Java Code Examples for org.hl7.fhir.r4.model.Bundle.BundleEntryComponent#getResource()

private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
  String folder = Utilities.getDirectoryForFile(src);
  Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
  for (BundleEntryComponent be : bnd.getEntry()) {
    Resource r = be.getResource();
    if (r != null) {
      if (StringUtils.isBlank(r.getId())) {
        if (r instanceof MetadataResource)
          r.setId(tail((MetadataResource) r));
      }
      if (!StringUtils.isBlank(r.getId())) {
        String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json");
        if (!new File(tgt).exists())
          new JsonParser().compose(new FileOutputStream(tgt), r);
      }
    }
  }
}
 

public static Resource getById(Bundle feed, ResourceType type, String reference) {
  for (BundleEntryComponent item : feed.getEntry()) {
    if (item.getResource().getId().equals(reference) && item.getResource().getResourceType() == type)
      return item.getResource();
  }
  return null;
}
 

/**
 * Find the provider entry in this bundle, and return the associated "fullUrl" attribute.
 *
 * @param provider A given provider.
 * @param bundle   The current bundle being generated.
 * @return Provider.fullUrl if found, otherwise null.
 */
private static String findProviderUrl(Provider provider, Bundle bundle) {
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource().fhirType().equals("Organization")) {
      Organization org = (Organization) entry.getResource();
      if (org.getIdentifierFirstRep().getValue() != null
          && org.getIdentifierFirstRep().getValue().equals(provider.getResourceID())) {
        return entry.getFullUrl();
      }
    }
  }
  return null;
}
 

/**
 * Find the Location entry in this bundle for the given provider, and return the
 * "fullUrl" attribute.
 *
 * @param provider A given provider.
 * @param bundle The current bundle being generated.
 * @return Location.fullUrl if found, otherwise null.
 */
private static String findLocationUrl(Provider provider, Bundle bundle) {
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource().fhirType().equals("Location")) {
      org.hl7.fhir.r4.model.Location location =
          (org.hl7.fhir.r4.model.Location) entry.getResource();
      if (location.getManagingOrganization()
          .getReference().endsWith(provider.getResourceID())) {
        return entry.getFullUrl();
      }
    }
  }
  return null;
}
 

/**
 * Create an entry for the given Claim, which references a Medication.
 *
 * @param person         The person being prescribed medication
 * @param personEntry     Entry for the person
 * @param bundle          The Bundle to add to
 * @param encounterEntry  The current Encounter
 * @param claim           the Claim object
 * @param medicationEntry The Entry for the Medication object, previously created
 * @return the added Entry
 */
private static BundleEntryComponent medicationClaim(
    Person person, BundleEntryComponent personEntry,
    Bundle bundle, BundleEntryComponent encounterEntry, Claim claim,
    BundleEntryComponent medicationEntry) {
  
  org.hl7.fhir.r4.model.Claim claimResource = new org.hl7.fhir.r4.model.Claim();
  org.hl7.fhir.r4.model.Encounter encounterResource =
      (org.hl7.fhir.r4.model.Encounter) encounterEntry.getResource();

  claimResource.setStatus(ClaimStatus.ACTIVE);
  CodeableConcept type = new CodeableConcept();
  type.getCodingFirstRep()
    .setSystem("http://terminology.hl7.org/CodeSystem/claim-type")
    .setCode("pharmacy");
  claimResource.setType(type);
  claimResource.setUse(org.hl7.fhir.r4.model.Claim.Use.CLAIM);

  // Get the insurance info at the time that the encounter occurred.
  InsuranceComponent insuranceComponent = new InsuranceComponent();
  insuranceComponent.setSequence(1);
  insuranceComponent.setFocal(true);
  insuranceComponent.setCoverage(new Reference().setDisplay(claim.payer.getName()));
  claimResource.addInsurance(insuranceComponent);

  // duration of encounter
  claimResource.setBillablePeriod(encounterResource.getPeriod());
  claimResource.setCreated(encounterResource.getPeriod().getEnd());

  claimResource.setPatient(new Reference(personEntry.getFullUrl()));
  claimResource.setProvider(encounterResource.getServiceProvider());

