private void saveClonedPOCs(SampleBean sampleBean) throws Exception {
savePointOfContact(sampleBean.getPrimaryPOCBean());
if (sampleBean.getOtherPOCBeans() != null && !sampleBean.getOtherPOCBeans().isEmpty()) {
for (PointOfContactBean pocBean : sampleBean.getOtherPOCBeans()) {
savePointOfContact(pocBean);
}
}
}
/**
* Persist a new sample or update an existing canano sample
*
* @param sample
* @throws SampleException , DuplicateEntriesException
*/
public void saveSample(SampleBean sampleBean)
throws SampleException, DuplicateEntriesException, NoAccessException {
if (user == null) {
throw new NoAccessException();
}
Boolean newSample = true;
if (sampleBean.getDomain().getId() != null) {
newSample = false;
}
Sample sample = sampleBean.getDomain();
try {
if (!newSample
&& !securityService.checkCreatePermission(sampleBean.getDomain().getId().toString())) {
throw new NoAccessException();
}
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
Sample dbSample = (Sample) appService.getObject(Sample.class, "name", sample.getName());
if (dbSample != null && !dbSample.getId().equals(sample.getId())) {
throw new DuplicateEntriesException();
}
if (sample.getKeywordCollection() != null) {
Collection<Keyword> keywords = new HashSet<Keyword>(sample.getKeywordCollection());
sample.getKeywordCollection().clear();
for (Keyword keyword : keywords) {
Keyword dbKeyword =
(Keyword) appService.getObject(Keyword.class, "name", keyword.getName());
if (dbKeyword != null) {
keyword.setId(dbKeyword.getId());
} else {
keyword.setId(null);
}
// turned off cascade save-update in order to share the same
// keyword instance with File keywords.
appService.saveOrUpdate(keyword);
sample.getKeywordCollection().add(keyword);
}
}
appService.saveOrUpdate(sample);
// save default access
if (newSample) {
super.saveDefaultAccessibilities(sample.getId().toString());
}
} catch (NoAccessException e) {
throw e;
} catch (DuplicateEntriesException e) {
throw e;
} catch (Exception e) {
String err = "Error in saving the sample";
logger.error(err, e);
throw new SampleException(err, e);
}
}
private SampleBean loadSampleBean(Sample sample) throws Exception {
SampleBean sampleBean = new SampleBean(sample);
if (user != null) {
List<AccessibilityBean> groupAccesses =
super.findGroupAccessibilities(sample.getId().toString());
List<AccessibilityBean> userAccesses =
super.findUserAccessibilities(sample.getId().toString());
sampleBean.setUserAccesses(userAccesses);
sampleBean.setGroupAccesses(groupAccesses);
sampleBean.setUser(user);
}
return sampleBean;
}
private void saveClonedPublications(SampleBean origSampleBean, SampleBean sampleBean)
throws Exception {
if (sampleBean.getDomain().getPublicationCollection() != null) {
for (Publication pub : sampleBean.getDomain().getPublicationCollection()) {
PublicationBean pubBean = new PublicationBean(pub);
pubBean.setFromSamplePage(true);
// don't need to reset sample names because savePublication
// takes care of empty sample names.
