/**
* Search for Data Elements using the Long Name
*
* @param args
*/
public static void main(String[] args) {
try {
System.out.println("...TestCaDsrApi Started...");
ApplicationService appService =
ApplicationServiceProvider.getApplicationServiceFromUrl(
"https://cadsrapi.nci.nih.gov/cadsrapi4");
System.out.println("Searching for DataElements");
// Search for the Data Element with the Long Name "Patient Race Category*". The asterisk (*)
// is a wild card.
DataElement dataElement = new DataElement();
dataElement.setLongName("Patient Race Category*");
// dataElement.setPublicID(2238438L);
// dataElement.setLatestVersionIndicator("Yes");
List<Object> results = appService.search(DataElement.class, dataElement);
System.out.println(" received results : " + results.size());
for (int i = 0; i < results.size(); i++) {
// Show the DE
Object curr = results.get(i);
DataElement de = (DataElement) curr;
System.out.println("===Data Element " + de.getLongName());
System.out.println("Data Element " + de.getVersion());
System.out.println("Data Element " + de.getPreferredDefinition());
}
} catch (Exception exception) {
System.out.println("--------Error in the TestCaDsrApi");
exception.printStackTrace();
}
}
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);
}
}
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 List<Characterization> loadCharacterizations(String sampleId) throws Exception {
List<Characterization> chars = new ArrayList<Characterization>();
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
DetachedCriteria crit = DetachedCriteria.forClass(Characterization.class);
crit.createAlias("sample", "sample");
crit.add(Property.forName("sample.id").eq(new Long(sampleId)));
// fully load characterization
crit.setFetchMode("pointOfContact", FetchMode.JOIN);
crit.setFetchMode("pointOfContact.organization", FetchMode.JOIN);
crit.setFetchMode("protocol", FetchMode.JOIN);
crit.setFetchMode("protocol.file", FetchMode.JOIN);
crit.setFetchMode("protocol.file.keywordCollection", FetchMode.JOIN);
crit.setFetchMode("experimentConfigCollection", FetchMode.JOIN);
crit.setFetchMode("experimentConfigCollection.technique", FetchMode.JOIN);
crit.setFetchMode("experimentConfigCollection.instrumentCollection", FetchMode.JOIN);
crit.setFetchMode("findingCollection", FetchMode.JOIN);
crit.setFetchMode("findingCollection.datumCollection", FetchMode.JOIN);
crit.setFetchMode("findingCollection.datumCollection.conditionCollection", FetchMode.JOIN);
crit.setFetchMode("findingCollection.fileCollection", FetchMode.JOIN);
crit.setFetchMode("findingCollection.fileCollection.keywordCollection", FetchMode.JOIN);
crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
List results = appService.query(crit);
for (int i = 0; i < results.size(); i++) {
Characterization achar = (Characterization) results.get(i);
chars.add(achar);
}
return chars;
}
/**
* 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 SampleComposition loadComposition(String sampleId) throws Exception {
SampleComposition composition = null;
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
DetachedCriteria crit = DetachedCriteria.forClass(SampleComposition.class);
crit.createAlias("sample", "sample");
crit.add(Property.forName("sample.id").eq(new Long(sampleId)));
crit.setFetchMode("nanomaterialEntityCollection", FetchMode.JOIN);
crit.setFetchMode("nanomaterialEntityCollection.fileCollection", FetchMode.JOIN);
crit.setFetchMode(
"nanomaterialEntityCollection.fileCollection.keywordCollection", FetchMode.JOIN);
