Example usage for org.hibernate Session save

List of usage examples for org.hibernate Session save

  1. HOME
  2. Java
  3. org.hibernate
  4. org.hibernate.*
  5. Session
  6. save

Introduction

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

Prototype

Serializable save(Object object);

Source Link

Document

Persist the given transient instance, first assigning a generated identifier.

Usage

From source file:au.org.theark.phenotypic.model.dao.PhenotypicDao.java

License:Open Source License

public void processPhenoCollectionsWithTheirDataToInsertBatch(
        List<PhenoDataSetCollection> phenoCollectionsWithTheirDataToInsert, Study study) {
    Session session = getSession();
    //      int count = 0;
    for (PhenoDataSetCollection collectionToInsert : phenoCollectionsWithTheirDataToInsert) {
        //TODO : investigate more efficient way to deal with null parent entity
        Set<PhenoDataSetData> dataToSave = collectionToInsert.getPhenoDataSetData();
        collectionToInsert.setPhenoDataSetData(new HashSet<PhenoDataSetData>());

        session.save(collectionToInsert);
        session.refresh(collectionToInsert);
        for (PhenoDataSetData data : dataToSave) {
            data.setPhenoDataSetCollection(collectionToInsert);
            session.save(data);/* w w  w .  ja  v a  2s . c om*/
        }
    }
    session.flush();
    session.clear();
}

From source file:au.org.theark.phenotypic.model.dao.PhenotypicDao.java

License:Open Source License

@Override
public void createPhenoDataSetFieldGroup(PhenoDataSetFieldGroupVO phenoDataSetFieldGroupVO)
        throws EntityExistsException, ArkSystemException {
    PhenoDataSetGroup phenoDataSetGroup = phenoDataSetFieldGroupVO.getPhenoDataSetGroup();
    Session session = getSession();
    session.save(phenoDataSetGroup);
    session.flush();//ww w . j av a2  s.c om
    insertToDispalyAndDeleteFromLinkAndPicked(phenoDataSetFieldGroupVO, phenoDataSetGroup, session);
    log.debug("Saved All PhenoDataSetDisplays for PhenoDataSet Group");
}

From source file:au.org.theark.phenotypic.model.dao.PhenotypicDao.java

License:Open Source License

private void insertToDispalyAndDeleteFromLinkAndPicked(PhenoDataSetFieldGroupVO phenoDataSetFieldGroupVO,
        PhenoDataSetGroup phenoDataSetGroup, Session session) {
    //Get the Picked Pheno Dataset categories.
    List<PickedPhenoDataSetCategory> phenoDataSetCategories = phenoDataSetFieldGroupVO
            .getPickedAvailableCategories();
    for (PickedPhenoDataSetCategory pickedPhenoDataSetCategory : phenoDataSetCategories) {
        //Get the Linked Pheno Dataset fields for  PickedPhenoDataSetCategory
        List<LinkPhenoDataSetCategoryField> linkPhenoDataSetCategoryFields = getLinkPhenoDataSetCategoryFieldsForPickedPhenoDataSetCategory(
                pickedPhenoDataSetCategory);
        if (!linkPhenoDataSetCategoryFields.isEmpty()) {
            for (LinkPhenoDataSetCategoryField linkPhenoDataSetCategoryField : linkPhenoDataSetCategoryFields) {
                PhenoDataSetFieldDisplay phenoDataSetFieldDisplay = new PhenoDataSetFieldDisplay();
                phenoDataSetFieldDisplay.setPhenoDataSetGroup(phenoDataSetGroup);
                phenoDataSetFieldDisplay
                        .setPhenoDataSetCategory(pickedPhenoDataSetCategory.getPhenoDataSetCategory());
                if (pickedPhenoDataSetCategory.getParentPickedPhenoDataSetCategory() != null) {
                    phenoDataSetFieldDisplay.setParentPhenoDataSetCategory(pickedPhenoDataSetCategory
                            .getParentPickedPhenoDataSetCategory().getPhenoDataSetCategory());
                }/*  w w w  .j av  a2s  .c om*/
                phenoDataSetFieldDisplay
                        .setPhenoDataSetCategoryOrderNumber(pickedPhenoDataSetCategory.getOrderNumber());
                phenoDataSetFieldDisplay
                        .setPhenoDataSetField(linkPhenoDataSetCategoryField.getPhenoDataSetField());
                phenoDataSetFieldDisplay
                        .setPhenoDataSetFiledOrderNumber(linkPhenoDataSetCategoryField.getOrderNumber());
                session.save(phenoDataSetFieldDisplay);
            }
        } else {
            PhenoDataSetFieldDisplay phenoDataSetFieldDisplay = new PhenoDataSetFieldDisplay();
            phenoDataSetFieldDisplay.setPhenoDataSetGroup(phenoDataSetGroup);
            phenoDataSetFieldDisplay
                    .setPhenoDataSetCategory(pickedPhenoDataSetCategory.getPhenoDataSetCategory());
            if (pickedPhenoDataSetCategory.getParentPickedPhenoDataSetCategory() != null) {
                phenoDataSetFieldDisplay.setParentPhenoDataSetCategory(pickedPhenoDataSetCategory
                        .getParentPickedPhenoDataSetCategory().getPhenoDataSetCategory());
            }
            phenoDataSetFieldDisplay
                    .setPhenoDataSetCategoryOrderNumber(pickedPhenoDataSetCategory.getOrderNumber());
            session.save(phenoDataSetFieldDisplay);
        }
    }
}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

public void create(Study study, Collection<ArkModule> selectedModules, Study parentStudy) {
    Session session = getSession();
    session.save(study);
    linkStudyToArkModule(study, selectedModules, session, au.org.theark.core.Constants.MODE_NEW);