publicationService.savePublication(pubBean);
// don't need to save access because the cloned publications
// shared the same IDs with the source publications
}
}
}
public void transferSampleBeanForDataAvailability(
SampleBean sampleBean, HttpServletRequest request, String[] availableEntityNames) {
if (sampleBean == null) return;
setSampleName(sampleBean.getDomain().getName());
setDataAvailability(sampleBean.getDataAvailabilityMetricsScore());
this.setCaNanoLabScore(sampleBean.getCaNanoLabScore());
this.setMincharScore(sampleBean.getMincharScore());
setCaNanoLabScore(sampleBean.getCaNanoLabScore());
setMincharScore(sampleBean.getMincharScore());
SortedSet<String> ca =
(SortedSet<String>) request.getSession().getServletContext().getAttribute("chemicalAssocs");
setChemicalAssocs(new ArrayList<String>(ca));
setCaNano2MINChar(
(Map<String, String>)
request.getSession().getServletContext().getAttribute("caNano2MINChar"));
SortedSet<String> pc =
(SortedSet<String>) request.getSession().getServletContext().getAttribute("physicoChars");
setPhysicoChars(new ArrayList<String>(pc));
SortedSet<String> iv =
(SortedSet<String>) request.getSession().getServletContext().getAttribute("invitroChars");
setInvitroChars(new ArrayList<String>(iv));
SortedSet<String> invivo =
(SortedSet<String>) request.getSession().getServletContext().getAttribute("invivoChars");
setInvivoChars(new ArrayList<String>(invivo));
if (availableEntityNames != null)
this.availableEntityNames = new ArrayList<String>(Arrays.asList(availableEntityNames));
// setSampleName(sampleBean.getDomain().getName());
// SortedSet<String> ca = (SortedSet<String>)
// request.getSession().getServletContext().getAttribute("chemicalAssocs");
// this.chemicalAssocs = SampleUtil.getStringArrayFromSortedSet(ca);
// // SampleUtil.getDefaultListFromSessionByType("chemicalAssocs", request.getSession());
//
//
// this.caNano2MINChar = (Map<String, String>) request.getSession().getServletContext()
// .getAttribute("caNano2MINChar");
//
// SortedSet<String> pc = (SortedSet<String>)
// request.getSession().getServletContext().getAttribute("physicoChars");
// this.physicoChars = SampleUtil.getStringArrayFromSortedSet(pc);
// SortedSet<String> iv = (SortedSet<String>)
// request.getSession().getServletContext().getAttribute("invitroChars");
// this.invitroChars = SampleUtil.getStringArrayFromSortedSet(iv);
// SortedSet<String> invivo = (SortedSet<String>)
// request.getSession().getServletContext().getAttribute("invivoChars");
// this.invivoChars = SampleUtil.getStringArrayFromSortedSet(invivo);
//
}
private void saveClonedCharacterizations(String origSampleName, SampleBean sampleBean)
throws Exception {
if (sampleBean.getDomain().getCharacterizationCollection() != null) {
String newSampleName = sampleBean.getDomain().getName();
for (Characterization achar : sampleBean.getDomain().getCharacterizationCollection()) {
CharacterizationBean charBean = new CharacterizationBean(achar);
if (charBean.getExperimentConfigs() != null) {
for (ExperimentConfigBean configBean : charBean.getExperimentConfigs()) {
charService.saveExperimentConfig(configBean);
}
}
if (charBean.getFindings() != null) {
for (FindingBean findingBean : charBean.getFindings()) {
for (FileBean fileBean : findingBean.getFiles()) {
fileUtils.updateClonedFileInfo(fileBean, origSampleName, newSampleName);
}
charService.saveFinding(findingBean);
}
}
charService.saveCharacterization(sampleBean, charBean);
}
}
}
private void saveClonedComposition(SampleBean origSampleBean, SampleBean sampleBean)
throws Exception {
String origSampleName = origSampleBean.getDomain().getName();
String newSampleName = sampleBean.getDomain().getName();
if (sampleBean.getDomain().getSampleComposition() != null) {
// save files
if (sampleBean.getDomain().getSampleComposition().getFileCollection() != null) {
for (File file : sampleBean.getDomain().getSampleComposition().getFileCollection()) {
FileBean fileBean = new FileBean(file);
fileUtils.updateClonedFileInfo(fileBean, origSampleName, newSampleName);
compService.saveCompositionFile(sampleBean, fileBean);
}
}
// save nanomaterial entities
if (sampleBean.getDomain().getSampleComposition().getNanomaterialEntityCollection() != null) {
for (NanomaterialEntity entity :
sampleBean.getDomain().getSampleComposition().getNanomaterialEntityCollection()) {
NanomaterialEntityBean entityBean = new NanomaterialEntityBean(entity);
