Example usage for org.hibernate Session persist

List of usage examples for org.hibernate Session persist

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Introduction

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

Prototype

void persist(Object object);

Source Link

Document

Make a transient instance persistent.

Usage

From source file:es.uvigo.ei.sing.gc.view.models.committee.dataset.DataSetViewModel.java

License:Open Source License

public void setDataSet(DataSetMetaData dataSet) {
    final Committee committee = this.getCommittee();
    final Integer dataSetId = dataSet.getId();

    if (!dataSet.equals(committee.getDataSet())) {
        this.dataLostNotification("Data Set Selection",
                "Data set changing will provoke data deletion (gene set, classifiers, etc.). Do you wish to continue?",
                CommitteeStatus.RANKED_GENES, CommitteeStatus.DATA_SET, new Runnable() {
                    public void run() {
                        final Session session = HibernateUtil.currentSession();
                        final Committee committee = DataSetViewModel.this.getCommittee();
                        final DataSetMetaData dataSet = (DataSetMetaData) session.get(DataSetMetaData.class,
                                dataSetId);
                        committee.setDataSet(dataSet);
                        committee.setName(dataSet.getName());
                        session.persist(committee);
                        DataSetViewModel.this.updateExecutions();

                        BindUtils.postNotifyChange(null, null, DataSetViewModel.this,
                                CommitteeViewModel.DATA_SET_STEP);
                    }/*from www  . j a v  a  2 s .  c o  m*/
                });
    }
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.enrichment.GeneEnrichmentSubtask.java

License:Open Source License

@Override
public Set<GeneSetMetaData> call() throws Exception {
    if (this.aborted)
        throw new AbortException();

    final ArrayOfString result = GeneEnrichmentSubtask.enrich("Homo sapiens (human)", geneList);

    if (this.aborted)
        throw new AbortException();

    final List<GeneSetMetaData> geneSets = new ArrayList<GeneSetMetaData>();

    int missingCount = 0;
    for (String data : result.getString()) {
        final String[] split = data.split(";");

        final String sourceId = split[0];
        final String sourceName = SOURCE_TRANSLATION.containsKey(sourceId) ? SOURCE_TRANSLATION.get(sourceId)
                : sourceId;/*from   w w  w  . ja v  a2 s.  c  o m*/
        final String id = split[1];
        final String name = split[2].equals("-.") ? "[" + sourceId + "-" + ++missingCount + "]" : split[2];
        final String[] genes = split[3].split(",");
        final String pvalueString = split[4].replace(",", ".");
        final double pvalue = Double.parseDouble(pvalueString);

        final GeneSetMetaData gs = new GeneSetMetaData();
        gs.setSource(sourceName);
        gs.setGeneSetId(id);
        gs.setName(name);
        gs.setPValue(pvalue);

        gs.changeGenes(new HashSet<String>(Arrays.asList(genes)));

        geneSets.add(gs);
    }

    if (this.aborted)
        throw new AbortException();

    final Session session = HibernateUtil.getSessionFactory().openSession();
    session.beginTransaction();
    final Committee committee = (Committee) session.get(Committee.class, committeeId);

    for (GeneSetMetaData geneSet : geneSets) {
        session.persist(geneSet);
    }
    session.flush();

    committee.getGeneSets().addAll(geneSets);
    session.update(committee);

    session.getTransaction().commit();
    session.close();

    return committee.getGeneSets();
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.evaluation.EvaluationViewModel.java

License:Open Source License

@Init
@Override/*from w w w  . java  2s  .  c  o  m*/
public void init() {
    super.init();

    this.currentPerformanceFunction = PerformanceFunction.KAPPA;
    this.currentClass = PerformanceFunction.ALL_CLASSES_LABEL;

    final Committee committee = this.getCommittee(false);

    final ExperimentMetaData experiment = committee.getExperiment();
    if (experiment == null) {
        final Session session = HibernateUtil.currentSession();

        final ExperimentMetaData newExperiment = new ExperimentMetaData(
                this.getUserId() + " - " + UUID.randomUUID().toString(), committee);

        session.persist(newExperiment);
        session.flush();

        committee.setExperiment(newExperiment);

        session.update(committee);
    } else if (experiment.getStatus() == ExperimentStatus.Finished && experiment.hasExpertResults()
            && !experiment.hasAnyExpertSelected()) {
        Clients.showNotification("Select the experts of your committee clicking on their performance",
                Clients.NOTIFICATION_TYPE_INFO, null, "middle_center", 0);
    }