  // set the required priority
  CodeableConcept priority = new CodeableConcept();
  priority.getCodingFirstRep()
    .setSystem("http://terminology.hl7.org/CodeSystem/processpriority")
    .setCode("normal");
  claimResource.setPriority(priority);

  // add item for encounter
  claimResource.addItem(new ItemComponent(new PositiveIntType(1),
        encounterResource.getTypeFirstRep())
      .addEncounter(new Reference(encounterEntry.getFullUrl())));

  // add prescription.
  claimResource.setPrescription(new Reference(medicationEntry.getFullUrl()));

  Money moneyResource = new Money();
  moneyResource.setValue(claim.getTotalClaimCost());
  moneyResource.setCurrency("USD");
  claimResource.setTotal(moneyResource);

  return newEntry(bundle, claimResource);
}
 

/**
 * Add a MedicationAdministration if needed for the given medication.
 * 
 * @param personEntry       The Entry for the Person
 * @param bundle            Bundle to add the MedicationAdministration to
 * @param encounterEntry    Current Encounter entry
 * @param medication        The Medication
 * @param medicationRequest The related medicationRequest
 * @return The added Entry
 */
private static BundleEntryComponent medicationAdministration(
    BundleEntryComponent personEntry, Bundle bundle, BundleEntryComponent encounterEntry,
    Medication medication, MedicationRequest medicationRequest) {

  MedicationAdministration medicationResource = new MedicationAdministration();

  medicationResource.setSubject(new Reference(personEntry.getFullUrl()));
  medicationResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = medication.codes.get(0);
  String system = code.system.equals("SNOMED-CT") ? SNOMED_URI : RXNORM_URI;

  medicationResource.setMedication(mapCodeToCodeableConcept(code, system));
  medicationResource.setEffective(new DateTimeType(new Date(medication.start)));

  medicationResource.setStatus("completed");

  if (medication.prescriptionDetails != null) {
    JsonObject rxInfo = medication.prescriptionDetails;
    MedicationAdministrationDosageComponent dosage =
        new MedicationAdministrationDosageComponent();

    // as_needed is false
    if ((rxInfo.has("dosage")) && (!rxInfo.has("as_needed"))) {
      Quantity dose = new SimpleQuantity()
          .setValue(rxInfo.get("dosage").getAsJsonObject().get("amount").getAsDouble());
      dosage.setDose((SimpleQuantity) dose);

      if (rxInfo.has("instructions")) {
        for (JsonElement instructionElement : rxInfo.get("instructions").getAsJsonArray()) {
          JsonObject instruction = instructionElement.getAsJsonObject();

          dosage.setText(instruction.get("display").getAsString());
        }
      }
    }
    if (rxInfo.has("refills")) {
      SimpleQuantity rate = new SimpleQuantity();
      rate.setValue(rxInfo.get("refills").getAsLong());
      dosage.setRate(rate);
    }
    medicationResource.setDosage(dosage);
  }

  if (!medication.reasons.isEmpty()) {
    // Only one element in list
    Code reason = medication.reasons.get(0);
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.getResource().fhirType().equals("Condition")) {
        Condition condition = (Condition) entry.getResource();
        // Only one element in list
        Coding coding = condition.getCode().getCoding().get(0);
        if (reason.code.equals(coding.getCode())) {
          medicationResource.addReasonReference().setReference(entry.getFullUrl());
        }
      }
    }
  }

  BundleEntryComponent medicationAdminEntry = newEntry(bundle, medicationResource);
  return medicationAdminEntry;
}
 

@Test
public void testSampledDataExport() throws Exception {

  Person person = new Person(0L);
  person.attributes.put(Person.GENDER, "F");
  person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
  person.attributes.put(Person.RACE, "other");
  person.attributes.put(Person.ETHNICITY, "hispanic");
  person.attributes.put(Person.INCOME, Integer.parseInt(Config
      .get("generate.demographics.socioeconomic.income.poverty")) * 2);
  person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);

  person.history = new LinkedList<>();
  Provider mock = Mockito.mock(Provider.class);
  mock.uuid = "Mock-UUID";
  person.setProvider(EncounterType.AMBULATORY, mock);
  person.setProvider(EncounterType.WELLNESS, mock);
  person.setProvider(EncounterType.EMERGENCY, mock);
  person.setProvider(EncounterType.INPATIENT, mock);

