public static Set<Set<Obs>> generateObsGroupFromSearchResults() {
Set<Set<Obs>> obsGroups = new HashSet<Set<Obs>>();
SearchAPI searchAPI = SearchAPI.getInstance();
List<ChartListItem> searchResultsList = searchAPI.getResults();
for (ChartListItem item :
searchResultsList) { // for each item in results we classify it by its obsGroup, and add all
// of the group.
if (item != null && item instanceof ObsItem && ((ObsItem) item).getObsId() != null) {
int itemObsId = ((ObsItem) item).getObsId();
Obs obsGrp = Context.getObsService().getObs(itemObsId).getObsGroup();
if (obsGrp != null) {
int groupId = obsGrp.getId();
Set<Obs> obsGroup = obsGrp.getGroupMembers();
boolean found = false; // if found == true then we don't need to add the group.
for (Set<Obs> grp : obsGroups) {
Obs ob = new Obs(-1);
if (grp.iterator().hasNext()) {
ob = grp.iterator().next();
}
if (ob.getObsGroup() != null && ob.getObsGroup().getId() != null) {
if (ob.getObsGroup().getId() == groupId) {
found = true;
}
}
}
if (!found) {
obsGroups.add(obsGroup);
}
}
}
}
return obsGroups;
}
private Obs doNotGoToServiceToFormatMembers(Obs obsGroup) {
Set<Obs> replacements = new HashSet<Obs>();
for (Obs member : obsGroup.getGroupMembers()) {
replacements.add(new DoNotGoToServiceWhenFormatting(member));
}
obsGroup.setGroupMembers(replacements);
return obsGroup;
}
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;
}
/**
* This is an equivalent to a copy constructor. Creates a new copy of the given <code>obsToCopy
* </code> with a null obs id
*
* @param obsToCopy The Obs that is going to be copied
* @return a new Obs object with all the same attributes as the given obs
*/
public static Obs newInstance(Obs obsToCopy) {
Obs newObs =
new Obs(
obsToCopy.getPerson(),
obsToCopy.getConcept(),
obsToCopy.getObsDatetime(),
obsToCopy.getLocation());
newObs.setObsGroup(obsToCopy.getObsGroup());
newObs.setAccessionNumber(obsToCopy.getAccessionNumber());
newObs.setValueCoded(obsToCopy.getValueCoded());
newObs.setValueDrug(obsToCopy.getValueDrug());
newObs.setValueGroupId(obsToCopy.getValueGroupId());
newObs.setValueDatetime(obsToCopy.getValueDatetime());
newObs.setValueNumeric(obsToCopy.getValueNumeric());
newObs.setValueModifier(obsToCopy.getValueModifier());
newObs.setValueText(obsToCopy.getValueText());
newObs.setComment(obsToCopy.getComment());
newObs.setOrder(obsToCopy.getOrder());
newObs.setEncounter(obsToCopy.getEncounter());
newObs.setDateStarted(obsToCopy.getDateStarted());
newObs.setDateStopped(obsToCopy.getDateStopped());
newObs.setCreator(obsToCopy.getCreator());
newObs.setDateCreated(obsToCopy.getDateCreated());
newObs.setVoided(obsToCopy.getVoided());
newObs.setVoidedBy(obsToCopy.getVoidedBy());
newObs.setDateVoided(obsToCopy.getDateVoided());
newObs.setVoidReason(obsToCopy.getVoidReason());
newObs.setValueComplex(obsToCopy.getValueComplex());
newObs.setComplexData(obsToCopy.getComplexData());
if (obsToCopy.getGroupMembers() != null)
for (Obs member : obsToCopy.getGroupMembers()) {
// if the obs hasn't been saved yet, no need to duplicate it
if (member.getObsId() == null) newObs.addGroupMember(member);
else newObs.addGroupMember(Obs.newInstance(member));
}
return newObs;
}
/** @see Encounter#addObs(Obs) */
@Test
@Verifies(
value = "should add encounter attrs to obs if attributes are null",
method = "addObs(Obs)")
public void addObs_shouldAddEncounterAttrsToObsGroupMembersIfAttributesAreNull()
throws Exception {
/// an encounter that will hav the date/location/patient on it
Encounter encounter = new Encounter();
Date date = new Date();
encounter.setEncounterDatetime(date);
Location location = new Location(1);
encounter.setLocation(location);
Patient patient = new Patient(1);
encounter.setPatient(patient);
// add an obs that doesn't have date/location/patient set on it.
