@SuppressWarnings("unused")
public static JSONObject createJsonObservation(Obs obs) {
JSONObject jsonObs = new JSONObject();
jsonObs.put("observation_id", obs.getObsId());
jsonObs.put("concept_name", obs.getConcept().getDisplayString());
Date obsDate = obs.getObsDatetime() == null ? new Date() : obs.getObsDatetime();
SimpleDateFormat formatDateJava = new SimpleDateFormat("dd/MM/yyyy HH:mm:ss");
String dateStr = obsDate.getTime() + "";
jsonObs.put("date", dateStr);
if (obs.getConcept().getDatatype().isNumeric()) { // ADD MORE DATATYPES
ConceptNumeric conceptNumeric =
Context.getConceptService().getConceptNumeric(obs.getConcept().getId());
jsonObs.put("units_of_measurement", conceptNumeric.getUnits());
jsonObs.put("absolute_high", conceptNumeric.getHiAbsolute());
jsonObs.put("absolute_low", conceptNumeric.getLowAbsolute());
jsonObs.put("critical_high", conceptNumeric.getHiCritical());
jsonObs.put("critical_low", conceptNumeric.getLowCritical());
jsonObs.put("normal_high", conceptNumeric.getHiNormal());
jsonObs.put("normal_low", conceptNumeric.getLowNormal());
}
jsonObs.put("value_type", obs.getConcept().getDatatype().getName());
jsonObs.put("value", obs.getValueAsString(Context.getLocale()));
jsonObs.put("location", obs.getLocation().getDisplayString());
jsonObs.put("creator", obs.getCreator().getDisplayString());
Set<EncounterProvider> encounterProviders = obs.getEncounter().getEncounterProviders();
if (encounterProviders != null && encounterProviders.iterator().hasNext()) {
EncounterProvider provider = encounterProviders.iterator().next();
if (provider.getProvider() != null) {
jsonObs.put("provider", provider.getProvider().getName());
}
}
SearchAPI searchAPI = SearchAPI.getInstance();
if (!searchAPI.getSearchPhrase().getPhrase().equals("")
&& !searchAPI.getSearchPhrase().getPhrase().equals("*")) {
for (ChartListItem item : searchAPI.getResults()) {
if (item != null && item instanceof ObsItem && ((ObsItem) item).getObsId() != null) {
if (((ObsItem) item).getObsId() == obs.getObsId()) {
jsonObs.put("chosen", "true");
}
}
}
}
return jsonObs;
}
/**
* 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;
}
}
}
/**
* Fails if there isn't an obs group with these exact characteristics
*
* @param groupingConceptId the concept id of the grouping obs
* @param conceptIdsAndValues these parameters must be given in pairs, the first element of
* which is the conceptId of a child obs (Integer) and the second element of which is the
* value of the child obs
*/
public void assertObsGroupCreated(int groupingConceptId, Object... conceptIdsAndValues) {
// quick checks
Assert.assertNotNull(encounterCreated);
Collection<Obs> temp = encounterCreated.getAllObs();
Assert.assertNotNull(temp);
List<ObsValue> expected = new ArrayList<ObsValue>();
for (int i = 0; i < conceptIdsAndValues.length; i += 2) {
int conceptId = (Integer) conceptIdsAndValues[i];
Object value = conceptIdsAndValues[i + 1];
expected.add(new ObsValue(conceptId, value));
}
for (Obs o : temp) {
if (o.getConcept().getConceptId() == groupingConceptId) {
if (o.getValueCoded() != null
|| o.getValueComplex() != null
|| o.getValueDatetime() != null
|| o.getValueDrug() != null
|| o.getValueNumeric() != null
|| o.getValueText() != null) {
Assert.fail(
"Obs group with groupingConceptId "
+ groupingConceptId
+ " should has a non-null value");
}
if (TestUtil.isMatchingObsGroup(o, expected)) {
return;
}
}
}
Assert.fail("Cannot find an obs group matching " + expected);
}
public void printEncounterCreated() {
if (encounterCreated == null) {
System.out.println("No encounter created");
} else {
System.out.println("=== Encounter created ===");
System.out.println(
"Created: "
+ encounterCreated.getDateCreated()
+ " Edited: "
+ encounterCreated.getDateChanged());
System.out.println("Date: " + encounterCreated.getEncounterDatetime());
System.out.println("Location: " + encounterCreated.getLocation().getName());
System.out.println("Provider: " + encounterCreated.getProvider().getPersonName());
System.out.println(" (obs)");
Collection<Obs> obs = encounterCreated.getAllObs(false);
if (obs == null) {
System.out.println("None");
} else {
for (Obs o : obs) {
System.out.println(
o.getConcept().getName() + " -> " + o.getValueAsString(Context.getLocale()));
}
}
}
}
@Test
public void shouldAddNewObservation() throws Exception {
executeDataSet("shouldAddNewObservation.xml");
String encounterDateTime = "2005-01-02T00:00:00.000+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\": \"d102c80f-1yz9-4da3-bb88-8122ce8868dd\"}, \"conceptName\":\"Should be Ignored\", \"value\":20}, "
