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

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

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Introduction

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

Prototype

public Collection<StepExecution> getStepExecutions()

Source Link

Document

Accessor for the step executions.

Usage

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

@Test
public void optionalStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();//from w  ww  . j  av  a2s .co  m

    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:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void annotationStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();//from   w ww  .ja  v a  2 s.  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()));
}

From source file:admin.jmx.BatchMBeanExporter.java

private void registerSteps() {
    if (!registerSteps) {
        return;//w  ww . j  a v a 2 s .  c  o m
    }
    for (String jobName : jobService.listJobs(0, Integer.MAX_VALUE)) {
        Collection<JobExecution> jobExecutions = Collections.emptySet();
        try {
            jobExecutions = jobService.listJobExecutionsForJob(jobName, 0, 1);
        } catch (NoSuchJobException e) {
            // do-nothing
            logger.error("Job listed but does not exist", e);
        }
        for (JobExecution jobExecution : jobExecutions) {
            for (StepExecution stepExecution : jobExecution.getStepExecutions()) {
                String stepName = stepExecution.getStepName();
                String stepKey = String.format("%s/%s", jobName, stepName);
                String beanKey = getBeanKeyForStepExecution(jobName, stepName);
                if (!stepKeys.contains(stepKey)) {
                    stepKeys.add(stepKey);
                    logger.info("Registering step execution " + stepKey);
                    registerBeanNameOrInstance(
                            stepExecutionMetricsFactory.createMetricsForStep(jobName, stepName), beanKey);
                }
            }
        }
    }
}

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

@Test
public void statsStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();//from  w w w.j  av a2  s .  c om
    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:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void allStepsShouldBeExecuted() throws Exception {
    initVariantConfigurationJob();//  w w w . j  a v  a  2 s  .co m

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(7, 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,
            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(PopulationStatisticsJob.CALCULATE_STATISTICS).getStartTime()));
    assertTrue(loadStep.getEndTime().before(parallelStepsNameToStepExecution
            .get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getEndTime()
            .before(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.LOAD_STATISTICS)
                    .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:uk.ac.ebi.eva.pipeline.jobs.AggregatedVcfJobTest.java

@Test
public void aggregatedTransformAndLoadShouldBeExecuted() throws Exception {
    Config.setOpenCGAHome(opencgaHome);//from   w w  w. j av a2 s .c om

    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.intact.editor.controller.dbmanager.ImportJobController.java

public List<Map.Entry<String, String>> getImportStatistics(JobExecution jobExecution) {
    Collection<StepExecution> stepExecutions = jobExecution.getStepExecutions();
    Map<String, String> statistics = new HashMap<String, String>();
    if (!stepExecutions.isEmpty()) {
        StepExecution firstStep = stepExecutions.iterator().next();
        ExecutionContext stepContext = firstStep.getExecutionContext();

        for (Map.Entry<String, Object> entry : stepContext.entrySet()) {
            // persisted count
            if (entry.getKey().startsWith(AbstractIntactDbImporter.PERSIST_MAP_COUNT)) {
                statistics.put(entry.getKey().substring(entry.getKey().lastIndexOf(".") + 1),
                        Integer.toString((Integer) entry.getValue()));
            }/* w  ww  .j a v  a  2  s . com*/
        }
    }
    return new ArrayList<Map.Entry<String, String>>(statistics.entrySet());
}

From source file:de.codecentric.batch.test.metrics.BatchMetricsFlatFileToDbIntegrationTest.java

@Test
public void testRunFlatFileToDbNoSkipJob_Failed() throws InterruptedException {
    JobExecution jobExecution = runJob("flatFileToDbNoSkipJob", "metrics/flatFileToDbNoSkipJob_Failed.csv");
    assertThat(jobExecution.getStatus(), is(BatchStatus.FAILED));
    ExecutionContext executionContext = jobExecution.getStepExecutions().iterator().next()
            .getExecutionContext();/*  www.j a v a2  s.  c  o  m*/
    long writeCount = 3L;
    MetricValidator validator = MetricValidatorBuilder.metricValidator().withExecutionContext(executionContext)
            .withBeforeChunkCount(1L).withStreamOpenCount(1L).withStreamUpdateCount(2L).withStreamCloseCount(0L)
            .withBeforeReadCount(6L).withReadCount(6L).withAfterReadCount(5L).withReadErrorCount(0L)
            .withBeforeProcessCount(3L).withProcessCount(3L).withAfterProcessCount(3L).withProcessErrorCount(1L)
            .withBeforeWriteCount(3L).withWriteCount(writeCount).withAfterWriteCount(3L).withAfterChunkCount(1L)
            .withChunkErrorCount(1L).withSkipInReadCount(0L).withSkipInProcessCount(0L).withSkipInWriteCount(0L)
            .build();
    validator.validate();
    // if one is correct, all will be in the metricReader, so I check just one
    assertThat((Double) metricReader
            .findOne("gauge.batch.flatFileToDbNoSkipJob.step." + MetricNames.PROCESS_COUNT.getName())
            .getValue(), is(notNullValue()));
    assertThat(jdbcTemplate.queryForObject("SELECT COUNT(*) FROM ITEM", Long.class), is(writeCount));
}

