Examples of org.broadinstitute.gatk.utils.runtime.ProcessController

Package org.broadinstitute.gatk.utils.runtime

Examples of org.broadinstitute.gatk.utils.runtime.ProcessController

org.broadinstitute.gatk.utils.runtime.ProcessController
Facade to Runtime.exec() and java.lang.Process. Handles running a process to completion and returns stdout and stderr as strings. Creates separate threads for reading stdout and stderr, then reuses those threads for each process most efficient use is to create one of these and use it repeatedly. Instances are not thread-safe, however. TODO: java.io sometimes zombies the backround threads locking up on read(). Supposedly NIO has better ways of interrupting a blocked stream but will require a little bit of refactoring. @author Michael Koehrsen @author Khalid Shakir

    }


    @Test(dataProvider = "ExtensionsTest")
    public void testExtensions(final CatVariantsTestProvider cfg) throws IOException {


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cfg.getCmdLine().split("\\s+"));
        pc.execAndCheck(ps);


        MD5DB.MD5Match result = md5db.testFileMD5("testExtensions", "CatVariantsTestProvider", cfg.outputFile, cfg.md5, false);
        if(result.failed) {
            final MD5Mismatch failure = new MD5Mismatch(result.actualMD5, result.expectedMD5, result.diffEngineOutput);
            Assert.fail(failure.toString());

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                BaseTest.b37KGReference,
                CatVariantsVcf1,
                CatVariantsVcf2,
                BaseTest.createTempFile("CatVariantsTest", ".bcf"));


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }

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                BaseTest.b37KGReference,
                CatVariantsVcf1,
                CatVariantsBcf2,
                BaseTest.createTempFile("CatVariantsTest", ".vcf"));


        ProcessController pc = ProcessController.getThreadLocal();
        ProcessSettings ps = new ProcessSettings(cmdLine.split("\\s+"));
        pc.execAndCheck(ps);
    }

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            if (logger.isDebugEnabled()) {
                processSettings.getStdoutSettings().printStandard(true);
                processSettings.getStderrSettings().printStandard(true);
            }


            ProcessController controller = ProcessController.getThreadLocal();


            if (logger.isDebugEnabled()) {
                logger.debug("Executing:");
                for (String arg: cmd)
                    logger.debug("  " + arg);
            }
            int exitValue = controller.exec(processSettings).getExitValue();
            logger.debug("Result: " + exitValue);


            if (exitValue != 0)
                throw new RScriptExecutorException(
                        "RScript exited with " + exitValue +

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Related Classes of org.broadinstitute.gatk.utils.runtime.ProcessController

org.broadinstitute.gatk.tools.CatVariantsIntegrationTest

org.broadinstitute.gatk.utils.R.RScriptExecutor

java.io.InputStream

java.io.IOException

java.io.ByteArrayInputStream

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

java.io.OutputStream

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