Example usage for org.springframework.batch.core ExitStatus COMPLETED

List of usage examples for org.springframework.batch.core ExitStatus COMPLETED

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ExitStatus COMPLETED

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Document

Convenient constant value representing finished processing.

Usage

From source file:org.jasig.ssp.util.importer.job.csv.RawItemCsvReader.java

@Override
public ExitStatus afterStep(StepExecution stepExecution) {
    logger.info("End Raw Read Step for " + itemResource.getFilename() + " lines read: "
            + stepExecution.getReadCount() + " lines skipped: " + stepExecution.getReadSkipCount());
    return ExitStatus.COMPLETED;
}

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

@Test
public void fullGenotypedVcfJob() throws Exception {
    String inputFile = GenotypedVcfJobTest.class.getResource(input).getFile();
    String mockVep = GenotypedVcfJobTest.class.getResource("/mockvep.pl").getFile();

    jobOptions.getPipelineOptions().put("input.vcf", inputFile);
    jobOptions.getPipelineOptions().put("app.vep.path", mockVep);

    Config.setOpenCGAHome(opencgaHome);/*from  w w w.j  av a 2  s.  c om*/

    // transformedVcf file init
    String transformedVcf = outputDir + input + ".variants.json" + compressExtension;
    File transformedVcfFile = new File(transformedVcf);
    transformedVcfFile.delete();
    assertFalse(transformedVcfFile.exists());

    //stats file init
    VariantSource source = (VariantSource) jobOptions.getVariantOptions()
            .get(VariantStorageManager.VARIANT_SOURCE);
    File statsFile = new File(Paths.get(outputDir).resolve(VariantStorageManager.buildFilename(source))
            + ".variants.stats.json.gz");
    statsFile.delete();
    assertFalse(statsFile.exists()); // ensure the stats file doesn't exist from previous executions

    // annotation files init
    File vepInputFile = new File(vepInput);
    vepInputFile.delete();
    assertFalse(vepInputFile.exists());

    File vepOutputFile = new File(vepOutput);
    vepOutputFile.delete();
    assertFalse(vepOutputFile.exists());

    VariantDBIterator iterator;

    // Run the Job
    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

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

    // 1 transform step: check transformed file
    long transformedLinesCount = getLines(new GZIPInputStream(new FileInputStream(transformedVcf)));
    assertEquals(300, transformedLinesCount);

    // 2 load step: check ((documents in DB) == (lines in transformed file))
    //variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    //variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    iterator = getVariantDBIterator();
    assertEquals(transformedLinesCount, count(iterator));

    // 3 create stats step
    assertTrue(statsFile.exists());

    // 4 load stats step: check ((documents in DB) == (lines in transformed file))
    //variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    //variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    iterator = getVariantDBIterator();
    assertEquals(transformedLinesCount, count(iterator));

    // check the DB docs have the field "st"
    iterator = getVariantDBIterator();

    assertEquals(1, iterator.next().getSourceEntries().values().iterator().next().getCohortStats().size());

    // 5 annotation flow
    // annotation input vep generate step
    BufferedReader testReader = new BufferedReader(new InputStreamReader(
            new FileInputStream(GenotypedVcfJobTest.class.getResource("/preannot.sorted").getFile())));
    BufferedReader actualReader = new BufferedReader(
            new InputStreamReader(new FileInputStream(vepInputFile.toString())));

    ArrayList<String> rows = new ArrayList<>();

    String s;
    while ((s = actualReader.readLine()) != null) {
        rows.add(s);
    }
    Collections.sort(rows);

    String testLine = testReader.readLine();
    for (String row : rows) {
        assertEquals(testLine, row);
        testLine = testReader.readLine();
    }
    assertNull(testLine); // if both files have the same length testReader should be after the last line

    // 6 annotation create step
    assertTrue(vepInputFile.exists());
    assertTrue(vepOutputFile.exists());

    // Check output file length
    assertEquals(537, getLines(new GZIPInputStream(new FileInputStream(vepOutput))));

