private List<String> getRefTermAncestors(
UiSessionContext context, String id, Locale locale, ConceptSource conceptSource)
throws Exception {
ConceptService conceptService = (ConceptService) Context.getService(ConceptService.class);
ConceptManagementAppsService conceptManagementAppsService =
(ConceptManagementAppsService) Context.getService(ConceptManagementAppsService.class);
// there are no mappings so we need to send it through blank and let the user know
if (StringUtils.isEmpty(id) || StringUtils.isBlank(id) || id.contains("empty")) {
id = "0";
Set<ConceptReferenceTerm> parentTerms = new HashSet<ConceptReferenceTerm>();
Set<ConceptReferenceTerm> childTerms = new HashSet<ConceptReferenceTerm>();
return formatByRefTermForUIWithGson(conceptService, id, childTerms, parentTerms, locale);
}
Set<ConceptReferenceTerm> parentTerms =
conceptManagementAppsService.getRefTermParentReferenceTerms(
conceptService.getConceptReferenceTerm(Integer.parseInt(id)), conceptSource);
Set<ConceptReferenceTerm> childTerms =
conceptManagementAppsService.getRefTermChildReferenceTerms(
conceptService.getConceptReferenceTerm(Integer.parseInt(id)), conceptSource);
return formatByRefTermForUIWithGson(conceptService, id, childTerms, parentTerms, locale);
}
@Test
public void shouldAddNewDrugOrderWhenPrnIsTrueWIthNoDosageFrequencyOrDosageInstruction() {
EncounterTransaction.DrugOrder drugOrder =
new DrugOrderBuilder()
.withBasicValues("drug-uuid", "test-concept-uuid", today, today, 3, "", "")
.withPrn(true)
.build();
Concept drugConcept = new Concept(3);
OrderType drugOrderType = new OrderType("Drug Order", "this is a drug order type");
when(orderService.getAllOrderTypes()).thenReturn(asList(drugOrderType));
when(conceptService.getConceptByUuid("test-concept-uuid")).thenReturn(drugConcept);
Drug drug = new Drug();
drug.setName("test drug");
when(conceptService.getDrugByUuid("drug-uuid")).thenReturn(drug);
encounterDrugOrderServiceHelper.update(encounter, asList(drugOrder));
assertThat(encounter.getOrders().size(), is(1));
org.openmrs.DrugOrder order = (org.openmrs.DrugOrder) encounter.getOrders().iterator().next();
assertEquals(drugConcept, order.getConcept());
assertEquals(drugOrderType, order.getOrderType());
assertEquals(patient, order.getPatient());
assertEquals(encounter, order.getEncounter());
assertEquals(today, order.getStartDate());
assertEquals(today, order.getAutoExpireDate());
assertEquals(drug.getDisplayName(), order.getDrug().getDisplayName());
assertEquals(Double.valueOf(3), order.getDose());
assertEquals(true, order.getPrn());
assertEquals(null, order.getFrequency());
assertEquals(null, order.getUnits());
}
@Test
public void testParsingDispositions() throws Exception {
Concept admit =
new ConceptBuilder(
null,
conceptService.getConceptDatatypeByName("N/A"),
conceptService.getConceptClassByName("Misc"))
.addName("Admit")
.get();
when(emrConceptService.getConcept("test:admit")).thenReturn(admit);
Obs dispositionObs =
dispositionDescriptor.buildObsGroup(
new Disposition(
"emrapi.admit",
"Admit",
"test:admit",
Collections.<String>emptyList(),
Collections.<DispositionObs>emptyList()),
emrConceptService);
encounter.addObs(doNotGoToServiceToFormatMembers(dispositionObs));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(1));
assertThat(parsed.getObs().size(), is(0));
assertThat(path(parsed.getDispositions(), 0, "disposition"), is((Object) "Admit"));
assertThat(
path(parsed.getDispositions(), 0, "additionalObs"), is((Object) Collections.emptyList()));
}
@Test
public void shouldPurgeAConceptSource() throws Exception {
