/**
  * Copy one ValueObject to another
  *
  * @param valueObjectDest to be updated
  * @param valueObjectSrc to copy values from
  */
 public static ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo copy(
     ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo valueObjectDest,
     ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo valueObjectSrc) {
   if (null == valueObjectSrc) {
     return valueObjectSrc;
   }
   valueObjectDest.setID_TumourGroup(valueObjectSrc.getID_TumourGroup());
   valueObjectDest.setIsRIE(valueObjectSrc.getIsRIE());
   // GroupName
   valueObjectDest.setGroupName(valueObjectSrc.getGroupName());
   // Sites
   valueObjectDest.setSites(valueObjectSrc.getSites());
   // TnmRequiresOver45
   valueObjectDest.setTnmRequiresOver45(valueObjectSrc.getTnmRequiresOver45());
   // isActive
   valueObjectDest.setIsActive(valueObjectSrc.getIsActive());
   // TNMValues
   valueObjectDest.setTNMValues(valueObjectSrc.getTNMValues());
   // SerumMarkers
   valueObjectDest.setSerumMarkers(valueObjectSrc.getSerumMarkers());
   // OtherClassifications
   valueObjectDest.setOtherClassifications(valueObjectSrc.getOtherClassifications());
   // AssociatedSpecialties
   valueObjectDest.setAssociatedSpecialties(valueObjectSrc.getAssociatedSpecialties());
   // hasTNM
   valueObjectDest.setHasTNM(valueObjectSrc.getHasTNM());
   // Histologies
   valueObjectDest.setHistologies(valueObjectSrc.getHistologies());
   // HistopathologicGrades
   valueObjectDest.setHistopathologicGrades(valueObjectSrc.getHistopathologicGrades());
   // Assessment
   valueObjectDest.setAssessment(valueObjectSrc.getAssessment());
   // isPrognosticGroupingRelevant
   valueObjectDest.setIsPrognosticGroupingRelevant(
       valueObjectSrc.getIsPrognosticGroupingRelevant());
   // PrognosticGroupingConfig
   valueObjectDest.setPrognosticGroupingConfig(valueObjectSrc.getPrognosticGroupingConfig());
   // TnmRequiresDiff
   valueObjectDest.setTnmRequiresDiff(valueObjectSrc.getTnmRequiresDiff());
   // TnmRequiresHisto
   valueObjectDest.setTnmRequiresHisto(valueObjectSrc.getTnmRequiresHisto());
   // TnmRequiresSMarkers
   valueObjectDest.setTnmRequiresSMarkers(valueObjectSrc.getTnmRequiresSMarkers());
   return valueObjectDest;
 }
  public static ims.oncology.configuration.domain.objects.TumourGroup extractTumourGroup(
      ims.domain.ILightweightDomainFactory domainFactory,
      ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo valueObject,
      HashMap domMap) {
    if (null == valueObject) {
      return null;
    }
    Integer id = valueObject.getID_TumourGroup();
    ims.oncology.configuration.domain.objects.TumourGroup domainObject = null;
    if (null == id) {
      if (domMap.get(valueObject) != null) {
        return (ims.oncology.configuration.domain.objects.TumourGroup) domMap.get(valueObject);
      }
      // ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo ID_TumourGroup field is
      // unknown
      domainObject = new ims.oncology.configuration.domain.objects.TumourGroup();
      domMap.put(valueObject, domainObject);
    } else {
      String key = (valueObject.getClass().getName() + "__" + valueObject.getID_TumourGroup());
      if (domMap.get(key) != null) {
        return (ims.oncology.configuration.domain.objects.TumourGroup) domMap.get(key);
      }
      domainObject =
          (ims.oncology.configuration.domain.objects.TumourGroup)
              domainFactory.getDomainObject(
                  ims.oncology.configuration.domain.objects.TumourGroup.class, id);

      // TODO: Not sure how this should be handled. Effectively it must be a staleobject exception,
      // but maybe should be handled as that further up.
      if (domainObject == null) return null;

      domMap.put(key, domainObject);
    }
    domainObject.setVersion(valueObject.getVersion_TumourGroup());

