@Override
public AnonymousEntityDescription convertTo(
ResolvedConceptReference source, AnonymousEntityDescription target) {
if (StringUtils.isBlank(source.getCode()) || StringUtils.isBlank(source.getCodeNamespace())) {
return target;
}
CodingScheme cs =
codingSchemeService.getCodingSchemeByUriAndVersion(
source.getCodingSchemeURI(), source.getCodingSchemeVersion());
for (org.LexGrid.concepts.Comment c : source.getEntity().getComment()) {
org.cts2.core.Comment comment = this.baseDozerBeanMapper.map(c, org.cts2.core.Comment.class);
// process supported mappings
if (cs != null) {
if (comment.getFormat() != null && !StringUtils.isEmpty(comment.getFormat().getContent())) {
SupportedDataType supportedDataType =
DaoUtility.getURIMap(cs, SupportedDataType.class, comment.getFormat().getContent());
if (supportedDataType != null) comment.getFormat().setMeaning(supportedDataType.getUri());
}
if (comment.getLanguage() != null
&& !StringUtils.isEmpty(comment.getLanguage().getContent())) {
SupportedLanguage supportedLanguage =
DaoUtility.getURIMap(cs, SupportedLanguage.class, comment.getLanguage().getContent());
if (supportedLanguage != null)
comment.getLanguage().setMeaning(supportedLanguage.getUri());
}
}
target.addNote(comment);
}
return target;
}
/**
* Resolve the Iterator
*
* @param iterator
* @param maxToReturn
* @param code
* @return
*/
public Vector<Entity> resolveIterator(
ResolvedConceptReferencesIterator iterator, int maxToReturn, String code) {
Vector<Entity> v = new Vector<Entity>();
if (iterator == null) {
_logger.warn("No match.");
return v;
}
try {
int iteration = 0;
while (iterator.hasNext()) {
iteration++;
iterator = iterator.scroll(maxToReturn);
ResolvedConceptReferenceList rcrl = iterator.getNext();
ResolvedConceptReference[] rcra = rcrl.getResolvedConceptReference();
for (int i = 0; i < rcra.length; i++) {
ResolvedConceptReference rcr = rcra[i];
Entity ce = rcr.getReferencedEntry();
if (code == null) {
v.add(ce);
} else {
if (ce.getEntityCode().compareTo(code) != 0) v.add(ce);
}
}
}
} catch (Exception e) {
_logger.warn(e.getMessage());
}
return v;
}
/** Force a refresh of all names assigned to graph nodes. */
@SuppressWarnings("unchecked")
void refreshNodeNames(boolean showCode, boolean abbreviate) {
for (Iterator<Tuple> tuples = getNodes().tuples(); tuples.hasNext(); ) {
Tuple t = tuples.next();
ResolvedConceptReference rcr = (ResolvedConceptReference) t.get("RCR");
if (rcr != null) {
String code = showCode ? rcr.getConceptCode() : null;
String desc =
rcr.getEntityDescription() != null ? rcr.getEntityDescription().getContent() : null;
t.set("name", getNodeName(code, desc, abbreviate, "\n"));
}
}
}
private boolean compareResolvedConceptReferenceList(
ResolvedConceptReferenceList list1, ResolvedConceptReferenceList list2) {
ResolvedConceptReference[] rcr1 = list1.getResolvedConceptReference();
ResolvedConceptReference[] rcr2 = list2.getResolvedConceptReference();
boolean found = false;
for (int i = 0; i < rcr1.length; i++) {
ResolvedConceptReference ref = rcr1[i];
String searchCode = ref.getConceptCode();
for (int j = 0; j < rcr2.length; j++) {
ResolvedConceptReference searchRef = rcr2[j];
String foundCode = searchRef.getConceptCode();
if (searchCode.equals(foundCode)) {
found = true;
}
}
}
return found;
}
/*
* (non-Javadoc)
*
* @see prefuse.data.Graph#addNode()
*/
public Node addNode(ResolvedConceptReference rcr, boolean showCode) {
// Limit length for nodes other than the focus item
// to allow more items in same horizontal space.