  Long time = System.currentTimeMillis();
  long birthTime = time - Utilities.convertTime("years", 35);
  person.attributes.put(Person.BIRTHDATE, birthTime);

  Payer.loadNoInsurance();
  for (int i = 0; i < person.payerHistory.length; i++) {
    person.setPayerAtAge(i, Payer.noInsurance);
  }
  
  Module module = TestHelper.getFixture("observation.json");
  
  State encounter = module.getState("SomeEncounter");
  assertTrue(encounter.process(person, time));
  person.history.add(encounter);
  
  State physiology = module.getState("Simulate_CVS");
  assertTrue(physiology.process(person, time));
  person.history.add(physiology);
  
  State sampleObs = module.getState("SampledDataObservation");
  assertTrue(sampleObs.process(person, time));
  person.history.add(sampleObs);
  
  FhirContext ctx = FhirContext.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Observation) {
      Observation obs = (Observation) entry.getResource();
      assertTrue(obs.getValue() instanceof SampledData);
      SampledData data = (SampledData) obs.getValue();
      assertEquals(10, data.getPeriod().doubleValue(), 0.001); // 0.01s == 10ms
      assertEquals(3, (int) data.getDimensions());
    }
  }
}
 

@Test
public void testObservationAttachment() throws Exception {

  Person person = new Person(0L);
  person.attributes.put(Person.GENDER, "F");
  person.attributes.put(Person.FIRST_LANGUAGE, "spanish");
  person.attributes.put(Person.RACE, "other");
  person.attributes.put(Person.ETHNICITY, "hispanic");
  person.attributes.put(Person.INCOME, Integer.parseInt(Config
      .get("generate.demographics.socioeconomic.income.poverty")) * 2);
  person.attributes.put(Person.OCCUPATION_LEVEL, 1.0);
  person.attributes.put("Pulmonary Resistance", 0.1552);
  person.attributes.put("BMI Multiplier", 0.055);
  person.setVitalSign(VitalSign.BMI, 21.0);

  person.history = new LinkedList<>();
  Provider mock = Mockito.mock(Provider.class);
  mock.uuid = "Mock-UUID";
  person.setProvider(EncounterType.AMBULATORY, mock);
  person.setProvider(EncounterType.WELLNESS, mock);
  person.setProvider(EncounterType.EMERGENCY, mock);
  person.setProvider(EncounterType.INPATIENT, mock);

  Long time = System.currentTimeMillis();
  long birthTime = time - Utilities.convertTime("years", 35);
  person.attributes.put(Person.BIRTHDATE, birthTime);

  Payer.loadNoInsurance();
  for (int i = 0; i < person.payerHistory.length; i++) {
    person.setPayerAtAge(i, Payer.noInsurance);
  }
  
  Module module = TestHelper.getFixture("observation.json");
  
  State physiology = module.getState("Simulate_CVS");
  assertTrue(physiology.process(person, time));
  person.history.add(physiology);
  
  State encounter = module.getState("SomeEncounter");
  assertTrue(encounter.process(person, time));
  person.history.add(encounter);
  
  State chartState = module.getState("ChartObservation");
  assertTrue(chartState.process(person, time));
  person.history.add(chartState);
  
  State urlState = module.getState("UrlObservation");
  assertTrue(urlState.process(person, time));
  person.history.add(urlState);
  
  FhirContext ctx = FhirContext.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
  Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
  
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource() instanceof Media) {
      Media media = (Media) entry.getResource();
      if (media.getContent().getData() != null) {
        assertEquals(400, media.getWidth());
        assertEquals(200, media.getHeight());
        assertEquals("Invasive arterial pressure", media.getReasonCode().get(0).getText());
        assertTrue(Base64.isBase64(media.getContent().getDataElement().getValueAsString()));
      } else if (media.getContent().getUrl() != null) {
        assertEquals("https://example.com/image/12498596132", media.getContent().getUrl());
        assertEquals("en-US", media.getContent().getLanguage());
        assertTrue(media.getContent().getSize() > 0);
      } else {
        fail("Invalid Media element in output JSON");
      }
    }
  }
}