private Obs getObsGroup() {
ConceptDatatype datatype = new ConceptDatatype();
datatype.setUuid(ConceptDatatype.CODED_UUID);
datatype.setHl7Abbreviation(ConceptDatatype.CODED);
Concept concept = new Concept(1);
concept.setDatatype(datatype);
concept.addName(new ConceptName("MedSet", Locale.ENGLISH));
ConceptSource source = new ConceptSource();
source.setName("LOCAL");
ConceptMap map = new ConceptMap();
map.setSourceCode("100");
map.setSource(source);
concept.addConceptMapping(map);
Date dateCreated = new Date(213231421890234L);
Obs obs = new Obs(1);
obs.setConcept(concept);
obs.setDateCreated(dateCreated);
return obs;
}
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();
}
public CodeableConceptDt addTRCoding(Concept concept) {
CodeableConceptDt codeableConcept = new CodeableConceptDt();
Collection<ConceptMap> conceptMappings = concept.getConceptMappings();
for (ConceptMap mapping : conceptMappings) {
if (mapping.getConceptMapType().getUuid().equals(ConceptMapType.SAME_AS_MAP_TYPE_UUID)) {
addTRCodingsForReferenceTerms(concept, idMappingsRepository, codeableConcept, mapping);
}
}
addTRCodingForConcept(concept, idMappingsRepository, codeableConcept);
return codeableConcept;
}
public List<String> getAncestors(
UiSessionContext context,
@RequestParam("termId") String termId,
@RequestParam("conceptId") String conceptId,
@RequestParam("updateBy") String updateBy)
throws Exception {
Locale locale = context.getLocale();
ConceptService conceptService = (ConceptService) Context.getService(ConceptService.class);
ConceptManagementAppsProperties conceptManagementAppsProperties =
new ConceptManagementAppsProperties();
ConceptSource conceptSource =
conceptService.getConceptSourceByUuid(
conceptManagementAppsProperties.getSnomedCTConceptSourceUuidGlobalProperty(
ConceptManagementAppsConstants.SNOMED_CT_CONCEPT_SOURCE_UUID_GP));
if (StringUtils.equals(updateBy, "conceptUpdate")) {
Collection<ConceptMap> mappings =
conceptService.getConcept(Integer.parseInt(conceptId)).getConceptMappings();
for (ConceptMap conceptMap : mappings) {
if (StringUtils.equals(
conceptMap.getConceptReferenceTerm().getConceptSource().getUuid(),
conceptSource.getUuid())
&& StringUtils.equals(
conceptMap.getConceptMapType().getUuid(),
ConceptManagementAppsConstants.SAME_AS_CONCEPT_MAP_TYPE_UUID)) {
termId =
Integer.toString(conceptMap.getConceptReferenceTerm().getConceptReferenceTermId());
}
}
return getRefTermAncestors(context, termId, locale, conceptSource);
} else {
return getRefTermAncestors(context, termId, locale, conceptSource);
}
}
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());
}
}
/**
* Gets the display string for a concept map.
*
* @param conceptMap the concept map object.
* @return the display string.