crit.setFetchMode("nanomaterialEntityCollection.composingElementCollection", FetchMode.JOIN);
crit.setFetchMode(
"nanomaterialEntityCollection.composingElementCollection.inherentFunctionCollection",
FetchMode.JOIN);
crit.setFetchMode(
"nanomaterialEntityCollection.composingElementCollection.inherentFunctionCollection.targetCollection",
FetchMode.JOIN);
crit.setFetchMode("functionalizingEntityCollection", FetchMode.JOIN);
crit.setFetchMode("functionalizingEntityCollection.fileCollection", FetchMode.JOIN);
crit.setFetchMode(
"functionalizingEntityCollection.fileCollection.keywordCollection", FetchMode.JOIN);
crit.setFetchMode("functionalizingEntityCollection.functionCollection", FetchMode.JOIN);
crit.setFetchMode(
"functionalizingEntityCollection.functionCollection.targetCollection", FetchMode.JOIN);
crit.setFetchMode("functionalizingEntityCollection.activationMethod", FetchMode.JOIN);
crit.setFetchMode("chemicalAssociationCollection", FetchMode.JOIN);
crit.setFetchMode("chemicalAssociationCollection.fileCollection", FetchMode.JOIN);
crit.setFetchMode(
"chemicalAssociationCollection.fileCollection.keywordCollection", FetchMode.JOIN);
crit.setFetchMode("chemicalAssociationCollection.associatedElementA", FetchMode.JOIN);
crit.setFetchMode("chemicalAssociationCollection.associatedElementB", FetchMode.JOIN);
crit.setFetchMode("fileCollection", FetchMode.JOIN);
crit.setFetchMode("fileCollection.keywordCollection", FetchMode.JOIN);
crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
List result = appService.query(crit);
if (!result.isEmpty()) {
composition = (SampleComposition) result.get(0);
}
return composition;
}
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);
}
}
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 updatePOCAssociatedWithCharacterizations(
String sampleName, Long oldPOCId, Long newPOCId) throws SampleException {
try {
CaNanoLabApplicationService appService =
(CaNanoLabApplicationService) ApplicationServiceProvider.getApplicationService();
DetachedCriteria crit = DetachedCriteria.forClass(Characterization.class);
crit.createAlias("sample", "sample");
crit.createAlias("pointOfContact", "poc");
crit.add(Property.forName("poc.id").eq(oldPOCId));
crit.add(Property.forName("sample.name").eq(sampleName));
crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
List results = appService.query(crit);
for (int i = 0; i < results.size(); i++) {
Characterization achar = (Characterization) results.get(i);
// update POC to the new ID
achar.getPointOfContact().setId(newPOCId);
appService.saveOrUpdate(achar);
}
} catch (Exception e) {
String err = "Error in updating POC associated sample characterizations " + sampleName;
logger.error(err, e);
throw new SampleException(err, e);
}
}
public GeneBySymbolQueryAction() throws Exception {
this.as = (CaBioApplicationService) ApplicationServiceProvider.getApplicationService();
this.rs = new ReportService(as);
}
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 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);
}
}
public static String getEVSCode(String prefName, String dtsVocab) {
LexEVSApplicationService evsService = null;
try {
evsService =
(LexEVSApplicationService)
ApplicationServiceProvider.getApplicationService("EvsServiceInfo");
} catch (Exception e) {
throw new RuntimeException(e);
}
if (dtsVocab == null) dtsVocab = "";
String CCode = "";
if (dtsVocab.equals("Thesaurus/Metathesaurus")
|| dtsVocab.equals("")
|| dtsVocab.equals("NCI Thesaurus")
|| dtsVocab.equals("NCI_Thesaurus")) dtsVocab = "NCI_Thesaurus";
ResolvedConceptReferenceList codes2 = null;
int codesSize = 0;
