@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()));
}
private Encounter buildEncounter(
EncounterType encounterType,
Patient patient,
Location location,
Form form,
Date when,
List<Obs> obsToCreate,
List<Order> ordersToCreate) {
Encounter encounter = new Encounter();
encounter.setPatient(patient);
encounter.setEncounterType(encounterType);
encounter.setLocation(location);
encounter.setForm(form);
encounter.setEncounterDatetime(when);
if (obsToCreate != null) {
for (Obs obs : obsToCreate) {
obs.setObsDatetime(new Date());
encounter.addObs(obs);
}
}
if (ordersToCreate != null) {
for (Order order : ordersToCreate) {
encounter.addOrder(order);
}
}
return encounter;
}
/**
* Adds a new encounter with the given observations and orders.
*
* @param observations a list of observations
* @param orderUuids a list of order UUIDs
* @param patient the patient for whom to add the encounter
* @param encounterTime the time of the encounter
* @param changeMessage a message to be recorded with the observation
* @param encounterTypeName the OpenMRS name for the encounter type, configured in OpenMRS
* @param locationUuid the UUID of the location where the encounter happened
*/
public static Encounter addEncounter(
List observations,
List orderUuids,
Patient patient,
Date encounterTime,
String changeMessage,
String encounterTypeName,
String locationUuid) {
// OpenMRS will reject the encounter if the time is in the past, even if
// the client's clock is off by only one millisecond; work around this.
encounterTime = Utils.fixEncounterDateTime(encounterTime);
EncounterService encounterService = Context.getEncounterService();
final Location location = Context.getLocationService().getLocationByUuid(locationUuid);
if (location == null) {
throw new InvalidObjectDataException("Location not found: " + locationUuid);
}
EncounterType encounterType = encounterService.getEncounterType(encounterTypeName);
if (encounterType == null) {
throw new InvalidObjectDataException("Encounter type not found: " + encounterTypeName);
}
List<Obs> obsList = new ArrayList<>();
if (observations != null) {
for (Object observation : observations) {
obsList.add(jsonObservationToObs(observation, patient, encounterTime, location));
}
}
if (orderUuids != null) {
for (Object item : orderUuids) {
obsList.add(orderUuidToObs((String) item, patient, encounterTime, location));
}
}
// Write the encounter and all the observations to the database.
Encounter encounter = new Encounter();
encounter.setEncounterDatetime(encounterTime);
encounter.setPatient(patient);
encounter.setLocation(location);
encounter.setEncounterType(encounterType);
encounter = encounterService.saveEncounter(encounter);
ObsService obsService = Context.getObsService();
for (Obs obs : obsList) {
if (obs != null) {
encounter.addObs(obs);
obsService.saveObs(obs, changeMessage);
}
}
return encounter;
}
@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 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));
}
@Test
public void testParsingDiagnoses() throws Exception {
encounter.addObs(
diagnosisMetadata.buildDiagnosisObsGroup(
new Diagnosis(new CodedOrFreeTextAnswer("Random Disease"), Diagnosis.Order.PRIMARY)));
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
assertThat(parsed.getDiagnoses().size(), is(1));
assertThat(parsed.getDispositions().size(), is(0));
assertThat(parsed.getObs().size(), is(0));
assertThat(
path(parsed.getDiagnoses(), 0, "question"),
is((Object) "coreapps.patientDashBoard.diagnosisQuestion.PRIMARY"));
assertThat(
path(parsed.getDiagnoses(), 0, "answer"),
is((Object) "(coreapps.Diagnosis.Certainty.PRESUMED) \"Random Disease\""));
assertThat(path(parsed.getDiagnoses(), 0, "order"), is((Object) 0));
}
@Test
public void testParsingSimpleObs() throws Exception {
ConceptDatatype textDatatype = conceptService.getConceptDatatypeByName("Text");
