Example usage for javax.persistence FlushModeType COMMIT

List of usage examples for javax.persistence FlushModeType COMMIT

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Introduction

In this page you can find the example usage for javax.persistence FlushModeType COMMIT.

Prototype

FlushModeType COMMIT

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Document

Flushing to occur at transaction commit.

Usage

From source file:uk.ac.ebi.intact.dataexchange.cvutils.CvUpdater.java

@Transactional
@IntactFlushMode(FlushModeType.COMMIT)
public CvUpdaterStatistics executeUpdate(OBOSession oboSession, AnnotationInfoDataset annotationInfoDataset)
        throws IOException {
    CvObjectOntologyBuilder builder = new CvObjectOntologyBuilder(oboSession);
    return createOrUpdateCVs(builder.getAllCvs(), annotationInfoDataset);
}

From source file:uk.ac.ebi.intact.dataexchange.cvutils.CvUpdater.java

@Transactional
@IntactFlushMode(FlushModeType.COMMIT)
public CvUpdaterStatistics executeUpdate(OBOSession oboSession) throws IOException {
    return executeUpdate(oboSession, new AnnotationInfoDataset());
}

From source file:uk.ac.ebi.intact.dataexchange.cvutils.CvUpdater.java

/**
 * Starts the creation and update of CVs by using the CVobject List provided
 *
 * @param allValidCvs           List of all valid  Cvs
 * @param annotationInfoDataset A seperate dataset specific for intact
 * @return An object containing some statistics about the update
 *//*from   w ww .ja  v  a  2 s. co m*/
@Transactional
@IntactFlushMode(FlushModeType.COMMIT)
public CvUpdaterStatistics createOrUpdateCVs(List<CvDagObject> allValidCvs,
        AnnotationInfoDataset annotationInfoDataset) {

    if (allValidCvs == null) {
        throw new IllegalArgumentException("You must give a non null collection of CvDagObject");
    }
    if (annotationInfoDataset == null) {
        throw new IllegalArgumentException("You must give a non null AnnotationInfoDataset");
    }

    List<CvDagObject> alreadyExistingObsoleteCvList = new ArrayList<CvDagObject>();
    List<CvDagObject> orphanCvList = dealWithOrphans(allValidCvs, alreadyExistingObsoleteCvList);

    if (log.isDebugEnabled()) {
        log.debug("Orphan count: " + orphanCvList.size());
        log.debug("AlreadyExisting cvs annotated with Obsolete: " + alreadyExistingObsoleteCvList.size());
    }

    //first step remove the orphan cvs that are not existing in database
    List<CvDagObject> cleanedList = (List<CvDagObject>) CollectionUtils.subtract(allValidCvs, orphanCvList);
    if (log.isDebugEnabled())
        log.debug("Size of CV list after removing orphans: " + cleanedList.size());
    //second step remove the orphan cvs that are are already existing in the database
    cleanedList = (List<CvDagObject>) CollectionUtils.subtract(cleanedList, alreadyExistingObsoleteCvList);

    if (log.isDebugEnabled())
        log.debug("Size of CV list after removing obsolete terms: " + cleanedList.size());

    CorePersister corePersister = persisterHelper.getCorePersister();
    corePersister.setUpdateWithoutAcEnabled(true);

    updateCVsUsingAnnotationDataset(cleanedList, annotationInfoDataset, corePersister);

    CvObject[] cvObjects = cleanedList.toArray(new CvObject[cleanedList.size()]);

    corePersister.saveOrUpdate(cvObjects);

    PersisterStatistics persisterStats = corePersister.getStatistics();

    addCvObjectsToUpdaterStats(persisterStats, stats);

    if (log.isDebugEnabled()) {
        log.debug("Persisted: " + persisterStats);
        log.debug("Processed: " + processed.size());
        log.debug(stats);
    }

    return stats;
}