Example usage for org.springframework.batch.core JobExecution getExitStatus

List of usage examples for org.springframework.batch.core JobExecution getExitStatus

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Introduction

In this page you can find the example usage for org.springframework.batch.core JobExecution getExitStatus.

Prototype

public ExitStatus getExitStatus()

Source Link

Usage

From source file:admin.jmx.SimpleJobExecutionMetrics.java

public String getLatestExitCode() {
    JobExecution jobExecution = getLatestJobExecution(jobName);
    return jobExecution == null ? "NONE" : jobExecution.getExitStatus().getExitCode();
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VepAnnotationGeneratorStepTest.java

@Test
public void shouldGenerateVepAnnotations() throws Exception {
    makeGzipFile("20\t60343\t60343\tG/A\t+", jobOptions.getVepInput());

    File vepOutputFile = JobTestUtils.createTempFile();
    jobOptions.setVepOutput(vepOutputFile.getAbsolutePath());

    vepOutputFile.delete();/*from   w  w w . jav  a2  s.  c  om*/
    TestCase.assertFalse(vepOutputFile.exists()); // ensure the annot file doesn't exist from previous executions

    // When the execute method in variantsAnnotCreate is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(AnnotationJob.GENERATE_VEP_ANNOTATION);

    //Then variantsAnnotCreate step should complete correctly
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // And VEP output should exist and annotations should be in the file
    TestCase.assertTrue(vepOutputFile.exists());
    Assert.assertEquals(537, JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(vepOutputFile))));
    vepOutputFile.delete();
}

From source file:uk.ac.ebi.eva.pipeline.jobs.AggregatedVcfJobTest.java

@Test
public void aggregationNoneOptionShouldNotLoadStats() throws Exception {
    VariantSource source = (VariantSource) jobOptions.getVariantOptions()
            .get(VariantStorageManager.VARIANT_SOURCE);
    jobOptions.getVariantOptions().put(VariantStorageManager.VARIANT_SOURCE,
            new VariantSource(input, source.getFileId(), source.getStudyId(), source.getStudyName(),
                    source.getType(), VariantSource.Aggregation.NONE));

    Config.setOpenCGAHome(opencgaHome);//  w  ww .j a  v  a 2s .c o  m

    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // check transformed file
    String outputFilename = getTransformedOutputPath(Paths.get(input).getFileName(), compressExtension,
            outputDir);

    long lines = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(outputFilename)));
    assertEquals(156, lines);

    // check ((documents in DB) == (lines in transformed file))
    VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions());

    Assert.assertEquals(JobTestUtils.count(iterator), lines);

    // check that stats are NOT loaded
    assertTrue(variantDBAdaptor.iterator(new QueryOptions()).next().getSourceEntries().values().iterator()
            .next().getCohortStats().isEmpty());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VariantNormalizerStepTest.java

/**
 * This test has to fail because the vcf FILE_WRONG_NO_ALT is malformed:
 * in a variant a reference and a alternate allele are the same
 */// ww w  .  ja va  2  s.co m
@Test
public void normalizerStepShouldFailIfVariantsAreMalformed() {
    final String FILE_WRONG_NO_ALT = "/wrong_no_alt.vcf.gz";
    Config.setOpenCGAHome(opencgaHome);

    //Given a malformed VCF input file
    String inputFile = VariantNormalizerStepTest.class.getResource(FILE_WRONG_NO_ALT).getFile();
    jobOptions.getPipelineOptions().put("input.vcf", inputFile);

    String outputFilename = getTransformedOutputPath(Paths.get(FILE_WRONG_NO_ALT).getFileName(), ".gz", "/tmp");

    File file = new File(outputFilename);
    file.delete();
    assertFalse(file.exists());

    //When the execute method in variantsTransform is invoked then a StorageManagerException is thrown
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(GenotypedVcfJob.NORMALIZE_VARIANTS);
    assertEquals(ExitStatus.FAILED.getExitCode(), jobExecution.getExitStatus().getExitCode());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.AggregatedVcfJobTest.java

@Test
public void aggregatedTransformAndLoadShouldBeExecuted() throws Exception {
    Config.setOpenCGAHome(opencgaHome);//from   w w w  .j  ava2 s  .co  m

    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // check execution flow
    Assert.assertEquals(2, jobExecution.getStepExecutions().size());
    List<StepExecution> steps = new ArrayList<>(jobExecution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Assert.assertEquals(AggregatedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    Assert.assertEquals(AggregatedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));

    // check transformed file
    String outputFilename = getTransformedOutputPath(Paths.get(input).getFileName(), compressExtension,
            outputDir);

    long lines = JobTestUtils.getLines(new GZIPInputStream(new FileInputStream(outputFilename)));
    assertEquals(156, lines);

    // check ((documents in DB) == (lines in transformed file))
    VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions());

    Assert.assertEquals(JobTestUtils.count(iterator), lines);

    // check that stats are loaded properly
    assertFalse(variantDBAdaptor.iterator(new QueryOptions()).next().getSourceEntries().values().iterator()
            .next().getCohortStats().isEmpty());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.AnnotationJobTest.java

@Test
public void allAnnotationStepsShouldBeExecuted() throws Exception {
    String dump = PopulationStatisticsJobTest.class.getResource("/dump/").getFile();
    JobTestUtils.restoreMongoDbFromDump(dump);

    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    Assert.assertEquals(3, jobExecution.getStepExecutions().size());
    List<StepExecution> steps = new ArrayList<>(jobExecution.getStepExecutions());
    StepExecution findVariantsToAnnotateStep = steps.get(0);
    StepExecution generateVepAnnotationsStep = steps.get(1);
    StepExecution loadVepAnnotationsStep = steps.get(2);