ConceptClass misc = conceptService.getConceptClassByName("Misc");
String consultNote =
"Consult note"; // intentionally the same as what will result from
// capitalizeFirstLetter(consultNote)
String valueText = "Patient is here for blah blah blah.";
Concept consultComments =
new ConceptBuilder(conceptService, textDatatype, misc).addName(consultNote).get();
encounter.addObs(new ObsBuilder().setConcept(consultComments).setValue(valueText).get());
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
assertThat(parsed.getDiagnoses().size(), is(0));
assertThat(parsed.getDispositions().size(), is(0));
assertThat(parsed.getObs().size(), is(1));
assertThat(path(parsed.getObs(), 0, "question"), is((Object) consultNote));
assertThat(path(parsed.getObs(), 0, "answer"), is((Object) valueText));
}
@Test
public void testParsingObsWithLocationAnswer() throws Exception {
ConceptDatatype textDatatype = conceptService.getConceptDatatypeByName("Text");
ConceptClass misc = conceptService.getConceptClassByName("Misc");
Location xanadu = new Location();
xanadu.setName("Xanadu");
when(locationService.getLocation(2)).thenReturn(xanadu);
Concept someLocation =
new ConceptBuilder(conceptService, textDatatype, misc).addName("Some location").get();
encounter.addObs(
new ObsBuilder()
.setConcept(someLocation)
.setValue("2")
.setComment("org.openmrs.Location")
.get());
ParsedObs parsed = parser.parseObservations(Locale.ENGLISH);
;
assertThat(parsed.getObs().size(), is(1));
assertThat(path(parsed.getObs(), 0, "question"), is((Object) "Some location"));
assertThat(path(parsed.getObs(), 0, "answer"), is((Object) "Xanadu"));
}
@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);
}
/**
*
* Returns the encounter with the obs that aren't used when populating form are removed.
* This *doesn't* save the encounter.
* TODO: handle Orders?
*
* @param e
* @param htmlform
* @return
* @throws Exception
*/
public static Encounter trimEncounterToMatchForm(Encounter e, HtmlForm htmlform) throws Exception {
//this should move existing obs from session to tag handlers.
FormEntrySession session = new FormEntrySession(e.getPatient(), e, FormEntryContext.Mode.VIEW, htmlform, null); // session gets a null HttpSession
session.getHtmlToDisplay();
if (log.isDebugEnabled()){
Map<Concept, List<Obs>> map = session.getContext().getExistingObs();
if (map != null){
for (Map.Entry<Concept, List<Obs>> existingObs : map.entrySet()){
List<Obs> oList = existingObs.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObs " + existingObs.getKey() + " " + oInner.getConcept());
}
}
Map<Obs, Set<Obs>> map2 = session.getContext().getExistingObsInGroups();
if (map2 != null){
for (Map.Entry<Obs, Set<Obs>> existingObsInGroups : map2.entrySet()){
Set<Obs> oList = existingObsInGroups.getValue();
for (Obs oInner : oList)
log.debug("Obs in existingObsInGroups " + existingObsInGroups.getKey().getConcept() + " " + oInner.getConcept());
}
}
}
Encounter ret = new Encounter();
ret.setCreator(e.getCreator());
ret.setEncounterDatetime(e.getEncounterDatetime());
EncounterCompatibility.setProvider(ret, EncounterCompatibility.getProvider(e));
ret.setLocation(e.getLocation());
ret.setDateCreated(e.getDateCreated());
ret.setPatient(e.getPatient());
//renders new encounter unsave-able:
ret.setEncounterId(e.getEncounterId());
for (Obs oTest : e.getAllObs()){
boolean found = false;
if (session.getContext().getExistingObs() != null && !oTest.isObsGrouping()){
List<Obs> obsList = session.getContext().getExistingObs().get(oTest.getConcept());
if (obsList != null && obsList.size() > 0){
for (Obs o : obsList){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
if (!found && session.getContext().getExistingObsInGroups() != null){
for (Map.Entry<Obs, Set<Obs>> mapEntry : session.getContext().getExistingObsInGroups().entrySet()){