Obs obs = new Obs(123);
Obs childObs = new Obs(456);
obs.addGroupMember(childObs);
// check for infinite recursion
// childObs-->childObs2 and childObs2-->childObs
Obs childObs2 = new Obs(456);
childObs.addGroupMember(childObs2);
childObs2.addGroupMember(childObs);
assertTrue(obs.getGroupMembers() != null && obs.getGroupMembers().size() == 1);
encounter.addObs(obs);
// check the values of the obs attrs to see if they were added
assertTrue(childObs.getObsDatetime().equals(date));
assertTrue(childObs.getLocation().equals(location));
assertTrue(childObs.getPerson().equals(patient));
assertTrue(childObs2.getObsDatetime().equals(date));
assertTrue(childObs2.getLocation().equals(location));
assertTrue(childObs2.getPerson().equals(patient));
}
public List<FHIRResource> mapToFhirObservation(
Obs observation, Encounter fhirEncounter, SystemProperties systemProperties) {
List<FHIRResource> result = new ArrayList<>();
FHIRResource entry = mapObservation(observation, fhirEncounter, systemProperties);
Observation fhirObservation = (Observation) entry.getResource();
fhirObservation.setStatus(ObservationStatusEnum.PRELIMINARY);
for (Obs member : observation.getGroupMembers()) {
mapGroupMember(member, fhirEncounter, fhirObservation, result, systemProperties);
}
result.add(entry);
return result;
}
/** @see org.openmrs.api.db.ObsDAO#saveObs(org.openmrs.Obs) */
public Obs saveObs(Obs obs) throws DAOException {
if (obs.hasGroupMembers() && obs.getObsId() != null) {
// hibernate has a problem updating child collections
// if the parent object was already saved so we do it
// explicitly here
for (Obs member : obs.getGroupMembers()) if (member.getObsId() == null) saveObs(member);
}
sessionFactory.getCurrentSession().saveOrUpdate(obs);
return obs;
}
@Test
public void shouldAddNewObservationGroup() throws Exception {
executeDataSet("shouldAddNewObservation.xml");
String encounterDateTime = "2005-01-02T00:00:00.000+0000";
String observationTime = "2005-01-02T12:00:00.000+0000";
String json =
"{ \"patientUuid\" : \"a76e8d23-0c38-408c-b2a8-ea5540f01b51\", "
+ "\"visitTypeUuid\" : \"b45ca846-c79a-11e2-b0c0-8e397087571c\", "
+ "\"encounterTypeUuid\": \"2b377dba-62c3-4e53-91ef-b51c68899890\", "
+ "\"encounterDateTime\" : \""
+ encounterDateTime
+ "\", "
+ "\"observations\":["
+ "{\"concept\":{\"uuid\": \"e102c80f-1yz9-4da3-bb88-8122ce8868dd\"}, "
+ " \"groupMembers\" : [{\"concept\":{\"uuid\": \"d102c80f-1yz9-4da3-bb88-8122ce8868dd\"}, \"value\":20, \"comment\":\"overweight\", \"observationDateTime\": \""
+ observationTime
+ "\"}] }"
+ "]}";
EncounterTransaction response =
deserialize(
handle(newPostRequest("/rest/emrapi/encounter", json)), EncounterTransaction.class);
Visit visit = visitService.getVisitByUuid(response.getVisitUuid());
Encounter encounter = (Encounter) visit.getEncounters().toArray()[0];
assertEquals(1, encounter.getObs().size());
Obs obs = (Obs) encounter.getAllObs().toArray()[0];
assertEquals("e102c80f-1yz9-4da3-bb88-8122ce8868dd", obs.getConcept().getUuid());
assertEquals(1, obs.getGroupMembers().size());
Obs member = obs.getGroupMembers().iterator().next();