From source file:fr.acxio.tools.agia.admin.StaleRunningJobsService.java

public void forceRunningJobsToFail() {
    if (logger.isInfoEnabled()) {
        logger.info("Reseting jobs...");
    }/*from w w w. j  a  v a  2 s  .  co  m*/

    List<String> aJobNames = jobExplorer.getJobNames();
    for (String aJobName : aJobNames) {
        Set<JobExecution> aJobExecutions = jobExplorer.findRunningJobExecutions(aJobName);
        for (JobExecution aJobExecution : aJobExecutions) {
            if (logger.isInfoEnabled()) {
                logger.info("  " + aJobName + " (" + aJobExecution.getId() + ")");
            }
            aJobExecution.setEndTime(new Date());
            aJobExecution.setStatus(BatchStatus.FAILED);
            aJobExecution.setExitStatus(ExitStatus.FAILED);
            jobRepository.update(aJobExecution);
            for (StepExecution aStepExecution : aJobExecution.getStepExecutions()) {
                if (aStepExecution.getStatus().isGreaterThan(BatchStatus.COMPLETED)) {
                    if (logger.isInfoEnabled()) {
                        logger.info("    " + aStepExecution.getStepName());
                    }
                    aStepExecution.setEndTime(new Date());
                    aStepExecution.setStatus(BatchStatus.FAILED);
                    aStepExecution.setExitStatus(ExitStatus.FAILED);
                    jobRepository.update(aStepExecution);
                }
            }
        }
    }
    if (logger.isInfoEnabled()) {
        logger.info("Done.");
    }
}

From source file:de.codecentric.batch.test.metrics.BatchMetricsFlatFileToDbIntegrationTest.java

@Test
public void testRunFlatFileToDbSkipJob_SkipInRead() throws InterruptedException {
    JobExecution jobExecution = runJob("flatFileToDbSkipJob", "metrics/flatFileToDbSkipJob_SkipInRead.csv");
    assertThat(jobExecution.getStatus(), is(BatchStatus.COMPLETED));
    ExecutionContext executionContext = jobExecution.getStepExecutions().iterator().next()
            .getExecutionContext();//from w ww  .  j  a va  2 s.  c o  m
    long writeCount = 7L;
    MetricValidator validator = MetricValidatorBuilder.metricValidator().withExecutionContext(executionContext)
            .withBeforeChunkCount(3L).withStreamOpenCount(1L).withStreamUpdateCount(4L).withStreamCloseCount(0L)
            .withBeforeReadCount(9L).withReadCount(9L).withAfterReadCount(7L).withReadErrorCount(1L)
            .withBeforeProcessCount(7L).withProcessCount(7L).withAfterProcessCount(7L).withProcessErrorCount(0L)
            .withBeforeWriteCount(7L).withWriteCount(writeCount).withAfterWriteCount(7L).withWriteErrorCount(0L)
            .withAfterChunkCount(3L).withChunkErrorCount(0L).withSkipInReadCount(1L).withSkipInProcessCount(0L)
            .withSkipInWriteCount(0L).build();
    validator.validate();
    // if one is correct, all will be in the metricReader, so I check just one
    assertThat((Double) metricReader
            .findOne("gauge.batch.flatFileToDbSkipJob.step." + MetricNames.PROCESS_COUNT.getName()).getValue(),
            is(notNullValue()));
    assertThat(jdbcTemplate.queryForObject("SELECT COUNT(*) FROM ITEM", Long.class), is(writeCount));
}