String code = showCode ? rcr.getConceptCode() : null;
String desc =
rcr.getEntityDescription() != null ? rcr.getEntityDescription().getContent() : null;
String nodeName = getNodeName(code, desc, false, "\n");
if (allNodes.containsKey(nodeName)) {
return allNodes.get(nodeName);
} else {
Node newNode = addNode();
newNode.setString("name", nodeName);
newNode.set("RCR", rcr);
allNodes.put(nodeName, newNode);
return newNode;
}
}
public void run() throws LBException {
ValueSetDefinition vsd = Util.promptForValueSetDefinition(message);
if (vsd != null) {
AbsoluteCodingSchemeVersionReferenceList acsvList = null;
Util.displayMessage("Now select Code System to use to resolve Value Set Definition");
CodingSchemeSummary css = Util.promptForCodeSystem();
if (css != null) {
acsvList = new AbsoluteCodingSchemeVersionReferenceList();
acsvList.addAbsoluteCodingSchemeVersionReference(
Constructors.createAbsoluteCodingSchemeVersionReference(
css.getCodingSchemeURI(), css.getRepresentsVersion()));
}
LexEVSValueSetDefinitionServices vsdServ =
LexEVSValueSetDefinitionServicesImpl.defaultInstance();
ResolvedValueSetDefinition rVSD = null;
try {
rVSD =
vsdServ.resolveValueSetDefinition(
new URI(vsd.getValueSetDefinitionURI()), null, acsvList, null, null);
} catch (URISyntaxException e) {
e.printStackTrace();
}
if (rVSD != null) {
Util.displayMessage(
"Member of Value Set Definition (" + vsd.getValueSetDefinitionURI() + ") are :");
ResolvedConceptReferencesIterator conceptItr = rVSD.getResolvedConceptReferenceIterator();
while (conceptItr.hasNext()) {
ResolvedConceptReference concept = conceptItr.next();
Util.displayMessage("Concept code : " + concept.getCode());
Util.displayMessage("\tCoding Scheme Name...: " + concept.getCodingSchemeName());
Util.displayMessage("\tCoding Scheme URI....: " + concept.getCodingSchemeURI());
Util.displayMessage("\tCoding Scheme Version: " + concept.getCodingSchemeVersion());
}
} else {
Util.displayMessage(
"No members found for Value Set Definition : '" + vsd.getValueSetDefinitionURI() + "'");
}
}
}
public void testNext() {
try {
LexBIGService lbs = ServiceHolder.instance().getLexBIGService();
CodedNodeSet cns = lbs.getCodingSchemeConcepts("NCI Thesaurus", null);
cns = cns.restrictToMatchingDesignations("heart", null, "startsWith", null);
ResolvedConceptReferencesIterator rcrl = cns.resolve(null, null, null, null, false);
String conceptCode = null;
while (rcrl.hasNext()) {
ResolvedConceptReference ref = rcrl.next();
String currentCode = ref.getConceptCode();
assertFalse(currentCode.equals(conceptCode));
conceptCode = currentCode;
}
} catch (Exception e) {
fail("Exception Thrown: " + e.getMessage());
e.printStackTrace();
}
}
/**
* Return list of Comments
*
* @param ref
* @return
*/
public Property[] getCommentValues(ResolvedConceptReference ref) {
return returnProperties(ref.getReferencedEntry().getComment());
}
/**
* Returns list of Child Concepts
*
* @param ref
* @return
*/
public Vector<String> getChildConcepts(ResolvedConceptReference ref) throws Exception {
String code = ref.getCode();
Vector<String> supconcepts = getAssociatedConcepts(code, false);
return supconcepts;
}
/**
* Return list of Definitions
*
* @param ref
* @return
*/
public Property[] getDefinitionValues(ResolvedConceptReference ref) {
return returnProperties(ref.getReferencedEntry().getDefinition());
}
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;
}