    // 8 Annotation load step: check documents in DB have annotation (only consequence type)
    iterator = getVariantDBIterator();

    int cnt = 0;
    int consequenceTypeCount = 0;
    while (iterator.hasNext()) {
        cnt++;
        Variant next = iterator.next();
        if (next.getAnnotation().getConsequenceTypes() != null) {
            consequenceTypeCount += next.getAnnotation().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(AnnotationLoaderStep.LOAD_VEP_ANNOTATION))
            .collect(Collectors.toList());
    assertEquals(1, variantAnnotationLoadStepExecution.get(0).getReadSkipCount());

}

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

@Test
public void optionalStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();//  w w w . j av a2  s .c  om

    jobOptions.getPipelineOptions().put(AnnotationJob.SKIP_ANNOT, true);
    jobOptions.getPipelineOptions().put(PopulationStatisticsJob.SKIP_STATS, true);

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(2, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

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

From source file:fr.acxio.tools.agia.alfresco.HibernateNodeReader.java

public ExitStatus afterStep(StepExecution sStepExecution) {
    synchronized (lock) {
        initialized = false;
        keys = null;
    }
    return ExitStatus.COMPLETED;
}

From source file:es.fcs.batch.integration.chunk.MyChunkMessageChannelItemWriter.java

@Override
public ExitStatus afterStep(StepExecution stepExecution) {
    if (!(stepExecution.getStatus() == BatchStatus.COMPLETED)) {
        return ExitStatus.EXECUTING;
    }//  w w  w. j a  v a2s  . c om
    long expecting = localState.getExpecting();
    boolean timedOut;
    try {
        logger.debug("Waiting for results in step listener...");
        timedOut = !waitForResults();
        logger.debug("Finished waiting for results in step listener.");
    } catch (RuntimeException e) {
        logger.debug("Detected failure waiting for results in step listener.", e);
        stepExecution.setStatus(BatchStatus.FAILED);
        return ExitStatus.FAILED.addExitDescription(e.getClass().getName() + ": " + e.getMessage());
    } finally {
        for (StepContribution contribution : getStepContributions()) {
            stepExecution.apply(contribution);
        }
    }
    if (timedOut) {
        stepExecution.setStatus(BatchStatus.FAILED);
        throw new ItemStreamException("Timed out waiting for back log at end of step");
    }
    return ExitStatus.COMPLETED.addExitDescription("Waited for " + expecting + " results.");
}

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

@Test
public void statsStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();/*w w w  .  ja  v  a  2  s.co m*/
    jobOptions.getPipelineOptions().put(PopulationStatisticsJob.SKIP_STATS, true);

    jobOptions.getPipelineOptions().put("db.name", "diegoTest");

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(5, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Map<String, StepExecution> parallelStepsNameToStepExecution = new HashMap<>();
    for (int i = 2; i <= steps.size() - 1; i++) {
        parallelStepsNameToStepExecution.put(steps.get(i).getStepName(), steps.get(i));
    }

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    Set<String> parallelStepNamesExecuted = parallelStepsNameToStepExecution.keySet();
    Set<String> parallelStepNamesToCheck = new HashSet<>(Arrays.asList(
            VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE, VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION,
            AnnotationLoaderStep.LOAD_VEP_ANNOTATION));

    assertEquals(parallelStepNamesToCheck, parallelStepNamesExecuted);

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
    assertTrue(loadStep.getEndTime().before(parallelStepsNameToStepExecution
            .get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE)
            .getEndTime().before(parallelStepsNameToStepExecution
                    .get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION).getStartTime()));
    assertTrue(parallelStepsNameToStepExecution.get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION)
            .getEndTime().before(parallelStepsNameToStepExecution.get(AnnotationLoaderStep.LOAD_VEP_ANNOTATION)
                    .getStartTime()));
}

From source file:com.philips.cn.hr.pps.App.java

private void startCaclBtnActionPerformed(java.awt.event.ActionEvent evt) {

    String f1 = this.filePath1.getText();
    String f2 = this.filePath2.getText();
    String saveTo = this.saveToPath.getText();