assertEquals("d102c80f-1yz9-4da3-bb88-8122ce8868dd", member.getConcept().getUuid());
assertEquals(new Double(20.0), member.getValueNumeric());
assertEquals("a76e8d23-0c38-408c-b2a8-ea5540f01b51", member.getPerson().getUuid());
assertEquals("f13d6fae-baa9-4553-955d-920098bec08f", member.getEncounter().getUuid());
assertEquals("overweight", member.getComment());
assertEquals(
new SimpleDateFormat(dateTimeFormat).parse(observationTime), member.getObsDatetime());
}
@Test
public void shouldChangeObservationsOfPreviousEncounters() throws Exception {
Date visitStartDate = getDateFromString("2014-06-22 00:00:00");
Date encounterDate = getDateFromString("2014-06-23 00:00:00");
List<Document> documents = new ArrayList<>();
documents.add(
new Document(
"/radiology/foo.jpg",
null,
"5f596de5-5caa-11e3-a4c0-0800271c1b75",
"6d0ae386-707a-4629-9850-f15206e63kj0",
encounterDate,
false));
VisitDocumentRequest visitDocumentRequest =
new VisitDocumentRequest(
patientUUID,
firstVisitUuid,
visitTypeUUID,
visitStartDate,
null,
secondEncounterTypeUUID,
encounterDate,
documents,
secondProviderUuid,
secondLocationUuid,
null);
executeDataSet("visitDocumentData.xml");
visitDocumentService.upload(visitDocumentRequest);
Context.flushSession();
Context.clearSession();
Encounter encounter = encounterService.getEncounterByUuid(secondEncounterUuid);
for (Obs obs : encounter.getAllObs(true)) {
if (obs.getUuid().equals("6d0ae386-707a-4629-9850-f15606e63666")
|| obs.getUuid().equals("6d0ae386-707a-4629-9850-f15206e63kj0")) {
assertThat(obs.getVoided(), is(true));
}
}
Obs savedDoc = getSavedDocument(encounter.getAllObs(), "5f596de5-5caa-11e3-a4c0-0800271c1b75");
assertNotNull(savedDoc);
assertThat(savedDoc.getConcept().getId(), is(333));
assertThat(
savedDoc.getGroupMembers().iterator().next().getValueText(), is("/radiology/foo.jpg"));
assertEquals(FIRST_LOCATION_UUID, encounter.getLocation().getUuid());
}
@Test
public void shouldUpdateObservations() throws Exception {
executeDataSet("shouldUpdateObservations.xml");
String json =
"{ \"patientUuid\" : \"a76e8d23-0c38-408c-b2a8-ea5540f01b51\", "
+ "\"visitTypeUuid\" : \"b45ca846-c79a-11e2-b0c0-8e397087571c\", "
+ "\"encounterTypeUuid\": \"2b377dba-62c3-4e53-91ef-b51c68899890\","
+ "\"encounterDateTime\" : \"2013-01-01T00:00:00.000+0000\", "
+ "\"observations\":["
+ "{\"uuid\":\"z9fb7f47-e80a-4056-9285-bd798be13c63\", "
+ " \"groupMembers\" : [{\"uuid\":\"ze48cdcb-6a76-47e3-9f2e-2635032f3a9a\", \"value\":20, \"comment\":\"new gc\" }] }, "
+ "{\"uuid\":\"zf616900-5e7c-4667-9a7f-dcb260abf1de\", \"comment\" : \"new c\", \"value\":100 }"
+ "]}";
EncounterTransaction response =
deserialize(
handle(newPostRequest("/rest/emrapi/encounter", json)), EncounterTransaction.class);
Visit visit = visitService.getVisitByUuid(response.getVisitUuid());
Encounter encounter = (Encounter) visit.getEncounters().toArray()[0];
assertEquals(2, encounter.getObsAtTopLevel(false).size());
Iterator<Obs> iterator = encounter.getObsAtTopLevel(false).iterator();
Obs obs1 = iterator.next();
assertEquals("zf616900-5e7c-4667-9a7f-dcb260abf1de", obs1.getUuid());
