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;
}
@Test
@Verifies(
value = "should return a list consisting of active, not retired, states",
method = "getPossibleNextStates")
public void getPossibleNextStates_shouldReturnNonRetiredStates() throws Exception {
executeDataSet(PROGRAM_NEXT_STATES_XML);
Integer patient = 11;
Integer workflow = 501;
Vector<ListItem> possibleNextStates;
/* retire a workflow state */
PatientProgram pp = Context.getProgramWorkflowService().getPatientProgram(patient);
ProgramWorkflow pw = pp.getProgram().getWorkflow(workflow);
Set<ProgramWorkflowState> pwss = pw.getStates();
for (ProgramWorkflowState pws : pwss) {
Concept cp = pws.getConcept();
ConceptName cn = cp.getName();
if (cn != null) {
String cnn = cn.getName();
if (cnn.equalsIgnoreCase("Test State 3")) {
pws.setRetired(true);
}
}
}
possibleNextStates = dwrProgramWorkflowService.getPossibleNextStates(patient, workflow);
assertFalse(possibleNextStates.isEmpty());
assertEquals(2, possibleNextStates.size());
}
/**
* Builds a coded result from an observation
*
* @param obs
*/
public Result(Obs obs) {
this(
obs.getObsDatetime(),
null,
obs.getValueAsBoolean(),
obs.getValueCoded(),
obs.getValueDatetime(),
obs.getValueNumeric(),
obs.getValueText(),
obs);
Concept concept = obs.getConcept();
ConceptDatatype conceptDatatype = null;
if (concept != null) {
conceptDatatype = concept.getDatatype();
if (conceptDatatype == null) {
return;
}
if (conceptDatatype.isCoded()) {
this.datatype = Datatype.CODED;
} else if (conceptDatatype.isNumeric()) {
this.datatype = Datatype.NUMERIC;
} else if (conceptDatatype.isDate()) {
this.datatype = Datatype.DATETIME;
} else if (conceptDatatype.isText()) {
this.datatype = Datatype.TEXT;
} else if (conceptDatatype.isBoolean()) {
this.datatype = Datatype.BOOLEAN;
}
}
}
/**
* Gets a concept by an identifier (mapping or UUID)
*
* @param identifier the identifier
* @return the concept
* @throws org.openmrs.module.metadatadeploy.MissingMetadataException if the concept could not be
* found
*/
public static Concept getConcept(String identifier) {
Concept concept;
if (identifier.contains(":")) {
String[] tokens = identifier.split(":");
concept = Context.getConceptService().getConceptByMapping(tokens[1].trim(), tokens[0].trim());
} else {
// Assume it's a UUID
concept = Context.getConceptService().getConceptByUuid(identifier);
}
if (concept == null) {
throw new MissingMetadataException(Concept.class, identifier);
}
// getConcept doesn't always return ConceptNumeric for numeric concepts
if (concept.getDatatype().isNumeric() && !(concept instanceof ConceptNumeric)) {
concept = Context.getConceptService().getConceptNumeric(concept.getId());
if (concept == null) {
throw new MissingMetadataException(ConceptNumeric.class, identifier);
}
}
return concept;
}
/** @param concept the concept to set */
public void setConcept(Concept concept) {
this.concept = concept;
if (concept != null) {
setName(concept.getName().getName());
setDescription(concept.getDisplayString());
}
}
private Concept newConcept(ConceptDatatype conceptDatatype, String conceptUuid) {
Concept concept = new Concept();
concept.setDatatype(conceptDatatype);
concept.setUuid(conceptUuid);
when(conceptService.getConceptByUuid(conceptUuid)).thenReturn(concept);
return concept;
}
/** @see {@link HtmlFormEntryUtil#getConcept(String)} mapping test */
@Test
@Verifies(value = "should find a concept by its mapping", method = "getConcept(String)")
public void getConcept_shouldFindAConceptByItsMapping() throws Exception {
String id = "XYZ:HT";
