org.hl7.fhir.dstu3.model.Patient Java Examples

public static void main(String[] theArgs) {
   FhirContext ctx = FhirContext.forDstu3();
   IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");

   // Build a search and execute it
   Bundle response = client.search()
      .forResource(Patient.class)
      .where(Patient.NAME.matches().value("Test"))
      .and(Patient.BIRTHDATE.before().day("2014-01-01"))
      .count(100)
      .returnBundle(Bundle.class)
      .execute();

   // How many resources did we find?
   System.out.println("Responses: " + response.getTotal());

   // Print the ID of the first one
   System.out.println("First response ID: " + response.getEntry().get(0).getResource().getId());
}
 

@Update
public MethodOutcome update(HttpServletRequest theRequest, @ResourceParam Patient patient, @IdParam IdType theId,@ConditionalUrlParam String theConditional, RequestDetails theRequestDetails) {

    log.debug("Update Patient Provider called");
    
    resourcePermissionProvider.checkPermission("update");

    MethodOutcome method = new MethodOutcome();
    method.setCreated(true);
    OperationOutcome opOutcome = new OperationOutcome();

    method.setOperationOutcome(opOutcome);
    Patient newPatient = null;
    try {
        newPatient = patientDao.update(ctx, patient, theId, theConditional);
    } catch (OperationOutcomeException ex) {
        ProviderResponseLibrary.handleException(method,ex);
    }
    method.setId(newPatient.getIdElement());
    method.setResource(newPatient);


    log.debug("called update Patient method");

    return method;
}
 

@Test
public void testFhirJsonMarshal() throws Exception {
    CamelContext camelctx = new DefaultCamelContext();
    camelctx.addRoutes(new RouteBuilder() {
        @Override
        public void configure() throws Exception {
            from("direct:start")
            .marshal().fhirXml();
        }
    });

    camelctx.start();
    try {
        Patient patient = createPatient();
        ProducerTemplate template = camelctx.createProducerTemplate();
        InputStream inputStream = template.requestBody("direct:start", patient, InputStream.class);
        IBaseResource result = FhirContext.forDstu3().newXmlParser().parseResource(new InputStreamReader(inputStream));
        Assert.assertTrue("Expected marshaled patient to be equal", patient.equalsDeep((Base)result));
    } finally {
        camelctx.close();
    }
}
 

@Test
public void testFhirJsonUnmarshal() throws Exception {
    CamelContext camelctx = new DefaultCamelContext();
    camelctx.addRoutes(new RouteBuilder() {
        @Override
        public void configure() throws Exception {
            from("direct:start")
            .unmarshal().fhirJson("DSTU3");
        }
    });

    camelctx.start();
    try {
        ProducerTemplate template = camelctx.createProducerTemplate();
        Patient result = template.requestBody("direct:start", PATIENT_JSON, Patient.class);
        Assert.assertTrue("Expected unmarshaled patient to be equal", result.equalsDeep(createPatient()));
    } finally {
        camelctx.close();
    }
}
 

@Test
public void testFhirJsonUnmarshal() throws Exception {
    CamelContext camelctx = new DefaultCamelContext();
    camelctx.addRoutes(new RouteBuilder() {
        @Override
        public void configure() throws Exception {
            from("direct:start")
            .unmarshal().fhirXml();
        }
    });

    camelctx.start();
    try {
        ProducerTemplate template = camelctx.createProducerTemplate();
        Patient result = template.requestBody("direct:start", PATIENT_XML, Patient.class);
        Assert.assertTrue("Expected unmarshaled patient to be equal", result.equalsDeep(createPatient()));
    } finally {
        camelctx.close();
    }
}
 

@Test
public void testFhirJsonMarshal() throws Exception {
    CamelContext camelctx = new DefaultCamelContext();
    camelctx.addRoutes(new RouteBuilder() {
        @Override
        public void configure() throws Exception {
            from("direct:start")
            .marshal().fhirJson("DSTU3");
        }
    });

    camelctx.start();
    try {
        Patient patient = createPatient();
        ProducerTemplate template = camelctx.createProducerTemplate();
        InputStream inputStream = template.requestBody("direct:start", patient, InputStream.class);
        IBaseResource result = FhirContext.forDstu3().newJsonParser().parseResource(new InputStreamReader(inputStream));
        Assert.assertTrue("Expected marshaled patient to be equal", patient.equalsDeep((Base)result));
    } finally {
        camelctx.close();
    }
}
 

public static void main(String[] theArgs) {

		// Create a Patient
		Patient pat = new Patient();
		pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");
		pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135");
		pat.addTelecom().setUse(ContactPointUse.HOME).setSystem(ContactPointSystem.PHONE).setValue("1 (416) 340-4800");
		pat.setGender(AdministrativeGender.MALE);

