Java Code Examples for org.hl7.fhir.dstu3.model.Bundle#getEntry()

private Bundle createTransactionBundle(Bundle bundle) {
    Bundle transactionBundle;
    if (bundle != null) {
        if (bundle.hasType() && bundle.getType() == Bundle.BundleType.TRANSACTION) {
            transactionBundle = bundle;
        } else {
            transactionBundle = new Bundle().setType(Bundle.BundleType.TRANSACTION);
            if (bundle.hasEntry()) {
                for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
                    if (entry.hasResource()) {
                        transactionBundle.addEntry(createTransactionEntry(entry.getResource()));
                    }
                }
            }
        }
    } else {
        transactionBundle = new Bundle().setType(Bundle.BundleType.TRANSACTION).setEntry(new ArrayList<>());
    }

    return transactionBundle;
}
 

private void addEvaluatedResourcesToParameters(Bundle contained, Parameters parameters) {
    Map<String, Resource> resourceMap = new HashMap<>();
    if (contained.hasEntry()) {
        for (Bundle.BundleEntryComponent entry : contained.getEntry()) {
            if (entry.hasResource() && !(entry.getResource() instanceof ListResource)) {
                if (!resourceMap.containsKey(entry.getResource().getIdElement().getValue())) {
                    parameters.addParameter(new Parameters.ParametersParameterComponent().setName("resource")
                            .setResource(entry.getResource()));

                    resourceMap.put(entry.getResource().getIdElement().getValue(), entry.getResource());

                    resolveReferences(entry.getResource(), parameters, resourceMap);
                }
            }
        }
    }
}
 

@Override
public void afterProducer(Exchange exchange) {
    Message in = exchange.getIn();
    Bundle bundle = in.getBody(Bundle.class);
    if (bundle == null) {
        return;
    }

    List<String> results = new ArrayList<>();
    for (Bundle.BundleEntryComponent entry: bundle.getEntry()) {
        String resource = fhirContext.newXmlParser().encodeResourceToString(entry.getResource());
        results.add(resource);
    }

    in.setBody(results);
}
 

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) {
      String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json");
      new JsonParser().compose(new FileOutputStream(tgt), r);
    }
  }
}
 

/**
 * Find the Practitioner entry in this bundle, and return the associated "fullUrl"
 * attribute.
 * @param clinician A given clinician.
 * @param bundle The current bundle being generated.
 * @return Practitioner.fullUrl if found, otherwise null.
 */
private static String findPractitioner(Clinician clinician, Bundle bundle) {
  for (BundleEntryComponent entry : bundle.getEntry()) {
    if (entry.getResource().fhirType().equals("Practitioner")) {
      Practitioner doc = (Practitioner) entry.getResource();
      if (doc.getIdentifierFirstRep().getValue().equals("" + clinician.identifier)) {
        return entry.getFullUrl();
      }
    }
  }
  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().equals(provider.getResourceID())) {
        return entry.getFullUrl();
      }
    }
  }
  return null;
}
 

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;
}
 

public boolean generate(Bundle b, boolean evenIfAlreadyHasNarrative) throws EOperationOutcome, FHIRException, IOException {
  boolean res = false;
  this.bundle = b;
  for (BundleEntryComponent be : b.getEntry()) {
    if (be.hasResource() && be.getResource() instanceof DomainResource) {
      DomainResource dr = (DomainResource) be.getResource();
      if (evenIfAlreadyHasNarrative || !dr.getText().hasDiv())
        res = generate(new ResourceContext(b, dr), dr) || res;
    }
  }
  return res;
}
 

private static boolean hasUnits(Bundle bundle) {
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (ToolingExtensions.getAllowedUnits(de.getElement().get(0)) != null)
      return true;
  }
  return false;
}
 

private static boolean hasType(Bundle bundle) {
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (de.getElement().get(0).hasType())
      return true;
  }
  return false;
}
 

private static boolean hasCode(Bundle bundle) {
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (de.getElement().get(0).hasCode())
      return true;
  }
  return false;
}
 

private static boolean hasBinding(Bundle bundle) {
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (de.getElement().get(0).hasBinding())
      return true;
  }
  return false;
}
 

private static boolean hasExtension(Bundle bundle, String url) {
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (ToolingExtensions.hasExtension(de, url))
      return true;
  }
  return false;
}
 

public static String representDataElementCollection(IWorkerContext context, Bundle bundle, boolean profileLink, String linkBase) {
  StringBuilder b = new StringBuilder();
  DataElement common = showDECHeader(b, bundle);
  b.append("<table class=\"grid\">\r\n"); 
  List<String> cols = chooseColumns(bundle, common, b, profileLink);
  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    renderDE(de, cols, b, profileLink, linkBase);
  }
  b.append("</table>\r\n");
  return b.toString();
}
 