    // Update parent study accordingly
    if (parentStudy != null) {
        parentStudy.setParentStudy(parentStudy);
        session.update(parentStudy);//www. j av a  2 s. c o m
    }
}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

/**
 * {@inheritDoc}/*from www.  j ava2  s .c  o  m*/
 */
public void processPedigreeBatch(List<LinkSubjectPedigree> parentsToInsert,
        List<LinkSubjectTwin> twinsToInsert) {
    Session session = getSession();
    int count = 0;
    for (LinkSubjectPedigree dataToInsert : parentsToInsert) {
        session.save(dataToInsert);
        count++;
        // based on recommended hibernate practice of <prop key="hibernate.jdbc.batch_size">50</prop>
        if (count % 50 == 0) {
            log.info("\n\n\n\n\n\n\n\n\nflush!!!!!!!!!!!!!!");
            session.flush();
            session.clear();
        }
    }
    count = 0;
    for (LinkSubjectTwin dataToInsert : twinsToInsert) {
        session.save(dataToInsert);
        count++;
        // based on recommended hibernate practice of <prop key="hibernate.jdbc.batch_size">50</prop>
        if (count % 50 == 0) {
            log.info("\n\n\n\n\n\n\n\n\nflush!!!!!!!!!!!!!!");
            session.flush();
            session.clear();
        }
    }
    session.flush();
    session.clear();

}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

/**
 * {@inheritDoc}//from w  w  w.  j a v  a 2s.  co  m
 */
public void processSubjectAttachmentBatch(List<SubjectFile> subjectFiles) {
    Session session = getSession();
    int count = 0;
    for (SubjectFile subjectFile : subjectFiles) {
        session.save(subjectFile);
        count++;
        // based on recommended hibernate practice of <prop key="hibernate.jdbc.batch_size">50</prop>
        if (count % 50 == 0) {
            log.info("\n\n\n\n\n\n\n\n\nflush!!!!!!!!!!!!!!");
            session.flush();
            session.clear();
        }
    }
    session.flush();
    session.clear();

}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

public void create(Study study, ArkUserVO arkUserVo, Collection<ArkModule> selectedModules) {
    Session session = getSession();
    session.save(study);
    linkStudyToArkModule(study, selectedModules, session, au.org.theark.core.Constants.MODE_NEW);

    // Update parent study accordingly
    Study parentStudy = study.getParentStudy();
    if (parentStudy != null) {
        parentStudy.setParentStudy(parentStudy);
        session.update(parentStudy);// www. ja  v a 2s  .c o m
    }

    // Assign user to newly created study
    try {
        iArkAuthorisationService.updateArkUser(arkUserVo);
    } catch (ArkSystemException e) {
        log.error(e.getMessage());
    } catch (EntityNotFoundException e) {
        log.error(e.getMessage());
    }
}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

private void linkStudyToArkModule(Study study, Collection<ArkModule> selectedModules, Session session,
        int mode) {
    for (ArkModule arkModule : selectedModules) {
        LinkStudyArkModule linkStudyArkModule = new LinkStudyArkModule();
        linkStudyArkModule.setStudy(study);
        linkStudyArkModule.setArkModule(arkModule);
        if (mode == au.org.theark.core.Constants.MODE_NEW) {
            session.save(linkStudyArkModule);
        } else {/*w ww . ja  v a  2s . co m*/
            session.update(linkStudyArkModule);
        }
    }
}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

public void updateStudy(Study study, Collection<ArkModule> selectedApplications)
        throws CannotRemoveArkModuleException {
    Session session = getSession();

    // session.update(study);
    // execute merge method instead of update to avoid org.hibernate.NonUniqueObjectException
    session.merge(study);//  w  w  w. j  ava2s. c o m

    Collection<LinkStudyArkModule> linkStudyArkModulesToAdd = getModulesToAddList(study, selectedApplications);
    // Determine Removal List here
    Collection<LinkStudyArkModule> linkStudyArkModulesToRemove = getModulesToRemoveList(study,
            selectedApplications);

    // Process the Removal of Linked ArkModules for this study
    for (LinkStudyArkModule linkStudyArkModule : linkStudyArkModulesToRemove) {
        session.delete(linkStudyArkModule);
    }
    // Insert the new modules for the Study
    for (LinkStudyArkModule linkStudyArkModule : linkStudyArkModulesToAdd) {
        session.save(linkStudyArkModule);
    }