    StringBuffer message = new StringBuffer();

    if (!isInputValidate(f1, f2, saveTo)) {
        message.append("file path null is not allowed");
        JOptionPane.showMessageDialog(null, message);
        //            System.exit(0);
        return;/*from   www  .  j  a  v  a  2  s . c o  m*/
    }

    System.out.println("going to execute application with parameters " + Arrays.asList(f1, f2, saveTo));

    JobExecution jobExecution = null;

    try {
        jobExecution = Application.execute(f1, f2, saveTo, false);
    } catch (Exception e) {
        e.printStackTrace();
        message.append(e.getMessage());
        JOptionPane.showMessageDialog(null, message);
        return;
    }

    if (jobExecution.getExitStatus().equals(ExitStatus.COMPLETED)) {
        //job completed;
        message.append("Job execution completed ,Please verify generated files in ");
        message.append(saveTo);
        JOptionPane.showMessageDialog(null, message);

    } else {
        //            for (Throwable exception : jobExecution.getAllFailureExceptions()) {
        //                message.append("cause:" + exception.getCause()).append("message " + exception.getMessage());
        //            }
        //            JOptionPane.showMessageDialog(null, message);

        for (StepExecution stepExecution : jobExecution.getStepExecutions()) {
            if (!stepExecution.getExitStatus().equals(ExitStatus.COMPLETED)) {
                message.append(stepExecution.getFailureExceptions());
                message.append(" occurred when executing ");
                message.append(stepExecution.getStepName());
                break;
            }
        }

        JOptionPane.showMessageDialog(null, message);
    }

    //        System.exit(0);don't exit;
    return;

}

From source file:lcn.module.batch.core.launch.support.CommandLineRunner.java

/**
 * Batch Job? ./* www .j  av a  2s  .com*/
 * ?  , Job ? / JobExecutionID, Job Parameter
 *  CommandLineRunner Option ? .
 * 
 * @param jobPath : Job Context ? XML ?  
 * @param jobIdentifier : Job ? /JobExecutionID
 * @param parameters : Job Parameter 
 * @param opts : CommandLineRunner (-restart, -next, -stop, -abandon)
 */
public int start(String jobPath, String jobIdentifier, String[] parameters, Set<String> opts) {

    ConfigurableApplicationContext context = null;

    try {
        //  ApplicationContext ?.
        context = new ClassPathXmlApplicationContext(jobPath);
        context.getAutowireCapableBeanFactory().autowireBeanProperties(this,
                AutowireCapableBeanFactory.AUTOWIRE_BY_TYPE, false);

        Assert.state(launcher != null, "A JobLauncher must be provided.  Please add one to the configuration.");
        // ? Batch Job? , ? Batch Job?  ? JobExplorer  ?.
        if (opts.contains("-restart") || opts.contains("-next")) {
            Assert.state(jobExplorer != null,
                    "A JobExplorer must be provided for a restart or start next operation.  Please add one to the configuration.");
        }

        // Job? ?? .
        String jobName = jobIdentifier;

        // JobParameters ?.
        JobParameters jobParameters = jobParametersConverter
                .getJobParameters(StringUtils.splitArrayElementsIntoProperties(parameters, "="));
        Assert.isTrue(parameters == null || parameters.length == 0 || !jobParameters.isEmpty(),
                "Invalid JobParameters " + Arrays.asList(parameters)
                        + ". If parameters are provided they should be in the form name=value (no whitespace).");

        // Batch Job? .
        if (opts.contains("-stop")) {
            List<JobExecution> jobExecutions = getRunningJobExecutions(jobIdentifier);
            if (jobExecutions == null) {
                throw new JobExecutionNotRunningException(
                        "No running execution found for job=" + jobIdentifier);
            }
            for (JobExecution jobExecution : jobExecutions) {
                jobExecution.setStatus(BatchStatus.STOPPING);
                jobRepository.update(jobExecution);
            }
            return exitCodeMapper.intValue(ExitStatus.COMPLETED.getExitCode());
        }