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

private static DataElement showDECHeader(StringBuilder b, Bundle bundle) {
  DataElement meta = new DataElement();
  DataElement prototype = (DataElement) bundle.getEntry().get(0).getResource();
  meta.setPublisher(prototype.getPublisher());
  meta.getContact().addAll(prototype.getContact());
  meta.setStatus(prototype.getStatus());
  meta.setDate(prototype.getDate());
  meta.addElement().getType().addAll(prototype.getElement().get(0).getType());

  for (BundleEntryComponent e : bundle.getEntry()) {
    DataElement de = (DataElement) e.getResource();
    if (!Base.compareDeep(de.getPublisherElement(), meta.getPublisherElement(), false))
      meta.setPublisherElement(null);
    if (!Base.compareDeep(de.getContact(), meta.getContact(), false))
      meta.getContact().clear();
    if (!Base.compareDeep(de.getStatusElement(), meta.getStatusElement(), false))
      meta.setStatusElement(null);
    if (!Base.compareDeep(de.getDateElement(), meta.getDateElement(), false))
      meta.setDateElement(null);
    if (!Base.compareDeep(de.getElement().get(0).getType(), meta.getElement().get(0).getType(), false))
      meta.getElement().get(0).getType().clear();
  }
  if (meta.hasPublisher() || meta.hasContact() || meta.hasStatus() || meta.hasDate() /* || meta.hasType() */) {
    b.append("<table class=\"grid\">\r\n"); 
    if (meta.hasPublisher())
      b.append("<tr><td>Publisher:</td><td>"+meta.getPublisher()+"</td></tr>\r\n");
    if (meta.hasContact()) {
      b.append("<tr><td>Contacts:</td><td>");
      boolean firsti = true;
      for (ContactDetail c : meta.getContact()) {
        if (firsti)
          firsti = false;
        else
          b.append("<br/>");
        if (c.hasName())
          b.append(Utilities.escapeXml(c.getName())+": ");
        boolean first = true;
        for (ContactPoint cp : c.getTelecom()) {
          if (first)
            first = false;
          else
            b.append(", ");
          renderContactPoint(b, cp);
        }
      }
      b.append("</td></tr>\r\n");
    }
    if (meta.hasStatus())
      b.append("<tr><td>Status:</td><td>"+meta.getStatus().toString()+"</td></tr>\r\n");
    if (meta.hasDate())
      b.append("<tr><td>Date:</td><td>"+meta.getDateElement().asStringValue()+"</td></tr>\r\n");
    if (meta.getElement().get(0).hasType())
      b.append("<tr><td>Type:</td><td>"+renderType(meta.getElement().get(0).getType())+"</td></tr>\r\n");
    b.append("</table>\r\n"); 
  }  
  return meta;
}
 

/**
 * 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(MedicationAdministrationStatus.fromCode("completed"));

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

    // as_needed is true if present
    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());
        }
      }
    }
    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;
}
 

/**
 * Map the given CarePlan to a FHIR CarePlan resource, and add it to the given Bundle.
 *
 * @param personEntry The Entry for the Person
 * @param bundle Bundle to add the CarePlan to
 * @param encounterEntry Current Encounter entry
 * @param carePlan The CarePlan to map to FHIR and add to the bundle
 * @return The added Entry
 */
private static BundleEntryComponent careplan(BundleEntryComponent personEntry, Bundle bundle,
    BundleEntryComponent encounterEntry, CarePlan carePlan) {
  org.hl7.fhir.dstu3.model.CarePlan careplanResource = new org.hl7.fhir.dstu3.model.CarePlan();
  careplanResource.setIntent(CarePlanIntent.ORDER);
  careplanResource.setSubject(new Reference(personEntry.getFullUrl()));
  careplanResource.setContext(new Reference(encounterEntry.getFullUrl()));

  Code code = carePlan.codes.get(0);
  careplanResource.addCategory(mapCodeToCodeableConcept(code, SNOMED_URI));

  CarePlanActivityStatus activityStatus;
  GoalStatus goalStatus;

  Period period = new Period().setStart(new Date(carePlan.start));
  careplanResource.setPeriod(period);
  if (carePlan.stop != 0L) {
    period.setEnd(new Date(carePlan.stop));
    careplanResource.setStatus(CarePlanStatus.COMPLETED);
    activityStatus = CarePlanActivityStatus.COMPLETED;
    goalStatus = GoalStatus.ACHIEVED;
  } else {
    careplanResource.setStatus(CarePlanStatus.ACTIVE);
    activityStatus = CarePlanActivityStatus.INPROGRESS;
    goalStatus = GoalStatus.INPROGRESS;
  }

  if (!carePlan.activities.isEmpty()) {
    for (Code activity : carePlan.activities) {
      CarePlanActivityComponent activityComponent = new CarePlanActivityComponent();
      CarePlanActivityDetailComponent activityDetailComponent =
          new CarePlanActivityDetailComponent();

      activityDetailComponent.setStatus(activityStatus);

      activityDetailComponent.setCode(mapCodeToCodeableConcept(activity, SNOMED_URI));
      activityComponent.setDetail(activityDetailComponent);

      careplanResource.addActivity(activityComponent);
    }
  }

  if (!carePlan.reasons.isEmpty()) {
    // Only one element in list
    Code reason = carePlan.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())) {
          careplanResource.addAddresses().setReference(entry.getFullUrl());
        }
      }
    }
  }

  for (JsonObject goal : carePlan.goals) {
    BundleEntryComponent goalEntry = caregoal(bundle, goalStatus, goal);
    careplanResource.addGoal().setReference(goalEntry.getFullUrl());
  }

  return newEntry(bundle, careplanResource);
}
 

@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.forDstu3();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirStu3.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.forDstu3();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  String fhirJson = FhirStu3.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");
      }
    }
  }
}