    // Flush must be the last thing to call. If there is any other code/logic to be added make sure session.flush() is invoked after that.
    session.flush();
}

From source file:au.org.theark.study.model.dao.StudyDao.java

License:Open Source License

public void createSubject(SubjectVO subjectVo) throws ArkUniqueException, ArkSubjectInsertException {
    Study study = subjectVo.getLinkSubjectStudy().getStudy();
    if (study.getAutoGenerateSubjectUid()) {
        String subjectUID = getNextGeneratedSubjectUID(study);

        if (isSubjectUIDUnique(subjectUID, study.getId(), "Insert")) {
            subjectVo.getLinkSubjectStudy().setSubjectUID(subjectUID);
        } else {// TODO : maybe a for loop to guard against a manual db insert, or just throw exception and holds someone up from further inserts until
                // investigated why?
            subjectUID = getNextGeneratedSubjectUID(study);
            subjectVo.getLinkSubjectStudy().setSubjectUID(subjectUID);
        }/*w w  w  .  j  a v  a  2 s.  c  o  m*/
    } else {
        if (!isSubjectUIDUnique(subjectVo.getLinkSubjectStudy().getSubjectUID(),
                subjectVo.getLinkSubjectStudy().getStudy().getId(), "Insert")) {
            throw new ArkUniqueException("Subject UID must be unique");
        }
    }

    // Set default foreign key reference
    if (subjectVo.getLinkSubjectStudy().getSubjectStatus() == null
            || StringUtils.isBlank(subjectVo.getLinkSubjectStudy().getSubjectStatus().getName())) {
        SubjectStatus subjectStatus = getSubjectStatusByName("Subject");
        subjectVo.getLinkSubjectStudy().setSubjectStatus(subjectStatus);
    }

    // Set default foreign key reference
    if (subjectVo.getLinkSubjectStudy().getPerson().getTitleType() == null
            || StringUtils.isBlank(subjectVo.getLinkSubjectStudy().getPerson().getTitleType().getName())) {
        TitleType titleType = getTitleType(new Long(0));
        subjectVo.getLinkSubjectStudy().getPerson().setTitleType(titleType);
    }

    // Set default foreign key reference
    if (subjectVo.getLinkSubjectStudy().getPerson().getGenderType() == null
            || StringUtils.isBlank(subjectVo.getLinkSubjectStudy().getPerson().getGenderType().getName())) {
        GenderType genderType = getGenderType(new Long(0));
        subjectVo.getLinkSubjectStudy().getPerson().setGenderType(genderType);
    }

    // Set default foreign key reference
    if (subjectVo.getLinkSubjectStudy().getPerson().getVitalStatus() == null
            || StringUtils.isBlank(subjectVo.getLinkSubjectStudy().getPerson().getVitalStatus().getName())) {
        VitalStatus vitalStatus = getVitalStatus(new Long(0));
        subjectVo.getLinkSubjectStudy().getPerson().setVitalStatus(vitalStatus);
    }

    //log.info("create subject otherIDs:  " + subjectVo.getLinkSubjectStudy().getPerson().getOtherIDs());

    if (subjectVo.getLinkSubjectStudy().getPerson().getOtherIDs() == null
            || subjectVo.getLinkSubjectStudy().getPerson().getOtherIDs().isEmpty()) { // get
                                                                                                                                                            // better
                                                                                                                                                            // values
                                                                                                                                                            // when
                                                                                                                                                            // implemented
                                                                                                                                                            // properly
        List<OtherID> otherIDs = new ArrayList<OtherID>();
        subjectVo.getLinkSubjectStudy().getPerson().setOtherIDs(otherIDs);
    }

    Session session = getSession();
    Person person = subjectVo.getLinkSubjectStudy().getPerson();

    if (person.getId() == null) {
        session.save(person);
        PersonLastnameHistory personLastNameHistory = null;

        // Previous LastName (if supplied on new Subject)
        if (subjectVo.getSubjectPreviousLastname() != null
                && !subjectVo.getSubjectPreviousLastname().isEmpty()) {
            personLastNameHistory = new PersonLastnameHistory();
            personLastNameHistory.setPerson(person);
            personLastNameHistory.setLastName(subjectVo.getSubjectPreviousLastname());
            session.save(personLastNameHistory);
        }

        /*
         * only keeping previous names from now on // Current lastName if (person.getLastName() != null) { personLastNameHistory = new
         * PersonLastnameHistory(); personLastNameHistory.setPerson(person); personLastNameHistory.setLastName(person.getLastName());
         * session.save(personLastNameHistory); }
         */
    }

    // Update subjectPreviousLastname TODO investigate
    subjectVo.setSubjectPreviousLastname(getPreviousLastname(person));

    LinkSubjectStudy linkSubjectStudy = subjectVo.getLinkSubjectStudy();
    session.save(linkSubjectStudy);// The hibernate session is the same. This should be automatically bound with Spring's

    autoConsentLinkSubjectStudy(subjectVo.getLinkSubjectStudy());

    // TODO EXCEPTIONHANDLING
}