		// Create a context
		FhirContext ctx = FhirContext.forDstu3();

		// Create a JSON parser
		IParser parser = ctx.newJsonParser();
		parser.setPrettyPrint(true);

		String encode = parser.encodeResourceToString(pat);
		System.out.println(encode);

	}
 

public static void main(String[] theArgs) {

      // Create a resource instance
      Patient pat = new Patient();

      // Add a "name" element
      HumanName name = pat.addName();
      name.setFamily("Simpson").addGiven("Homer").addGiven("J");

      // Add an "identifier" element
      Identifier identifier = pat.addIdentifier();
      identifier.setSystem("http://acme.org/MRNs").setValue("7000135");

      // Model is designed to be chained
      pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("12345");

   }
 

public static void main(String[] args) {

      // Create an Observation
      Observation obs = new Observation();
      obs.setStatus(Observation.ObservationStatus.FINAL);
      obs.setValue(new StringType("This is a value"));

      // Create a Patient
      Patient pat = new Patient();
      pat.addName().setFamily("Simpson").addGiven("Homer");

      // Assign the Patient to the Observation
      obs.getSubject().setResource(pat);

      FhirContext ctx = FhirContext.forDstu3();
      String output = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(obs);
      System.out.println(output);

   }
 

@Test
public void searchTest() {
    Patient one = new Patient();
    one.setId("one");
    one.setGender(Enumerations.AdministrativeGender.UNKNOWN);
    Patient two = new Patient();
    two.setId("two");
    two.setGender(Enumerations.AdministrativeGender.UNKNOWN);

    Bundle bundle = new Bundle();
    bundle.getEntry().add(new Bundle.BundleEntryComponent().setResource(one));
    bundle.getEntry().add(new Bundle.BundleEntryComponent().setResource(two));

    stubFhirRequest(get(urlEqualTo("/Patient?gender=unknown&_format=xml")).willReturn(okXml(toXml(bundle))));

    FhirResourceQuery query = new FhirResourceQuery();
    query.setQuery("gender=unknown");

    String result = template.requestBody("direct:start", query, String.class);

    Assertions.assertThat(result).isEqualTo(
        "[<Patient xmlns=\"http://hl7.org/fhir\"><id value=\"one\"/><gender value=\"unknown\"/></Patient>, " +
        "<Patient xmlns=\"http://hl7.org/fhir\"><id value=\"two\"/><gender value=\"unknown\"/></Patient>]");
}
 

public static void main(String[] theArgs) {
Patient pat = new Patient();
pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");

// Add an extension on the resource
pat.addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-importance")
		.setValue(new CodeableConcept().setText("Patient is a VIP"));

// Add an extension on a primitive
pat.getBirthDateElement().setValueAsString("1955-02-22");
pat.getBirthDateElement().addExtension()
		.setUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime")
		.setValue(new TimeType("23:30"));

    IParser parser = FhirContext.forDstu3().newJsonParser().setPrettyPrint(true);
    System.out.println(parser.encodeResourceToString(pat));
 }
 

public static void main(String[] theArgs) {

		// Create a client
      IGenericClient client = FhirContext.forDstu3().newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3");

      // Register some interceptors
      client.registerInterceptor(new CookieInterceptor("mycookie=Chips Ahoy"));
      client.registerInterceptor(new LoggingInterceptor());

      // Read a Patient
      Patient patient = client.read().resource(Patient.class).withId("example").execute();

		// Change the gender
		patient.setGender(patient.getGender() == AdministrativeGender.MALE ? AdministrativeGender.FEMALE : AdministrativeGender.MALE);

		// Update the patient
		MethodOutcome outcome = client.update().resource(patient).execute();
		
