Example usage for org.hibernate Session clear

List of usage examples for org.hibernate Session clear

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Introduction

In this page you can find the example usage for org.hibernate Session clear.

Prototype

void clear();

Source Link

Document

Completely clear the session.

Usage

From source file:edu.scripps.fl.pubchem.app.curves.CommitCurveStage.java

License:Apache License

@Override
public void doSave(Object obj) throws StageException {
    Session session = getSession();
    session.save(obj);//from w  w  w.j a v  a2 s.  co m
    session.flush();
    session.clear();
}

From source file:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public void populateAssayResults(Session session, PCAssay assay, InputStream is) throws Exception {
    long counter = 0L;
    PCAssayColumn activeColumn = assay.getActiveColumn();
    List<PCAssayColumn> testedCols = assay.getTestedColumns();

    CsvReader reader = new CsvReader(new BufferedReader(new InputStreamReader(is)), ',');
    reader.readHeaders();// w w  w .  j  av  a2  s .  c o  m
    String[] headers = reader.getHeaders();

    Transaction trx = session.beginTransaction();
    while (reader.readRecord()) {

        String[] values = reader.getValues();

        String[] sids = reader.get("PUBCHEM_SID").split("\\s*,\\s*");

        if (sids.length > 1) {
            log.warn(String.format("AID %s has %s SIDS on a line", assay.getAID(), sids.length));
        }

        for (String sid : sids) {

            PCAssayResult result = new PCAssayResult();

            result.setSID(Long.parseLong(sid));

            String cid = reader.get("PUBCHEM_CID");
            if (!"".equals(cid))
                result.setCID(Long.parseLong(cid));

            result.setComments(reader.get("PUBCHEM_ASSAYDATA_COMMENT"));

            int outcome = Integer.parseInt(reader.get("PUBCHEM_ACTIVITY_OUTCOME"));
            result.setOutcome(getOutcome(outcome));

            String score = reader.get("PUBCHEM_ACTIVITY_SCORE");
            if (!"".equals(score))
                result.setRankScore(Integer.parseInt(score));

            result.setURL(reader.get("PUBCHEM_ACTIVITY_URL"));

            result.setXref(reader.get("PUBCHEM_EXT_DATASOURCE_REGID"));

            // if a dose response assay with a marked activeConcentration
            if ("confirmatory".equals(assay.getActivityOutcomeMethod()) && activeColumn != null) {
                String actConc = reader.get("" + activeColumn.getTID());
                if (!"".equals(actConc)) {
                    result.setPrimaryValue(Double.valueOf(actConc));
                    result.setPrimaryColumn(activeColumn);

                    PCAssayColumn qualCol = assay.getQualifierColumn();
                    if (qualCol != null) {
                        String qual = reader.get("" + qualCol.getTID()); // get(String)
                        if (!"".equals(qual))
                            result.setQualifier(qual);
                    }
                }

            } else if ("screening".equals(assay.getActivityOutcomeMethod()) && testedCols.size() > 0) {
                PCAssayColumn testedCol = testedCols.get(0);
                String value = reader.get("" + testedCol.getTID());
                result.setPrimaryColumn(testedCol);
                if (!"".equals(value))
                    if ("float".equals(testedCol.getType()) || "int".equals(testedCol.getType()))
                        result.setPrimaryValue(Double.parseDouble(value));
                    else
                        result.setPrimaryValueAsString(value);
            }
            // put all testedConcentration columns into an ordered array.
            // Interested in numbers here only.
            result.getTestedValues().clear();
            for (int ii = 0; ii < testedCols.size(); ii++) {
                String value = reader.get("" + testedCols.get(ii).getTID());
                try {
                    Double dbl = Double.parseDouble(value);
                    result.getTestedValues().set(ii, dbl);
                } catch (NumberFormatException ex) {
                    // if not a number then don't worry about it.
                }
            }

            List<String> list = result.getAllValues();
            list.clear();
            for (PCAssayColumn col : assay.getColumns()) {
                if (col.getTID() > 0) { // not the outcome and score
                    String value = reader.get("" + col.getTID());
                    list.set(col.getTID() - 1, value);
                }
            }

            result.setAssay(assay);

            session.save(result);

            if (++counter % 100 == 0) {
                trx.commit();
                session.clear(); // else huge build up of hibernate memory
                // cache
                trx = session.beginTransaction();
            }
            if (counter % 10000 == 0)
                log.debug(String.format("AID %s: processed %s results", assay.getAID(), counter));
        }
    }
    log.debug(String.format("Processed AID: %s, contained %s results", assay.getAID(), counter));
    assay = (PCAssay) session.merge(assay);
    assay.setVersionChanged(false);
    session.save(assay);
    trx.commit();
}

From source file:edu.scripps.fl.pubchem.PubChemFactory.java

License:Apache License

public int populateRelations(Session session, Document document) throws IOException, DocumentException {
    String fromDb = document.selectSingleNode("/eLinkResult/LinkSet/DbFrom").getText();
    String idStr = document.selectSingleNode("/eLinkResult/LinkSet/IdList/Id").getText();
    Long id = Long.parseLong(idStr);
    List<Node> linkSetDbs = document.selectNodes("/eLinkResult/LinkSet/LinkSetDb");

