private void deleteSampleWhenError(String sampleName) throws Exception {
Sample sample = this.findFullyLoadedSampleByName(sampleName);
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
// delete characterizations
if (sample.getCharacterizationCollection() != null) {
for (Characterization achar : sample.getCharacterizationCollection()) {
charService.deleteCharacterization(achar);
}
}
// delete composition
if (sample.getSampleComposition() != null) {
compService.deleteComposition(sample.getSampleComposition());
}
sample.setSampleComposition(null);
// remove publication associations
if (sample.getPublicationCollection() != null) {
sample.setPublicationCollection(null);
}
// remove keyword associations
if (sample.getKeywordCollection() != null) {
sample.setKeywordCollection(null);
}
appService.saveOrUpdate(sample);
appService.delete(sample);
// remove all csm entries associated with sample
this.accessUtils.removeCSMEntries(sample.getId().toString());
}
private Sample findFullyLoadedSampleByName(String sampleName) throws Exception {
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
// load composition and characterization separate because of Hibernate
// join limitation
DetachedCriteria crit =
DetachedCriteria.forClass(Sample.class)
.add(Property.forName("name").eq(sampleName).ignoreCase());
Sample sample = null;
// load composition and characterization separate because of
// Hibernate join limitation
crit.setFetchMode("primaryPointOfContact", FetchMode.JOIN);
crit.setFetchMode("primaryPointOfContact.organization", FetchMode.JOIN);
crit.setFetchMode("otherPointOfContactCollection", FetchMode.JOIN);
crit.setFetchMode("otherPointOfContactCollection.organization", FetchMode.JOIN);
crit.setFetchMode("keywordCollection", FetchMode.JOIN);
crit.setFetchMode("publicationCollection", FetchMode.JOIN);
crit.setFetchMode("publicationCollection.authorCollection", FetchMode.JOIN);
crit.setFetchMode("publicationCollection.keywordCollection", FetchMode.JOIN);
crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
List result = appService.query(crit);
if (!result.isEmpty()) {
sample = (Sample) result.get(0);
}
if (sample == null) {
throw new NotExistException("Sample doesn't exist in the database");
}
// fully load composition
SampleComposition comp = this.loadComposition(sample.getId().toString());
sample.setSampleComposition(comp);
// fully load characterizations
List<Characterization> chars = this.loadCharacterizations(sample.getId().toString());
if (chars != null && !chars.isEmpty()) {
sample.setCharacterizationCollection(new HashSet<Characterization>(chars));
} else {
sample.setCharacterizationCollection(null);
}
return sample;
}
public void deleteSample(String sampleName)
throws SampleException, NoAccessException, NotExistException {
if (user == null) {
throw new NoAccessException();
}
Sample sample = null;
try {
// / / fully load original sample
sample = findFullyLoadedSampleByName(sampleName);
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
// / / delete characterizations
if (sample.getCharacterizationCollection() != null) {
for (Characterization achar : sample.getCharacterizationCollection()) {
charService.deleteCharacterization(achar);
}
}
// / / delete composition
if (sample.getSampleComposition() != null) {
compService.deleteComposition(sample.getSampleComposition());
}
sample.setSampleComposition(null);
// / / remove publication associations
if (sample.getPublicationCollection() != null) {
sample.setPublicationCollection(null);
}
// / / remove keyword associations
if (sample.getKeywordCollection() != null) {
sample.setKeywordCollection(null);
}
appService.saveOrUpdate(sample);
appService.delete(sample);
} catch (NotExistException e) {
throw e;
} catch (Exception e) {
String err = "Error in deleting the sample " + sampleName;
logger.error(err, e);
throw new SampleException(err, e);
}
}