		System.out.println("Now have ID: " + outcome.getId());
	}
 

public static void main(String[] theArgs) {

      // Create a resource instance
      Patient pat = new Patient();

      // Add a "name" element
      HumanName name = pat.addName();
      name.setFamily("Simpson").addGiven("Homer").addGiven("J");

      // Add an "identifier" element
      Identifier identifier = pat.addIdentifier();
      identifier.setSystem("http://acme.org/MRNs").setValue("7000135");

      // Model is designed to be chained
      pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("12345");

   }
 

@Test
@SuppressWarnings("JdkObsolete")
public void transactionTest() {
    Bundle bundle = new Bundle();
    bundle.addEntry(new Bundle.BundleEntryComponent().setResource(new Account().setId("1").setMeta(new Meta().setLastUpdated(new Date()))));
    bundle.addEntry(new Bundle.BundleEntryComponent().setResource(new Patient().setId("2").setMeta(new Meta().setLastUpdated(new Date()))));
    stubFhirRequest(post(urlEqualTo("/?_format=xml")).withRequestBody(containing(
        "<type value=\"transaction\"/><total value=\"2\"/><link><relation value=\"fhir-base\"/></link>" +
            "<link><relation value=\"self\"/></link>" +
            "<entry><resource><Account xmlns=\"http://hl7.org/fhir\"><name value=\"Joe\"/></Account></resource>" +
            "<request><method value=\"POST\"/></request></entry><entry><resource>" +
            "<Patient xmlns=\"http://hl7.org/fhir\"><name><family value=\"Jackson\"/></name></Patient></resource>" +
            "<request><method value=\"POST\"/></request></entry>")).willReturn(okXml(toXml(bundle))));

    template.requestBody("direct:start",
        "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>" +
            "<tns:Transaction xmlns:tns=\"http://hl7.org/fhir\">" +
            "<tns:Account><tns:name value=\"Joe\"/></tns:Account>" +
            "<tns:Patient><name><tns:family value=\"Jackson\"/></name></tns:Patient></tns:Transaction>");
}
 

private void addPopulationCriteriaReport(MeasureReport report, MeasureReport.MeasureReportGroupComponent reportGroup, Measure.MeasureGroupPopulationComponent populationCriteria, int populationCount, Iterable<Patient> patientPopulation) {
     if (populationCriteria != null) {
         MeasureReport.MeasureReportGroupPopulationComponent populationReport = new MeasureReport.MeasureReportGroupPopulationComponent();
         populationReport.setIdentifier(populationCriteria.getIdentifier());
         populationReport.setCode(populationCriteria.getCode());
         if (report.getType() == MeasureReport.MeasureReportType.PATIENTLIST && patientPopulation != null) {
             ListResource subjectList = new ListResource();
	subjectList.setId(UUID.randomUUID().toString());
             populationReport.setPatients(new Reference().setReference("#" + subjectList.getId()));
             for (Patient patient : patientPopulation) {
                 ListResource.ListEntryComponent entry = new ListResource.ListEntryComponent()
                         .setItem(new Reference().setReference(
                                 patient.getIdElement().getIdPart().startsWith("Patient/") ?
                                         patient.getIdElement().getIdPart() :
                                         String.format("Patient/%s", patient.getIdElement().getIdPart()))
                                 .setDisplay(patient.getNameFirstRep().getNameAsSingleString()));
                 subjectList.addEntry(entry);
             }
             report.addContained(subjectList);
         }            
populationReport.setCount(populationCount);
         reportGroup.addPopulation(populationReport);
     }
 }
 

@Test
public void testXmlBundleStrings() {

  JavaRDD<String> xmlBundlesRdd = spark.sparkContext()
      .wholeTextFiles("src/test/resources/xml/bundles", 1)
      .toJavaRDD()
      .map(tuple -> tuple._2());

  Dataset<String> xmlBundles = spark.createDataset(xmlBundlesRdd.rdd(),
      Encoders.STRING());

  xmlBundles.write().saveAsTable("xml_bundle_table");

  JavaRDD<BundleContainer> bundles = BundlesTest.bundles.fromXml(
      spark.sql("select value from xml_bundle_table"), "value");