Assert.assertNotNull(service.getConceptSourceByUuid(getUuid()));
MockHttpServletRequest req = request(RequestMethod.DELETE, getURI() + "/" + getUuid());
req.addParameter("purge", "");
handle(req);
Assert.assertNull(service.getConceptSourceByUuid(getUuid()));
}
/**
* Processes requests to display a list of the current concept map types in the database
*
* @param model the {@link ModelMap} object
* @param request the {@link WebRequest} object
*/
@RequestMapping(method = RequestMethod.GET, value = CONCEPT_MAP_TYPE_LIST_URL)
public void showConceptMapTypeList(ModelMap model, WebRequest request) {
ConceptService conceptService = Context.getConceptService();
List<ConceptMapType> conceptMapTypeList = null;
conceptMapTypeList = conceptService.getConceptMapTypes(true, true);
model.addAttribute("conceptMapTypeList", conceptMapTypeList);
}
@Test
public void shouldRetireAConceptSource() throws Exception {
Assert.assertEquals(false, service.getConceptSourceByUuid(getUuid()).isRetired());
MockHttpServletRequest req = request(RequestMethod.DELETE, getURI() + "/" + getUuid());
req.addParameter("!purge", "");
final String reason = "none";
req.addParameter("reason", reason);
handle(req);
Assert.assertEquals(true, service.getConceptSourceByUuid(getUuid()).isRetired());
Assert.assertEquals(reason, service.getConceptSourceByUuid(getUuid()).getRetireReason());
}
/** 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;
}
/**
* This is called prior to displaying a form for the first time. It tells Spring the form/command
* object to load into the request
*
* @see
* org.springframework.web.servlet.mvc.AbstractFormController#formBackingObject(javax.servlet.http.HttpServletRequest)
*/
protected Object formBackingObject(HttpServletRequest request) throws ServletException {
// default empty Object
List<ConceptClass> conceptClassList = new Vector<ConceptClass>();
// only fill the Object if the user has authenticated properly
if (Context.isAuthenticated()) {
ConceptService cs = Context.getConceptService();
conceptClassList = cs.getAllConceptClasses();
}
return conceptClassList;
}
/**
* Takes a "program_id:list" where program_id is the id of the program that this collection is for
* (or not present, if it's a new program) and list is a space-separated list of concept ids. This
* class is a bit of a hack, because I don't know a better way to do this. -DJ The purpose is to
* retire and un-retire workflows where possible rather than deleting and creating them.
*/
public void setAsText(String text) throws IllegalArgumentException {
if (StringUtils.hasText(text)) {
ConceptService cs = Context.getConceptService();
ProgramWorkflowService pws = Context.getProgramWorkflowService();
try {
int ind = text.indexOf(":");
String progIdStr = text.substring(0, ind);
text = text.substring(ind + 1);
if (program == null)
// if a program wasn't passed in, try to look it up now
program = pws.getProgram(Integer.valueOf(progIdStr));
} catch (Exception ex) {
}
String[] conceptIds = text.split(" ");
Set<ProgramWorkflow> oldSet =
program == null ? new HashSet<ProgramWorkflow>() : program.getAllWorkflows();
Set<Integer> newConceptIds = new HashSet<Integer>();
for (String id : conceptIds) {
if (id.trim().length() == 0) continue;
log.debug("trying " + id);
newConceptIds.add(Integer.valueOf(id.trim()));
}
// go through oldSet and see what we need to keep and what we need to unvoid
Set<Integer> alreadyDone = new HashSet<Integer>();
for (ProgramWorkflow pw : oldSet) {
if (!newConceptIds.contains(pw.getConcept().getConceptId())) {
pw.setRetired(true);
} else if (pw.isRetired()) { // && newConceptIds.contains(pw...)