    // This is to overcome a bug in both Sybase and Oracle which prevents them from storing an empty
    // string correctly
    // Sybase stores it as a single space, Oracle stores it as NULL. This fix will make them
    // consistent at least.
    if (valueObject.getGroupName() != null && valueObject.getGroupName().equals("")) {
      valueObject.setGroupName(null);
    }
    domainObject.setGroupName(valueObject.getGroupName());
    domainObject.setSites(
        ims.clinicaladmin.vo.domain.TumourSiteLiteVoAssembler.extractTumourSiteList(
            domainFactory, valueObject.getSites(), domainObject.getSites(), domMap));
    domainObject.setTnmRequiresOver45(valueObject.getTnmRequiresOver45());
    domainObject.setIsActive(valueObject.getIsActive());
    domainObject.setTNMValues(
        ims.clinicaladmin.vo.domain.TumourGroupSiteTNMValueListVoAssembler
            .extractTumourGroupSiteTNMValueList(
                domainFactory, valueObject.getTNMValues(), domainObject.getTNMValues(), domMap));
    domainObject.setSerumMarkers(
        ims.clinicaladmin.vo.domain.TumourSerumMarkersVoAssembler.extractTumourSerumMarkerSet(
            domainFactory, valueObject.getSerumMarkers(), domainObject.getSerumMarkers(), domMap));
    domainObject.setOtherClassifications(
        ims.oncology.vo.domain.TumourGroupClassificationVoAssembler
            .extractTumourGroupClassificationSet(
                domainFactory,
                valueObject.getOtherClassifications(),
                domainObject.getOtherClassifications(),
                domMap));
    domainObject.setAssociatedSpecialties(
        ims.oncology.vo.domain.TumourGroupSpecialtyVoAssembler.extractTumourGroupSpecialtySet(
            domainFactory,
            valueObject.getAssociatedSpecialties(),
            domainObject.getAssociatedSpecialties(),
            domMap));
    domainObject.setHasTNM(valueObject.getHasTNM());

    // SaveAsRefVO treated as RefValueObject
    ims.oncology.configuration.vo.TumourGroupHistologyRefVoCollection refCollection10 =
        new ims.oncology.configuration.vo.TumourGroupHistologyRefVoCollection();
    if (valueObject.getHistologies() != null) {
      for (int i10 = 0; i10 < valueObject.getHistologies().size(); i10++) {
        ims.oncology.configuration.vo.TumourGroupHistologyRefVo ref10 =
            (ims.oncology.configuration.vo.TumourGroupHistologyRefVo)
                valueObject.getHistologies().get(i10);
        refCollection10.add(ref10);
      }
    }
    int size10 = (null == refCollection10) ? 0 : refCollection10.size();
    java.util.List domainHistologies10 = domainObject.getHistologies();
    if (domainHistologies10 == null) {
      domainHistologies10 = new java.util.ArrayList();
    }
    for (int i = 0; i < size10; i++) {
      ims.oncology.configuration.vo.TumourGroupHistologyRefVo vo = refCollection10.get(i);
      ims.oncology.configuration.domain.objects.TumourGroupHistology dom = null;
      if (null != vo) {
        if (vo.getBoId() == null) {
          if (domMap.get(vo) != null) {
            dom = (ims.oncology.configuration.domain.objects.TumourGroupHistology) domMap.get(vo);
          }
        } else {
          dom =
              (ims.oncology.configuration.domain.objects.TumourGroupHistology)
                  domainFactory.getDomainObject(
                      ims.oncology.configuration.domain.objects.TumourGroupHistology.class,
                      vo.getBoId());
        }
      }

      int domIdx = domainHistologies10.indexOf(dom);
      if (domIdx == -1) {
        domainHistologies10.add(i, dom);
      } else if (i != domIdx && i < domainHistologies10.size()) {
        Object tmp = domainHistologies10.get(i);
        domainHistologies10.set(i, domainHistologies10.get(domIdx));
        domainHistologies10.set(domIdx, tmp);
      }
    }

