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

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);
      }
    }
  }
}
 

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);
                }
            }
        }
    }
}
 

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;
}
 

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 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;
}
 

/**
 * 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;
}
 

private void handleResource(IBaseResource resource) {
  if (resource instanceof Bundle) {
    Bundle bundle = (Bundle) resource;
    for (BundleEntryComponent entry : bundle.getEntry()) {
      if (entry.hasResource()) {
        handleResource(entry.getResource());
      }
    }
  } else {
    resources.add(resource);
    if (resource instanceof CodeSystem) {
      CodeSystem cs = (CodeSystem) resource;
      resourcesMap.put(cs.getUrl(), cs);
      codeSystemMap.put(cs.getUrl(), cs);
    } else if (resource instanceof ValueSet) {
      ValueSet vs = (ValueSet) resource;
      resourcesMap.put(vs.getUrl(), vs);

      if (vs.hasExpansion() && vs.getExpansion().hasContains()) {
        processExpansion(vs.getExpansion().getContains());
      }
    } else if (resource instanceof StructureDefinition) {
      StructureDefinition sd = (StructureDefinition) resource;
      resourcesMap.put(sd.getUrl(), sd);
      definitions.add(sd);
      definitionsMap.put(sd.getUrl(), sd);
    }
  }
}
 

/**
 * 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 testFHIRR4Export() throws Exception {
  TestHelper.loadTestProperties();
  Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
  Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());

  FhirContext ctx = FhirContext.forR4();
  IParser parser = ctx.newJsonParser().setPrettyPrint(true);
  ValidationResources validator = new ValidationResources();
  List<String> validationErrors = new ArrayList<String>();

  int numberOfPeople = 10;
  Generator generator = new Generator(numberOfPeople);
  
  generator.options.overflow = false;

  for (int i = 0; i < numberOfPeople; i++) {
    int x = validationErrors.size();
    TestHelper.exportOff();
    Person person = generator.generatePerson(i);
    FhirR4.TRANSACTION_BUNDLE = person.random.nextBoolean();
    FhirR4.USE_US_CORE_IG = person.random.nextBoolean();
    FhirR4.USE_SHR_EXTENSIONS = false;
    String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
    // Check that the fhirJSON doesn't contain unresolved SNOMED-CT strings
    // (these should have been converted into URIs)
    if (fhirJson.contains("SNOMED-CT")) {
      validationErrors.add(
          "JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
    }
    // Now validate the resource...
    IBaseResource resource = ctx.newJsonParser().parseResource(fhirJson);
    ValidationResult result = validator.validateR4(resource);
    if (!result.isSuccessful()) {
      // If the validation failed, let's crack open the Bundle and validate
      // each individual entry.resource to get context-sensitive error
      // messages...
      Bundle bundle = parser.parseResource(Bundle.class, fhirJson);
      for (Bundle.BundleEntryComponent entry : bundle.getEntry()) {
        ValidationResult eresult = validator.validateR4(entry.getResource());
        if (!eresult.isSuccessful()) {
          for (SingleValidationMessage emessage : eresult.getMessages()) {
            boolean valid = false;
            if (emessage.getMessage().contains("@ AllergyIntolerance ait-2")) {
              /*
               * The ait-2 invariant:
               * Description:
               * AllergyIntolerance.clinicalStatus SHALL NOT be present
               * if verification Status is entered-in-error
               * Expression:
               * verificationStatus!='entered-in-error' or clinicalStatus.empty()
               */
              valid = true;
            } else if (emessage.getMessage().contains("@ ExplanationOfBenefit dom-3")) {
              /*
               * For some reason, it doesn't like the contained ServiceRequest and contained
               * Coverage resources in the ExplanationOfBenefit, both of which are
               * properly referenced. Running $validate on test servers finds this valid...
               */
              valid = true;
            } else if (emessage.getMessage().contains(
                "per-1: If present, start SHALL have a lower value than end")) {
              /*
               * The per-1 invariant does not account for daylight savings time... so, if the
               * daylight savings switch happens between the start and end, the validation
               * fails, even if it is valid.
               */
              valid = true; // ignore this error
            } else if (emessage.getMessage().contains("[active, inactive, entered-in-error]")
                || emessage.getMessage().contains("MedicationStatusCodes-list")) {
              /*
               * MedicationStatement.status has more legal values than this... including
               * completed and stopped.
               */
              valid = true;
            }
            if (!valid) {
              System.out.println(parser.encodeResourceToString(entry.getResource()));
              System.out.println("ERROR: " + emessage.getMessage());
              validationErrors.add(emessage.getMessage());
            }
          }
        }
      }
    }
    int y = validationErrors.size();
    if (x != y) {
      Exporter.export(person, System.currentTimeMillis());
    }
  }
  assertTrue("Validation of exported FHIR bundle failed: "
      + String.join("|", validationErrors), validationErrors.size() == 0);
}
 

@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");
      }
    }
  }
}