if (mapEntry.getKey().equals(oTest)){
found = true;
continue;
} else {
Set<Obs> oSet = mapEntry.getValue();
//note: oSet.contains fails for some reason
for (Obs o:oSet){
if (o.getObsId().equals(oTest.getObsId())){
found = true;
continue;
}
}
}
}
}
if (!found)
ret.addObs(oTest);
}
session = null;
return ret;
}
@RequestMapping(method = RequestMethod.POST)
public void savePatientInfo(
@RequestParam("patientId") Integer patientId,
@RequestParam(value = "encounterId", required = false) Integer encounterId,
HttpServletRequest request,
HttpServletResponse response)
throws ParseException, IOException {
Map<String, String> parameters = RegistrationWebUtils.optimizeParameters(request);
// get patient
Patient patient = Context.getPatientService().getPatient(patientId);
/*
* SAVE ENCOUNTER
*/
Encounter encounter = null;
if (encounterId != null) {
encounter = Context.getEncounterService().getEncounter(encounterId);
} else {
encounter = RegistrationWebUtils.createEncounter(patient, true);
// create OPD obs
Concept opdWardConcept =
Context.getConceptService().getConcept(RegistrationConstants.CONCEPT_NAME_OPD_WARD);
Concept selectedOPDConcept =
Context.getConceptService()
.getConcept(
Integer.parseInt(
parameters.get(RegistrationConstants.FORM_FIELD_PATIENT_OPD_WARD)));
Obs opd = new Obs();
opd.setConcept(opdWardConcept);
opd.setValueCoded(selectedOPDConcept);
encounter.addObs(opd);
// send patient to opd room/bloodbank
// harsh 5/10/2012 changed the way to get blood bank concept->shifted hardcoded dependency
// from id to name
// Concept bloodbankConcept = Context.getConceptService().getConcept(
// GlobalPropertyUtil.getInteger(RegistrationConstants.PROPERTY_BLOODBANK_CONCEPT_ID,
// 6425));
String bloodBankWardName =
GlobalPropertyUtil.getString(
RegistrationConstants.PROPERTY_BLOODBANK_OPDWARD_NAME, "Blood Bank Room");
// ghanshyam 03-sept-2013 Bug #394 [Blood bank]queue
String socn = new String(selectedOPDConcept.getName().toString());
String substringofsocn = socn.substring(0, 15);
if (!substringofsocn.equalsIgnoreCase(bloodBankWardName)) {
RegistrationWebUtils.sendPatientToOPDQueue(patient, selectedOPDConcept, true);
} else {
OrderType orderType = null;
String orderTypeName =
Context.getAdministrationService().getGlobalProperty("bloodbank.orderTypeName");
orderType = OrderUtil.getOrderTypeByName(orderTypeName);
Order order = new Order();
order.setConcept(selectedOPDConcept);
order.setCreator(Context.getAuthenticatedUser());
order.setDateCreated(new Date());
order.setOrderer(Context.getAuthenticatedUser());
order.setPatient(patient);
order.setStartDate(new Date());
order.setAccessionNumber("0");
order.setOrderType(orderType);
order.setEncounter(encounter);
encounter.addOrder(order);
}
}
// create temporary attributes
for (String name : parameters.keySet()) {
if ((name.contains(".attribute.")) && (!StringUtils.isBlank(parameters.get(name)))) {
String[] parts = name.split("\\.");
String idText = parts[parts.length - 1];
Integer id = Integer.parseInt(idText);
Concept tempCatConcept = Context.getConceptService().getConceptByName("TEMPORARY CATEGORY");
Concept temporaryAttributeConcept =
Context.getConceptService().getConcept(tempCatConcept.getConceptId());
Obs temporaryAttribute = new Obs();
temporaryAttribute.setConcept(temporaryAttributeConcept);
logger.info("concept: " + temporaryAttributeConcept);
logger.info("value: " + parameters.get(name));
temporaryAttribute.setValueAsString(parameters.get(name));
encounter.addObs(temporaryAttribute);
}
}
// save encounter
Context.getEncounterService().saveEncounter(encounter);
logger.info(
String.format(
"Save encounter for the visit of patient [encounterId=%s, patientId=%s]",
encounter.getId(), patient.getId()));
response.setContentType("text/html;charset=UTF-8");
PrintWriter out = response.getWriter();
out.print("success");
}