+ "{\"concept\": {\"uuid\": \"8f8e7340-a067-11e3-a5e2-0800200c9a66\"}, \"value\": {\"uuid\": \"e7167090-a067-11e3-a5e2-0800200c9a66\"}}, "
+ "{\"concept\": {\"uuid\": \"e102c80f-1yz9-4da3-bb88-8122ce8868dd\"}, \"value\":\"text value\", \"comment\":\"overweight\"}]}";
MockHttpServletResponse response1 = handle(newPostRequest("/rest/emrapi/encounter", json));
EncounterTransaction response = deserialize(response1, EncounterTransaction.class);
Visit visit = visitService.getVisitByUuid(response.getVisitUuid());
Encounter encounter = visit.getEncounters().iterator().next();
assertEquals(3, encounter.getObs().size());
Iterator<Obs> obsIterator = encounter.getObs().iterator();
Map<String, Obs> map = new HashMap<String, Obs>();
while (obsIterator.hasNext()) {
Obs obs = obsIterator.next();
map.put(obs.getConcept().getDatatype().getHl7Abbreviation(), obs);
}
Obs textObservation = map.get(ConceptDatatype.TEXT);
assertEquals("text value", textObservation.getValueText());
assertEquals("a76e8d23-0c38-408c-b2a8-ea5540f01b51", textObservation.getPerson().getUuid());
assertEquals("e102c80f-1yz9-4da3-bb88-8122ce8868dd", textObservation.getConcept().getUuid());
assertEquals("f13d6fae-baa9-4553-955d-920098bec08f", textObservation.getEncounter().getUuid());
assertEquals("overweight", textObservation.getComment());
// TODO : change the observation startTime logic to take current time as start time when
// startTime is not passed by the client
// assertEquals(DateUtils.parseDate(encounterDateTime, dateTimeFormat),
// textObservation.getObsDatetime());
assertEquals(
"e7167090-a067-11e3-a5e2-0800200c9a66",
map.get(ConceptDatatype.CODED).getValueCoded().getUuid());
assertEquals(new Double(20.0), map.get(ConceptDatatype.NUMERIC).getValueNumeric());
}
public boolean matches(Obs obs) {
if (!obs.getConcept().getConceptId().equals(conceptId)) {
return false;
}
return OpenmrsUtil.nullSafeEquals(
TestUtil.valueAsStringHelper(value), obs.getValueAsString(Context.getLocale()));
}
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;
}
private List<Obs> getSavedDocuments(Set<Obs> allObs, String conceptUuid) {
List<Obs> obsList = new ArrayList<>();
for (Obs obs : allObs) {
if (obs.getConcept().getUuid().equals(conceptUuid)) {
obsList.add(obs);
}
}
Collections.sort(obsList, new IdBasedComparator());
return obsList;
}
public static List<Chemotherapy> generateChemotherapies(Patient patient) {
List<Encounter> encounters =
getEncountersByTreatment(patient, PatientPortalToolkitConstants.CHEMOTHERAPY_ENCOUNTER);
List<Chemotherapy> chemotherapiesList = new ArrayList<Chemotherapy>();
for (Encounter e : encounters) {
Chemotherapy chemotherapy = new Chemotherapy();
List<String> chemomedications = new ArrayList<String>();
Set<Obs> obsList = e.getObs();
chemotherapy.setEncounterUuid(e.getUuid());
for (Obs o : obsList) {
if (o.getConcept().getUuid().equals("8481b9da-74e3-45a9-9124-d69ab572d636"))
chemomedications.add(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("85c3a99e-0598-4c63-912b-796dee9c75b2"))
chemotherapy.setChemoStartDate(o.getValueDate());
if (o.getConcept().getUuid().equals("7dd8b8aa-b0f1-4eb1-862d-b6d737bdd315"))
chemotherapy.setChemoEndDate(o.getValueDate());
if (o.getConcept().getUuid().equals("361b7f9b-a985-4b18-9055-03af3b41b8b3")) {
if (o.getValueCoded().getUuid().equals("1065AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"))
chemotherapy.setCentralLine(true);
else chemotherapy.setCentralLine(false);
}
// doctors name
if (o.getConcept().getUuid().equals("c2cb2220-c07d-47c6-a4df-e5918aac3fc2"))
chemotherapy.setPcpName(o.getValueText());
// doctors email
if (o.getConcept().getUuid().equals("898a0028-8c65-4db9-a802-1577fce59864"))
chemotherapy.setPcpEmail(o.getValueText());
// doctors phone
if (o.getConcept().getUuid().equals("9285b227-4054-4830-ac32-5ea78462e8c4"))
chemotherapy.setPcpPhone(o.getValueText());
if (o.getConcept().getUuid().equals("47d58999-d3b5-4869-a52e-841e2e6bdbb3"))
chemotherapy.setInstitutionName(o.getValueText());
if (o.getConcept().getUuid().equals("bfa752d6-2037-465e-b0a2-c4c2d485ec32"))
chemotherapy.setInstitutionCity(o.getValueText());
if (o.getConcept().getUuid().equals("34489100-487e-443a-bf27-1b6869fb9332"))
chemotherapy.setInstitutionState(o.getValueText());
}
chemotherapy.setChemoMedications(chemomedications);
chemotherapiesList.add(chemotherapy);
}
return chemotherapiesList;
}
public static List<Surgery> generateSurgeries(Patient patient) {
List<Encounter> encounters =
getEncountersByTreatment(patient, PatientPortalToolkitConstants.SURGERY_ENCOUNTER);