    Transaction trx = session.beginTransaction();
    int counter = 0;
    for (Node linkSetDb : linkSetDbs) {
        String toDb = linkSetDb.selectSingleNode("DbTo").getText();
        String linkName = linkSetDb.selectSingleNode("LinkName").getText();
        List<Node> ids = linkSetDb.selectNodes("Link/Id");
        for (Node idNode : ids) {
            long relatedId = Long.parseLong(idNode.getText());
            if (id == relatedId)
                continue;
            Relation relation = new Relation();
            relation.setRelationName(linkName);
            relation.setFromDb(fromDb);//from   w w  w.j  a v a 2 s . c  o m
            relation.setFromId(id);
            relation.setToDb(toDb);
            relation.setToId(relatedId);
            session.save(relation);
            if (counter++ % 100 == 0) {
                trx.commit();
                session.clear(); // cache grows hugely during very large
                // inserts
                trx = session.beginTransaction();
            }
        }
    }
    trx.commit();
    return counter;
}

From source file:edu.utah.further.ds.impl.service.query.processor.PageFinalizerHibernateQp.java

License:Apache License

/**
 * @param request//from w w  w. jav a  2s .c o m
 * @return
 * @see edu.utah.further.core.api.chain.RequestProcessor#process(edu.utah.further.core.api.chain.ChainRequest)
 */
@Override
public boolean process(final ChainRequest request) {
    // Read inputs from chain request
    final QueryContext queryContext = request.getAttribute(QUERY_CONTEXT);
    final List<?> resultPage = request.getAttribute(QUERY_RESULT);
    final PagingLoopController controller = request.getAttribute(AttributeName.PAGING_LOOP_CONTROLLER);

    // Perform finalization logic
    // In the future pass only selected attributes to the delegate. For simplicity,
    // pass all of them for now.
    final QueryContext newQueryContext = getDelegate().finalizePage(queryContext, resultPage, controller);

    // Clear persistent session
    final SessionFactory sessionFactory = request.getAttribute(SESSION_FACTORY);
    final Session session = sessionFactory.getCurrentSession();
    // Flush the current page's batch of reads, inserts and updates and release memory
    session.flush();
    session.clear();

    // Save results in the chain request
    request.setAttribute(QUERY_CONTEXT, newQueryContext);

    return false;
}

From source file:edu.wustl.cab2b.server.queryengine.QueryOperations.java

License:BSD License

public void deleteQuery(Long id) {

    logger.info("id to delete:" + id);

    Session session = HibernateUtil.getSessionFactory().openSession();
    Transaction tx = session.beginTransaction();

    try {/*from  w w w  .  j a va 2  s  .  c  o m*/
        session.connection().createStatement()
                .execute("update query_abstract_query set created_by=-1 where identifier=" + id);

    } catch (Exception e) {
        logger.error(e);

    }

    tx.commit();
    session.clear();
    session.close();

    EntityCache.getCache().refreshCache();
    CategoryCache.getInstance().refreshCategoryCache();
    UtilityOperations.refreshCache();

}

From source file:ee.ria.xroad.opmonitordaemon.OperationalDataRecordManager.java

License:Open Source License

private static Void storeInTransaction(Session session, List<OperationalDataRecord> records, long timestamp) {
    int storedCount = 0;
    int batchSize = getConfiguredBatchSize(session);

    for (OperationalDataRecord record : records) {
        record.setMonitoringDataTs(timestamp);
        session.save(record);//  w  ww.  j av a 2s .c  om

        if (++storedCount % batchSize == 0) {
            session.flush();
            session.clear();
        }
    }

    return null;
}

From source file:eionet.webq.dao.ProjectFileStorageImplTest.java

License:Mozilla Public License

@Test(expected = LazyInitializationException.class)
public void allFilesQueryDoesNotReturnFileContent() throws Exception {
    addOneFile("fileName1");
    Session currentSession = sessionFactory.getCurrentSession();
    currentSession.clear();

    Collection<ProjectFile> projectFiles = projectFileStorage.findAllFilesFor(projectEntry);
    assertThat(projectFiles.size(), equalTo(1));
    ProjectFile file = projectFiles.iterator().next();
    currentSession.evict(file);//  w w w  . j a  v  a 2  s  .c o  m

    file.getFileContent();
}

From source file:eionet.webq.dao.UserFileStorageImplTest.java

License:Mozilla Public License

@Test(expected = LazyInitializationException.class)
public void filesContentIsFetchedLazily() throws Exception {
    storage.save(fileWithContentAndXmlSchema("test-content".getBytes()), userId);
    Session currentSession = sessionFactory.getCurrentSession();
    currentSession.clear();

    UserFile theOnlyFile = getFirstUploadedFileAndAssertThatItIsTheOnlyOneAvailableFor(userId);
    currentSession.evict(theOnlyFile);//from   w  ww.  j a va  2  s . co m

    theOnlyFile.getContent();// content must be not initialized
}

From source file:eionet.webq.dao.UserFileStorageImplTest.java

License:Mozilla Public License

@Test
public void fileContentWillBeLoadedOnDemand() throws Exception {
    byte[] testContent = "aaaaa".getBytes();
    storage.save(fileWithContentAndXmlSchema(testContent), userId);
    Session currentSession = sessionFactory.getCurrentSession();
    currentSession.clear();

    UserFile theOnlyFile = getFirstUploadedFileAndAssertThatItIsTheOnlyOneAvailableFor(userId);

    assertThat(theOnlyFile.getContent(), equalTo(testContent));
}

From source file:es.emergya.bbdd.dao.BandejaEntradaHome.java

License:Open Source License

@SuppressWarnings("unchecked")
@Transactional(propagation = Propagation.REQUIRES_NEW, readOnly = true, rollbackFor = Throwable.class)
public List<Inbox> getNotProcessed() {
    Session currentSession = getSession();
    currentSession.clear();
    return (List<Inbox>) getSession().createCriteria(Inbox.class).add(Restrictions.eq("procesado", false))
            .addOrder(Order.asc("marcaTemporal")).setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY).list();
}