        // ? Batch Job? ? abandon .
        if (opts.contains("-abandon")) {
            List<JobExecution> jobExecutions = getStoppedJobExecutions(jobIdentifier);
            if (jobExecutions == null) {
                throw new JobExecutionNotStoppedException(
                        "No stopped execution found for job=" + jobIdentifier);
            }
            for (JobExecution jobExecution : jobExecutions) {
                jobExecution.setStatus(BatchStatus.ABANDONED);
                jobRepository.update(jobExecution);
            }
            return exitCodeMapper.intValue(ExitStatus.COMPLETED.getExitCode());
        }

        // Batch Job? .
        if (opts.contains("-restart")) {
            JobExecution jobExecution = getLastFailedJobExecution(jobIdentifier);
            if (jobExecution == null) {
                throw new JobExecutionNotFailedException(
                        "No failed or stopped execution found for job=" + jobIdentifier);
            }
            jobParameters = jobExecution.getJobInstance().getJobParameters();
            jobName = jobExecution.getJobInstance().getJobName();
        }

        Job job;

        // JobLocator  Job?  null? ApplicationContext? Job? .
        if (jobLocator != null) {
            job = jobLocator.getJob(jobName);
        } else {
            job = (Job) context.getBean(jobName);
        }

        // ? Batch Job?   Job Parameters ?.
        if (opts.contains("-next")) {
            JobParameters nextParameters = getNextJobParameters(job);
            Map<String, JobParameter> map = new HashMap<String, JobParameter>(nextParameters.getParameters());
            map.putAll(jobParameters.getParameters());
            jobParameters = new JobParameters(map);
        }

        // Batch Job? .
        JobExecution jobExecution = launcher.run(job, jobParameters);
        logger.warn("CommandLineRunner's Job Information");
        logger.warn("jobName=" + jobExecution.getJobInstance().getJobName());
        logger.warn("jobParamters=" + jobParameters.toString());
        logger.warn("jobExecutionTime="
                + (jobExecution.getEndTime().getTime() - jobExecution.getStartTime().getTime()) / 1000f + "s");

        return exitCodeMapper.intValue(jobExecution.getExitStatus().getExitCode());
    } catch (Throwable e) {
        String message = "Job Terminated in error: " + e.getMessage();
        logger.error(message, e);
        CommandLineRunner.message = message;
        return exitCodeMapper.intValue(ExitStatus.FAILED.getExitCode());
    } finally {
        if (context != null) {
            context.close();
        }
    }
}

From source file:egovframework.rte.bat.core.launch.support.EgovCommandLineRunner.java

/**
 * Batch Job? ./*  w w  w.j  a v  a  2  s  .c om*/
 * ?  , Job ? / JobExecutionID, Job Parameter
 *  CommandLineRunner Option ? .
 * 
 * @param jobPath : Job Context ? XML ?  
 * @param jobIdentifier : Job ? /JobExecutionID
 * @param parameters : Job Parameter 
 * @param opts : CommandLineRunner (-restart, -next, -stop, -abandon)
 */
public int start(String jobPath, String jobIdentifier, String[] parameters, Set<String> opts) {

    ConfigurableApplicationContext context = null;

    try {
        //  ApplicationContext ?.
        context = new ClassPathXmlApplicationContext(jobPath);
        context.getAutowireCapableBeanFactory().autowireBeanProperties(this,
                AutowireCapableBeanFactory.AUTOWIRE_BY_TYPE, false);

        Assert.state(launcher != null, "A JobLauncher must be provided.  Please add one to the configuration.");
        // ? Batch Job? , ? Batch Job?  ? JobExplorer  ?.
        if (opts.contains("-restart") || opts.contains("-next")) {
            Assert.state(jobExplorer != null,
                    "A JobExplorer must be provided for a restart or start next operation.  Please add one to the configuration.");
        }

        // Job? ?? .
        String jobName = jobIdentifier;

        // JobParameters ?.
        JobParameters jobParameters = jobParametersConverter
                .getJobParameters(StringUtils.splitArrayElementsIntoProperties(parameters, "="));
        Assert.isTrue(parameters == null || parameters.length == 0 || !jobParameters.isEmpty(),
                "Invalid JobParameters " + Arrays.asList(parameters)
                        + ". If parameters are provided they should be in the form name=value (no whitespace).");