try {
CodedNodeSet metaNodes = evsService.getNodeSet("NCI MetaThesaurus", null, null);
metaNodes =
metaNodes.restrictToMatchingDesignations(
prefName, // the text to match
CodedNodeSet.SearchDesignationOption
.PREFERRED_ONLY, // whether to search all designation, only Preferred or only
// Non-Preferred
"exactMatch", // the match algorithm to use
null); // the language to match (null matches all)
metaNodes = metaNodes.restrictToStatus(ActiveOption.ACTIVE_ONLY, null);
codes2 =
metaNodes.resolveToList(
null, // Sorts used to sort results (null means sort by match score)
null, // PropertyNames to resolve (null resolves all)
new CodedNodeSet.PropertyType[] {
PropertyType.DEFINITION, PropertyType.PRESENTATION
}, // PropertyTypess to resolve (null resolves all) //PropertyTypess to resolve (null
// resolves all)
10 // cap the number of results returned (-1 resolves all)
);
codesSize = codes2.getResolvedConceptReferenceCount();
} catch (Exception ex) {
System.err.println("Error do_getEVSCode:resolveToList: " + ex.toString());
ex.printStackTrace();
}
if (codes2 != null) {
ResolvedConceptReference conceptReference = new ResolvedConceptReference();
// logger.debug("Got "+codesSize+" results for the do_getEVSCode search using prefName and
// exactMatch");
for (int i = 0; i < codesSize; i++) {
conceptReference = (ResolvedConceptReference) codes2.getResolvedConceptReference(i);
CCode = (String) conceptReference.getConceptCode();
}
}
evsService = null;
return CCode;
}
public static List searchEVS(
String term,
String dtsVocab,
String retired,
String sSearchInEVS,
String sUISearchType,
String sMetaSource,
int sMetaLimit)
throws Exception {
String algorithm;
String altNameType;
String CCode;
String prefName = "";
Boolean isRetired = new Boolean(false);
Boolean bTrue = new Boolean(true);
Boolean bFalse = new Boolean(false);
boolean isMetaCodeSearch = false;
Boolean codeFoundInThesaurus = new Boolean(false);
String source = "";
String definition = "";
List vCon = new ArrayList();
String sDefDefault = "No value exists.";
String sDef = "";
String sDefSrc = "";
// List vCon = null;
List vMetaDefs = new ArrayList();
// List vMetaDefs = null;
if (dtsVocab.equals("Thesaurus/Metathesaurus")
|| dtsVocab.equals("")
|| dtsVocab.equals("NCI Thesaurus")
|| dtsVocab.equals("NCI_Thesaurus")) {
dtsVocab = "NCI Thesaurus";
altNameType = "NCI_CONCEPT_CODE";
}
// for search Meta by (LOINC) code
else if (dtsVocab.equals("Metathesaurus") || sSearchInEVS.equals("Code")) {
dtsVocab = "NCI_Thesaurus";
altNameType = "NCI_CONCEPT_CODE";
isMetaCodeSearch = true;
sUISearchType = "term";
}
// for Meta searches only (no Thes search), like in getSuperConcepts Meta
else if (dtsVocab.equals("NCI Metathesaurus")) {
altNameType = "UMLS_CUI";
isMetaCodeSearch = false;
sUISearchType = "term";
} else altNameType = "";
LexEVSApplicationService evsService =
(LexEVSApplicationService)
ApplicationServiceProvider.getApplicationService("EvsServiceInfo");
/* if (!sSearchInEVS.equals("Concept Code") || term.equals("")) {*/
Pattern pattern = Pattern.compile("^C\\d{2,8}");
Matcher matcher = pattern.matcher(term);
algorithm = getAlgorithm(term);
term = cleanTerm(term);
int totalReturnCount = 0;
try {
if (retired.equals(
"Include")) // do this if all concepts, including retired, should be included
isRetired = new Boolean(false);
else {
try {
ResolvedConceptReferenceList rcrl =
searchPrefTerm(evsService, dtsVocab, term, sMetaLimit, algorithm);
if (rcrl != null && rcrl.getResolvedConceptReferenceCount() > 0)
isRetired = (Boolean) (!rcrl.getResolvedConceptReference(0).getEntity().isIsActive());
