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 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);
}
}