List<Surgery> surgeriesList = new ArrayList<Surgery>();
for (Encounter e : encounters) {
Surgery surgery = new Surgery();
List<String> surgeryTypes = new ArrayList<String>();
Set<Obs> obsList = e.getObs();
surgery.setEncounterUuid(e.getUuid());
for (Obs o : obsList) {
if (o.getConcept().getUuid().equals("d409122c-8a0b-4282-a17f-07abad81f278"))
surgeryTypes.add(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("99ef1d68-05ed-4f37-b98b-c982e3574138")) {
if (o.getValueCoded().getUuid().equals("1065AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"))
surgery.setHasMajorComplications(true);
else surgery.setHasMajorComplications(false);
}
if (o.getConcept().getUuid().equals("c2d9fca3-1e0b-4007-8c3c-b3ebb4e67963"))
surgery.setMajorComplications(o.getValueText());
if (o.getConcept().getUuid().equals("87a69397-65ef-4576-a709-ae0a526afd85"))
surgery.setSurgeryDate(o.getValueDate());
// doctors name
if (o.getConcept().getUuid().equals("c2cb2220-c07d-47c6-a4df-e5918aac3fc2"))
surgery.setPcpName(o.getValueText());
// doctors email
if (o.getConcept().getUuid().equals("898a0028-8c65-4db9-a802-1577fce59864"))
surgery.setPcpEmail(o.getValueText());
// doctors phone
if (o.getConcept().getUuid().equals("9285b227-4054-4830-ac32-5ea78462e8c4"))
surgery.setPcpPhone(o.getValueText());
if (o.getConcept().getUuid().equals("47d58999-d3b5-4869-a52e-841e2e6bdbb3"))
surgery.setInstitutionName(o.getValueText());
if (o.getConcept().getUuid().equals("bfa752d6-2037-465e-b0a2-c4c2d485ec32"))
surgery.setInstitutionCity(o.getValueText());
if (o.getConcept().getUuid().equals("34489100-487e-443a-bf27-1b6869fb9332"))
surgery.setInstitutionState(o.getValueText());
}
surgery.setSurgeryTypes(surgeryTypes);
surgeriesList.add(surgery);
}
return surgeriesList;
}
/**
* Iterate over all encounters to determine occurrence number based on concept duplication at same
* level For instance, an obs group 'functional review of symptoms' might occur twice in the same
* form In this case, it is important to maintain which children belong to which parent
*
* @param fieldMap
* @param e the encounter to add to the fieldMap
* @return fieldMap
*/
public static Map<Obs, Integer> addEncounterToFieldMap(Map<Obs, Integer> fieldMap, Encounter e) {
Map<Concept, Integer> parentMap = new HashMap<Concept, Integer>();
for (Obs obs : e.getObsAtTopLevel(false)) {
Integer occurrence =
(parentMap.get(obs.getConcept()) != null) ? parentMap.get(obs.getConcept()) : 0;
occurrence++;
parentMap.put(obs.getConcept(), occurrence);
// Add top level obs to the fieldMap
fieldMap.put(obs, occurrence);
// Add children observations to the fieldMap recursively.
// fieldMap will have each obs with the occurrence number
// for a given concept on a given level of the tree structure
addChildrenObsToFieldMap(fieldMap, obs);
}
return fieldMap;
}
/** @see java.util.Iterator#next() */
public Map<String, Object> next() {
Locale locale = Context.getLocale();
Obs obs = iter.next();
Map<String, Object> ret = new HashMap<String, Object>();
ret.put("patientId", obs.getPersonId());
ret.put("question", obs.getConcept().getName(locale, false));
ret.put("questionConceptId", obs.getConcept().getConceptId());
ret.put("answer", obs.getValueAsString(locale));
if (obs.getValueCoded() != null) {
ret.put("answerConceptId", obs.getValueCoded());
}
ret.put("obsDatetime", obs.getObsDatetime());
if (obs.getEncounter() != null) {
ret.put("encounterId", obs.getEncounter().getEncounterId());
}
if (obs.getObsGroup() != null) {
ret.put("obsGroupId", obs.getObsGroup().getObsId());
}
return ret;
}
@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());
}
/**
* 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;
}
private boolean hasIgnoredConcept(Obs obs) {
String globalPropertyValue =
globalPropertyLookUpService.getGlobalPropertyValue(
MRSProperties.GLOBAL_PROPERTY_IGNORED_CONCEPT_LIST);
if (StringUtils.isBlank(globalPropertyValue)) return false;
List<String> conceptIds = asList(StringUtils.split(globalPropertyValue, ","));
for (String conceptId : conceptIds) {
if (obs.getConcept().getId().equals(Integer.parseInt(conceptId.trim()))) {
return true;
}
}
return false;
}
private FHIRResource mapObservation(
Obs openmrsObs, Encounter fhirEncounter, SystemProperties systemProperties) {
FHIRResource fhirObservationResource =
observationBuilder.buildObservationResource(
fhirEncounter,
systemProperties,
openmrsObs.getUuid(),
openmrsObs.getConcept().getName().getName());
Observation fhirObservation = (Observation) fhirObservationResource.getResource();
