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

Example 66 with IParser

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

the class FHIRR4ExporterTest 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 = 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 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 67 with IParser

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

the class FHIRSTU3ExporterTest method testFHIRSTU3Export.

@Test
public void testFHIRSTU3Export() throws Exception {
    TestHelper.loadTestProperties();
    Generator.DEFAULT_STATE = Config.get("test_state.default", "Massachusetts");
    Config.set("exporter.baseDirectory", tempFolder.newFolder().toString());
    FhirContext ctx = FhirStu3.getContext();
    IParser parser = ctx.newJsonParser().setPrettyPrint(true);
    FhirValidator validator = ctx.newValidator();
    validator.setValidateAgainstStandardSchema(true);
    validator.setValidateAgainstStandardSchematron(true);
    ValidationResources validationResources = new ValidationResources();
    List<String> errors = ParallelTestingService.runInParallel((person) -> {
        List<String> validationErrors = new ArrayList<String>();
        TestHelper.exportOff();
        Config.set("exporter.fhir_stu3.export", "true");
        Config.set("exporter.fhir.use_shr_extensions", "true");
        FhirStu3.TRANSACTION_BUNDLE = person.randBoolean();
        String fhirJson = FhirStu3.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 (BundleEntryComponent entry : bundle.getEntry()) {
            ValidationResult eresult = validator.validateWithResult(entry.getResource());
            if (!eresult.isSuccessful()) {
                for (SingleValidationMessage emessage : eresult.getMessages()) {
                    boolean valid = false;
                    if (emessage.getMessage().contains("@ Observation obs-7")) {
                        /*
               * The obs-7 invariant basically says that Observations should have values, unless
               * they are made of components. This test replaces an invalid XPath expression
               * that was causing correct instances to fail validation.
               */
                        valid = validateObs7((Observation) entry.getResource());
                    } else if (emessage.getMessage().contains("@ Condition con-4")) {
                        /*
               * The con-4 invariant says "If condition is abated, then clinicalStatus must be
               * either inactive, resolved, or remission" which is very clear and sensical.
               * However, the XPath expression does not evaluate correctly for valid instances,
               * so we must manually validate.
               */
                        valid = validateCon4((Condition) entry.getResource());
                    } else if (emessage.getMessage().contains("@ MedicationRequest mps-1")) {
                        /*
               * The mps-1 invariant says MedicationRequest.requester.onBehalfOf can only be
               * specified if MedicationRequest.requester.agent is practitioner or device.
               * But the invariant is poorly written and does not correctly handle references
               * starting with "urn:uuid"
               */
                        // ignore this error
                        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.
               */
                        // ignore this error
                        valid = true;
                    }
                    if (!valid) {
                        System.out.println(parser.encodeResourceToString(entry.getResource()));
                        System.out.println("ERROR: " + emessage.getMessage());
                        validationErrors.add(emessage.getMessage());
                    }
                }
            }
            // Check ExplanationOfBenefit Resources against BlueButton
            if (entry.getResource().fhirType().equals("ExplanationOfBenefit")) {
                ValidationResult bbResult = validationResources.validateSTU3(entry.getResource());
                for (SingleValidationMessage message : bbResult.getMessages()) {
                    if (message.getMessage().contains("extension https://bluebutton.cms.gov/assets")) {
                        /*
               * The instance validator complains about the BlueButton extensions, ignore
               */
                        continue;
                    } else if (message.getSeverity() == ResultSeverityEnum.ERROR) {
                        if (!(message.getMessage().contains("Element 'ExplanationOfBenefit.id': minimum required = 1, but only found 0") || message.getMessage().contains("Could not verify slice for profile"))) {
                            // For some reason the validator is not detecting the IDs on the resources,
                            // even though they appear to be present while debugging and during normal
                            // operations.
                            System.out.println(message.getSeverity() + ": " + message.getMessage());
                            Assert.fail(message.getSeverity() + ": " + message.getMessage());
                        }
                    }
                }
            }
        }
        if (!validationErrors.isEmpty()) {
            FailedExportHelper.dumpInfo("FHIRSTU3", fhirJson, validationErrors, person);
        }
        return validationErrors;
    });
    assertTrue("Validation of exported FHIR bundle failed: " + String.join("|", errors), errors.size() == 0);
}