  Dataset<Row> patients = BundlesTest.bundles.extractEntry(spark,
      bundles,
      Patient.class);

  checkPatients(patients);
}
 

@Test
public void testJsonBundleStrings() {

  JavaRDD<String> jsonBundlesRdd = spark.sparkContext()
      .wholeTextFiles("src/test/resources/json/bundles", 1)
      .toJavaRDD()
      .map(tuple -> tuple._2());

  Dataset<String> jsonBundles = spark.createDataset(jsonBundlesRdd.rdd(),
      Encoders.STRING());

  jsonBundles.write().saveAsTable("json_bundle_table");

  JavaRDD<BundleContainer> bundlesRdd = bundles.fromJson(
      spark.sql("select value from json_bundle_table"), "value");

  Dataset<Row> patients = BundlesTest.bundles.extractEntry(spark,
      bundlesRdd,
      Patient.class);

  checkPatients(patients);
}
 

public MeasureReport evaluatePatientMeasure(Measure measure, Context context, String patientId) {
    logger.info("Generating individual report");

    if (patientId == null) {
        return evaluatePopulationMeasure(measure, context);
    }

    Patient patient = registry.getResourceDao(Patient.class).read(new IdType(patientId));
    // Iterable<Object> patientRetrieve = provider.retrieve("Patient", "id",
    // patientId, "Patient", null, null, null, null, null, null, null, null);
    // Patient patient = null;
    // if (patientRetrieve.iterator().hasNext()) {
    // patient = (Patient) patientRetrieve.iterator().next();
    // }

    return evaluate(measure, context,
            patient == null ? Collections.emptyList() : Collections.singletonList(patient),
            MeasureReport.MeasureReportType.INDIVIDUAL);
}
 

private Iterable<Resource> evaluateCriteria(Context context, Patient patient,
        Measure.MeasureGroupPopulationComponent pop) {
    if (!pop.hasCriteria()) {
        return Collections.emptyList();
    }

    context.setContextValue("Patient", patient.getIdElement().getIdPart());
    // Hack to clear expression cache
    // See cqf-ruler github issue #153
    try {
        Field privateField = Context.class.getDeclaredField("expressions");
        privateField.setAccessible(true);
        LinkedHashMap<String, Object> expressions = (LinkedHashMap<String, Object>)privateField.get(context);
        expressions.clear();
        
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
 
    Object result = context.resolveExpressionRef(pop.getCriteria()).evaluate(context);
    if (result == null) {
        return Collections.emptyList();
    }

    if (result instanceof Boolean) {
        if (((Boolean)result)) {
            return Collections.singletonList(patient);
        }
        else {
            return Collections.emptyList();
        }
    }

    return (Iterable)result;
}
 

public static void main(String[] theArgs) {

      Patient pat = new Patient();

      pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");
      pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135");

      // Enumerated types are provided for many coded elements
      ContactPoint contact = pat.addTelecom();
      contact.setUse(ContactPoint.ContactPointUse.HOME);
      contact.setSystem(ContactPoint.ContactPointSystem.PHONE);
      contact.setValue("1 (416) 340-4800");

      pat.setGender(Enumerations.AdministrativeGender.MALE);
   }
 

private Patient createPatient() {
    Patient patient = new Patient();
    patient.addName(new HumanName()
        .addGiven("Sherlock")
        .setFamily("Holmes"))
        .addAddress(new Address().addLine("221b Baker St, Marylebone, London NW1 6XE, UK"));
    return patient;
}
 

public static void main(String[] theArgs) {

      Patient pat = new Patient();

      pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("J");
      pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135");

      // Enumerated types are provided for many coded elements
      ContactPoint contact = pat.addTelecom();
      contact.setUse(ContactPoint.ContactPointUse.HOME);
      contact.setSystem(ContactPoint.ContactPointSystem.PHONE);
      contact.setValue("1 (416) 340-4800");

      pat.setGender(Enumerations.AdministrativeGender.MALE);
   }
 

@Search
List<Patient> search(
		@OptionalParam(name="family") StringParam theFamily,
		@OptionalParam(name="given") StringParam theGiven
		) {
	return null; // populate this
}
 

public static void main(String[] args) {
	
	// Create an encounter with an invalid status and no class
	Patient pat = new Patient();
	pat.addName().setFamily("Simpson").addGiven("Homer").addGiven("Jay");
	pat.addAddress().addLine("342 Evergreen Terrace").addLine("Springfield");
	pat.addIdentifier().setSystem("http://acme.org/mrns").setValue("12345");
	