fhirObservation.setStatus(ObservationStatusEnum.PRELIMINARY);
mapCode(openmrsObs, fhirObservation);
mapValue(openmrsObs, fhirObservation);
return fhirObservationResource;
}
@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());
}
private void assertObsExists(boolean lookForVoided, int conceptId, Object value) {
// quick checks
Assert.assertNotNull(encounterCreated);
Collection<Obs> temp = encounterCreated.getAllObs(lookForVoided);
Assert.assertNotNull(temp);
String valueAsString = TestUtil.valueAsStringHelper(value);
for (Obs obs : temp) {
if (lookForVoided && !obs.isVoided()) continue;
if (obs.getConcept().getConceptId() == conceptId) {
if (valueAsString == null) return;
if (valueAsString.equals(obs.getValueAsString(Context.getLocale()))) return;
}
}
Assert.fail("Could not find obs with conceptId " + conceptId + " and value " + valueAsString);
}
public static Set<String> generateDatatypesFromResults() {
Set<String> res = new HashSet<String>();
SearchAPI searchAPI = SearchAPI.getInstance();
for (ChartListItem item : searchAPI.getResults()) {
if (item != null && item instanceof ObsItem && ((ObsItem) item).getObsId() != null) {
int itemObsId = ((ObsItem) item).getObsId();
Obs obs = Context.getObsService().getObs(itemObsId);
if (obs != null) {
res.add(obs.getConcept().getDatatype().getName());
}
}
}
return res;
}
/**
* 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;
}
public static List<Radiation> generateRadiations(Patient patient) {
List<Encounter> encounters =
getEncountersByTreatment(patient, PatientPortalToolkitConstants.RADIATION_ENCOUNTER);
List<Radiation> radiationsList = new ArrayList<Radiation>();
for (Encounter e : encounters) {
Radiation radiation = new Radiation();
List<String> radiationTypes = new ArrayList<String>();
Set<Obs> obsList = e.getObs();
radiation.setEncounterUuid(e.getUuid());
for (Obs o : obsList) {
if (o.getConcept().getUuid().equals("42fb7bb5-f840-4518-814c-893813211cba"))
radiationTypes.add(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("85c3a99e-0598-4c63-912b-796dee9c75b2"))
radiation.setStartDate(o.getValueDate());
if (o.getConcept().getUuid().equals("7dd8b8aa-b0f1-4eb1-862d-b6d737bdd315"))
radiation.setEndDate(o.getValueDate());
// doctors name
if (o.getConcept().getUuid().equals("c2cb2220-c07d-47c6-a4df-e5918aac3fc2"))
radiation.setPcpName(o.getValueText());
// doctors email
if (o.getConcept().getUuid().equals("898a0028-8c65-4db9-a802-1577fce59864"))
radiation.setPcpEmail(o.getValueText());
// doctors phone
if (o.getConcept().getUuid().equals("9285b227-4054-4830-ac32-5ea78462e8c4"))
radiation.setPcpPhone(o.getValueText());
if (o.getConcept().getUuid().equals("47d58999-d3b5-4869-a52e-841e2e6bdbb3"))
radiation.setInstitutionName(o.getValueText());
if (o.getConcept().getUuid().equals("bfa752d6-2037-465e-b0a2-c4c2d485ec32"))
radiation.setInstitutionCity(o.getValueText());
if (o.getConcept().getUuid().equals("34489100-487e-443a-bf27-1b6869fb9332"))
radiation.setInstitutionState(o.getValueText());
}
radiation.setRadiationTypes(radiationTypes);
radiationsList.add(radiation);
}
return radiationsList;
}
/**
* 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;
}
public static List<GeneralHistory> generateGeneralHistory(Patient patient) {
List<Encounter> encounters =
getEncountersByTreatment(patient, PatientPortalToolkitConstants.TREATMENTSUMMARY_ENCOUNTER);
List<GeneralHistory> generalHistoryList = new ArrayList<GeneralHistory>();
for (Encounter e : encounters) {
GeneralHistory generalHistory = new GeneralHistory();
generalHistory.setEncounterUuid(e.getUuid());
Set<Obs> obsList = e.getObs();
for (Obs o : obsList) {
if (o.getConcept().getUuid().equals("efa3f9eb-ade4-4ddb-92c9-0fc1119d112d"))
generalHistory.setCancerStage(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("cdf6d767-2aa3-40b6-ae78-0386eebe2411"))
generalHistory.setCancerType(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("395878ae-5108-4aad-8ad8-9b88e812d278")) {
if (o.getValueCoded().getUuid().equals("1065AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"))
generalHistory.setHasGeneticOrPredisposingAbnormality(true);
else generalHistory.setHasGeneticOrPredisposingAbnormality(false);
}
if (o.getConcept().getUuid().equals("8719adbe-0975-477f-a95f-2fae4d6cbdae"))
generalHistory.setGeneticOrPredisposingAbnormality(o.getValueCoded().getName().getName());
if (o.getConcept().getUuid().equals("654e32f0-8b57-4d1f-845e-500922e800f6"))
generalHistory.setDiagnosisDate(o.getValueDate());
// doctors name
