Examples with DashboardEntity gov.nih.nci.ctd2.dashboard.model.DashboardEntity used on opensource projects

Example 11 with DashboardEntity

use of gov.nih.nci.ctd2.dashboard.model.DashboardEntity in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method batchSave.

@Override
public void batchSave(Collection<? extends DashboardEntity> entities, int batchSize) {
    if (entities == null || entities.isEmpty())
        return;
    Session session = getSessionFactory().openSession();
    session.beginTransaction();
    int i = 0;
    for (DashboardEntity entity : entities) {
        if (entity instanceof Subject) {
            Subject subject = (Subject) entity;
            for (Xref x : subject.getXrefs()) {
                session.save(x);
            }
            for (Synonym x : subject.getSynonyms()) {
                session.save(x);
            }
        }
        session.save(entity);
        i++;
        if (batchSize != 0 && i % batchSize == 0) {
            session.flush();
            session.clear();
        }
    }
    session.flush();
    session.clear();
    session.getTransaction().commit();
    session.close();
}

Example 12 with DashboardEntity

use of gov.nih.nci.ctd2.dashboard.model.DashboardEntity in project nci-ctd2-dashboard by CBIIT.

the class ProteinDataWriter method write.

public void write(List<? extends ProteinData> items) throws Exception {
    ArrayList<DashboardEntity> entities = new ArrayList<DashboardEntity>();
    for (ProteinData proteinData : items) {
        Set<Transcript> transcripts = proteinData.transcripts;
        for (Transcript tra : transcripts) {
            String traStableURL = new StableURL().createURLWithPrefix("transcript", tra.getRefseqId());
            tra.setStableURL(traStableURL);
        }
        entities.addAll(proteinData.transcripts);
        log.info("Storing protein: " + proteinData.protein.getDisplayName());
        String stableURL = new StableURL().createURLWithPrefix("protein", proteinData.protein.getUniprotId());
        proteinData.protein.setStableURL(stableURL);
        entities.add(proteinData.protein);
    }
    dashboardDao.batchSave(entities, batchSize);
}

Example 13 with DashboardEntity

use of gov.nih.nci.ctd2.dashboard.model.DashboardEntity in project nci-ctd2-dashboard by CBIIT.

the class ControlledVocabularyPerColumnWriter method write.

public void write(List<? extends ControlledVocabulary> items) throws Exception {
    if (entityCache == null)
        entityCache = new HashSet<DashboardEntity>();
    if (entities == null)
        entities = new ArrayList<DashboardEntity>();
    for (ControlledVocabulary controlledVocabulary : items) {
        String observedRoleName = "";
        if (controlledVocabulary.observedRole instanceof ObservedSubjectRole) {
            observedRoleName = ((ObservedSubjectRole) controlledVocabulary.observedRole).getColumnName();
        } else if (controlledVocabulary.observedRole instanceof ObservedEvidenceRole) {
            observedRoleName = ((ObservedEvidenceRole) controlledVocabulary.observedRole).getColumnName();
        }
        log.info("Storing Observed Role: " + observedRoleName);
        if (!entityCache.contains(controlledVocabulary.role)) {
            entityCache.add(controlledVocabulary.role);
            entities.add(controlledVocabulary.role);
        }
        ObservationTemplate ot = (ObservationTemplate) controlledVocabulary.observationTemplate;
        if (!entityCache.contains(ot.getSubmissionCenter())) {
            SubmissionCenter submissionCenter = dashboardDao.findSubmissionCenterByName(ot.getSubmissionCenter().getDisplayName());
            if (submissionCenter == null) {
                entities.add(ot.getSubmissionCenter());
            }
            entityCache.add(ot.getSubmissionCenter());
        }
        if (!entityCache.contains(controlledVocabulary.observationTemplate)) {
            entityCache.add(controlledVocabulary.observationTemplate);
            entities.add(controlledVocabulary.observationTemplate);
        }
        if (!entityCache.contains(controlledVocabulary.observedRole)) {
            entityCache.add(controlledVocabulary.observedRole);
            entities.add(controlledVocabulary.observedRole);
        }
    }
    dashboardDao.batchSave(entities, batchSize);
}

Example 14 with DashboardEntity

use of gov.nih.nci.ctd2.dashboard.model.DashboardEntity in project nci-ctd2-dashboard by CBIIT.

the class CellLineDataWriter method execute.

public RepeatStatus execute(StepContribution arg0, ChunkContext arg1) throws Exception {
    ArrayList<DashboardEntity> entities = new ArrayList<DashboardEntity>();
    for (CellSample cellSample : cellSampleMap.values()) {
        entities.addAll(cellSample.getAnnotations());
        String stableURL = new StableURL().createURLWithPrefix("cell-sample", cellSample.getDisplayName());
        cellSample.setStableURL(stableURL);
        entities.add(cellSample);
    }
    dashboardDao.batchSave(entities, batchSize);
    return RepeatStatus.FINISHED;
}