pw.setRetired(false);
}
alreadyDone.add(pw.getConcept().getConceptId());
}
// now add any new ones
newConceptIds.removeAll(alreadyDone);
for (Integer conceptId : newConceptIds) {
ProgramWorkflow pw = new ProgramWorkflow();
pw.setProgram(program);
pw.setConcept(cs.getConcept(conceptId));
oldSet.add(pw);
}
setValue(oldSet);
} else {
setValue(null);
}
}
private void verifySentinelData() {
// Verify a few pieces of sentinel data that should have been in the packages
assertNotNull(userService.getRole("Organizational: Doctor"));
MetadataUtils.existing(Role.class, RolePrivilegeMetadata._Role.ORGANIZATIONAL_DOCTOR);
MetadataUtils.existing(
Privilege.class, RolePrivilegeMetadata._Privilege.APP_COREAPPS_FIND_PATIENT);
assertThat(
conceptService.getConcept(5085).getUuid(), is("5085AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"));
assertThat(
conceptService.getConcept(159947).getUuid(), is("159947AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"));
assertThat(conceptService.getAllConcepts().size(), is(435));
}
@Test
public void testParsingDispositionWithTransferLocation() throws Exception {
Concept admit =
new ConceptBuilder(
null,
conceptService.getConceptDatatypeByName("N/A"),
conceptService.getConceptClassByName("Misc"))
.addName("Transfer")
.get();
when(emrConceptService.getConcept("test:transfer")).thenReturn(admit);
Obs dispositionObs =
dispositionDescriptor.buildObsGroup(
new Disposition(
"emrapi.transfer",
"Transfer",
"test:transfer",
Collections.<String>emptyList(),
Collections.<DispositionObs>emptyList()),
emrConceptService);
Obs transferLocationObs = new Obs();
transferLocationObs.setObsId(100);
transferLocationObs.setConcept(dispositionDescriptor.getInternalTransferLocationConcept());
transferLocationObs.setValueText("3");
dispositionObs.addGroupMember(transferLocationObs);
Location transferLocation = new Location();
transferLocation.setName("Outpatient clinic");
when(locationService.getLocation(3)).thenReturn(transferLocation);
encounter.addObs(doNotGoToServiceToFormatMembers(dispositionObs));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
SimpleObject expectedTransferLocationObject =
SimpleObject.create("obsId", transferLocationObs.getObsId());
expectedTransferLocationObject.put("question", "Transfer location");
expectedTransferLocationObject.put("answer", "Outpatient clinic");
List<SimpleObject> expectedAdditionalObsList = new ArrayList<SimpleObject>();
expectedAdditionalObsList.add(expectedTransferLocationObject);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(1));
assertThat(parsed.getObs().size(), is(0));
assertThat(path(parsed.getDispositions(), 0, "disposition"), is((Object) "Transfer"));
assertThat(
path(parsed.getDispositions(), 0, "additionalObs"), is((Object) expectedAdditionalObsList));
}
@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
public void should_fail_to_persist_if_conceptSetRow_introduces_cycle() throws Exception {
ConceptSetRow row1 = new ConceptSetRow();
row1.name = "ConceptA";
row1.conceptClass = "New Class";
row1.description = "some description";
List<KeyValue> children = new ArrayList<>();
children.add(new KeyValue("1", "Child1"));
children.add(new KeyValue("2", "Child2"));
row1.children = children;
Messages persistErrorMessages = conceptSetPersister.persist(row1);
assertTrue(persistErrorMessages.isEmpty());
Context.openSession();
Context.authenticate("admin", "test");
Concept persistedConcept = conceptService.getConceptByName(row1.name);
assertNotNull(persistedConcept);
ConceptSetRow row2 = new ConceptSetRow();
row2.name = "Child2";
row2.conceptClass = "New Class";
row2.description = "some description";
List<KeyValue> children1 = new ArrayList<>();
children1.add(new KeyValue("1", "ConceptA"));
children1.add(new KeyValue("2", "Child3"));
row2.children = children1;
Messages persistErrorMessages1 = conceptSetPersister.persist(row2);
assertFalse(persistErrorMessages1.isEmpty());
Context.flushSession();
Context.closeSession();
}
// loading MDS packages is expensive, so we do everything in a single test. This is typically not
// best practice, but it speeds the build significantly.