if (o.getConcept().getUuid().equals("c2cb2220-c07d-47c6-a4df-e5918aac3fc2"))
generalHistory.setPcpName(o.getValueText());
// doctors email
if (o.getConcept().getUuid().equals("898a0028-8c65-4db9-a802-1577fce59864"))
generalHistory.setPcpEmail(o.getValueText());
// doctors phone
if (o.getConcept().getUuid().equals("9285b227-4054-4830-ac32-5ea78462e8c4"))
generalHistory.setPcpPhone(o.getValueText());
}
generalHistoryList.add(generalHistory);
}
return generalHistoryList;
}
@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());
}
/**
* Creates an OpenMRS Obs instance
*
* @param concept concept associated with the Obs
* @param value value associated with the Obs
* @param datetime date/time associated with the Obs (may be null)
* @param accessionNumber accession number associatd with the Obs (may be null)
* @return the created Obs instance
*/
public static Obs createObs(
Concept concept, Object value, Date datetime, String accessionNumber) {
Obs obs = new Obs();
obs.setConcept(concept);
ConceptDatatype dt = obs.getConcept().getDatatype();
if (dt.isNumeric()) {
obs.setValueNumeric(Double.parseDouble(value.toString()));
} else if (dt.isText()) {
if (value instanceof Location) {
obs.setValueText(((Location) value).getLocationId().toString());
} else {
obs.setValueText(value.toString());
}
} else if (dt.isCoded()) {
if (value instanceof Concept) obs.setValueCoded((Concept) value);
else obs.setValueCoded((Concept) convertToType(value.toString(), Concept.class));
} else if (dt.isBoolean()) {
boolean booleanValue =
value != null && !Boolean.FALSE.equals(value) && !"false".equals(value);
obs.setValueNumeric(booleanValue ? 1.0 : 0.0);
} else if (dt.isDate()) {
Date date = (Date) value;
obs.setValueDatetime(date);
} else if ("ZZ".equals(dt.getHl7Abbreviation())) {
// don't set a value
} else {
throw new IllegalArgumentException(
"concept datatype not yet implemented: "
+ dt.getName()
+ " with Hl7 Abbreviation: "
+ dt.getHl7Abbreviation());
}
if (datetime != null) obs.setObsDatetime(datetime);
if (accessionNumber != null) obs.setAccessionNumber(accessionNumber);
return obs;
}
@Override
public Concept getConcept() {
return obs.getConcept();
}
/**
* This method produces a model containing the following mappings:
*
* <pre>
* (always)
* (java.util.Date) now
* (String) size
* (Locale) locale
* (String) portletUUID // unique for each instance of any portlet
* (other parameters)
* (if there's currently an authenticated user)
* (User) authenticatedUser
* (if the request has a patientId attribute)
* (Integer) patientId
* (Patient) patient
* (List<Obs>) patientObs
* (List<Encounter>) patientEncounters
* (List<DrugOrder>) patientDrugOrders
* (List<DrugOrder>) currentDrugOrders
* (List<DrugOrder>) completedDrugOrders
* (Obs) patientWeight // most recent weight obs
* (Obs) patientHeight // most recent height obs
* (Double) patientBmi // BMI derived from most recent weight and most recent height
* (String) patientBmiAsString // BMI rounded to one decimal place, or "?" if unknown
* (Integer) personId
* (if the patient has any obs for the concept in the global property 'concept.reasonExitedCare')
* (Obs) patientReasonForExit
* (if the request has a personId or patientId attribute)
* (Person) person
* (List<Relationship>) personRelationships
* (Map<RelationshipType, List<Relationship>>) personRelationshipsByType
* (if the request has an encounterId attribute)
* (Integer) encounterId
* (Encounter) encounter
* (Set<Obs>) encounterObs
* (if the request has a userId attribute)
* (Integer) userId
* (User) user
* (if the request has a patientIds attribute, which should be a (String) comma-separated list of patientIds)
* (PatientSet) patientSet
* (String) patientIds
* (if the request has a conceptIds attribute, which should be a (String) commas-separated list of conceptIds)
* (Map<Integer, Concept>) conceptMap
* (Map<String, Concept>) conceptMapByStringIds
* </pre>
*
* @should calculate bmi into patientBmiAsString
* @should not fail with empty height and weight properties
*/
@SuppressWarnings("unchecked")
public ModelAndView handleRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
AdministrationService as = Context.getAdministrationService();
ConceptService cs = Context.getConceptService();
// find the portlet that was identified in the openmrs:portlet taglib
Object uri = request.getAttribute("javax.servlet.include.servlet_path");
String portletPath = "";
Map<String, Object> model = null;
{
HttpSession session = request.getSession();
String uniqueRequestId = (String) request.getAttribute(WebConstants.INIT_REQ_UNIQUE_ID);
