Examples with IParser org.hl7.fhir.r4b.formats.IParser used on opensource projects

Example 76 with IParser

use of org.hl7.fhir.r4b.formats.IParser in project dpc-app by CMSgov.

the class ParamResourceFactoryTest method testNonParameter.

@Test
void testNonParameter() throws IOException {
    final HttpServletRequest mock = Mockito.mock(HttpServletRequest.class);
    final ServletInputStream mockStream = Mockito.mock(ServletInputStream.class);
    final Injector mockInjector = Mockito.mock(Injector.class);
    Mockito.when(mockInjector.getInstance(HttpServletRequest.class)).thenReturn(mock);
    Mockito.when(mock.getInputStream()).thenReturn(mockStream);
    final IParser parser = Mockito.mock(IParser.class);
    Mockito.when(parser.parseResource(Mockito.eq(Parameters.class), Mockito.any(InputStream.class))).thenThrow(DataFormatException.class);
    final ParamResourceFactory factory = new ParamResourceFactory(mockInjector, null, parser);
    final WebApplicationException exception = assertThrows(WebApplicationException.class, factory::provide, "Should throw exception");
    assertAll(() -> assertEquals(HttpStatus.BAD_REQUEST_400, exception.getResponse().getStatus(), "Should be a bad request"), () -> assertEquals("Resource type must be `Parameters`", exception.getMessage(), "Should have wrong resource message"));
}

Example 77 with IParser

use of org.hl7.fhir.r4b.formats.IParser in project dpc-app by CMSgov.

the class ParamResourceFactoryTest method testCannotReadIS.

@Test
void testCannotReadIS() throws IOException {
    final HttpServletRequest mock = Mockito.mock(HttpServletRequest.class);
    final ServletInputStream mockStream = Mockito.mock(ServletInputStream.class);
    final Injector mockInjector = Mockito.mock(Injector.class);
    Mockito.when(mockInjector.getInstance(HttpServletRequest.class)).thenReturn(mock);
    Mockito.when(mock.getInputStream()).thenReturn(mockStream);
    final IParser parser = Mockito.mock(IParser.class);
    Mockito.when(parser.parseResource(Mockito.eq(Parameters.class), Mockito.any(InputStream.class))).thenAnswer(answer -> {
        throw new IOException();
    });
    final ParamResourceFactory factory = new ParamResourceFactory(mockInjector, null, parser);
    final WebApplicationException exception = assertThrows(WebApplicationException.class, factory::provide, "Should throw exception");
    assertAll(() -> assertEquals(HttpStatus.INTERNAL_SERVER_ERROR_500, exception.getResponse().getStatus(), "Should be an internal exception"), () -> assertEquals("Cannot read input stream", exception.getMessage(), "Should have wrong resource message"));
}

Example 78 with IParser

use of org.hl7.fhir.r4b.formats.IParser in project dpc-app by CMSgov.

the class DPCProfileSupport method loadProfiles.

private Map<String, StructureDefinition> loadProfiles(FhirContext ctx) {
    logger.info("Loading resource profiles");
    final Map<String, StructureDefinition> definitionMap = new HashMap<>();
    // Generate a validator to pull the base definitions from.
    final DefaultProfileValidationSupport defaultValidation = new DefaultProfileValidationSupport();
    final HapiWorkerContext hapiWorkerContext = new HapiWorkerContext(ctx, defaultValidation);
    final ProfileUtilities profileUtilities = new ProfileUtilities(hapiWorkerContext, new ArrayList<>(), null);
    final IParser parser = ctx.newJsonParser();
    ServiceLoaderHelpers.getLoaderStream(IProfileLoader.class).map(profileLoader -> toStructureDefinition(parser, profileLoader.getPath())).filter(Objects::nonNull).map(diffStructure -> mergeDiff(ctx, defaultValidation, profileUtilities, diffStructure)).forEach(structure -> definitionMap.put(structure.getUrl(), structure));
    return definitionMap;
}

Example 79 with IParser

use of org.hl7.fhir.r4b.formats.IParser in project synthea by synthetichealth.

the class FHIRSTU3ExporterTest method testSampledDataExport.

@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.attributes.put(Person.CONTACT_EMAIL, "test@test.test");
    person.attributes.put(Person.CONTACT_GIVEN_NAME, "John");
    person.attributes.put(Person.CONTACT_FAMILY_NAME, "Appleseed");
    person.history = new LinkedList<>();
    Provider mock = Mockito.mock(Provider.class);
    Mockito.when(mock.getResourceID()).thenReturn("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();
    int age = 35;
    long birthTime = time - Utilities.convertTime("years", age);
    person.attributes.put(Person.BIRTHDATE, birthTime);
    Payer.loadNoInsurance();
    for (int i = 0; i < age; i++) {
        long yearTime = time - Utilities.convertTime("years", i);
        person.coverage.setPayerAtTime(yearTime, 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 = FhirStu3.getContext();
    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();
            // 0.01s == 10ms
            assertEquals(10, data.getPeriod().doubleValue(), 0.001);
            assertEquals(3, (int) data.getDimensions());
        }
    }
}

Example 80 with IParser

use of org.hl7.fhir.r4b.formats.IParser in project synthea by synthetichealth.

the class FHIRSTU3ExporterTest method testObservationAttachment.

@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);
    Mockito.when(mock.getResourceID()).thenReturn("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();
    int age = 35;
    long birthTime = time - Utilities.convertTime("years", age);
    person.attributes.put(Person.BIRTHDATE, birthTime);
    Payer.loadNoInsurance();
    for (int i = 0; i < age; i++) {
        long yearTime = time - Utilities.convertTime("years", i);
        person.coverage.setPayerAtTime(yearTime, 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 = FhirStu3.getContext();
    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");
            }
        }
    }
}