	// Create a new context and enable the narrative generator
	FhirContext ctx = FhirContext.forDstu2();
	ctx.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
	
	String res = ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(pat);
	System.out.println(res);
}
 

private List<Patient> getAllPatients() {
    List<Patient> patients = new ArrayList<>();
    IBundleProvider patientProvider = registry.getResourceDao("Patient").search(new SearchParameterMap());
    List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
    patientList.forEach(x -> patients.add((Patient) x));
    return patients;
}
 

private List<Patient> getPractitionerPatients(String practitionerRef) {
    SearchParameterMap map = new SearchParameterMap();
    map.add("general-practitioner", new ReferenceParam(
            practitionerRef.startsWith("Practitioner/") ? practitionerRef : "Practitioner/" + practitionerRef));

    List<Patient> patients = new ArrayList<>();
    IBundleProvider patientProvider = registry.getResourceDao("Patient").search(map);
    List<IBaseResource> patientList = patientProvider.getResources(0, patientProvider.size());
    patientList.forEach(x -> patients.add((Patient) x));
    return patients;
}
 

@Test 
public void resolveMissingPropertyReturnsNull() {
    ModelResolver resolver = new Dstu3FhirModelResolver();
    
    Patient p = new Patient();

    Object result = resolver.resolvePath(p, "notapath");
    assertNull(result);
}
 

@Test
public void testTransformSimplePatientEntity() throws FHIRException {

    LocalDate dateOfBirth = LocalDate.of(1996, 6, 21);

    final PatientEntity patientEntity = new PatientEntityBuilder()
            .setDateOfBirth(dateOfBirth)
            .build();

    final Patient patient = transformer.transform(patientEntity);

    assertThat(patient, not(nullValue()));
    assertThat(patient.getActive(), equalTo(true));
    assertThat(patient.getName().size(), equalTo(1));

    HumanName name = patient.getName().get(0);
    assertThat(name.getGivenAsSingleString(), equalTo("John"));
    assertThat(name.getFamily(), equalTo("Smith"));
    assertThat(name.getUse(), equalTo(HumanName.NameUse.OFFICIAL));
    assertThat(name.getPrefixAsSingleString(), equalTo("Mr"));

    assertThat(patient.getGender(), equalTo(Enumerations.AdministrativeGender.MALE));

    assertThat(patient.getBirthDate(), not(nullValue()));
    LocalDate patientDoB = DateUtils.asLocalDate(patient.getBirthDate());
    assertThat(patientDoB, equalTo(dateOfBirth));
}
 

@Create
  public MethodOutcome createPatient(HttpServletRequest theRequest, @ResourceParam Patient patient) {

      log.info("Update Patient Provider called");
      resourcePermissionProvider.checkPermission("create");
      /*
      if(CRUD_create.equals("false"))
{
	throw OperationOutcomeFactory.buildOperationOutcomeException(
	new InvalidRequestException("Invalid Request"),
	OperationOutcome.IssueSeverity.ERROR, OperationOutcome.IssueType.INVALID);
}
*/
      MethodOutcome method = new MethodOutcome();
      method.setCreated(true);
      OperationOutcome opOutcome = new OperationOutcome();

      method.setOperationOutcome(opOutcome);
      Patient newPatient = null;
      try {
          newPatient = patientDao.update(ctx, patient, null, null);
          method.setId(newPatient.getIdElement());
          method.setResource(newPatient);
      } catch (BaseServerResponseException srv) {
          // HAPI Exceptions pass through
          throw srv;
      } catch(Exception ex) {
          ProviderResponseLibrary.handleException(method,ex);
      }

      log.debug("called create Patient method");

      return method;
  }
 

@Test
@EnabledIf(FhirFlags.Dstu2Enabled.class)
public void jsonDstu2() {
    LOG.info("Running DSTU2 JSON test");

    final ca.uhn.fhir.model.dstu2.resource.Patient patient = getDstu2Patient();
    final String patientString = FhirContext.forDstu2().newJsonParser().encodeResourceToString(patient);

    RestAssured.given()
            .contentType(ContentType.JSON).body(patientString).post("/dstu2/fhir2json")
            .then().statusCode(201);
}