String lastRequestId =
(String) session.getAttribute(WebConstants.OPENMRS_PORTLET_LAST_REQ_ID);
if (uniqueRequestId.equals(lastRequestId)) {
model =
(Map<String, Object>) session.getAttribute(WebConstants.OPENMRS_PORTLET_CACHED_MODEL);
// remove cached parameters
List<String> parameterKeys = (List<String>) model.get("parameterKeys");
for (String key : parameterKeys) {
model.remove(key);
}
}
if (model == null) {
log.debug("creating new portlet model");
model = new HashMap<String, Object>();
session.setAttribute(WebConstants.OPENMRS_PORTLET_LAST_REQ_ID, uniqueRequestId);
session.setAttribute(WebConstants.OPENMRS_PORTLET_CACHED_MODEL, model);
}
}
if (uri != null) {
long timeAtStart = System.currentTimeMillis();
portletPath = uri.toString();
// Allowable extensions are '' (no extension) and '.portlet'
if (portletPath.endsWith("portlet")) portletPath = portletPath.replace(".portlet", "");
else if (portletPath.endsWith("jsp"))
throw new ServletException(
"Illegal extension used for portlet: '.jsp'. Allowable extensions are '' (no extension) and '.portlet'");
log.debug("Loading portlet: " + portletPath);
String id = (String) request.getAttribute("org.openmrs.portlet.id");
String size = (String) request.getAttribute("org.openmrs.portlet.size");
Map<String, Object> params =
(Map<String, Object>) request.getAttribute("org.openmrs.portlet.parameters");
Map<String, Object> moreParams =
(Map<String, Object>) request.getAttribute("org.openmrs.portlet.parameterMap");
model.put("now", new Date());
model.put("id", id);
model.put("size", size);
model.put("locale", Context.getLocale());
model.put("portletUUID", UUID.randomUUID().toString().replace("-", ""));
List<String> parameterKeys = new ArrayList<String>(params.keySet());
model.putAll(params);
if (moreParams != null) {
model.putAll(moreParams);
parameterKeys.addAll(moreParams.keySet());
}
model.put("parameterKeys", parameterKeys); // so we can clean these up in the next request
// if there's an authenticated user, put them, and their patient set, in the model
if (Context.getAuthenticatedUser() != null) {
model.put("authenticatedUser", Context.getAuthenticatedUser());
}
Integer personId = null;
// if a patient id is available, put patient data documented above in the model
Object o = request.getAttribute("org.openmrs.portlet.patientId");
if (o != null) {
String patientVariation = "";
Integer patientId = (Integer) o;
if (!model.containsKey("patient")) {
// we can't continue if the user can't view patients
if (Context.hasPrivilege(PrivilegeConstants.VIEW_PATIENTS)) {
Patient p = Context.getPatientService().getPatient(patientId);
model.put("patient", p);
// add encounters if this user can view them
if (Context.hasPrivilege(PrivilegeConstants.VIEW_ENCOUNTERS))
model.put(
"patientEncounters", Context.getEncounterService().getEncountersByPatient(p));
if (Context.hasPrivilege(PrivilegeConstants.VIEW_OBS)) {
List<Obs> patientObs = Context.getObsService().getObservationsByPerson(p);
model.put("patientObs", patientObs);
Obs latestWeight = null;
Obs latestHeight = null;
String bmiAsString = "?";
try {
String weightString = as.getGlobalProperty("concept.weight");
ConceptNumeric weightConcept = null;
if (StringUtils.hasLength(weightString))
weightConcept =
cs.getConceptNumeric(
cs.getConcept(Integer.valueOf(weightString)).getConceptId());
String heightString = as.getGlobalProperty("concept.height");
ConceptNumeric heightConcept = null;
if (StringUtils.hasLength(heightString))
heightConcept =
cs.getConceptNumeric(
cs.getConcept(Integer.valueOf(heightString)).getConceptId());
for (Obs obs : patientObs) {
if (obs.getConcept().equals(weightConcept)) {
if (latestWeight == null
|| obs.getObsDatetime().compareTo(latestWeight.getObsDatetime()) > 0)
latestWeight = obs;
} else if (obs.getConcept().equals(heightConcept)) {
if (latestHeight == null
|| obs.getObsDatetime().compareTo(latestHeight.getObsDatetime()) > 0)
latestHeight = obs;
}
}
if (latestWeight != null) model.put("patientWeight", latestWeight);
if (latestHeight != null) model.put("patientHeight", latestHeight);
if (latestWeight != null && latestHeight != null) {
double weightInKg;
double heightInM;
if (weightConcept.getUnits().equals("kg"))
weightInKg = latestWeight.getValueNumeric();
else if (weightConcept.getUnits().equals("lb"))
weightInKg = latestWeight.getValueNumeric() * 0.45359237;
else
throw new IllegalArgumentException(
"Can't handle units of weight concept: " + weightConcept.getUnits());
if (heightConcept.getUnits().equals("cm"))
heightInM = latestHeight.getValueNumeric() / 100;