    // Remove all ones in domList where index > voCollection.size() as these should
    // now represent the ones removed from the VO collection. No longer referenced.
    int i10 = domainHistologies10.size();
    while (i10 > size10) {
      domainHistologies10.remove(i10 - 1);
      i10 = domainHistologies10.size();
    }

    domainObject.setHistologies(domainHistologies10);
    domainObject.setHistopathologicGrades(
        ims.clinicaladmin.vo.domain.TumourGroupHistopathologyGradeVoAssembler
            .extractTumourGroupHistopathologicGradeSet(
                domainFactory,
                valueObject.getHistopathologicGrades(),
                domainObject.getHistopathologicGrades(),
                domMap));
    ims.assessment.configuration.domain.objects.UserAssessment value12 = null;
    if (null != valueObject.getAssessment()) {
      if (valueObject.getAssessment().getBoId() == null) {
        if (domMap.get(valueObject.getAssessment()) != null) {
          value12 =
              (ims.assessment.configuration.domain.objects.UserAssessment)
                  domMap.get(valueObject.getAssessment());
        }
      } else if (valueObject.getBoVersion()
          == -1) // RefVo was not modified since obtained from the Assembler, no need to update the
      // BO field
      {
        value12 = domainObject.getAssessment();
      } else {
        value12 =
            (ims.assessment.configuration.domain.objects.UserAssessment)
                domainFactory.getDomainObject(
                    ims.assessment.configuration.domain.objects.UserAssessment.class,
                    valueObject.getAssessment().getBoId());
      }
    }
    domainObject.setAssessment(value12);
    domainObject.setIsPrognosticGroupingRelevant(valueObject.getIsPrognosticGroupingRelevant());
    // SaveAsRefVO - treated as a refVo in extract methods
    ims.oncology.configuration.domain.objects.PrognosticGroupingConfig value14 = null;
    if (null != valueObject.getPrognosticGroupingConfig()) {
      if (valueObject.getPrognosticGroupingConfig().getBoId() == null) {
        if (domMap.get(valueObject.getPrognosticGroupingConfig()) != null) {
          value14 =
              (ims.oncology.configuration.domain.objects.PrognosticGroupingConfig)
                  domMap.get(valueObject.getPrognosticGroupingConfig());
        }
      } else {
        value14 =
            (ims.oncology.configuration.domain.objects.PrognosticGroupingConfig)
                domainFactory.getDomainObject(
                    ims.oncology.configuration.domain.objects.PrognosticGroupingConfig.class,
                    valueObject.getPrognosticGroupingConfig().getBoId());
      }
    }
    domainObject.setPrognosticGroupingConfig(value14);
    domainObject.setTnmRequiresDiff(valueObject.getTnmRequiresDiff());
    domainObject.setTnmRequiresHisto(valueObject.getTnmRequiresHisto());
    domainObject.setTnmRequiresSMarkers(valueObject.getTnmRequiresSMarkers());

    return domainObject;
  }
  /**
   * Update the ValueObject with the Domain Object.
   *
   * @param map DomainObjectMap of DomainObjects to already created ValueObjects.
   * @param valueObject to be updated
   * @param domainObject ims.oncology.configuration.domain.objects.TumourGroup
   */
  public static ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo insert(
      DomainObjectMap map,
      ims.clinicaladmin.vo.TumourGroupListForPrimaryTumourDetailsVo valueObject,
      ims.oncology.configuration.domain.objects.TumourGroup domainObject) {
    if (null == domainObject) {
      return valueObject;
    }
    if (null == map) {
      map = new DomainObjectMap();
    }

    valueObject.setID_TumourGroup(domainObject.getId());
    valueObject.setIsRIE(domainObject.getIsRIE());

    // If this is a recordedInError record, and the domainObject
    // value isIncludeRecord has not been set, then we return null and
    // not the value object
    if (valueObject.getIsRIE() != null
        && valueObject.getIsRIE().booleanValue() == true
        && !domainObject.isIncludeRecord()) return null;