assertEquals(new Double(100), obs1.getValueNumeric());
assertEquals("new c", obs1.getComment());
Obs obs2 = iterator.next();
assertEquals("z9fb7f47-e80a-4056-9285-bd798be13c63", obs2.getUuid());
assertEquals(1, obs2.getGroupMembers().size());
Obs member = obs2.getGroupMembers().iterator().next();
assertEquals(new Double(20), member.getValueNumeric());
assertEquals("new gc", member.getComment());
}
private void mapGroupMember(
Obs obs,
Encounter fhirEncounter,
Observation parentObservation,
List<FHIRResource> result,
SystemProperties systemProperties) {
if (hasIgnoredConcept(obs)) {
return;
}
FHIRResource entry = mapObservation(obs, fhirEncounter, systemProperties);
Observation observation = (Observation) entry.getResource();
mapRelatedObservation(observation).mergeWith(parentObservation, systemProperties);
for (Obs member : obs.getGroupMembers()) {
mapGroupMember(member, fhirEncounter, observation, result, systemProperties);
}
result.add(entry);
}
@Test
public void shouldAddDiagnosesAdObservation() throws Exception {
executeDataSet("baseMetaData.xml");
executeDataSet("diagnosisMetaData.xml");
executeDataSet("shouldAddDiagnosisAsObservation.xml");
String cancerDiagnosisUuid = "d102c80f-1yz9-4da3-bb88-8122ce8868dh";
String encounterDateTime = "2005-01-02T00:00:00.000+0000";
String diagnosisDateTime = "2005-01-02T01:00:00.000+0000";
String postData =
"{"
+ "\"patientUuid\" : \"a76e8d23-0c38-408c-b2a8-ea5540f01b51\", "
+ "\"visitTypeUuid\" : \"b45ca846-c79a-11e2-b0c0-8e397087571c\", "
+ "\"encounterTypeUuid\": \"2b377dba-62c3-4e53-91ef-b51c68899891\", "
+ "\"encounterDateTime\" : \""
+ encounterDateTime
+ "\", "
+ "\"diagnoses\":["
+ "{\"order\":\"PRIMARY\", \"certainty\": \"CONFIRMED\", \"codedAnswer\": { \"uuid\": \""
+ cancerDiagnosisUuid
+ "\"}, \"diagnosisDateTime\": \""
+ diagnosisDateTime
+ "\" }"
+ "]"
+ "}";
EncounterTransaction response =
deserialize(
handle(newPostRequest("/rest/emrapi/encounter", postData)), EncounterTransaction.class);
Visit visit = visitService.getVisitByUuid(response.getVisitUuid());
Encounter encounter = visit.getEncounters().iterator().next();
Set<Obs> obsAtTopLevel = encounter.getObsAtTopLevel(false);
assertEquals(1, obsAtTopLevel.size());
Obs parentObservation = obsAtTopLevel.iterator().next();
assertTrue(parentObservation.isObsGrouping());
assertEquals(
DateUtils.parseDate(diagnosisDateTime, dateTimeFormat), parentObservation.getObsDatetime());
Set<Obs> diagnosisObservationGroupMembers = parentObservation.getGroupMembers();
assertEquals(3, diagnosisObservationGroupMembers.size());
ArrayList<String> valueCodedNames = getValuCodedNames(diagnosisObservationGroupMembers);
assertTrue(valueCodedNames.contains("Confirmed"));
assertTrue(valueCodedNames.contains("Primary"));
assertTrue(valueCodedNames.contains("Cancer"));
}
@Test
public void shouldPreferVoidOverUpdateWhenEditingADocument() throws Exception {
Date visitStartDate = getDateFromString("2014-06-22 00:00:00");
Date encounterDate = getDateFromString("2014-06-23 00:00:00");
List<Document> documents = new ArrayList<>();
String obsUuid = "6d0ae386-707a-4629-9850-f15206e63kj0";
