executeTest(queueTest, _)) } /** - * Runs the pipelineTest. - * @param pipelineTest test to run. + * Runs the queueTest. + * @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) - if (BaseTest.pipelineTestRunModeIsSet) { - assertMatchingMD5s(name, pipelineTest.fileMD5s.map{case (file, md5) => new File(runDir(name, jobRunner), file) -> md5}, pipelineTest.parameterize) - if (pipelineTest.evalSpec != null) - validateEval(name, pipelineTest.evalSpec, jobRunner) - for (path <- pipelineTest.expectedFilePaths) + executeTest(name, queueTest.args, queueTest.jobQueue, queueTest.expectedException, jobRunner) + if (BaseTest.queueTestRunModeIsSet) { + assertMatchingMD5s(name, queueTest.fileMD5s.map{case (file, md5) => new File(runDir(name, jobRunner), file) -> md5}, queueTest.parameterize) + if (queueTest.evalSpec != null) + validateEval(name, queueTest.evalSpec, jobRunner) + 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 diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestEvalSpec.scala similarity index 98% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestEvalSpec.scala index 4beb81c93..2295d7185 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala +++ b/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 = _ diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestSpec.scala similarity index 96% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/QueueTestSpec.scala index 3dc761382..e05350bce 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala +++ b/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 diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociQueueTest.scala similarity index 90% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociQueueTest.scala index 291894244..b1149054a 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala +++ b/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) } } \ No newline at end of file diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsQueueTest.scala similarity index 89% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsQueueTest.scala index 2ec84e85f..e023a9dda 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala +++ b/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) } } diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala similarity index 90% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsQueueTest.scala index b9964d187..667187bd2 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExamplePrintReadsPipelineTest.scala +++ b/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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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) } } diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterQueueTest.scala similarity index 95% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterQueueTest.scala index 7d74e1a5c..82fd57ee3 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala +++ b/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) } } diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala similarity index 87% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitQueueTest.scala index e98ca6756..3e314708c 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala +++ b/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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + QueueTest.executeTest(spec) } } diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala similarity index 87% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperQueueTest.scala index b054164a1..20f97ea61 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleUnifiedGenotyperPipelineTest.scala +++ b/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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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) } } diff --git a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldQueueTest.scala similarity index 79% rename from public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldQueueTest.scala index 0f645cb2a..5d3923250 100644 --- a/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala +++ b/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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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 - PipelineTest.executeTest(spec) + spec.jobRunners = QueueTest.allJobRunners + 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) } } diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml index 4ff9a1381..89b547b2f 100644 --- a/public/queue-package/pom.xml +++ b/public/queue-package/pom.xml @@ -144,9 +144,9 @@ - pipeline-tests + queue-tests - ${sting.serialpipelinetests.skipped} + ${sting.serialqueuetests.skipped} org.broadinstitute.sting:.* diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml index 44644e13d..5b3dfe43b 100644 --- a/public/sting-root/pom.xml +++ b/public/sting-root/pom.xml @@ -31,10 +31,10 @@ true ${sting.committests.skipped} ${sting.committests.skipped} - ${sting.committests.skipped} + ${sting.committests.skipped} true true - false + false 1g 4g 4 @@ -412,7 +412,7 @@ diff true - ${sting.pipelinetests.run} + ${sting.queuetests.run} ${java.io.tmpdir} @@ -435,19 +435,19 @@ - pipeline-tests + queue-tests integration-test verify - + - - ${sting.pipelinetests.skipped} - ${project.build.directory}/failsafe-reports/pipeline/${it.test} - ${project.build.directory}/failsafe-reports/pipeline/failsafe-summary-${it.test}.xml + + ${sting.queuetests.skipped} + ${project.build.directory}/failsafe-reports/queuetest/${it.test} + ${project.build.directory}/failsafe-reports/queuetest/failsafe-summary-${it.test}.xml - **/*PipelineTest.class + **/*QueueTest.class