public Throwable fhir(SparseArray<GlucoseRecord> records) {
try {
Patient p = getPatient();
Log.d(TAG, "converting glucoserecrods to observations now");
Device d = initializeDevice(p);
// do conditional update here so the device is updated if needed
String ident = getConditionalUrl(d, d.getIdentifierFirstRep());
String a = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(d);
IdDt id = (IdDt) client.update().resource(d).conditionalByUrl(ident).execute().getId();
d.setId(id);
DeviceMetric metric = initializeDeviceMetric(d);
metric.setId(
client
.create()
.resource(metric)
.conditionalByUrl(getConditionalUrl(metric, metric.getIdentifier()))
.execute()
.getId());
for (int i = 0; i < records.size(); i++) {
int j = records.keyAt(i);
GlucoseRecord r = records.get(j);
Log.d(TAG, "creating quantity");
QuantityDt qdt = initializeQuantityDt(r);
Observation o = initializeObservation(p, metric, r, qdt);
Log.d(TAG, "submitting to server...");
// client.update().resource(o).conditionalByUrl("Observation?identifier=http://...%7Cid").encodedJson().execute();
IdDt did =
(IdDt)
client
.update()
.resource(o)
.conditionalByUrl(getConditionalUrl(o, o.getIdentifierFirstRep()))
.execute()
.getId();
o.setId(did);
String s = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o);
Log.d(TAG, "... done");
}
} catch (Throwable e) {
return e;
}
return null;
}
@Search(queryName = "stitchedInclude")
public List<DiagnosticReport> stitchedInclude() {
Practitioner pr1 = new Practitioner();
pr1.setId("Practitioner/001");
pr1.getName().addFamily("Pract1");
Practitioner pr2 = new Practitioner();
pr2.setId("Practitioner/002");
pr2.getName().addFamily("Pract2");
Practitioner pr3 = new Practitioner();
pr3.setId("Practitioner/003");
pr3.getName().addFamily("Pract3");
Observation o1 = new Observation();
o1.getCode().setText("Obs1");
o1.addPerformer().setResource(pr1);
Observation o2 = new Observation();
o2.getCode().setText("Obs2");
o2.addPerformer().setResource(pr2);
Observation o3 = new Observation();
o3.getCode().setText("Obs3");
o3.addPerformer().setResource(pr3);
DiagnosticReport rep = new DiagnosticReport();
rep.setId("DiagnosticReport/999");
rep.getName().setText("Rep");
rep.addResult().setResource(o1);
rep.addResult().setResource(o2);
rep.addResult().setResource(o3);
return Collections.singletonList(rep);
}
private Observation newObservation(QuantityDt value) {
Log.d(TAG, "creating new observation");
Observation o = new Observation();
o.setValue(value);
o.getResourceMetadata()
.put(
ResourceMetadataKeyEnum.PROFILES,
"http://hl7.org/fhir/StructureDefinition/devicemetricobservation");
o.setStatus(ObservationStatusEnum.FINAL);
return o;
}
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;
}
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 testNullFlavorCompositeXml() throws Exception {
Observation observation = new Observation();
observation
.getCode()
.addCoding()
.addUndeclaredExtension(
false,
"http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor",
new StringDt("UNK"));
IParser parser = ctx.newXmlParser().setPrettyPrint(true);
String xml = parser.encodeResourceToString(observation);
ourLog.info(xml);
observation = (Observation) parser.parseResource(xml);
assertEquals(1, observation.getCode().getCoding().get(0).getUndeclaredExtensions().size());
}
@Test
public void testNullFlavorPrimitiveJson() throws Exception {
Observation observation = new Observation();
observation
.getCode()
.getCoding()
.add(new CodingDt().setSystem("http://loinc.org").setCode("3141-9"));
observation
.getStatusElement()
.addUndeclaredExtension(
false,
"http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor",
new StringDt("UNK"));
IParser parser = ctx.newJsonParser().setPrettyPrint(true);
String json = parser.encodeResourceToString(observation);
ourLog.info(json);
observation = (Observation) parser.parseResource(json);
assertEquals(1, observation.getStatusElement().getUndeclaredExtensions().size());
}
private Observation initializeObservation(
Patient p, DeviceMetric metric, GlucoseRecord r, QuantityDt qdt) {
log("Initializing observation");
Observation o = newObservation(qdt);
o.setCode(createCode(r.unit));
o.setSubject(newResourceReference(p.getId()));
o.setDevice(newResourceReference(metric.getId()));
// set date and time for observation
DateTimeDt dt = new DateTimeDt();
dt.setValue(r.time.getTime());
o.setEffective(dt);
o.setIdentifier(
Arrays.asList(
getIdentifier(
"/devices/".concat("" + deviceInfo.getSysID()), "" + r.getSequenceNumber())));
// set narrative
o.setText(getNarrative(o));
log("Initializing observation done");
return o;
}
private void mapCode(Obs openmrsObs, Observation fhirObservation) {
CodeableConceptDt name = buildCode(openmrsObs);
if (null != name) {
fhirObservation.setCode(name);
}
}
private void mapValue(Obs openmrsObs, Observation fhirObservation) {
IDatatype value = observationValueMapper.map(openmrsObs);
if (null != value) {
fhirObservation.setValue(value);
}
}