@Test
public void testEverything() throws Exception {
initializeInMemoryDatabase();
executeDataSet("requiredDataTestDataset.xml");
authenticate();
// we need to make sure that if emrapi has already created its concept source, we don't
// duplicate it
ConceptSource emrapiSource = new EmrApiActivator().createConceptSource(conceptService);
activator = new ReferenceMetadataActivator();
activator.willRefreshContext();
activator.contextRefreshed();
activator.willStart();
activator.started();
verifyMetadataPackagesConfigured();
verifySentinelData();
// verify there's only one concept source representing the emrapi module (and we haven't
// duplicated it)
int count = 0;
for (ConceptSource candidate : conceptService.getAllConceptSources()) {
if (candidate.getName().equals(emrapiSource.getName())) {
++count;
}
}
assertThat(count, is(1));
}
@Test
public void createNewOrderFromEtOrder() throws Exception {
Provider provider = mock(Provider.class);
handleEncounterProvider(provider);
Concept mrsBloodConcept = mock(Concept.class);
when(conceptService.getConceptByUuid("bloodConceptUuid")).thenReturn(mrsBloodConcept);
Date currentDate = new Date();
EncounterTransaction.Concept blood =
new EncounterTransaction.Concept("bloodConceptUuid", "blood");
EncounterTransaction.Order etOrder = new EncounterTransaction.Order();
etOrder.setConcept(blood);
etOrder.setDateCreated(currentDate);
OpenMRSOrderMapper orderMapper = new OpenMRSOrderMapper(orderService, conceptService);
Order order = orderMapper.map(etOrder, encounter);
Assert.assertEquals(encounter, order.getEncounter());
Assert.assertEquals(mrsBloodConcept, order.getConcept());
Assert.assertEquals(provider, order.getOrderer());
}
/**
* This is called prior to displaying a form for the first time. It tells Spring the form/command
* object to load into the request
*
* @see
* org.springframework.web.servlet.mvc.AbstractFormController#formBackingObject(javax.servlet.http.HttpServletRequest)
*/
protected Object formBackingObject(HttpServletRequest request) throws ServletException {
Drug drug = null;
if (Context.isAuthenticated()) {
ConceptService cs = Context.getConceptService();
String id = request.getParameter("drugId");
if (id != null) {
drug = cs.getDrug(Integer.valueOf(id));
}
}
if (drug == null) drug = new Drug();
return drug;
}
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;
}
private HashMap<ConceptReferenceTerm, List<Concept>> getAssociatedConceptsToRefTerms(
Set<ConceptReferenceTerm> terms) {
ConceptService conceptService = (ConceptService) Context.getService(ConceptService.class);
HashMap<ConceptReferenceTerm, List<Concept>> hmconceptsToRefTerms =
new HashMap<ConceptReferenceTerm, List<Concept>>();
for (ConceptReferenceTerm refTerm : terms) {
List<Concept> mappedConcept =
conceptService.getConceptsByMapping(
refTerm.getCode(), refTerm.getConceptSource().getName(), false);
hmconceptsToRefTerms.put(refTerm, mappedConcept);
}
return hmconceptsToRefTerms;
}
@Test
public void testStarted() throws Exception {
new EbolaExampleActivator().started();
assertThat(
conceptService.getConceptByUuid("162599AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA").getConceptId(),
is(162599));
}
@Test
public void testParsingDispositionWithDateOfDeath() throws Exception {
Concept admit =
new ConceptBuilder(
null,
conceptService.getConceptDatatypeByName("N/A"),
conceptService.getConceptClassByName("Misc"))
.addName("Death")
.get();
when(emrConceptService.getConcept("test:death")).thenReturn(admit);
Obs dispositionObs =