documents.add(
new Document(
"/radiology/foo.jpg",
null,
"3f596de5-5caa-11e3-a4c0-0800271c1b75",
obsUuid,
encounterDate,
true));
VisitDocumentRequest visitDocumentRequest =
new VisitDocumentRequest(
patientUUID,
firstVisitUuid,
visitTypeUUID,
visitStartDate,
null,
secondEncounterTypeUUID,
encounterDate,
documents,
secondProviderUuid,
secondLocationUuid,
null);
visitDocumentService.upload(visitDocumentRequest);
Context.flushSession();
Context.clearSession();
Encounter encounter = encounterService.getEncounterByUuid(secondEncounterUuid);
Obs savedObs = obsService.getObsByUuid(obsUuid);
assertTrue("Observation is not voided", savedObs.getVoided());
assertTrue(
"Observation is not voided", savedObs.getGroupMembers(true).iterator().next().getVoided());
Obs savedDoc = getSavedDocument(encounter.getAllObs(), "3f596de5-5caa-11e3-a4c0-0800271c1b75");
assertNull(savedDoc);
}
/**
* Auto generated method comment
*
* @param obs
* @param conceptId
* @return
*/
public static String convsetObsValueByConcept(Obs obs, Integer conceptId) {
String res = "-";
try {
if (obs != null) {
for (Obs ob : obs.getGroupMembers()) {
if (ob.getConcept().getConceptId() == conceptId.intValue()) {
res = ob.getValueAsString(Context.getLocale());
break;
}
}
}
} catch (Exception e) {
log.error(">>>>>>>>>>>>>>>>>>>VCT>>Module>>Tag>>>> An error occured : " + e.getMessage());
e.printStackTrace();
}
return res;
}
@Test
public void shouldNotChangeObservationsIfSameDetailsProvidedOnceAgain() throws Exception {
Date visitStartDate = getDateFromString("2014-06-22 00:00:00");
Date encounterDate = getDateFromString("2014-06-23 00:00:00");
List<Document> documents = new ArrayList<>();
documents.add(
new Document(
"/radiology/foo.jpg",
null,
conceptUuid,
"6d0ae386-707a-4629-9850-f15206e63kj0",
encounterDate,
false));
VisitDocumentRequest visitDocumentRequest =
new VisitDocumentRequest(
patientUUID,
firstVisitUuid,
visitTypeUUID,
visitStartDate,
null,
secondEncounterTypeUUID,
encounterDate,
documents,
secondProviderUuid,
secondLocationUuid,
null);
visitDocumentService.upload(visitDocumentRequest);
Context.flushSession();
Context.clearSession();
Encounter encounter = encounterService.getEncounterByUuid(secondEncounterUuid);
Obs savedDoc = getSavedDocument(encounter.getAllObs(), conceptUuid);
assertNotNull(savedDoc);
Set<Obs> groupMembers = savedDoc.getGroupMembers();
assertThat(groupMembers.size(), is(equalTo(1)));
assertThat(groupMembers.iterator().next().getValueText(), is("/radiology/foo.jpg"));
assertThat(
groupMembers.iterator().next().getUuid(), is("6d0ae386-707a-4629-9850-f15606e63666"));
}
/**
* Column headers must be unique to avoid clobbering and to ensure it is clear which columns are
* grouped together by obsgroup. As such, duplicate concepts at the parent level or duplicate
* concepts in the same obs group are given a unique occurrence number. For instance, in an obs
* group Functional Review Of Symptoms, there might be two child obs with the concept Symptom
* Present. To distinguish them, one is given an occurrence number of 1 and the next an occurrence
* number of 2.