else if (heightConcept.getUnits().equals("m"))
heightInM = latestHeight.getValueNumeric();
else if (heightConcept.getUnits().equals("in"))
heightInM = latestHeight.getValueNumeric() * 0.0254;
else
throw new IllegalArgumentException(
"Can't handle units of height concept: " + heightConcept.getUnits());
double bmi = weightInKg / (heightInM * heightInM);
model.put("patientBmi", bmi);
String temp = "" + bmi;
bmiAsString = temp.substring(0, temp.indexOf('.') + 2);
}
} catch (Exception ex) {
if (latestWeight != null && latestHeight != null)
log.error(
"Failed to calculate BMI even though a weight and height were found", ex);
}
model.put("patientBmiAsString", bmiAsString);
} else {
model.put("patientObs", new HashSet<Obs>());
}
// information about whether or not the patient has exited care
Obs reasonForExitObs = null;
String reasonForExitConceptString = as.getGlobalProperty("concept.reasonExitedCare");
if (StringUtils.hasLength(reasonForExitConceptString)) {
Concept reasonForExitConcept = cs.getConcept(reasonForExitConceptString);
if (reasonForExitConcept != null) {
List<Obs> patientExitObs =
Context.getObsService()
.getObservationsByPersonAndConcept(p, reasonForExitConcept);
if (patientExitObs != null) {
log.debug("Exit obs is size " + patientExitObs.size());
if (patientExitObs.size() == 1) {
reasonForExitObs = patientExitObs.iterator().next();
Concept exitReason = reasonForExitObs.getValueCoded();
Date exitDate = reasonForExitObs.getObsDatetime();
if (exitReason != null && exitDate != null) {
patientVariation = "Exited";
}
} else {
if (patientExitObs.size() == 0) {
log.debug("Patient has no reason for exit");
} else {
log.error("Too many reasons for exit - not putting data into model");
}
}
}
}
}
model.put("patientReasonForExit", reasonForExitObs);
if (Context.hasPrivilege(PrivilegeConstants.VIEW_ORDERS)) {
List<DrugOrder> drugOrderList = Context.getOrderService().getDrugOrdersByPatient(p);
model.put("patientDrugOrders", drugOrderList);
List<DrugOrder> currentDrugOrders = new ArrayList<DrugOrder>();
List<DrugOrder> discontinuedDrugOrders = new ArrayList<DrugOrder>();
Date rightNow = new Date();
for (Iterator<DrugOrder> iter = drugOrderList.iterator(); iter.hasNext(); ) {
DrugOrder next = iter.next();
if (next.isCurrent() || next.isFuture()) currentDrugOrders.add(next);
if (next.isDiscontinued(rightNow)) discontinuedDrugOrders.add(next);
}
model.put("currentDrugOrders", currentDrugOrders);
model.put("completedDrugOrders", discontinuedDrugOrders);
List<RegimenSuggestion> standardRegimens =
Context.getOrderService().getStandardRegimens();
if (standardRegimens != null) model.put("standardRegimens", standardRegimens);
}
if (Context.hasPrivilege(PrivilegeConstants.VIEW_PROGRAMS)
&& Context.hasPrivilege(PrivilegeConstants.VIEW_PATIENT_PROGRAMS)) {
model.put(
"patientPrograms",
Context.getProgramWorkflowService()
.getPatientPrograms(p, null, null, null, null, null, false));
model.put(
"patientCurrentPrograms",
Context.getProgramWorkflowService()
.getPatientPrograms(p, null, null, new Date(), new Date(), null, false));
}
model.put("patientId", patientId);
if (p != null) {
personId = p.getPatientId();
model.put("personId", personId);
}
model.put("patientVariation", patientVariation);
}
}
}
// if a person id is available, put person and relationships in the model
if (personId == null) {
o = request.getAttribute("org.openmrs.portlet.personId");
if (o != null) {
personId = (Integer) o;
model.put("personId", personId);
}
}
if (personId != null) {
if (!model.containsKey("person")) {
Person p = (Person) model.get("patient");
if (p == null) p = Context.getPersonService().getPerson(personId);
model.put("person", p);
if (Context.hasPrivilege(PrivilegeConstants.VIEW_RELATIONSHIPS)) {
List<Relationship> relationships = new ArrayList<Relationship>();
relationships.addAll(Context.getPersonService().getRelationshipsByPerson(p));
Map<RelationshipType, List<Relationship>> relationshipsByType =
new HashMap<RelationshipType, List<Relationship>>();
for (Relationship rel : relationships) {
List<Relationship> list = relationshipsByType.get(rel.getRelationshipType());
if (list == null) {
list = new ArrayList<Relationship>();
relationshipsByType.put(rel.getRelationshipType(), list);
}
list.add(rel);
}
model.put("personRelationships", relationships);
model.put("personRelationshipsByType", relationshipsByType);
}
}
}
// if an encounter id is available, put "encounter" and "encounterObs" in the model
o = request.getAttribute("org.openmrs.portlet.encounterId");