dispositionDescriptor.buildObsGroup(
new Disposition(
"emrapi.death",
"Death",
"test:death",
Collections.<String>emptyList(),
Collections.<DispositionObs>emptyList()),
emrConceptService);
Date dateOfDeath = new DateTime(2012, 2, 20, 10, 10, 10).toDate();
Obs dateOfDeathObs = new Obs();
dateOfDeathObs.setObsId(100);
dateOfDeathObs.setConcept(dispositionDescriptor.getDateOfDeathConcept());
dateOfDeathObs.setValueDate(dateOfDeath);
dispositionObs.addGroupMember(dateOfDeathObs);
encounter.addObs(doNotGoToServiceToFormatMembers(dispositionObs));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
SimpleObject expectedAdmissionLocationObject =
SimpleObject.create("obsId", dateOfDeathObs.getObsId());
expectedAdmissionLocationObject.put("question", "Date of death");
expectedAdmissionLocationObject.put("answer", "20 Feb 2012 10:10 AM");
List<SimpleObject> expectedAdditionalObsList = new ArrayList<SimpleObject>();
expectedAdditionalObsList.add(expectedAdmissionLocationObject);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(1));
assertThat(parsed.getObs().size(), is(0));
assertThat(path(parsed.getDispositions(), 0, "disposition"), is((Object) "Death"));
assertThat(
path(parsed.getDispositions(), 0, "additionalObs"), is((Object) expectedAdditionalObsList));
}
private List<String> formatByRefTermForUIWithGson(
ConceptService conceptService,
String id,
Set<ConceptReferenceTerm> childTerms,
Set<ConceptReferenceTerm> parentTerms,
Locale locale) {
List<String> data = new ArrayList<String>();
try {
Gson gson = new Gson();
ConceptReferenceTerm currentRefTerm =
conceptService.getConceptReferenceTerm(Integer.parseInt(id));
HashMap<ConceptReferenceTerm, List<Concept>> parentMappings =
getAssociatedConceptsToRefTerms(parentTerms);
HashMap<ConceptReferenceTerm, List<Concept>> childMappings =
getAssociatedConceptsToRefTerms(childTerms);
List<String> parents = new ArrayList<String>();
for (ConceptReferenceTerm term : parentTerms) {
List<Concept> mappedConcepts = parentMappings.get(term);
List<DataObject> mappedConceptsDOList = new ArrayList<DataObject>();
for (Concept concept : mappedConcepts) {
DataObject mappedConceptDataObject = simplifyConcept(concept, locale);
mappedConceptsDOList.add(mappedConceptDataObject);
}
DataObject refTermDataObject = simplifyReferenceTerm(term);
parents.add(gson.toJson(simplifyMapping(mappedConceptsDOList, refTermDataObject)));
}
List<String> children = new ArrayList<String>();
for (ConceptReferenceTerm term : childTerms) {
List<Concept> mappedConcepts = childMappings.get(term);
List<DataObject> mappedConceptsDOList = new ArrayList<DataObject>();
for (Concept concept : mappedConcepts) {
DataObject mappedConceptDataObject = simplifyConcept(concept, locale);
mappedConceptsDOList.add(mappedConceptDataObject);
}
DataObject refTermDataObject = simplifyReferenceTerm(term);
children.add(gson.toJson(simplifyMapping(mappedConceptsDOList, refTermDataObject)));
}
String currentTerm = gson.toJson(simplifyReferenceTerm(currentRefTerm));
DataObject ancestorsDataObject = simplifyAncestors(parents, children, currentTerm);
data.add(gson.toJson(ancestorsDataObject));
} catch (Exception e) {
log.error("Error generated", e);
}
return data;
}
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;
}
@Test
public void setPreferredConceptName_shouldTagShortName() throws Exception {
metadataDeployService.installBundles(Arrays.<MetadataBundle>asList(ebolaMetadata));
ConceptNameTag nameTag =
MetadataUtils.existing(ConceptNameTag.class, EbolaMetadata._ConceptNameTag.PREFERRED);