    // If this is not a recordedInError record, and the domainObject
    // value isIncludeRecord has been set, then we return null and
    // not the value object
    if ((valueObject.getIsRIE() == null || valueObject.getIsRIE().booleanValue() == false)
        && domainObject.isIncludeRecord()) return null;

    // GroupName
    valueObject.setGroupName(domainObject.getGroupName());
    // Sites
    valueObject.setSites(
        ims.clinicaladmin.vo.domain.TumourSiteLiteVoAssembler
            .createTumourSiteLiteVoCollectionFromTumourSite(map, domainObject.getSites()));
    // TnmRequiresOver45
    valueObject.setTnmRequiresOver45(domainObject.isTnmRequiresOver45());
    // isActive
    valueObject.setIsActive(domainObject.isIsActive());
    // TNMValues
    valueObject.setTNMValues(
        ims.clinicaladmin.vo.domain.TumourGroupSiteTNMValueListVoAssembler
            .createTumourGroupSiteTNMValueListVoCollectionFromTumourGroupSiteTNMValue(
                map, domainObject.getTNMValues()));
    // SerumMarkers
    valueObject.setSerumMarkers(
        ims.clinicaladmin.vo.domain.TumourSerumMarkersVoAssembler
            .createTumourSerumMarkersVoCollectionFromTumourSerumMarker(
                map, domainObject.getSerumMarkers()));
    // OtherClassifications
    valueObject.setOtherClassifications(
        ims.oncology.vo.domain.TumourGroupClassificationVoAssembler
            .createTumourGroupClassificationVoCollectionFromTumourGroupClassification(
                map, domainObject.getOtherClassifications()));
    // AssociatedSpecialties
    valueObject.setAssociatedSpecialties(
        ims.oncology.vo.domain.TumourGroupSpecialtyVoAssembler
            .createTumourGroupSpecialtyVoCollectionFromTumourGroupSpecialty(
                map, domainObject.getAssociatedSpecialties()));
    // hasTNM
    valueObject.setHasTNM(domainObject.isHasTNM());
    // Histologies
    valueObject.setHistologies(
        ims.clinicaladmin.vo.domain.TumourGroupHistologyVoAssembler
            .createTumourGroupHistologyVoCollectionFromTumourGroupHistology(
                map, domainObject.getHistologies()));
    // HistopathologicGrades
    valueObject.setHistopathologicGrades(
        ims.clinicaladmin.vo.domain.TumourGroupHistopathologyGradeVoAssembler
            .createTumourGroupHistopathologyGradeVoCollectionFromTumourGroupHistopathologicGrade(
                map, domainObject.getHistopathologicGrades()));
    // Assessment
    if (domainObject.getAssessment() != null) {
      if (domainObject.getAssessment()
          instanceof
          HibernateProxy) // If the proxy is set, there is no need to lazy load, the proxy knows the
      // id already.
      {
        HibernateProxy p = (HibernateProxy) domainObject.getAssessment();
        int id = Integer.parseInt(p.getHibernateLazyInitializer().getIdentifier().toString());
        valueObject.setAssessment(new ims.assessment.configuration.vo.UserAssessmentRefVo(id, -1));
      } else {
        valueObject.setAssessment(
            new ims.assessment.configuration.vo.UserAssessmentRefVo(
                domainObject.getAssessment().getId(), domainObject.getAssessment().getVersion()));
      }
    }
    // isPrognosticGroupingRelevant
    valueObject.setIsPrognosticGroupingRelevant(domainObject.isIsPrognosticGroupingRelevant());
    // PrognosticGroupingConfig
    valueObject.setPrognosticGroupingConfig(
        ims.clinicaladmin.vo.domain.PrognosticGroupingCongfigVoAssembler.create(
            map, domainObject.getPrognosticGroupingConfig()));
    // TnmRequiresDiff
    valueObject.setTnmRequiresDiff(domainObject.isTnmRequiresDiff());
    // TnmRequiresHisto
    valueObject.setTnmRequiresHisto(domainObject.isTnmRequiresHisto());
    // TnmRequiresSMarkers
    valueObject.setTnmRequiresSMarkers(domainObject.isTnmRequiresSMarkers());
    return valueObject;
  }