*/
@Override
@PropertyGetter("display")
public String getDisplayString(ConceptMap conceptMap) {
if (conceptMap.getConceptReferenceTerm() == null
|| conceptMap.getConceptReferenceTerm().getConceptSource() == null) {
return "";
}
String display =
conceptMap.getConceptReferenceTerm().getConceptSource().getName()
+ ": "
+ conceptMap.getConceptReferenceTerm().getCode();
if (!StringUtils.isBlank(conceptMap.getConceptReferenceTerm().getName())) {
display += " (" + conceptMap.getConceptReferenceTerm().getName() + ")";
}
return display;
}
@Test
public void shouldEvaluateOBRORUR01TemplateForOBSGroup() throws Exception {
// given
Encounter encounter = new Encounter();
Date date = new Date();
encounter.setEncounterDatetime(date);
encounter.setUuid("ENCOUNTER UUID");
EncounterType encounterType = new EncounterType();
encounterType.setName("ENCOUNTER TYPE NAME");
encounter.setEncounterType(encounterType);
Location location = new Location(1);
location.setUuid("LOCATION UUID");
location.setName("LOCATION NAME");
encounter.setLocation(location);
Person provider = new Person(1);
provider.setUuid("PROVIDER UUID");
provider.addName(
new PersonName("PROVIDER GIVENNAME", "PROVIDER MIDDLENAME", "PROVIDER FAMILYNAME"));
encounter.setProvider(provider);
ConceptSource source = new ConceptSource();
source.setName("AMPATH");
ConceptMap map = new ConceptMap();
map.setSourceCode("200");
map.setSource(source);
ConceptDatatype datatype = new ConceptDatatype();
datatype.setUuid(ConceptDatatype.NUMERIC_UUID);
datatype.setHl7Abbreviation(ConceptDatatype.NUMERIC);
ConceptNumeric concept = new ConceptNumeric();
concept.setDatatype(datatype);
concept.addConceptMapping(map);
concept.addName(new ConceptName("NumericConcept", Locale.ENGLISH));
concept.setUnits("mg");
Date dateCreated = new Date(213231421890234L);
Obs obs = new Obs(2);
obs.setConcept(concept);
obs.setDateCreated(dateCreated);
obs.setValueNumeric(10d);
obs.setObsGroup(getObsGroup());
obs.getObsGroup().addGroupMember(obs);
encounter.addObs(obs);
obs = new Obs(3);
obs.setConcept(concept);
obs.setDateCreated(dateCreated);
obs.setValueNumeric(23d);
encounter.addObs(obs);
Map<String, Object> bindings = new HashMap<String, Object>();
bindings.put("encounter", encounter);
bindings.put("implementationId", "MVP");
// when
HL7Template hl7Template = hl7QueryService.getHL7TemplateByName("Generic Obs Group");
String evaluatedTemplate = hl7QueryService.evaluateTemplate(hl7Template, bindings);
// then
evaluatedTemplate = StringUtils.deleteWhitespace(evaluatedTemplate);
Assert.assertEquals(
"<ORU_R01.ORDER_OBSERVATION><OBR><OBR.1>0</OBR.1><OBR.4><CE.1>100</CE.1>"
+ "<CE.2>MEDICALRECORDOBSERVATIONS</CE.2><CE.3>LOCAL</CE.3></OBR.4><OBR.18>0</OBR.18>"
+ "<OBR.29><EIP.2><EI.3>ENCOUNTERUUID</EI.3></EIP.2></OBR.29></OBR><ORU_R01.OBSERVATION>"
+ "<OBX><OBX.1>1</OBX.1><OBX.2>NM</OBX.2><OBX.3><CE.1>200</CE.1><CE.2>NumericConcept</CE.2>"
+ "<CE.3>AMPATH</CE.3></OBX.3><OBX.5>23.0</OBX.5><OBX.6><CE.1>mg</CE.1><CE.3>UCUM</CE.3></OBX.6>"
+ "<OBX.14><TS.1>"
+ new HL7TemplateFunctions().formatDate(dateCreated, null)
+ "</TS.1>"
+ "</OBX.14></OBX></ORU_R01.OBSERVATION></ORU_R01.ORDER_OBSERVATION>"
+ "<ORU_R01.ORDER_OBSERVATION><OBR><OBR.1>2</OBR.1><OBR.4><CE.1>100</CE.1><CE.2>MedSet</CE.2>"
+ "<CE.3>LOCAL</CE.3></OBR.4><OBR.18>0</OBR.18><OBR.29><EIP.2><EI.3>ENCOUNTERUUID</EI.3></EIP.2></OBR.29"
+ "></OBR><ORU_R01.OBSERVATION><OBX><OBX.1>2</OBX.1><OBX.2>NM</OBX.2><OBX.3><CE.1>200</CE.1>"
+ "<CE.2>NumericConcept</CE.2><CE.3>AMPATH</CE.3></OBX.3><OBX.5>10.0</OBX.5><OBX.6><CE.1>mg</CE.1>"
+ "<CE.3>UCUM</CE.3></OBX.6><OBX.14><TS.1>"
+ new HL7TemplateFunctions().formatDate(dateCreated, null)
+ "</TS.1></OBX.14></OBX></ORU_R01.OBSERVATION></ORU_R01.ORDER_OBSERVATION>",
evaluatedTemplate);
}