/**
* @param nanomaterialEntityClassNames
* @param functionalizingEntityClassNames
* @param otherFunctionalizingEntityTypes
* @param functionClassNames
* @param otherFunctionTypes
* @param characterizationClassNames
* @param wordList
* @param samplePointOfContacts
* @return
* @throws SampleException
*/
public List<String> findSampleIdsBy(
String sampleName,
String samplePointOfContact,
String[] nanomaterialEntityClassNames,
String[] otherNanomaterialEntityTypes,
String[] functionalizingEntityClassNames,
String[] otherFunctionalizingEntityTypes,
String[] functionClassNames,
String[] otherFunctionTypes,
String[] characterizationClassNames,
String[] otherCharacterizationTypes,
String[] wordList)
throws SampleException {
try {
List<String> sampleIds =
helper.findSampleIdsBy(
sampleName,
samplePointOfContact,
nanomaterialEntityClassNames,
otherNanomaterialEntityTypes,
functionalizingEntityClassNames,
otherFunctionalizingEntityTypes,
functionClassNames,
otherFunctionTypes,
characterizationClassNames,
otherCharacterizationTypes,
wordList);
return sampleIds;
} catch (Exception e) {
String err = "Problem finding samples with the given search parameters.";
logger.error(err, e);
throw new SampleException(err, e);
}
}
public int getNumberOfPublicSampleSources() throws SampleException {
try {
int count = helper.getNumberOfPublicSampleSources();
return count;
} catch (Exception e) {
String err = "Error finding counts of public sample sources.";
logger.error(err, e);
throw new SampleException(err, e);
}
}
public List<String> findSampleIdsByOwner(String currentOwner) throws SampleException {
List<String> sampleIds = new ArrayList<String>();
try {
sampleIds = helper.findSampleIdsByOwner(currentOwner);
} catch (Exception e) {
String error = "Error in retrieving sampleIds by owner";
throw new SampleException(error, e);
}
return sampleIds;
}
public PointOfContactBean findPointOfContactById(String pocId) throws PointOfContactException {
PointOfContactBean pocBean = null;
try {
PointOfContact poc = helper.findPointOfContactById(pocId);
pocBean = new PointOfContactBean(poc);
} catch (Exception e) {
String err = "Problem finding point of contact for the given id.";
logger.error(err, e);
throw new PointOfContactException(err, e);
}
return pocBean;
}
public List<String> findOtherSampleNamesFromSamePrimaryOrganization(String sampleId)
throws SampleException {
List<String> sortedNames = null;
try {
Set<String> names = helper.findOtherSamplesFromSamePrimaryOrganization(sampleId);
sortedNames = new ArrayList<String>(names);
Collections.sort(sortedNames, new Comparators.SortableNameComparator());
} catch (Exception e) {
String err = "Error in deleting the sample " + sampleId;
logger.error(err, e);
throw new SampleException(err, e);
}
return sortedNames;
}
public SampleBean findSampleByName(String sampleName) throws SampleException, NoAccessException {
try {
Sample sample = helper.findSampleByName(sampleName);
SampleBean sampleBean = null;
if (sample != null) {
sampleBean = loadSampleBean(sample);
}
return sampleBean;
} catch (NoAccessException e) {
throw e;
} catch (Exception e) {
String err = "Problem finding the sample by name: " + sampleName;
logger.error(err, e);
throw new SampleException(err, e);
}
}
/**
* Only load sample core data.
*
* <p>Do not check read permission because workspace items are owned by user.
