public CodeableConceptDt addTRCodingOrDisplay(Concept concept) {
CodeableConceptDt codeableConceptDt = addTRCoding(concept);
if (CollectionUtils.isEmpty(codeableConceptDt.getCoding())) {
CodingDt coding = codeableConceptDt.addCoding();
coding.setDisplay(concept.getName().getName());
}
return codeableConceptDt;
}
public CodeableConceptDt getTRValueSetCodeableConcept(
Concept concept, String valueSetURL, CodeableConceptDt codeableConcept) {
CodingDt coding = codeableConcept.addCoding();
if (null != idMappingsRepository.findByInternalId(concept.getUuid())) {
coding.setCode(getTRValueSetCode(concept));
coding.setSystem(valueSetURL);
}
coding.setDisplay(concept.getName().getName());
return codeableConcept;
}
public String getTRValueSetCode(Concept concept) {
for (ConceptMap mapping : concept.getConceptMappings()) {
if (mapping.getConceptMapType().getUuid().equals(ConceptMapType.SAME_AS_MAP_TYPE_UUID)) {
return mapping.getConceptReferenceTerm().getCode();
}
}
for (ConceptName conceptName : concept.getShortNames()) {
return conceptName.getName();
}
return concept.getName().getName();
}
private Concept mockConcept() {
QNameUtil qnames = QNameUtil.instance();
Concept mocked = mock(Concept.class);
try {
when(mocked.getName())
.thenReturn(qnames.createQNameInPreconstructedNamespace(CONCEPT_LOCALNAME));
} catch (Exception ex) {
throw new Error(ex);
}
return mocked;
}
private void addTRCodingForConcept(
Concept concept,
IdMappingsRepository idMappingsRepository,
CodeableConceptDt codeableConcept) {
IdMapping idMapping = idMappingsRepository.findByInternalId(concept.getUuid());
if (idMapping != null) {
addFHIRCoding(
codeableConcept,
idMapping.getExternalId(),
idMapping.getUri(),
concept.getName().getName());
}
}
private void addTRCodingsForReferenceTerms(
Concept concept,
IdMappingsRepository idMappingsRepository,
CodeableConceptDt codeableConcept,
ConceptMap mapping) {
ConceptReferenceTerm conceptReferenceTerm = mapping.getConceptReferenceTerm();
IdMapping idMapping = idMappingsRepository.findByInternalId(conceptReferenceTerm.getUuid());
if (idMapping != null) {
addFHIRCoding(
codeableConcept,
conceptReferenceTerm.getCode(),
idMapping.getUri(),
concept.getName().getName());
}
}
private void processMatchedConcepts(
List<Concept> matchedConcepts,
String matchedText,
int tokenPosn,
Map<Concept, Score> tokTable,
PrintWriter pw) {
// Increment match score of the matched concept and record information
// about where in the article it was found
for (Concept c : matchedConcepts) {
Score cnt = tokTable.get(c);
if (cnt == null) {
tokTable.put(c, new Score(tokenPosn));
} else {
cnt.addMatch(tokenPosn);
}
// Output the concept to the token file for debugging purposes
if (pw != null) {
pw.println(c.getName() + "<" + c.getKey() + ">:" + tokenPosn + ":TEXT=" + matchedText);
}
System.out.println(
c.getName() + "<" + c.getKey() + ">:" + tokenPosn + ":TEXT=" + matchedText);
}
}