    Assert.assertEquals(FIND_VARIANTS_TO_ANNOTATE, findVariantsToAnnotateStep.getStepName());
    Assert.assertEquals(GENERATE_VEP_ANNOTATION, generateVepAnnotationsStep.getStepName());
    Assert.assertEquals(LOAD_VEP_ANNOTATION, loadVepAnnotationsStep.getStepName());

    //check list of variants without annotation output file
    assertTrue(vepInputFile.exists());/*from   w  ww . j  a v a2  s .  c  o m*/
    assertEquals("20\t60343\t60343\tG/A\t+", JobTestUtils.readFirstLine(vepInputFile));

    //check that documents have the annotation
    DBCursor cursor = collection(dbName, jobOptions.getDbCollectionsVariantsName()).find();

    int cnt = 0;
    int consequenceTypeCount = 0;
    while (cursor.hasNext()) {
        cnt++;
        DBObject dbObject = (DBObject) cursor.next().get("annot");
        if (dbObject != null) {
            VariantAnnotation annot = converter.convertToDataModelType(dbObject);
            assertNotNull(annot.getConsequenceTypes());
            consequenceTypeCount += annot.getConsequenceTypes().size();
        }
    }

    assertEquals(300, cnt);
    assertEquals(536, consequenceTypeCount);

    //check that one line is skipped because malformed
    List<StepExecution> variantAnnotationLoadStepExecution = jobExecution.getStepExecutions().stream()
            .filter(stepExecution -> stepExecution.getStepName().equals(LOAD_VEP_ANNOTATION))
            .collect(Collectors.toList());
    assertEquals(1, variantAnnotationLoadStepExecution.get(0).getReadSkipCount());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.PopulationStatisticsGeneratorStepTest.java

/**
 * This test has to fail because it will try to extract variants from a non-existent DB.
 * Variants not loaded.. so nothing to query!
 *///w  w w  . j a v a 2 s.c  o m
@Test
public void statisticsGeneratorStepShouldFailIfVariantLoadStepIsNotCompleted() throws Exception {
    //Given a valid VCF input file
    String input = SMALL_VCF_FILE;

    pipelineOptions.put("input.vcf", input);
    variantOptions.put(VariantStorageManager.DB_NAME, STATS_DB);

    VariantSource source = new VariantSource(input, "1", "1", "studyName", VariantStudy.StudyType.COLLECTION,
            VariantSource.Aggregation.NONE);

    variantOptions.put(VARIANT_SOURCE, source);

    statsFile = new File(Paths.get(pipelineOptions.getString("output.dir.statistics"))
            .resolve(VariantStorageManager.buildFilename(source)) + ".variants.stats.json.gz");
    statsFile.delete();
    assertFalse(statsFile.exists()); // ensure the stats file doesn't exist from previous executions

    // When the execute method in variantsStatsCreate is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(PopulationStatisticsJob.CALCULATE_STATISTICS);
    assertEquals(ExitStatus.FAILED.getExitCode(), jobExecution.getExitStatus().getExitCode());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VariantNormalizerStepTest.java

@Test
public void normalizerStepShouldTransformAllVariants() throws Exception {
    Config.setOpenCGAHome(opencgaHome);//from  w ww  .  ja v a2s. c  o m

    String inputFile = VariantNormalizerStepTest.class.getResource(input).getFile();
    jobOptions.getPipelineOptions().put("input.vcf", inputFile);

    String outputFilename = getTransformedOutputPath(Paths.get(input).getFileName(), ".gz", "/tmp");

    File file = new File(outputFilename);
    if (file.exists())
        file.delete();
    assertFalse(file.exists());

    // When the execute method in variantsTransform is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(GenotypedVcfJob.NORMALIZE_VARIANTS);

    //Then variantsTransform should complete correctly
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // And the transformed file should contain the same number of line of the Vcf input file
    Assert.assertEquals(300, getLines(new GZIPInputStream(new FileInputStream(outputFilename))));

    file.delete();
    new File(outputDir, "small20.vcf.gz.file.json.gz").delete();
}

From source file:org.cloudfoundry.workers.stocks.batch.NightlyStockSymbolRecorder.java

@Scheduled(fixedRate = 10 * 1000)
public void runNightlyStockPriceRecorder() throws Throwable {
    JobParameters params = new JobParametersBuilder().addDate("date", new Date()).toJobParameters();

    JobExecution jobExecution = jobLauncher.run(job, params);
    BatchStatus batchStatus = jobExecution.getStatus();
    while (batchStatus.isRunning()) {
        logger.info("Still running...");
        Thread.sleep(1000);//from  w w  w  . j av a  2s.c o m
    }
    logger.info(String.format("Exit status: %s", jobExecution.getExitStatus().getExitCode()));
    JobInstance jobInstance = jobExecution.getJobInstance();
    logger.info(String.format("job instance Id: %d", jobInstance.getId()));
}

From source file:org.cloudfoundry.workers.twitter.batch.NightlyTweetRecorder.java

@Scheduled(fixedRate = 10 * 1000)
public void runNightlyTweetRecorder() throws Throwable {
    logger.info("Running nightly tweet recorder");
    JobParameters params = new JobParametersBuilder().addDate("date", new Date()).toJobParameters();

    JobExecution jobExecution = jobLauncher.run(job, params);
    BatchStatus batchStatus = jobExecution.getStatus();
    while (batchStatus.isRunning()) {
        logger.info("Still running...");
        Thread.sleep(1000);//from   ww  w  . j  a va 2  s.c o m
    }
    logger.info(String.format("Exit status: %s", jobExecution.getExitStatus().getExitCode()));
    JobInstance jobInstance = jobExecution.getJobInstance();
    logger.info(String.format("job instance Id: %d", jobInstance.getId()));
}