Example 68 with IParser

use of org.hl7.fhir.r5.formats.IParser in project bunsen by cerner.

the class BunsenTestStu3ProfileProvider method load.

private static void load(PrePopulatedValidationSupport support, IParser jsonParser, String resource) {
    try (InputStream input = BunsenTestStu3ProfileProvider.class.getClassLoader().getResourceAsStream(resource)) {
        StructureDefinition definition = (StructureDefinition) jsonParser.parseResource(new InputStreamReader(input));
        support.addStructureDefinition(definition);
    } catch (IOException exception) {
        throw new RuntimeException(exception);
    }
}

Example 69 with IParser

use of org.hl7.fhir.r5.formats.IParser in project bunsen by cerner.

the class UsCoreStu3ProfileProvider method load.

private static void load(PrePopulatedValidationSupport support, IParser jsonParser, String resource) {
    try (InputStream input = UsCoreStu3ProfileProvider.class.getClassLoader().getResourceAsStream(resource)) {
        StructureDefinition definition = (StructureDefinition) jsonParser.parseResource(new InputStreamReader(input));
        support.addStructureDefinition(definition);
    } catch (IOException exception) {
        throw new RuntimeException(exception);
    }
}

Example 70 with IParser

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

the class OrganizationResourceTest method testUpdateOrganization.

@Test
void testUpdateOrganization() throws IOException, URISyntaxException, GeneralSecurityException {
    final String orgID = UUID.randomUUID().toString();
    final IParser parser = ctx.newJsonParser();
    final IGenericClient attrClient = APITestHelpers.buildAttributionClient(ctx);
    final String macaroon = FHIRHelpers.registerOrganization(attrClient, parser, orgID, "1111121111", getAdminURL());
    final Pair<UUID, PrivateKey> uuidPrivateKeyPair = APIAuthHelpers.generateAndUploadKey("org-update-key", orgID, GOLDEN_MACAROON, getBaseURL());
    final IGenericClient client = APIAuthHelpers.buildAuthenticatedClient(ctx, getBaseURL(), macaroon, uuidPrivateKeyPair.getLeft(), uuidPrivateKeyPair.getRight());
    Organization organization = client.read().resource(Organization.class).withId(orgID).encodedJson().execute();
    assertNotNull(organization);
    organization.setName("New Org Name");
    organization.setContact(Lists.emptyList());
    MethodOutcome outcome = client.update().resource(organization).execute();
    Organization result = (Organization) outcome.getResource();
    assertEquals("1111121111", result.getIdentifierFirstRep().getValue());
    assertEquals(organization.getName(), result.getName(), "Name should be updated");
    assertTrue(organization.getContact().isEmpty(), "Contact list should be updated");
    assertEquals(1, result.getEndpoint().size(), "Endpoint list should be unchanged");
    // Try to update when authenticated as different organization
    final String org2ID = UUID.randomUUID().toString();
    final String org2Macaroon = FHIRHelpers.registerOrganization(attrClient, parser, org2ID, "4321234211", getAdminURL());
    final Pair<UUID, PrivateKey> org2UUIDPrivateKeyPair = APIAuthHelpers.generateAndUploadKey("org2-update-key", org2ID, GOLDEN_MACAROON, getBaseURL());
    final IGenericClient org2Client = APIAuthHelpers.buildAuthenticatedClient(ctx, getBaseURL(), org2Macaroon, org2UUIDPrivateKeyPair.getLeft(), org2UUIDPrivateKeyPair.getRight());
    IUpdateTyped update = org2Client.update().resource(organization);
    assertThrows(AuthenticationException.class, update::execute);
}