        // Batch Job? .
        if (opts.contains("-stop")) {
            List<JobExecution> jobExecutions = getRunningJobExecutions(jobIdentifier);
            if (jobExecutions == null) {
                throw new JobExecutionNotRunningException(
                        "No running execution found for job=" + jobIdentifier);
            }
            for (JobExecution jobExecution : jobExecutions) {
                jobExecution.setStatus(BatchStatus.STOPPING);
                jobRepository.update(jobExecution);
            }
            return exitCodeMapper.intValue(ExitStatus.COMPLETED.getExitCode());
        }

        // ? Batch Job? ? abandon .
        if (opts.contains("-abandon")) {
            List<JobExecution> jobExecutions = getStoppedJobExecutions(jobIdentifier);
            if (jobExecutions == null) {
                throw new JobExecutionNotStoppedException(
                        "No stopped execution found for job=" + jobIdentifier);
            }
            for (JobExecution jobExecution : jobExecutions) {
                jobExecution.setStatus(BatchStatus.ABANDONED);
                jobRepository.update(jobExecution);
            }
            return exitCodeMapper.intValue(ExitStatus.COMPLETED.getExitCode());
        }

        // Batch Job? .
        if (opts.contains("-restart")) {
            JobExecution jobExecution = getLastFailedJobExecution(jobIdentifier);
            if (jobExecution == null) {
                throw new JobExecutionNotFailedException(
                        "No failed or stopped execution found for job=" + jobIdentifier);
            }
            jobParameters = jobExecution.getJobInstance().getJobParameters();
            jobName = jobExecution.getJobInstance().getJobName();
        }

        Job job;

        // JobLocator  Job?  null? ApplicationContext? Job? .
        if (jobLocator != null) {
            job = jobLocator.getJob(jobName);
        } else {
            job = (Job) context.getBean(jobName);
        }

        // ? Batch Job?   Job Parameters ?.
        if (opts.contains("-next")) {
            JobParameters nextParameters = getNextJobParameters(job);
            Map<String, JobParameter> map = new HashMap<String, JobParameter>(nextParameters.getParameters());
            map.putAll(jobParameters.getParameters());
            jobParameters = new JobParameters(map);
        }

        // Batch Job? .
        JobExecution jobExecution = launcher.run(job, jobParameters);
        logger.warn("EgovCommandLineRunner's Job Information");
        logger.warn("jobName=" + jobExecution.getJobInstance().getJobName());
        logger.warn("jobParamters=" + jobParameters.toString());
        logger.warn("jobExecutionTime="
                + (jobExecution.getEndTime().getTime() - jobExecution.getStartTime().getTime()) / 1000f + "s");

        return exitCodeMapper.intValue(jobExecution.getExitStatus().getExitCode());
    } catch (Throwable e) {
        String message = "Job Terminated in error: " + e.getMessage();
        logger.error(message, e);
        EgovCommandLineRunner.message = message;
        return exitCodeMapper.intValue(ExitStatus.FAILED.getExitCode());
    } finally {
        if (context != null) {
            context.close();
        }
    }
}

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

@Test
public void annotationStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();/*w  w w . jav  a 2s. c o  m*/
    jobOptions.getPipelineOptions().put(AnnotationJob.SKIP_ANNOT, true);

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(4, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Map<String, StepExecution> parallelStepsNameToStepExecution = new HashMap<>();
    for (int i = 2; i <= steps.size() - 1; i++) {
        parallelStepsNameToStepExecution.put(steps.get(i).getStepName(), steps.get(i));
    }

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    Set<String> parallelStepNamesExecuted = parallelStepsNameToStepExecution.keySet();
    Set<String> parallelStepNamesToCheck = new HashSet<>(Arrays
            .asList(PopulationStatisticsJob.CALCULATE_STATISTICS, PopulationStatisticsJob.LOAD_STATISTICS));

    assertEquals(parallelStepNamesToCheck, parallelStepNamesExecuted);

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
    assertTrue(loadStep.getEndTime().before(
            parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getEndTime()
            .before(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.LOAD_STATISTICS)
                    .getStartTime()));
}