if (o != null && !model.containsKey("encounterId")) {
if (!model.containsKey("encounter")) {
if (Context.hasPrivilege(PrivilegeConstants.VIEW_ENCOUNTERS)) {
Encounter e = Context.getEncounterService().getEncounter((Integer) o);
model.put("encounter", e);
if (Context.hasPrivilege(PrivilegeConstants.VIEW_OBS))
model.put("encounterObs", e.getObs());
}
model.put("encounterId", (Integer) o);
}
}
// if a user id is available, put "user" in the model
o = request.getAttribute("org.openmrs.portlet.userId");
if (o != null) {
if (!model.containsKey("user")) {
if (Context.hasPrivilege(PrivilegeConstants.VIEW_USERS)) {
User u = Context.getUserService().getUser((Integer) o);
model.put("user", u);
}
model.put("userId", (Integer) o);
}
}
// if a list of patient ids is available, make a patientset out of it
o = request.getAttribute("org.openmrs.portlet.patientIds");
if (o != null && !"".equals(o) && !model.containsKey("patientIds")) {
if (!model.containsKey("patientSet")) {
Cohort ps = new Cohort((String) o);
model.put("patientSet", ps);
model.put("patientIds", (String) o);
}
}
o = model.get("conceptIds");
if (o != null && !"".equals(o)) {
if (!model.containsKey("conceptMap")) {
log.debug("Found conceptIds parameter: " + o);
Map<Integer, Concept> concepts = new HashMap<Integer, Concept>();
Map<String, Concept> conceptsByStringIds = new HashMap<String, Concept>();
String conceptIds = (String) o;
String[] ids = conceptIds.split(",");
for (String cId : ids) {
try {
Integer i = Integer.valueOf(cId);
Concept c = cs.getConcept(i);
concepts.put(i, c);
conceptsByStringIds.put(i.toString(), c);
} catch (Exception ex) {
}
}
model.put("conceptMap", concepts);
model.put("conceptMapByStringIds", conceptsByStringIds);
}
}
populateModel(request, model);
log.debug(portletPath + " took " + (System.currentTimeMillis() - timeAtStart) + " ms");
}
return new ModelAndView(portletPath, "model", model);
}
/**
*
* 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;
}
/**
* @see EligibleForArtTriggerCalculation#evaluate(java.util.Collection, java.util.Map,
* org.openmrs.calculation.patient.PatientCalculationContext)
* @verifies calculate the obs which triggered a patient to become eligible for ART
* @verifies return null for patients who have never been eligible for ART
*/
@Test
public void evaluate_shouldCalculateEligibilityTrigger() throws Exception {
PatientService ps = Context.getPatientService();
// Confirm patient #6 HIV+ when they're 1 year old and give them very low CD4 soon after
TestUtils.saveObs(
ps.getPatient(6),
Dictionary.getConcept(Dictionary.DATE_OF_HIV_DIAGNOSIS),
TestUtils.date(2008, 05, 27),
TestUtils.date(2010, 1, 1));
TestUtils.saveObs(
ps.getPatient(6),
Dictionary.getConcept(Dictionary.CD4_COUNT),
300.0,
TestUtils.date(2009, 1, 1));
// Give patient #7 low CD4 when they're 3 years old and very low CD4 after
TestUtils.saveObs(
ps.getPatient(7),
Dictionary.getConcept(Dictionary.CD4_COUNT),
900.0,
TestUtils.date(1979, 8, 25));
TestUtils.saveObs(
ps.getPatient(7),
Dictionary.getConcept(Dictionary.CD4_COUNT),
300.0,
TestUtils.date(2009, 1, 1));
// Give patient #8 WHO stage of 3
TestUtils.saveObs(
ps.getPatient(8),
Dictionary.getConcept(Dictionary.CURRENT_WHO_STAGE),
Dictionary.getConcept(Dictionary.WHO_STAGE_3_PEDS),
TestUtils.date(2009, 1, 1));
Context.flushSession();
List<Integer> cohort = Arrays.asList(6, 7, 8, 999);
CalculationResultMap resultMap =
new EligibleForArtTriggerCalculation()
.evaluate(
cohort,
null,
Context.getService(PatientCalculationService.class).createCalculationContext());
Obs patient6Trigger = (Obs) resultMap.get(6).getValue(); // Eligible through HIV confirmation
Assert.assertEquals(Dictionary.DATE_OF_HIV_DIAGNOSIS, patient6Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(2008, 05, 27), patient6Trigger.getValueDate());
Obs patient7Trigger = (Obs) resultMap.get(7).getValue(); // Eligible through CD4 count
Assert.assertEquals(Dictionary.CD4_COUNT, patient7Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(1979, 8, 25), patient7Trigger.getObsDatetime());
Obs patient8Trigger = (Obs) resultMap.get(8).getValue(); // Eligible through WHO stage
Assert.assertEquals(Dictionary.CURRENT_WHO_STAGE, patient8Trigger.getConcept().getUuid());
Assert.assertEquals(TestUtils.date(2009, 1, 1), patient8Trigger.getObsDatetime());
Assert.assertNull(resultMap.get(999)); // Was never eligible for ART
}
private CodeableConceptDt buildCode(Obs observation) {
if (null == observation.getConcept()) {
return null;
}
return codeableConceptService.addTRCodingOrDisplay(observation.getConcept());
}
