Examples with IParser org.hl7.fhir.r5.formats.IParser used on opensource projects

Example 61 with IParser

use of org.hl7.fhir.r5.formats.IParser in project dpc-app by CMSgov.

the class SeedCommand method seedOrganizationBundle.

private void seedOrganizationBundle(FHIREntityConverter converter, DSLContext context, IParser parser) throws IOException {
    try (final InputStream orgBundleStream = SeedCommand.class.getClassLoader().getResourceAsStream(ORGANIZATION_BUNDLE)) {
        if (orgBundleStream == null) {
            throw new MissingResourceException("Can not find seeds file", this.getClass().getName(), CSV);
        }
        final Bundle bundle = parser.parseResource(Bundle.class, orgBundleStream);
        final List<EndpointEntity> endpointEntities = BundleParser.parse(Endpoint.class, bundle, (endpoint) -> converter.fromFHIR(EndpointEntity.class, endpoint), ORGANIZATION_ID);
        final List<OrganizationEntity> organizationEntities = BundleParser.parse(Organization.class, bundle, (org) -> converter.fromFHIR(OrganizationEntity.class, org), ORGANIZATION_ID);
        organizationEntities.stream().map(entity -> organizationEntityToRecord(context, entity)).forEach(context::executeInsert);
        endpointEntities.stream().map(entity -> endpointsEntityToRecord(context, entity)).forEach(context::executeInsert);
    }
}

Example 62 with IParser

use of org.hl7.fhir.r5.formats.IParser in project dpc-app by CMSgov.

the class SeedCommand method seedPatientBundle.

private Map<String, Reference> seedPatientBundle(FHIREntityConverter converter, DSLContext context, IParser parser, UUID organizationID) throws IOException {
    try (final InputStream providerBundleStream = SeedCommand.class.getClassLoader().getResourceAsStream(PATIENT_BUNDLE)) {
        final Parameters parameters = parser.parseResource(Parameters.class, providerBundleStream);
        final Bundle patientBundle = (Bundle) parameters.getParameterFirstRep().getResource();
        final List<PatientEntity> patients = BundleParser.parse(Patient.class, patientBundle, (patient) -> converter.fromFHIR(PatientEntity.class, patient), organizationID);
        Map<String, Reference> patientReferences = new HashMap<>();
        patients.stream().peek(entity -> {
            final OrganizationEntity organization = new OrganizationEntity();
            organization.setId(organizationID);
            entity.setOrganization(organization);
        }).map(entity -> patientEntityToRecord(context, entity)).peek(context::executeInsert).forEach(record -> {
            final Reference ref = new Reference(new IdType("Patient", record.getId().toString()));
            patientReferences.put(record.getBeneficiaryId(), ref);
        });
        return patientReferences;
    }
}

Example 63 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class FHIRDSTU2ExporterTest method testFHIRDSTU2Export.

@Test
public void testFHIRDSTU2Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirDstu2.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        Config.set("exporter.fhir_dstu2.export", "true");
        FhirDstu2.TRANSACTION_BUNDLE = person.randBoolean();
        String fhirJson = FhirDstu2.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // 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 (Entry entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateWithResult(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    if (emessage.getMessage().contains("start SHALL have a lower value than end")) {
                        continue;
                    }
                    System.out.println(parser.encodeResourceToString(entry.getResource()));
                    System.out.println("ERROR: " + emessage.getMessage());
                    validationErrors.add(emessage.getMessage());
                }
            }
            if (entry.getResource() instanceof DiagnosticReport) {
                DiagnosticReport report = (DiagnosticReport) entry.getResource();
                if (report.getPerformer().isEmpty()) {
                    validationErrors.add("Performer is a required field on DiagnosticReport!");
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            Exporter.export(person, System.currentTimeMillis());
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 64 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class FHIRR4ExporterTest method testFHIRR4Export.

@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 = FhirR4.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    ValidationResources validator = new ValidationResources();
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        TestHelper.exportOff();
        FhirR4.TRANSACTION_BUNDLE = person.randBoolean();
        FhirR4.USE_US_CORE_IG = person.randBoolean();
        FhirR4.USE_SHR_EXTENSIONS = false;
        String fhirJson = FhirR4.convertToFHIRJson(person, System.currentTimeMillis());
        // (these should have been converted into URIs)
        if (fhirJson.contains("SNOMED-CT")) {
            validationErrors.add("JSON contains unconverted references to 'SNOMED-CT' (should be URIs)");
        }
        // Let's crack open the Bundle and validate
        // each individual entry.resource to get context-sensitive error
        // messages...
        // IMPORTANT: this approach significantly reduces memory usage when compared to
        // validating the entire bundle at a time, but means that validating references
        // is impossible.
        // As of 2021-01-05, validating the bundle didn't validate references anyway,
        // but at some point we may want to do that.
        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.getSeverity() == ResultSeverityEnum.INFORMATION || emessage.getSeverity() == ResultSeverityEnum.WARNING) {
                        /*
               * Ignore warnings.
               */
                        valid = true;
                    }
                    if (!valid) {
                        System.out.println(parser.encodeResourceToString(entry.getResource()));
                        System.out.println("ERROR: " + emessage.getMessage());
                        validationErrors.add(emessage.getMessage());
                    }
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            FailedExportHelper.dumpInfo("FHIRR4", fhirJson, validationErrors, person);
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 65 with IParser

use of org.hl7.fhir.r5.formats.IParser in project synthea by synthetichealth.

the class FHIRR4ExporterTest 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-Provider");
    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 = FhirR4.getContext();
    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");
            }
        }
    }
}