Concept cpt = HtmlFormEntryUtil.getConcept(id);
Assert.assertEquals("XYZ", cpt.getConceptMappings().iterator().next().getSource().getName());
Assert.assertEquals("HT", cpt.getConceptMappings().iterator().next().getSourceCode());
}
/**
* @see BaseOpenmrsDatatype#doGetTextSummary(Object)
* @should use the name in summary instance
*/
@Override
public Summary doGetTextSummary(Concept concept) {
String name = "";
if (concept.getName() != null) {
name = concept.getName().getName();
}
return new CustomDatatype.Summary(name, true);
}
private void assertMappedCorrectly() {
Concept concept = Context.getConceptService().getConceptByUuid("23423a2982236623");
if (concept.isNumeric()) {
Assert.fail();
}
Assert.assertEquals("N/A", concept.getDatatype().getName());
}
private Concept setupConcept(ConceptService mockConceptService, String name, String mappingCode) {
Concept concept = new Concept();
concept.addName(new ConceptName(name, Locale.ENGLISH));
concept.addConceptMapping(
new ConceptMap(new ConceptReferenceTerm(emrConceptSource, mappingCode, null), sameAs));
when(mockConceptService.getConceptByMapping(mappingCode, emrConceptSource.getName()))
.thenReturn(concept);
return concept;
}
/**
* Auto generated method comment
*
* @param conceptId
* @return
*/
public static String getConceptName(Integer conceptId) {
try {
if (null == conceptId) return "-";
Concept concept = Context.getConceptService().getConcept(conceptId);
return (concept != null) ? concept.getDisplayString() : "-";
} catch (Exception e) {
log.info(e.getMessage());
return "-";
}
}
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;
}
/**
* Auto generated method comment
*
* @param conceptId
* @return
*/
public static String getConceptNameByIdAsString(String conceptId) {
String res = "-";
try {
if (conceptId.trim().compareTo("") == 0) return "-";
Concept concept = Context.getConceptService().getConcept(Integer.parseInt(conceptId));
res = (concept != null) ? concept.getDisplayString() : "-";
} catch (Exception e) {
log.info(e.getMessage());
}
return res;
}
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();
}
/**
* Auto generated method comment
*
* @param conceptId
* @return
*/
public static String checkIfConceptExistByIdAsString(String conceptId) {
String res = "";
try {
if (conceptId.trim().compareTo("") == 0) return res;
Concept concept = Context.getConceptService().getConcept(Integer.parseInt(conceptId));
res = (concept != null) ? "" + concept.getConceptId() : "";
} catch (Exception e) {
log.info(e.getMessage());
}
return res;
}
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());
}
}
/** Gets or creates a Concept with a given UUID and name. */
public static Concept getConcept(String name, String uuid, String typeUuid) {
ConceptService conceptService = Context.getConceptService();
Concept concept = conceptService.getConceptByUuid(uuid);
if (concept == null) {
concept = new Concept();
concept.setUuid(uuid);
concept.setShortName(new ConceptName(name, new Locale("en")));
concept.setDatatype(conceptService.getConceptDatatypeByUuid(typeUuid));
concept.setConceptClass(conceptService.getConceptClassByUuid(ConceptClass.MISC_UUID));
conceptService.saveConcept(concept);
}
return concept;
}
@Test
public void addSetMembers() throws Exception {
ConceptSetRow conceptRow = new ConceptSetRow();
conceptRow.name = "New concept";
conceptRow.conceptClass = "New Class";
conceptRow.description = "some description";
List<KeyValue> children = new ArrayList<>();
children.add(new KeyValue("1", "Child1"));
children.add(new KeyValue("2", "Child2"));
conceptRow.children = children;
