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

private void loadStructureDefinitions(FhirContext theContext, Map<String, StructureDefinition> theCodeSystems, String theClasspath) {
  logD("SNOMEDMOCK Loading structure definitions from classpath: "+ theClasspath);
  InputStream valuesetText = SNOMEDUKMockValidationSupport.class.getResourceAsStream(theClasspath);
  if (valuesetText != null) {
    InputStreamReader reader = new InputStreamReader(valuesetText, Charsets.UTF_8);

    Bundle bundle = theContext.newXmlParser().parseResource(Bundle.class, reader);
    for (BundleEntryComponent next : bundle.getEntry()) {
      if (next.getResource() instanceof StructureDefinition) {
        StructureDefinition nextSd = (StructureDefinition) next.getResource();
        nextSd.getText().setDivAsString("");
        String system = nextSd.getUrl();
        if (isNotBlank(system)) {
          theCodeSystems.put(system, nextSd);
        }
      }
    }
  } else {
    log.warn("Unable to load resource: {}", theClasspath);
  }
}
 

public Resource resolve(String value) {
  if (value.startsWith("#")) {
    for (Resource r : resourceResource.getContained()) {
      if (r.getId().equals(value.substring(1)))
        return r;
    }
    return null;
  }
  if (bundleResource != null) {
    for (BundleEntryComponent be : bundleResource.getEntry()) {
      if (be.getFullUrl().equals(value))
        return be.getResource();
      if (value.equals(be.getResource().fhirType()+"/"+be.getResource().getId()))
        return be.getResource();
    }
  }
  return null;
}
 

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();
}
 

/**
 * Create an entry for the given Claim, which references a 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(BundleEntryComponent personEntry,
    Bundle bundle, BundleEntryComponent encounterEntry, Claim claim,
    BundleEntryComponent medicationEntry) {
  org.hl7.fhir.dstu3.model.Claim claimResource = new org.hl7.fhir.dstu3.model.Claim();
  org.hl7.fhir.dstu3.model.Encounter encounterResource =
      (org.hl7.fhir.dstu3.model.Encounter) encounterEntry.getResource();

  claimResource.setStatus(ClaimStatus.ACTIVE);
  claimResource.setUse(org.hl7.fhir.dstu3.model.Claim.Use.COMPLETE);

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

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

  // add item for encounter
  claimResource.addItem(new org.hl7.fhir.dstu3.model.Claim.ItemComponent(new PositiveIntType(1))
      .addEncounter(new Reference(encounterEntry.getFullUrl())));

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

  Money moneyResource = new Money();
  moneyResource.setValue(claim.getTotalClaimCost());
  moneyResource.setCode("USD");
  moneyResource.setSystem("urn:iso:std:iso:4217");
  claimResource.setTotal(moneyResource);

  return newEntry(bundle, claimResource);
}
 

/**
 * 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;
}
 

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);
    }
  }
}
 

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 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;
}
 

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;
}
 

@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
  if (codeSystems.containsKey(system)) {
    return true;
  } else if (nonSupportedCodeSystems.contains(system)) {
    return false;
  } else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com")
    || system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:")) {
    return false;
  } else {
    if (noTerminologyServer) {
      return false;
    }
    if (bndCodeSystems == null) {
      try {
        tlog("Terminology server: Check for supported code systems for " + system);
        bndCodeSystems = txServer.fetchFeed(txServer.getAddress()
          + "/CodeSystem?content-mode=not-present&_summary=true&_count=1000");
      } catch (Exception e) {
        if (canRunWithoutTerminology) {
          noTerminologyServer = true;
          log("==============!! Running without terminology server !!============== (" + e
            .getMessage() + ")");
          return false;
        } else {
          throw new TerminologyServiceException(e);
        }
      }
    }
    if (bndCodeSystems != null) {
      for (BundleEntryComponent be : bndCodeSystems.getEntry()) {
        CodeSystem cs = (CodeSystem) be.getResource();
        if (!codeSystems.containsKey(cs.getUrl())) {
          codeSystems.put(cs.getUrl(), null);
        }
      }
    }
    if (codeSystems.containsKey(system)) {
      return true;
    }
  }
  nonSupportedCodeSystems.add(system);
  return false;
}
 

/**
 * 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");
      }
    }
  }
}