*
* @param fieldMap
* @param obs
* @return Map<Obs, Integer> the filled in fieldMap
*/
public static Map<Obs, Integer> addChildrenObsToFieldMap(Map<Obs, Integer> fieldMap, Obs obs) {
if (obs != null && obs.isObsGrouping()) {
Set<Obs> childSet = obs.getGroupMembers();
List<Obs> children = new ArrayList<Obs>(childSet);
Map<Concept, Integer> childMap = new HashMap<Concept, Integer>();
for (Obs o : children) {
// check for duplicate concepts among this batch of children
Integer occurrence =
(childMap.get(o.getConcept()) != null) ? childMap.get(o.getConcept()) : 0;
occurrence++;
childMap.put(o.getConcept(), occurrence);
fieldMap.put(o, occurrence);
addChildrenObsToFieldMap(fieldMap, o);
}
}
return fieldMap;
}
@Test
public void shouldCreateObservations() throws Exception {
Date visitStartDate = getDateFromString("2014-06-22 00:00:00");
Date encounterDate = getDateFromString("2014-06-23 00:00:00");
Date obsDate = getDateFromString("2014-06-24 00:10:00");
List<Document> documents = new ArrayList<>();
documents.add(new Document("/radiology/fooo-bar.jpg", null, conceptUuid, null, obsDate, false));
visitDocumentRequest =
new VisitDocumentRequest(
patientUUID,
secondVisitUuid,
visitTypeUUID,
visitStartDate,
null,
firstEncounterTypeUUID,
encounterDate,
documents,
firstProviderUuid,
FIRST_LOCATION_UUID,
null);
visitDocumentService.upload(visitDocumentRequest);
Context.flushSession();
Context.clearSession();
Encounter encounter = encounterService.getEncounterByUuid(firstEncounterUuid);
Obs savedDoc = getSavedDocument(encounter.getAllObs(), conceptUuid);
assertNotNull(savedDoc);
assertThat(savedDoc.getConcept().getId(), is(222));
assertThat(
savedDoc.getGroupMembers().iterator().next().getValueText(), is("/radiology/fooo-bar.jpg"));
assertEquals(FIRST_LOCATION_UUID, encounter.getLocation().getUuid());
}
@Test
public void shouldDeleteObservationsOfPreviousEncounters() throws ParseException {
Date visitStartDate = getDateFromString("2014-06-22 00:00:00");
Date encounterDate = getDateFromString("2014-06-23 00:00:00");
List<Document> documents = new ArrayList<>();
String testUuid = "3f596de5-5caa-11e3-a4c0-0800271c1b75";
String obsUuid = "6d0ae386-707a-4629-9850-f15206e63j8s";
String providerUuid = "331c6bf8-7846-11e3-a96a-0800271c1b75";
documents.add(new Document("/patient_file", null, testUuid, obsUuid, encounterDate, true));
visitDocumentRequest =
new VisitDocumentRequest(
patientUUID,
secondVisitUuid,
visitTypeUUID,
visitStartDate,
null,
firstEncounterTypeUUID,
encounterDate,
documents,
providerUuid,
null,
null);
visitDocumentService.upload(visitDocumentRequest);
Context.flushSession();
Context.clearSession();
Encounter encounter = encounterService.getEncounterByUuid(firstEncounterUuid);
for (Obs obs : encounter.getAllObs(true)) {
if (obs.getUuid().equals(obsUuid)) {
assertThat(obs.getVoided(), is(true));
assertThat(obs.getGroupMembers(true).iterator().next().getVoided(), is(true));
}
}
}
private String getImageName(Obs obs) {
Set<Obs> groupMembers = obs.getGroupMembers();
return groupMembers.iterator().hasNext() ? groupMembers.iterator().next().getValueText() : null;
}