/** 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"));
}
}
}
/*
* (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 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;
}