Messages persistErrorMessages = conceptSetPersister.persist(conceptRow);
assertTrue(persistErrorMessages.isEmpty());
Context.openSession();
Context.authenticate("admin", "test");
Concept persistedConcept = conceptService.getConceptByName(conceptRow.name);
assertNotNull(persistedConcept);
assertEquals(conceptRow.name, persistedConcept.getName(Context.getLocale()).getName());
assertEquals(conceptRow.conceptClass, persistedConcept.getConceptClass().getName());
assertEquals("some description", persistedConcept.getDescription().getDescription());
assertEquals(2, persistedConcept.getSetMembers().size());
assertEquals("some description", persistedConcept.getDescription().getDescription());
assertEquals(0, persistedConcept.getSynonyms().size());
assertTrue(persistedConcept.isSet());
Context.flushSession();
Context.closeSession();
}
@Test
@Verifies(
value = "shouldSetTheValueComplexOfObsIfConceptIsComplex",
method = "createObs(Concept concept, Object value, Date datetime, String accessionNumber)")
public void createObs_shouldSetTheValueComplexOfObsIfConceptIsComplex() {
ComplexData complexData = new ComplexData("test", null);
Concept c = new Concept();
ConceptDatatype cd = new ConceptDatatype();
cd.setUuid(HtmlFormEntryConstants.COMPLEX_UUID);
c.setDatatype(cd);
Obs o = HtmlFormEntryUtil.createObs(c, complexData, null, null);
Assert.assertEquals(o.getValueComplex(), complexData.getTitle());
}
/**
* @return string representation of the result. For non-text results, this will either be the
* overridden text value (if specifically defined) or a string representation of the default
* datatype value. If the result is a list, then the string representation of all members a
* joined with commas.
*/
public String toString() {
if (isSingleResult()) {
if (datatype == null) {
return valueText == null ? "" : valueText;
}
switch (datatype) {
case BOOLEAN:
return (valueBoolean ? "true" : "false");
case CODED:
return (valueCoded == null ? "" : valueCoded.getBestName(Context.getLocale()).getName());
case DATETIME:
return (valueDatetime == null ? "" : Context.getDateFormat().format(valueDatetime));
case NUMERIC:
return (valueNumeric == null ? "" : String.valueOf(valueNumeric));
case TEXT:
return (valueText == null ? "" : valueText);
default:
return valueText;
}
}
StringBuffer s = new StringBuffer();
for (Result r : this) {
if (s.length() > 0) {
s.append(",");
}
s.append(r.toString());
}
return s.toString();
}
@Test
public void testController_createdProperPriorDiagnoses() throws Exception {
EncounterDiagnosesFragmentController controller = new EncounterDiagnosesFragmentController();
ConceptName specificName = new ConceptName("Specific Name", Context.getLocale());
specificName.setId(1);
specificName.setLocalePreferred(true);
Concept conceptForSpecificName = new Concept();
conceptForSpecificName.setId(2);
conceptForSpecificName.addName(specificName);
Concept nonSpecificConcept = new Concept();
nonSpecificConcept.setId(3);
ConceptName nonSpecificConceptName =
new ConceptName("Non-specific concept", Context.getLocale());
nonSpecificConceptName.setId(4);
nonSpecificConceptName.setLocalePreferred(true);
nonSpecificConcept.addName(nonSpecificConceptName);
List<Diagnosis> diagnoses = new ArrayList<Diagnosis>();
diagnoses.add(new Diagnosis(new CodedOrFreeTextAnswer(specificName), Diagnosis.Order.PRIMARY));
diagnoses.add(
new Diagnosis(new CodedOrFreeTextAnswer(nonSpecificConcept), Diagnosis.Order.SECONDARY));
diagnoses.add(
new Diagnosis(new CodedOrFreeTextAnswer("Unknown Disease"), Diagnosis.Order.SECONDARY));
for (Diagnosis d : diagnoses) {