String uuid = "c607c80f-1ea9-4da3-bb88-6276ce8868dd";
assertThat(
conceptService.getConceptByUuid(uuid).getPreferredName(Locale.ENGLISH).getName(),
is("WEIGHT (KG)"));
new EbolaExampleActivator().setPreferredConceptName(conceptService, uuid, "WT");
assertThat(
conceptService.getConceptByUuid(uuid).getPreferredName(Locale.ENGLISH).getName(),
is("WEIGHT (KG)"));
assertThat(
conceptService.getConceptByUuid(uuid).findNameTaggedWith(nameTag).getName(), is("WT"));
}
private void verifyMetadataPackagesConfigured() throws Exception {
MetadataPackagesConfig config;
{
InputStream inputStream =
activator.getClass().getClassLoader().getResourceAsStream(MetadataUtil.PACKAGES_FILENAME);
String xml = IOUtils.toString(inputStream);
config =
Context.getSerializationService()
.getDefaultSerializer()
.deserialize(xml, MetadataPackagesConfig.class);
}
MetadataSharingService metadataSharingService =
Context.getService(MetadataSharingService.class);
// To catch the (common) case where someone gets the groupUuid wrong, we look for any installed
// packages that
// we are not expecting
List<String> groupUuids = new ArrayList<String>();
for (MetadataPackageConfig metadataPackage : config.getPackages()) {
groupUuids.add(metadataPackage.getGroupUuid());
}
for (ImportedPackage importedPackage : metadataSharingService.getAllImportedPackages()) {
if (!groupUuids.contains(importedPackage.getGroupUuid())) {
fail(
"Found a package with an unexpected groupUuid. Name: "
+ importedPackage.getName()
+ " , groupUuid: "
+ importedPackage.getGroupUuid());
}
}
for (MetadataPackageConfig metadataPackage : config.getPackages()) {
ImportedPackage installedPackage =
metadataSharingService.getImportedPackageByGroup(metadataPackage.getGroupUuid());
Integer actualVersion = installedPackage == null ? null : installedPackage.getVersion();
assertEquals(
"Failed to install "
+ metadataPackage.getFilenameBase()
+ ". Expected version: "
+ metadataPackage.getVersion()
+ " Actual version: "
+ actualVersion,
metadataPackage.getVersion(),
actualVersion);
}
// this doesn't strictly belong here, but we include it as an extra sanity check on the MDS
// module
for (Concept concept : conceptService.getAllConcepts()) {
ValidateUtil.validate(concept);
}
}
@Test
public void shouldGetAConceptSourceByName() throws Exception {
final String name = "SNOMED CT";
MockHttpServletRequest req = request(RequestMethod.GET, getURI() + "/" + name);
SimpleObject result = deserialize(handle(req));
ConceptSource conceptSource = service.getConceptSourceByName(name);
Assert.assertEquals(conceptSource.getUuid(), PropertyUtils.getProperty(result, "uuid"));
Assert.assertEquals(conceptSource.getName(), PropertyUtils.getProperty(result, "name"));
}
void updateDiagnosisStatus(
Obs diagnosisObs, BahmniDiagnosis bahmniDiagnosis, Concept bahmniDiagnosisStatusConcept) {
Obs obs = findOrCreateObs(diagnosisObs, bahmniDiagnosisStatusConcept);
if (bahmniDiagnosis.getDiagnosisStatusConcept() != null) {
Concept statusConcept =
conceptService.getConcept(bahmniDiagnosis.getDiagnosisStatusConcept().getName());
obs.setValueCoded(statusConcept);
addToObsGroup(diagnosisObs, obs);
}
}
@RequestMapping("/module/htmlformentry/drugSearch")
public void localizedMessage(@RequestParam("term") String query, HttpServletResponse response)
throws IOException {
List<Drug> drugs;
// we want to use a later API method from 1.8+ if it is available, so we need to access it via
// reflection
if (OpenmrsConstants.OPENMRS_VERSION_SHORT.startsWith("1.6")
|| OpenmrsConstants.OPENMRS_VERSION_SHORT.startsWith("1.7")) {
