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

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

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In this page you can find the example usage for org.springframework.batch.core ExitStatus COMPLETED.

Prototype

ExitStatus COMPLETED

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Document

Convenient constant value representing finished processing.

Usage

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

@Test
public void allStepsShouldBeExecuted() throws Exception {
    initVariantConfigurationJob();//ww  w  .  jav a 2 s. c  o 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:com.javaetmoi.elasticsearch.musicbrainz.batch.TestMusicAlbumJob.java

@Test
public void indexMusicAlbum() throws Exception {
    JobExecution execution = testUtils.launchJob();

    // Batch Status
    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    StepExecution indexMusicAlbum = getStepExecution(execution, "indexMusicAlbum");
    assertEquals(13, indexMusicAlbum.getWriteCount());
    assertEquals(2 * 2, indexMusicAlbum.getCommitCount());

    // Elasticsearch status
    ElasticSearchHelper.refreshIndex(client);
    DocsStatus docs = getDocStatus();//from   w  ww.  ja  v a 2  s .c o  m
    assertEquals(13, docs.getNumDocs());
}

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

@Test
public void shouldLoadAllAnnotations() throws Exception {
    DBObjectToVariantAnnotationConverter converter = new DBObjectToVariantAnnotationConverter();

    String dump = AnnotationLoaderStepTest.class.getResource("/dump/").getFile();
    restoreMongoDbFromDump(dump);//from   w ww .ja v a2s . c  o m

    String vepOutput = jobOptions.getVepOutput();
    makeGzipFile(VepOutputContent.vepOutputContent, vepOutput);

    JobExecution jobExecution = jobLauncherTestUtils.launchStep(AnnotationLoaderStep.LOAD_VEP_ANNOTATION);

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

    //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);
            Assert.assertNotNull(annot.getConsequenceTypes());
            consequenceTypeCount += annot.getConsequenceTypes().size();
        }
    }

    assertEquals(300, cnt);
    assertTrue("Annotations not found", consequenceTypeCount > 0);
}

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

@Test
public void aggregatedTransformAndLoadShouldBeExecuted() throws Exception {
    Config.setOpenCGAHome(opencgaHome);/*  w w w  .j a  va2  s  . c  o 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:org.jasig.ssp.util.importer.job.listener.ParsingListener.java

@SuppressWarnings("unchecked")
@Override/*w  ww .j av a2  s .  c  o m*/
@AfterStep
public ExitStatus afterStep(StepExecution arg0) {
    // The "fileName" context property has been normalized so the file separator is
    // not platform-specific
    String fileSeparatorRegex = "/";
    String fileName = this.getStepExecution().getExecutionContext().getString("fileName");
    String[] split = fileName.split(fileSeparatorRegex);
    String pathname = split[split.length - 1];
    String[] split1 = pathname.split("\\.");
    String currentEntity = split1[0];

    if (currentEntity != null) {
        Map<String, ReportEntry> report = (Map<String, ReportEntry>) this.getStepExecution().getJobExecution()
                .getExecutionContext().get("report");
        if (report == null) {
            report = new HashMap<String, ReportEntry>();
        }
        ReportEntry currentEntry = report.get(currentEntity);
        if (currentEntry != null) {
            currentEntry.setTableName(currentEntity);
            currentEntry.setNumberParsed(this.getStepExecution().getReadCount());
            currentEntry.setNumberSkippedOnParse(this.getStepExecution().getProcessSkipCount());
        } else {
            currentEntry = new ReportEntry();
            currentEntry.setTableName(currentEntity);
            currentEntry.setNumberParsed(this.getStepExecution().getReadCount());
            currentEntry.setNumberSkippedOnParse(this.getStepExecution().getProcessSkipCount());
        }
        report.put(currentEntity, currentEntry);
        arg0.getJobExecution().getExecutionContext().put("report", report);
    }

    return ExitStatus.COMPLETED;
}

From source file:com.github.jrrdev.mantisbtsync.core.common.auth.PortalAuthManager.java