d.setExistingObs(new Obs());
}
FragmentModel model = new FragmentModel();
controller.controller(new TestUiUtils(), null, diagnoses, model);
assertThat(((List<String>) model.getAttribute("jsForExisting")).size(), is(0));
List<String> jsForPrior = (List<String>) model.getAttribute("jsForPrior");
assertThat(
jsForPrior.get(0),
is(
"{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer({\"word\":null,\"conceptName\":{\"id\":1,\"uuid\":\""
+ specificName.getUuid()
+ "\",\"conceptNameType\":\"FULLY_SPECIFIED\",\"name\":\"Specific Name\"},\"concept\":{\"id\":2,\"uuid\":\""
+ conceptForSpecificName.getUuid()
+ "\",\"conceptMappings\":[],\"preferredName\":\"Specific Name\"}}), confirmed: false, primary: true, existingObs: null }"));
assertThat(
jsForPrior.get(1),
is(
"{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer({\"word\":null,\"conceptName\":null,\"concept\":{\"id\":3,\"uuid\":\""
+ nonSpecificConcept.getUuid()
+ "\",\"conceptMappings\":[],\"preferredName\":\"Non-specific concept\"}}), confirmed: false, primary: false, existingObs: null }"));
assertThat(
jsForPrior.get(2),
is(
"{ diagnosis: diagnoses.CodedOrFreeTextConceptAnswer('Unknown Disease'), confirmed: false, primary: false, existingObs: null }"));
}
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 DataObject simplifyConcept(Concept concept, Locale locale) throws Exception {
List<Object> propertyNamesAndValues = new ArrayList<Object>();
ConceptName preferredName = concept.getPreferredName(locale);
propertyNamesAndValues.add("conceptId");
propertyNamesAndValues.add(Integer.toString((concept.getConceptId())));
if (preferredName != null && preferredName.getName() != null) {
propertyNamesAndValues.add("conceptName");
propertyNamesAndValues.add(preferredName.getName());
} else if (preferredName == null && concept.getName() != null) {
propertyNamesAndValues.add("conceptName");
propertyNamesAndValues.add(concept.getName().getName());
}
DataObject dataObject = DataObject.create(propertyNamesAndValues);
return dataObject;
}
private Obs findOrCreateObs(Obs diagnosisObs, Concept concept) {
for (Obs o : diagnosisObs.getGroupMembers()) {
if (concept.equals(o.getConcept())) {
return o;
}
}
Obs obs = new Obs();
obs.setConcept(concept);
return obs;
}
public ConceptSearchResult(Concept con) {
this.conceptId = con.getConceptId();
if (con.getName() != null) {
this.conceptName = con.getName().getName();
}
if (con.getDescription() != null) {
this.conceptDescription = con.getDescription().getDescription();
}
if (con.getConceptClass() != null) {
this.conceptClass = con.getConceptClass().getName();
}
if (con.getDatatype() != null) {
this.conceptDatatype = con.getDatatype().getName();
}
this.otherNames = new Vector<String>();
for (ConceptName cn : con.getNames()) {
this.otherNames.add(cn.getName());
}
}
@Test
public void shouldSaveOrdersToEncounterWithExistingOrders() throws ParseException {
EmrOrderServiceImpl_1_10 emrOrderService =
new EmrOrderServiceImpl_1_10(openMRSDrugOrderMapper, encounterService, openMRSOrderMapper);
EncounterTransaction.Order order1 =
new OrderBuilder().withConceptUuid("concept-uuid1").withComment("Comment").build();
EncounterTransaction.Order order2 =
new OrderBuilder().withConceptUuid("concept-uuid2").withComment("Comment").build();
Order mappedOrder1 = new Order();
Concept concept = new Concept();
concept.setUuid("concept-uuid1");
mappedOrder1.setConcept(concept);
mappedOrder1.setCommentToFulfiller("Comment");
Order mappedOrder2 = new Order();
concept = new Concept();
concept.setUuid("concept-uuid2");