drugs =
conceptService.getDrugs(query); // this method returns retired drugs, so it is not ideal
} else {
try {
Object conceptService =
Context.getService(Context.loadClass("org.openmrs.api.ConceptService"));
Method getDrugsMethod =
conceptService
.getClass()
.getMethod(
"getDrugs",
String.class,
Concept.class,
boolean.class,
boolean.class,
boolean.class,
Integer.class,
Integer.class);
drugs =
(List<Drug>)
getDrugsMethod.invoke(
conceptService,
query,
null,
true,
false,
false,
0,
100); // this method excludes retired drugs
} catch (Exception ex) {
throw new RuntimeException(
"Unable to access ConceptService getDrugs method via reflection", ex);
}
}
List<Map<String, Object>> simplified = drugCompatibility.simplify(drugs);
response.setContentType("application/json");
response.setCharacterEncoding("UTF-8");
PrintWriter out = response.getWriter();
new ObjectMapper().writeValue(out, simplified);
}
static Obs jsonObservationToObs(
Object jsonObservation, Patient patient, Date encounterTime, Location location) {
Map observationObject = (Map) jsonObservation;
String questionUuid = (String) observationObject.get(QUESTION_UUID);
ConceptService conceptService = Context.getConceptService();
Concept questionConcept = conceptService.getConceptByUuid(questionUuid);
if (questionConcept == null) {
log.warn("Question concept not found: " + questionUuid);
return null;
}
Obs obs = new Obs(patient, questionConcept, encounterTime, location);
String answerUuid = (String) observationObject.get(ANSWER_UUID);
String answerDate = (String) observationObject.get(ANSWER_DATE);
String answerNumber = (String) observationObject.get(ANSWER_NUMBER);
if (answerUuid != null) {
Concept answerConcept = conceptService.getConceptByUuid(answerUuid);
if (answerConcept == null) {
log.warn("Answer concept not found: " + answerUuid);
return null;
}
obs.setValueCoded(answerConcept);
} else if (answerDate != null) {
try {
obs.setValueDate(Utils.YYYYMMDD_UTC_FORMAT.parse(answerDate));
} catch (ParseException e) {
log.warn("Invalid date answer: " + answerDate);
return null;
}
} else if (observationObject.containsKey(ANSWER_NUMBER)) {
try {
obs.setValueNumeric(Double.parseDouble(answerNumber));
} catch (IllegalArgumentException e) {
log.warn("Invalid numeric answer: " + answerUuid);
return null;
}
} else {
log.warn("Invalid answer type: " + observationObject);
return null;
}
return obs;
}
@Test
public void shouldEditAConceptSource() throws Exception {
final String newName = "updated name";
SimpleObject conceptSource = new SimpleObject();
conceptSource.add("name", newName);
String json = new ObjectMapper().writeValueAsString(conceptSource);
MockHttpServletRequest req = request(RequestMethod.POST, getURI() + "/" + getUuid());
req.setContent(json.getBytes());
handle(req);
Assert.assertEquals(newName, service.getConceptSourceByUuid(getUuid()).getName());
}
@Test
public void shouldGetAConceptSourceByUuid() throws Exception {
MockHttpServletRequest req = request(RequestMethod.GET, getURI() + "/" + getUuid());
SimpleObject result = deserialize(handle(req));
ConceptSource conceptSource = service.getConceptSourceByUuid(getUuid());
Assert.assertEquals(conceptSource.getUuid(), PropertyUtils.getProperty(result, "uuid"));
Assert.assertEquals(conceptSource.getName(), PropertyUtils.getProperty(result, "name"));
Assert.assertEquals(conceptSource.getHl7Code(), PropertyUtils.getProperty(result, "hl7Code"));
Assert.assertEquals(
conceptSource.getDescription(), PropertyUtils.getProperty(result, "description"));
}