    StatusViewModel.changeInitialStatus("Execute the evaluation of the classifiers using selected gene sets");
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.evaluation.ExpertEvaluationSubtask.java

License:Open Source License

private void storeResult(ExpertResult result, Integer experimentId) throws StorageException {
    synchronized (ExpertEvaluationSubtask.class) {
        boolean done = false;
        int tries = 0;
        do {//from ww  w.j  av  a 2 s .  co m
            Session session = null;
            Transaction transaction = null;
            ExperimentMetaData experiment = null;
            try {
                this.checkAbort();

                session = HibernateUtil.getSessionFactory().openSession();
                transaction = session.beginTransaction();

                this.checkAbort();

                experiment = (ExperimentMetaData) session.load(ExperimentMetaData.class, experimentId);

                for (SampleClassification sample : result.getSamples()) {
                    session.persist(sample);
                }

                this.checkAbort();

                session.flush();
                session.persist(result);

                this.checkAbort();

                session.flush();
                experiment.getResults().add(result);

                this.checkAbort();

                session.update(experiment);
                transaction.commit();

                done = true;
            } catch (Exception e) {
                try {
                    if (transaction != null)
                        transaction.rollback();
                } catch (Exception ex) {
                    ex.printStackTrace();
                }

                result.setId(null);
                for (SampleClassification sample : result.getSamples()) {
                    sample.setId(null);
                }
                if (experiment != null)
                    experiment.getResults().remove(result);

                if (this.aborted)
                    return;

                e.printStackTrace();
            } finally {
                try {
                    if (session != null && session.isOpen())
                        session.close();
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        } while (!done && ++tries < ExpertEvaluationSubtask.MAX_TRIES);

        if (!done) {
            final String message = "Evaluation result could not be stored: " + result.toString();
            System.err.println(message);
            throw new StorageException(message);
        }
    }
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.geneset.GeneSetViewModel.java

License:Open Source License

@Init
@Override// ww w  .j a  va  2 s  . co m
public void init() {
    super.init();

    this.geneURL = "/loading.zul";
    this.geneURLVisible = false;

    final Committee committee = this.getCommittee(false); // Refreshed in init
    if (!committee.hasGeneSelection()) {
        final Session session = HibernateUtil.currentSession();
        final GeneSelectionMetaData geneSelection = GeneSelectionType.getDefault().buildGeneSelection();
        committee.setGeneSelection(geneSelection);

        session.persist(geneSelection);
        session.flush();
        session.update(geneSelection);
    }

    StatusViewModel.changeInitialStatus("Select the best genes using a feature selection algorithm");
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.geneset.SelectGenesSubtask.java

License:Open Source License

@Override
public Set<RankedGene> call() throws Exception {
    try {//w  w w. j  ava 2  s.c  om
        if (this.aborted)
            throw new AbortException();

        final FeatureSelectionResults fsResults = fs.obtainFeatureSelection();
        final List<Variable> selectedVariables = fsResults.getSelectedVariables();
        final List<Double> ranking = fsResults.getRanking();

        final Session session = HibernateUtil.getSessionFactory().openSession();
        session.beginTransaction();
        final Set<RankedGene> genes = new HashSet<RankedGene>();

        int i = 0;
        for (Variable selectedVariable : selectedVariables) {
            if (this.aborted)
                throw new AbortException();
            final RankedGene gene = new RankedGene(i + 1, selectedVariable.getName(), ranking.get(i++));
            session.persist(gene);
            session.flush();
            genes.add(gene);
        }

        if (this.aborted)
            throw new AbortException();

        final Committee committee = (Committee) session.get(Committee.class, committeeId);

        committee.getRankedGenes().clear();
        committee.getRankedGenes().addAll(genes);
        session.update(committee);

        session.getTransaction().commit();
        session.close();
        return committee.getRankedGenes();
    } catch (Exception e) {
        e.printStackTrace();
        throw e;
    }
}