/**
 * EGet the authenfication by executing the defined requests sequence.
 *
 * @throws IOException//from w w w  . j a v a 2  s  .  co m
 * @throws ClientProtocolException
 */
public ExitStatus authentificate() throws ClientProtocolException, IOException {
    authCookie = null;

    if (firstRequest != null) {

        final CookieStore cookieStore = new BasicCookieStore();
        client = HttpClients.custom().setDefaultCookieStore(cookieStore)
                .setRedirectStrategy(new LaxRedirectStrategy()).useSystemProperties().build();

        lastResponse = firstRequest.executeSequence(client);

        final List<Cookie> cookies = cookieStore.getCookies();
        final StringBuilder strBuff = new StringBuilder();
        for (final Cookie cookie : cookies) {
            strBuff.append(cookie.getName());
            strBuff.append("=");
            strBuff.append(cookie.getValue());
            strBuff.append(";");
        }

        authCookie = strBuff.toString();
    }

    return ExitStatus.COMPLETED;
}

From source file:org.emonocot.job.common.GetResourceClientTest.java

/**
 *
 * @throws IOException// w ww  .  j a v a2  s  . co  m
 *             if a temporary file cannot be created or if there is a http
 *             protocol error.
 * @throws SAXException
 *             if the content retrieved is not valid xml.
 */
@Test
public final void testGetResourceSuccessfully() throws IOException, SAXException {
    File tempFile = File.createTempFile("test", "zip");
    tempFile.deleteOnExit();

    EasyMock.expect(httpClient.getParams()).andReturn(new BasicHttpParams());
    EasyMock.expect(httpClient.execute(EasyMock.isA(HttpGet.class))).andReturn(httpResponse);
    EasyMock.replay(httpClient);

    ExitStatus exitStatus = getResourceClient.getResource(testzip, Long.toString(new Date().getTime()),
            tempFile.getAbsolutePath());

    EasyMock.verify(httpClient);

    assertNotNull("ExitStatus should not be null", exitStatus);
    assertEquals("ExitStatus should be COMPLETED", exitStatus, ExitStatus.COMPLETED);
}

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

@Test
public void normalizerStepShouldTransformAllVariants() throws Exception {
    Config.setOpenCGAHome(opencgaHome);//w ww  . j  a va2  s  . co 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:uk.ac.ebi.eva.pipeline.jobs.steps.IndexesGeneratorStepTest.java

@Test(expected = DuplicateKeyException.class)
public void testNoDuplicatesCanBeInserted() throws Exception {
    String dbCollectionGenesName = jobOptions.getDbCollectionsFeaturesName();
    JobExecution jobExecution = jobLauncherTestUtils
            .launchStep(DatabaseInitializationJob.CREATE_DATABASE_INDEXES);

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

    MongoClient mongoClient = new MongoClient();
    DBCollection genesCollection = mongoClient.getDB(dbName).getCollection(dbCollectionGenesName);
    genesCollection.insert(new BasicDBObject("_id", "example_id"));
    genesCollection.insert(new BasicDBObject("_id", "example_id"));
}

From source file:com.github.jrrdev.mantisbtsync.core.jobs.issues.tasklets.IssuesLastRunExtractorTasklet.java

/**
 * {@inheritDoc}//  w  w w .ja va 2s . c  o  m
 * @see org.springframework.batch.core.step.tasklet.Tasklet#execute(org.springframework.batch.core.StepContribution, org.springframework.batch.core.scope.context.ChunkContext)
 */
@Override
public RepeatStatus execute(final StepContribution contribution, final ChunkContext chunkContext)
        throws Exception {

    final StepContext stepContext = chunkContext.getStepContext();
    final String jobName = stepContext.getJobName();
    final JobParameters jobParams = stepContext.getStepExecution().getJobParameters();
    final Map<String, JobParameter> currParams = new HashMap<String, JobParameter>(jobParams.getParameters());
    currParams.remove("run.id");

    Date lastJobRun = null;

    final List<JobInstance> jobInstances = jobExplorer.getJobInstances(jobName, 0, 1000);
    for (final JobInstance jobInstance : jobInstances) {
        final List<JobExecution> jobExecutions = jobExplorer.getJobExecutions(jobInstance);
        for (final JobExecution jobExecution : jobExecutions) {

            final JobParameters oldJobParams = jobExecution.getJobParameters();
            final Map<String, JobParameter> oldParams = new HashMap<String, JobParameter>(
                    oldJobParams.getParameters());
            oldParams.remove("run.id");

            if (ExitStatus.COMPLETED.equals(jobExecution.getExitStatus()) && oldParams.equals(currParams)) {

                if (lastJobRun == null || lastJobRun.before(jobExecution.getStartTime())) {
                    lastJobRun = jobExecution.getStartTime();
                }
            }
        }
    }

    if (lastJobRun != null) {
        stepContext.getStepExecution().getExecutionContext().put("mantis.update.last_job_run", lastJobRun);
    }

    stepContext.getStepExecution().getExecutionContext().put("mantis.update.current_job_run",
            Calendar.getInstance());

    return RepeatStatus.FINISHED;
}