for (FileBean fileBean : entityBean.getFiles()) {
fileUtils.updateClonedFileInfo(fileBean, origSampleName, newSampleName);
}
compService.saveNanomaterialEntity(sampleBean, entityBean);
}
}
// save functionalizing entities
if (sampleBean.getDomain().getSampleComposition().getFunctionalizingEntityCollection()
!= null) {
for (FunctionalizingEntity entity :
sampleBean.getDomain().getSampleComposition().getFunctionalizingEntityCollection()) {
FunctionalizingEntityBean entityBean = new FunctionalizingEntityBean(entity);
for (FileBean fileBean : entityBean.getFiles()) {
fileUtils.updateClonedFileInfo(fileBean, origSampleName, newSampleName);
}
compService.saveFunctionalizingEntity(sampleBean, entityBean);
}
}
// save chemical association
if (sampleBean.getDomain().getSampleComposition().getChemicalAssociationCollection()
!= null) {
for (ChemicalAssociation assoc :
sampleBean.getDomain().getSampleComposition().getChemicalAssociationCollection()) {
ChemicalAssociationBean assocBean = new ChemicalAssociationBean(assoc);
// set the correct IDs for associated elements
updateAssociatedElementId(
sampleBean.getDomain().getSampleComposition(), assoc.getAssociatedElementA());
updateAssociatedElementId(
sampleBean.getDomain().getSampleComposition(), assoc.getAssociatedElementB());
for (FileBean fileBean : assocBean.getFiles()) {
fileUtils.updateClonedFileInfo(fileBean, origSampleName, newSampleName);
}
compService.saveChemicalAssociation(sampleBean, assocBean);
}
}
}
}
public SampleBean cloneSample(String originalSampleName, String newSampleName)
throws SampleException, NoAccessException, DuplicateEntriesException, NotExistException {
if (user == null) {
throw new NoAccessException();
}
SampleBean newSampleBean = null;
Sample origSample = null;
SampleBean origSampleBean = null;
Sample newSample0 = new Sample();
try {
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
Sample dbNewSample = (Sample) appService.getObject(Sample.class, "name", newSampleName);
if (dbNewSample != null) {
throw new DuplicateEntriesException();
}
// fully load original sample
origSample = findFullyLoadedSampleByName(originalSampleName);
origSampleBean = new SampleBean(origSample);
newSample0.setName(newSampleName);
newSample0.setCreatedBy(user.getLoginName() + ":" + Constants.AUTO_COPY_ANNOTATION_PREFIX);
newSample0.setCreatedDate(new Date());
// save the sample so later up just update the cloned the
// associations.
SampleBean newSampleBean0 = new SampleBean(newSample0);
// save the sample to get an ID before saving associations
saveSample(newSampleBean0);
} catch (NotExistException e) {
throw e;
} catch (DuplicateEntriesException e) {
throw e;
} catch (Exception e) {
String err = "Error in loading the original sample " + originalSampleName;
logger.error(err, e);
throw new SampleException(err, e);
}
try {
// clone the sample
Sample newSample = origSampleBean.getDomainCopy(user.getLoginName());
newSample.setName(newSampleName);
// keep the id
newSample.setId(newSample0.getId());
newSampleBean = new SampleBean(newSample);
// retrieve accessibilities of the original sample
List<AccessibilityBean> groupAccesses =
super.findGroupAccessibilities(origSample.getId().toString());
List<AccessibilityBean> userAccesses =
super.findUserAccessibilities(origSample.getId().toString());
origSampleBean.setGroupAccesses(groupAccesses);
origSampleBean.setUserAccesses(userAccesses);
// need to save associations one by one (except keywords)
// Hibernate mapping settings for most use cases
saveClonedPOCs(newSampleBean);
saveClonedCharacterizations(origSample.getName(), newSampleBean);
saveClonedComposition(origSampleBean, newSampleBean);
saveClonedPublications(origSampleBean, newSampleBean);
saveSample(newSampleBean);
newSampleBean.setUser(user);
// assign accessibility for the new sample
for (AccessibilityBean access : origSampleBean.getAllAccesses()) {
this.assignAccessibility(access, newSampleBean.getDomain());
}
} catch (Exception e) {
// delete the already persisted new sample in case of error
try {
this.deleteSampleWhenError(newSample0.getName());
} catch (Exception ex) {
String err = "Error in deleting the errored cloned-sample " + newSample0.getName();
logger.error(err, e);
throw new SampleException(err, ex);
}
String err = "Error in cloning the sample " + originalSampleName;
logger.error(err, e);
throw new SampleException(err, e);
}
return newSampleBean;
}