From source file:es.uvigo.ei.sing.gc.view.models.committee.summary.SummaryViewModel.java

License:Open Source License

@Command("saveAndFinish")
public void saveAndFinish() throws Exception {
    final Committee committee = this.getCommittee();

    if (committee.isFinished()) {
        throw new IllegalStateException("Committee is already completed");
    } else {/*from ww  w  .  j  av  a  2s  .  com*/
        final Session session = HibernateUtil.currentSession();

        Committee sameName = (Committee) session.createCriteria(Committee.class).setMaxResults(1)
                .add(Restrictions.eq("user", committee.getUser()))
                .add(Restrictions.eq("name", committee.getName()))
                .add(Restrictions.not(Restrictions.eq("id", committee.getId()))).uniqueResult();

        if (sameName == null) {
            committee.setFinished(true);

            session.persist(committee);

            Executions.sendRedirect("/home.zul");
        } else {
            Messagebox.show(
                    "There is another committee with the same name. Please, change the name in order to continue.",
                    "Invalid Name", Messagebox.OK, Messagebox.ERROR);
        }
    }
}

From source file:es.uvigo.ei.sing.gc.view.models.datasets.UploadDataSubTask.java

License:Open Source License

@Override
public DataSetMetaData call() throws Exception {
    Transaction transaction = null;//from  www  . j ava 2 s .  c o  m
    Session session = null;

    DataSetMetaData dataSet = null;
    try {
        if (this.aborted)
            throw new AbortException();

        final Data data = ZKUtils.loadDataFromMedia(this.media);

        if (this.aborted)
            throw new AbortException();

        session = HibernateUtil.getSessionFactory().openSession();
        transaction = session.beginTransaction();
        final User user = ZKUtils.hLoad(User.class, this.userId, session);
        dataSet = user.addDataSet(data);
        session.persist(user);

        if (this.aborted)
            throw new AbortException();

        session.flush();

        transaction.commit();

        return dataSet;
    } catch (Throwable e) {
        e.printStackTrace();

        if (transaction != null)
            try {
                transaction.rollback();
            } catch (HibernateException he) {
            }

        if (dataSet != null && dataSet.hasFile()) {
            new File(dataSet.getFileName()).delete();
        }

        if (e instanceof Exception) {
            throw (Exception) e;
        } else {
            throw new Exception(e);
        }
    } finally {
        if (session.isOpen())
            try {
                session.close();
            } catch (HibernateException e) {
            }
    }
}

From source file:es.uvigo.ei.sing.gc.view.models.PasswordRecoveryViewModel.java

License:Open Source License

@Command
public void changePassword() {
    if (this.isPasswordOk()) {
        final Session session = HibernateUtil.currentSession();

        final User user = ZKUtils.hLoad(User.class, this.email, session);

        user.setPassword(DigestUtils.md5Hex(this.newPassword));
        session.persist(user);
        session.flush();/*from  w ww  .ja  va2  s  . com*/

        Messagebox.show("Password successfully changed. Press 'Ok' to go to the login page.",
                "Password Changed", Messagebox.OK, Messagebox.INFORMATION, new EventListener<Event>() {
                    @Override
                    public void onEvent(Event event) throws Exception {
                        Executions.sendRedirect("index.zul");
                    }
                });
    }
}

From source file:eu.trentorise.opendata.ckanalyze.managers.PersistencyManager.java

License:Open Source License

public static void insert(Object o) {
    Session ss = PersistencyManager.getSessionFactory().openSession();
    ss.beginTransaction();//ww w  .  j a v a  2 s .  c om
    ss.persist(o);
    ss.getTransaction().commit();
    ss.close();
}