*/
public SampleBasicBean findSWorkspaceSampleById(String sampleId, boolean loadAccessInfo)
throws SampleException, NoAccessException {
SampleBasicBean sampleBean = null;
try {
Sample sample = helper.findSampleBasicById(sampleId);
if (sample != null) {
if (loadAccessInfo) {
sampleBean = loadSampleBean(sample, false);
} else {
sampleBean = new SampleBasicBean(sample);
}
}
} catch (NoAccessException e) {
throw e;
} catch (Exception e) {
String err = "Problem finding the sample by id: " + sampleId;
logger.error(err, e);
throw new SampleException(err, e);
}
return sampleBean;
}
public SortedSet<String> getAllOrganizationNames() throws PointOfContactException {
try {
SortedSet<String> names = new TreeSet<String>(new Comparators.SortableNameComparator());
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
HQLCriteria crit =
new HQLCriteria(
"select org.name from gov.nih.nci.cananolab.domain.common.Organization org");
List results = appService.query(crit);
logger.debug(
"Completed select org.name from gov.nih.nci.cananolab.domain.common.Organization org");
for (int i = 0; i < results.size(); i++) {
String name = ((String) results.get(i)).trim();
names.add(name);
}
return names;
} catch (Exception e) {
String err = "Error finding organization for " + helper.getUser().getLoginName();
logger.error(err, e);
throw new PointOfContactException(err, e);
}
}
public void savePointOfContact(PointOfContactBean pocBean)
throws PointOfContactException, NoAccessException {
if (user == null) {
throw new NoAccessException();
}
try {
PointOfContact dbPointOfContact = null;
Long oldPOCId = null;
String oldOrgName = null;
Boolean newPOC = true;
Boolean newOrg = true;
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
PointOfContact domainPOC = pocBean.getDomain();
Organization domainOrg = domainPOC.getOrganization();
// get existing organization from database and reuse ID,
// created by and created date
// address information will be updated
Organization dbOrganization = helper.findOrganizationByName(domainOrg.getName());
if (dbOrganization != null) {
domainOrg.setId(dbOrganization.getId());
domainOrg.setCreatedBy(dbOrganization.getCreatedBy());
domainOrg.setCreatedDate(dbOrganization.getCreatedDate());
newOrg = false;
}
// create a new org if not an existing one
else {
domainOrg.setId(null);
}
// if point of contact has no ID
if (domainPOC.getId() == null) {
// check if org name, first name and last name matches existing
// one
dbPointOfContact =
helper.findPointOfContactByNameAndOrg(
domainPOC.getFirstName(),
domainPOC.getLastName(),
domainPOC.getOrganization().getName());
// if found, reuse ID, created_date and created_by
if (dbPointOfContact != null) {
domainPOC.setId(dbPointOfContact.getId());
domainPOC.setCreatedDate(dbPointOfContact.getCreatedDate());
domainPOC.setCreatedBy(dbPointOfContact.getCreatedBy());
newPOC = false;
}
} else {
// check if organization is changed
dbPointOfContact = helper.findPointOfContactById(domainPOC.getId().toString());
Organization dbOrg = dbPointOfContact.getOrganization();
// if organization information is changed, create a new POC
if (!dbOrg.getName().equals(domainOrg.getName())) {
oldPOCId = domainPOC.getId();
oldOrgName = dbOrg.getName();
domainPOC.setId(null);
newPOC = true;
}
// if name information is changed, create a new POC
else if (domainPOC.getFirstName() != null
&& !domainPOC.getFirstName().equalsIgnoreCase(dbPointOfContact.getFirstName())
|| domainPOC.getLastName() != null
&& !domainPOC.getLastName().equalsIgnoreCase(dbPointOfContact.getLastName())) {
newPOC = true;
} else {
domainPOC.setId(dbPointOfContact.getId());
domainPOC.setCreatedBy(dbPointOfContact.getCreatedBy());
domainPOC.setCreatedDate(dbPointOfContact.getCreatedDate());
newPOC = false;
}
}
appService.saveOrUpdate(domainPOC);
if (newPOC) {
this.saveAccessibility(AccessibilityBean.CSM_PUBLIC_ACCESS, domainPOC.getId().toString());
}
if (newOrg) {
this.saveAccessibility(
AccessibilityBean.CSM_PUBLIC_ACCESS, domainPOC.getOrganization().getId().toString());
}
} catch (Exception e) {
String err = "Error in saving the PointOfContact.";
logger.error(err, e);
throw new PointOfContactException(err, e);
}
}