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());
}
public void removeAccessibility(AccessibilityBean access, Sample sample)
throws SampleException, NoAccessException {
if (!isOwnerByCreatedBy(sample.getCreatedBy())) {
throw new NoAccessException();
}
String sampleId = sample.getId().toString();
try {
super.deleteAccessibility(access, sampleId);
// fully load sample
sample = this.findFullyLoadedSampleByName(sample.getName());
// keep POC public
// remove characterization accessibility
if (sample.getCharacterizationCollection() != null) {
for (Characterization achar : sample.getCharacterizationCollection()) {
accessUtils.removeAccessibility(access, achar, false);
}
}
// remove composition accessibility
if (sample.getSampleComposition() != null) {
accessUtils.removeAccessibility(access, sample.getSampleComposition(), false);
}
} catch (NoAccessException e) {
throw e;
} catch (Exception e) {
String err = "Error in deleting the access for sample " + sampleId;
logger.error(err, e);
throw new SampleException(err, e);
}
}
public List<String> removeAccesses(Sample sample, Boolean removeLater)
throws SampleException, NoAccessException {
List<String> ids = new ArrayList<String>();
try {
if (!securityService.checkCreatePermission(sample.getId().toString())) {
throw new NoAccessException();
}
ids.add(sample.getId().toString());
// fully load sample
Sample fullSample = this.findFullyLoadedSampleByName(sample.getName());
// find sample accesses
List<AccessibilityBean> sampleAccesses = super.findSampleAccesses(sample.getId().toString());
for (AccessibilityBean access : sampleAccesses) {
if (fullSample.getCharacterizationCollection() != null) {
for (Characterization achar : fullSample.getCharacterizationCollection()) {
ids.addAll(accessUtils.removeAccessibility(access, achar, removeLater));
}
}
if (fullSample.getSampleComposition() != null) {
ids.addAll(
accessUtils.removeAccessibility(
access, fullSample.getSampleComposition(), removeLater));
}
}
} catch (NoAccessException e) {
throw e;
} catch (Exception e) {
String error = "Error in removing sample accesses";
throw new SampleException(error, e);
}
return ids;
}
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);
}
}
public void assignAccessibility(AccessibilityBean access, Sample sample)
throws SampleException, NoAccessException {
if (!isOwnerByCreatedBy(sample.getCreatedBy())) {
throw new NoAccessException();
}
String sampleId = sample.getId().toString();
try {
if (!isOwnerByCreatedBy(sample.getCreatedBy())) {
throw new NoAccessException();
}
// get existing accessibilities
List<AccessibilityBean> groupAccesses = this.findGroupAccessibilities(sampleId);
List<AccessibilityBean> userAccesses = this.findUserAccessibilities(sampleId);
// if access is Public, remove all other access except Public
// Curator and owner
if (access.getGroupName().equals(AccessibilityBean.CSM_PUBLIC_GROUP)) {
for (AccessibilityBean acc : groupAccesses) {
// remove group accesses that are not public or curator
if (!acc.getGroupName().equals(AccessibilityBean.CSM_PUBLIC_GROUP)
&& !acc.getGroupName().equals((AccessibilityBean.CSM_DATA_CURATOR))) {
this.removeAccessibility(acc, sample);
}
}
SecuredDataBean securedDataBean = new SecuredDataBean();
for (AccessibilityBean acc : userAccesses) {
// remove accesses that are not owner
if (!securedDataBean.retrieveUserIsOwner(acc.getUserBean(), sample.getCreatedBy())) {
this.removeAccessibility(acc, sample);
}
}
}
// if sample is already public, retract from public
else {
if (groupAccesses.contains(AccessibilityBean.CSM_PUBLIC_ACCESS)) {
this.removeAccessibility(AccessibilityBean.CSM_PUBLIC_ACCESS, sample);
}
}
super.saveAccessibility(access, sampleId);
// fully load sample
sample = this.findFullyLoadedSampleByName(sample.getName());
// assign POC to public is handled when adding POC
// TODO check this logic when working with COPPA on organization
// assign characterization accessibility
if (sample.getCharacterizationCollection() != null) {
for (Characterization achar : sample.getCharacterizationCollection()) {
accessUtils.assignAccessibility(access, achar);
}
}
// assign composition accessibility
if (sample.getSampleComposition() != null) {
accessUtils.assignAccessibility(access, sample.getSampleComposition());
}
} catch (NoAccessException e) {
throw e;
} catch (Exception e) {
String err = "Error in assigning accessibility to the sample " + sampleId;
logger.error(err, e);
throw new SampleException(err, e);
}
}
