public List<PointOfContactBean> findPointOfContactsBySampleId(String sampleId)
throws PointOfContactException {
try {
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
DetachedCriteria crit =
DetachedCriteria.forClass(Sample.class)
.add(Property.forName("id").eq(new Long(sampleId)));
crit.setFetchMode("primaryPointOfContact", FetchMode.JOIN);
crit.setFetchMode("primaryPointOfContact.organization", FetchMode.JOIN);
crit.setFetchMode("otherPointOfContactCollection", FetchMode.JOIN);
crit.setFetchMode("otherPointOfContactCollection.organization", FetchMode.JOIN);
crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
List results = appService.query(crit);
List<PointOfContactBean> pointOfContactCollection = new ArrayList<PointOfContactBean>();
for (int i = 0; i < results.size(); i++) {
Sample particle = (Sample) results.get(i);
PointOfContact primaryPOC = particle.getPrimaryPointOfContact();
Collection<PointOfContact> otherPOCs = particle.getOtherPointOfContactCollection();
pointOfContactCollection.add(new PointOfContactBean(primaryPOC));
for (PointOfContact poc : otherPOCs) {
pointOfContactCollection.add(new PointOfContactBean(poc));
}
}
return pointOfContactCollection;
} catch (Exception e) {
String err = "Problem finding all PointOfContact collections with the given sample ID.";
logger.error(err, e);
throw new PointOfContactException(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 loadAccessesForBasicSampleBean(SampleBasicBean sampleBean) throws Exception {
Sample sample = sampleBean.getDomain();
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);
}
}
/**
* 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;
}
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);
}
}
private SampleBasicBean loadSampleBean(Sample sample, boolean checkReadPermission)
throws Exception {
SampleBasicBean sampleBean = new SampleBasicBean(sample);
if (user != null) {
logger.debug("=== Loading group accesses");
List<AccessibilityBean> groupAccesses =
super.findGroupAccessibilities(sample.getId().toString(), checkReadPermission);
logger.debug("=== Done Loading group accesses");
logger.debug("=== Loading user accesses");
List<AccessibilityBean> userAccesses =
super.findUserAccessibilities(sample.getId().toString(), checkReadPermission);
logger.debug("=== Done Loading user accesses");
sampleBean.setUserAccesses(userAccesses);
sampleBean.setGroupAccesses(groupAccesses);
sampleBean.setUser(user);
}
return sampleBean;
}
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);
}
}
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;
}
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 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;
}
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);
}
}