diff --git a/public/java/test/org/broadinstitute/sting/BaseTest.java b/public/java/test/org/broadinstitute/sting/BaseTest.java index d6cba26d6..f86a9b513 100644 --- a/public/java/test/org/broadinstitute/sting/BaseTest.java +++ b/public/java/test/org/broadinstitute/sting/BaseTest.java @@ -131,6 +131,8 @@ public abstract class BaseTest { public static final String exampleFASTA = publicTestDir + "exampleFASTA.fasta"; + public static final boolean pipelineTestRunModeIsSet = System.getProperty("pipeline.run").equals("run"); + /** before the class starts up */ static { // setup a basic log configuration diff --git a/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java b/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java index d2da0e228..5a6a1b769 100644 --- a/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java +++ b/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/JnaSessionPipelineTest.java @@ -29,6 +29,7 @@ import org.apache.commons.io.FileUtils; import org.broadinstitute.sting.BaseTest; import org.ggf.drmaa.*; import org.testng.Assert; +import org.testng.SkipException; import org.testng.annotations.Test; import java.io.File; @@ -51,19 +52,23 @@ 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 (implementation.contains("LSF")) { System.err.println(" ***********************************************************"); System.err.println(" *************************************************************"); System.err.println(" **** ****"); - System.err.println(" **** Skipping JnaSessionIntegrationTest.testSubmitEcho() ****"); + System.err.println(" **** Skipping JnaSessionPipelineTest.testSubmitEcho() ****"); System.err.println(" **** Are you using the dotkit .combined_LSF_SGE? ****"); System.err.println(" **** ****"); System.err.println(" *************************************************************"); System.err.println(" ***********************************************************"); - return; + throw new SkipException("Skipping testSubmitEcho because correct DRMAA implementation not found"); } - File outFile = tryCreateNetworkTempFile("JnaSessionIntegrationTest.out"); + File outFile = tryCreateNetworkTempFile("JnaSessionPipelineTest.out"); Session session = factory.getSession(); session.init(null); try { diff --git a/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java b/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java index efeeb3640..13bad765b 100644 --- a/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java +++ b/public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaPipelineTest.java @@ -34,6 +34,7 @@ import com.sun.jna.ptr.PointerByReference; import org.apache.commons.io.FileUtils; import org.broadinstitute.sting.BaseTest; import org.testng.Assert; +import org.testng.SkipException; import org.testng.annotations.Test; import java.io.File; @@ -87,22 +88,26 @@ public class LibDrmaaPipelineTest 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 (implementation.contains("LSF")) { System.err.println(" *********************************************************"); System.err.println(" ***********************************************************"); System.err.println(" **** ****"); - System.err.println(" **** Skipping LibDrmaaIntegrationTest.testSubmitEcho() ****"); + System.err.println(" **** Skipping LibDrmaaPipelineTest.testSubmitEcho() ****"); System.err.println(" **** Are you using the dotkit .combined_LSF_SGE? ****"); System.err.println(" **** ****"); System.err.println(" ***********************************************************"); System.err.println(" *********************************************************"); - return; + throw new SkipException("Skipping testSubmitEcho because correct DRMAA implementation not found"); } Memory error = new Memory(LibDrmaa.DRMAA_ERROR_STRING_BUFFER); int errnum; - File outFile = tryCreateNetworkTempFile("LibDrmaaIntegrationTest.out"); + File outFile = tryCreateNetworkTempFile("LibDrmaaPipelineTest.out"); errnum = LibDrmaa.drmaa_init(null, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN); diff --git a/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java b/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java index af8d0e7b1..4db600fc1 100644 --- a/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java +++ b/public/java/test/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBatPipelineTest.java @@ -30,6 +30,7 @@ import com.sun.jna.ptr.IntByReference; import org.apache.commons.io.FileUtils; import org.broadinstitute.sting.utils.Utils; import org.testng.Assert; +import org.testng.SkipException; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import org.broadinstitute.sting.BaseTest; @@ -43,7 +44,7 @@ import java.io.File; public class LibBatPipelineTest extends BaseTest { @BeforeClass public void initLibBat() { - Assert.assertFalse(LibBat.lsb_init("LibBatIntegrationTest") < 0, LibBat.lsb_sperror("lsb_init() failed")); + Assert.assertFalse(LibBat.lsb_init("LibBatPipelineTest") < 0, LibBat.lsb_sperror("lsb_init() failed")); } @Test @@ -93,15 +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"); + } + String queue = "hour"; - File outFile = tryCreateNetworkTempFile("LibBatIntegrationTest.out"); + File outFile = tryCreateNetworkTempFile("LibBatPipelineTest.out"); submit req = new submit(); for (int i = 0; i < LibLsf.LSF_RLIM_NLIMITS; i++) req.rLimits[i] = LibLsf.DEFAULT_RLIMIT; - req.projectName = "LibBatIntegrationTest"; + req.projectName = "LibBatPipelineTest"; req.options |= LibBat.SUB_PROJECT_NAME; req.queue = queue; diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala index 6741e4107..e990b5233 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala @@ -45,8 +45,6 @@ object PipelineTest extends BaseTest with Logging { private val validationReportsDataLocation = "/humgen/gsa-hpprojects/GATK/validationreports/submitted/" private val md5DB = new MD5DB() - final val run = System.getProperty("pipeline.run") == "run" - final val allJobRunners = { val commandLinePluginManager = new CommandLinePluginManager commandLinePluginManager.getPlugins.map(commandLinePluginManager.getName(_)).toSeq @@ -100,7 +98,7 @@ object PipelineTest extends BaseTest with Logging { Assert.fail("PipelineTestSpec.name is null") println(Utils.dupString('-', 80)); executeTest(name, pipelineTest.args, pipelineTest.jobQueue, pipelineTest.expectedException, jobRunner) - if (run) { + 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) @@ -169,7 +167,7 @@ object PipelineTest extends BaseTest with Logging { if (jobQueue != null) command = Utils.appendArray(command, "-jobQueue", jobQueue) - if (run) + if (BaseTest.pipelineTestRunModeIsSet) command = Utils.appendArray(command, "-run") // run the executable