} catch (Exception ex) {
ex.printStackTrace();
}
}
if (isRetired.equals(bFalse)) {
ResolvedConceptReferenceList concepts = null;
// CCode = term;
int codesSize = 0;
try {
if (sSearchInEVS.equals("Concept Code") || matcher.matches())
concepts = searchConceptCode(evsService, dtsVocab, term, sMetaLimit);
else concepts = searchPrefTerm(evsService, dtsVocab, term, sMetaLimit, algorithm);
codesSize = concepts.getResolvedConceptReferenceCount();
} catch (Exception ex) {
System.out.println("Error do_EVSSearch get concept: " + ex.toString());
}
if (concepts != null && codesSize > 0) {
codeFoundInThesaurus = new Boolean(true);
prefName = concepts.getResolvedConceptReference(0).getEntityDescription().getContent();
concepts = new ResolvedConceptReferenceList();
try {
concepts = searchPrefTerm(evsService, dtsVocab, prefName, sMetaLimit, algorithm);
codesSize = concepts.getResolvedConceptReferenceCount();
} catch (Exception ex) {
// ex.printStackTrace();
System.out.println("Error do_EVSSearch DescLogic: " + ex.toString());
}
if (concepts != null) {
ResolvedConceptReference rcr = new ResolvedConceptReference();
for (int i = 0; i < codesSize; i++) {
rcr = concepts.getResolvedConceptReference(i);
prefName = rcr.getEntityDescription().getContent();
CCode = rcr.getConceptCode();
Definition[] defs = rcr.getEntity().getDefinition();
if (defs == null) defs = new Definition[0];
sDef = sDefDefault; // "No Value Exists.";
sDefSrc = "";
for (int k = 0; k < defs.length; k++) {
Definition def = defs[k];
if (def != null) {
if (def.getIsPreferred() != null) {
sDef = def.getValue().getContent();
if (def.getSourceCount() > 0)
sDefSrc = def.getSource(0).getContent(); // get def source
}
}
}
EVSBean conBean = new EVSBean();
conBean.setCode(CCode);
conBean.setDefinition(sDef);
conBean.setDictionary(dtsVocab);
conBean.setName(prefName);
conBean.setSource(sDefSrc);
conBean.setType(altNameType);
vCon.add(conBean);
totalReturnCount++;
if (totalReturnCount >= sMetaLimit) return vCon;
}
}
}
}
} catch (Exception ex) {
System.out.println("Error do_EVSSearch Concept code: " + ex.toString());
}
// Search Meta
int length = 0;
length = term.length();
ResolvedConceptReferenceList concepts = null;
if (sSearchInEVS.equals("Concept Code"))
concepts = searchConceptCode(evsService, "NCI Metathesaurus", term, sMetaLimit);
else if (!sSearchInEVS.equals("Concept Code"))
concepts = searchPrefTerm(evsService, "NCI Metathesaurus", term, sMetaLimit, algorithm);
if (concepts != null) {
ResolvedConceptReference rcr = new ResolvedConceptReference();
for (int i = 0; i < concepts.getResolvedConceptReferenceCount(); i++) {
if (totalReturnCount >= sMetaLimit) break;
rcr = concepts.getResolvedConceptReference(i);
prefName = rcr.getEntityDescription().getContent();
CCode = rcr.getConceptCode();
Definition[] defs = rcr.getEntity().getDefinition();
if (defs == null) defs = new Definition[0];
sDef = sDefDefault; // "No Value Exists.";
sDefSrc = "";
for (int k = 0; k < defs.length; k++) {
Definition def = defs[k];
if (def != null) {
sDef = def.getValue().getContent();
if (def.getSourceCount() > 0) sDefSrc = def.getSource(0).getContent(); // get def source
}
EVSBean conBean = new EVSBean();
conBean.setCode(CCode);
conBean.setDefinition(sDef);
conBean.setDictionary("NCI Metathesaurus");
conBean.setName(prefName);
conBean.setSource(sDefSrc);
conBean.setType("UMLS_CUI");
vCon.add(conBean);
totalReturnCount++;
if (totalReturnCount >= sMetaLimit) break;
}
}
}
evsService = null;
System.out.println(vCon.size());
return vCon;
}