mappedOrder2.setConcept(concept);
mappedOrder2.setCommentToFulfiller("Comment");
Order existingOrder1 = new Order();
Order existingOrder2 = new Order();
Encounter encounter = new Encounter();
encounter.addOrder(existingOrder1);
encounter.addOrder(existingOrder2);
when(openMRSOrderMapper.map(order1, encounter)).thenReturn(mappedOrder1);
when(openMRSOrderMapper.map(order2, encounter)).thenReturn(mappedOrder2);
emrOrderService.saveOrders(Arrays.asList(order1, order2), encounter);
ArgumentCaptor<Encounter> encounterArgumentCaptor = ArgumentCaptor.forClass(Encounter.class);
verify(encounterService).saveEncounter(encounterArgumentCaptor.capture());
Encounter savedEncounter = encounterArgumentCaptor.getValue();
ArrayList<org.openmrs.Order> savedOrders =
new ArrayList<org.openmrs.Order>(savedEncounter.getOrders());
assertThat(savedOrders.size(), is(4));
assertTrue(existsInOrdersList(mappedOrder1, savedOrders));
assertTrue(existsInOrdersList(mappedOrder2, savedOrders));
}
/**
* @return true if result contains a coded value with the given concept id (if the result is a
* list, then returns true if <em>any</em> member has a matching coded value)
*/
public boolean containsConcept(Integer conceptId) {
if (isSingleResult()) {
return (valueCoded != null && valueCoded.getConceptId().equals(conceptId));
}
for (Result r : this) {
if (r.containsConcept(conceptId)) {
return true;
}
}
return false;
}
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;
}
@Test
public void setPreferredConceptName_shouldSetPreferredName() throws Exception {
metadataDeployService.installBundles(Arrays.<MetadataBundle>asList(ebolaMetadata));
ConceptNameTag nameTag =
MetadataUtils.existing(ConceptNameTag.class, EbolaMetadata._ConceptNameTag.PREFERRED);
String uuid = "c607c80f-1ea9-4da3-bb88-6276ce8868dd";
Concept weight = conceptService.getConceptByUuid(uuid);
weight.addName(new ConceptName("Weight", Locale.ENGLISH));
conceptService.saveConcept(weight);
assertThat(
conceptService.getConceptByUuid(uuid).getPreferredName(Locale.ENGLISH).getName(),
is("WEIGHT (KG)"));
new EbolaExampleActivator().setPreferredConceptName(conceptService, uuid, "Weight");
assertThat(
conceptService.getConceptByUuid(uuid).getPreferredName(Locale.ENGLISH).getName(),
is("Weight"));
assertThat(
conceptService.getConceptByUuid(uuid).findNameTaggedWith(nameTag).getName(), is("Weight"));
}
/** @see java.lang.Object#equals(java.lang.Object) */
@Override
public boolean equals(Object obj) {
if (obj == null || !(obj instanceof Result)) {
return false;
}
Result r = (Result) obj;
if (EmptyResult.class.isAssignableFrom(r.getClass()) && this.isEmpty()) {
return true;
}
if (EmptyResult.class.isAssignableFrom(this.getClass()) && r.isEmpty()) {
return true;
}
if (isSingleResult() && r.isSingleResult()) {
if (datatype == null) {
return false;
}
// both are single results
switch (datatype) {
case BOOLEAN:
return (valueBoolean.equals(r.valueBoolean));
case CODED:
return (valueCoded.equals(r.valueCoded));
case DATETIME:
return (valueDatetime.equals(r.valueDatetime));
case NUMERIC:
return (valueNumeric.equals(r.valueNumeric));
case TEXT:
return (valueText.equals(r.valueText));
default:
return false;
}
}
if (isSingleResult() || r.isSingleResult()) {
// we already know they're not both single results, so if one is
// single, it's not a match
return false;
}
if (this.size() != r.size()) {
return false;
}
// at this point, we have two results that are lists, so members must
// match exactly
for (int i = 0; i < this.size(); i++) {
if (!this.get(i).equals(r.get(i))) {
return false;
}
}
return true;
}
