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

Example 56 with IParser

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

the class OrganizationRegistration method run.

@Override
public void run(Bootstrap<?> bootstrap, Namespace namespace) throws Exception {
    System.out.println("Registering Organization");
    // Read the file and parse it
    final Path filePath = FileSystems.getDefault().getPath(namespace.getString(ORG_FILE)).normalize().toAbsolutePath();
    Bundle organization;
    try (FileInputStream fileInputStream = new FileInputStream(new File(filePath.toUri()))) {
        final IParser parser = ctx.newJsonParser();
        organization = (Bundle) parser.parseResource(fileInputStream);
    }
    final boolean noToken = Boolean.parseBoolean(namespace.getString("no-token"));
    final String apiService = namespace.getString("api-service");
    registerOrganization(organization, namespace.getString(ATTR_HOSTNAME), noToken, apiService);
}

Example 57 with IParser

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

the class ParamResourceFactoryTest method testUnnamedResource.

@Test
void testUnnamedResource() throws IOException {
    final Parameters parameters = new Parameters();
    final Patient dummyPatient = new Patient();
    parameters.addParameter().setResource(dummyPatient);
    final HttpServletRequest mock = Mockito.mock(HttpServletRequest.class);
    final ServletInputStream mockStream = Mockito.mock(ServletInputStream.class);
    final IParser parser = Mockito.mock(IParser.class);
    Mockito.when(parser.parseResource(Mockito.eq(Parameters.class), Mockito.any(InputStream.class))).thenReturn(parameters);
    final Injector mockInjector = Mockito.mock(Injector.class);
    Mockito.when(mockInjector.getInstance(HttpServletRequest.class)).thenReturn(mock);
    Mockito.when(mock.getInputStream()).thenReturn(mockStream);
    final Parameter parameter = Mockito.mock(Parameter.class);
    final FHIRParameter annotation = Mockito.mock(FHIRParameter.class);
    Mockito.when(annotation.name()).thenReturn("");
    Mockito.when(parameter.getAnnotation(FHIRParameter.class)).thenReturn(annotation);
    Mockito.when(parameter.getRawType()).thenAnswer(answer -> Patient.class);
    final ParamResourceFactory factory = new ParamResourceFactory(mockInjector, parameter, parser);
    assertTrue(dummyPatient.equalsDeep((Patient) factory.provide()), "Should have returned dummy patient");
}

Example 58 with IParser

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

the class ParamResourceFactoryTest method testMismatchedParameterType.

@Test
void testMismatchedParameterType() throws IOException {
    final Parameters parameters = new Parameters();
    final Patient dummyPatient = new Patient();
    parameters.addParameter().setResource(dummyPatient);
    final HttpServletRequest mock = Mockito.mock(HttpServletRequest.class);
    final ServletInputStream mockStream = Mockito.mock(ServletInputStream.class);
    final IParser parser = Mockito.mock(IParser.class);
    Mockito.when(parser.parseResource(Mockito.eq(Parameters.class), Mockito.any(InputStream.class))).thenReturn(parameters);
    final Injector mockInjector = Mockito.mock(Injector.class);
    Mockito.when(mockInjector.getInstance(HttpServletRequest.class)).thenReturn(mock);
    Mockito.when(mock.getInputStream()).thenReturn(mockStream);
    final Parameter parameter = Mockito.mock(Parameter.class);
    final FHIRParameter annotation = Mockito.mock(FHIRParameter.class);
    Mockito.when(annotation.name()).thenReturn("");
    Mockito.when(parameter.getAnnotation(FHIRParameter.class)).thenReturn(annotation);
    Mockito.when(parameter.getRawType()).thenAnswer(answer -> Practitioner.class);
    final ParamResourceFactory factory = new ParamResourceFactory(mockInjector, parameter, parser);
    final WebApplicationException exception = assertThrows(WebApplicationException.class, factory::provide, "Should throw an exception");
    assertAll(() -> assertEquals(HttpStatus.BAD_REQUEST_400, exception.getResponse().getStatus(), "Should be a bad request"), () -> assertEquals("Provided resource must be: `Practitioner`, not `Patient`", exception.getMessage(), "Should have useful message"));
}

Example 59 with IParser

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

the class FHIRHelpers method registerOrganization.

/**
 * Register an organization with the Attribution Service
 * Organizations are pulled from the `organization_bundle.json` file and filtered based on the provided resource ID
 *
 * @param client         - {@link IGenericClient} client to communicate to attribution service
 * @param parser         - {@link IParser} to use for reading {@link Bundle} JSON
 * @param organizationID - {@link String} organization ID to filter for
 * @param adminURL       - {@link String} Base url for executing admin tasks
 * @return - {@link String} Access token generated for the {@link Organization}
 * @throws IOException - Throws if HTTP client fails
 */
public static String registerOrganization(IGenericClient client, IParser parser, String organizationID, String organizationNPI, String adminURL) throws IOException {
    // Random number generator for Org NPI
    // Register an organization, and a token
    // Read in the test file
    String macaroon;
    try (InputStream inputStream = FHIRHelpers.class.getClassLoader().getResourceAsStream("organization.tmpl.json")) {
        final Bundle orgBundle = (Bundle) parser.parseResource(inputStream);
        // Update the Organization resource and set a random NPI
        final Organization origOrg = (Organization) orgBundle.getEntryFirstRep().getResource();
        origOrg.getIdentifierFirstRep().setValue(organizationNPI);
        origOrg.setId(organizationID);
        final Parameters parameters = new Parameters();
        parameters.addParameter().setResource(orgBundle).setName("resource");
        client.operation().onType(Organization.class).named("submit").withParameters(parameters).returnResourceType(Organization.class).encodedJson().execute();
        try (CloseableHttpClient httpClient = HttpClients.createDefault()) {
            final URIBuilder uriBuilder = new URIBuilder(String.format("%s/generate-token", adminURL));
            uriBuilder.setParameter("organization", organizationID);
            // Now, create a Macaroon
            final HttpPost tokenPost = new HttpPost(uriBuilder.build());
            try (CloseableHttpResponse response = httpClient.execute(tokenPost)) {
                if (response.getStatusLine().getStatusCode() != HttpStatus.OK_200) {
                    throw new IllegalStateException(String.format("Unable to generate token: %s", response.getStatusLine().getReasonPhrase()));
                }
                macaroon = EntityUtils.toString(response.getEntity());
            }
        } catch (URISyntaxException e) {
            throw new IllegalArgumentException("Cannot parse URI", e);
        }
    }
    return macaroon;
}

Example 60 with IParser

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

the class PractitionerResourceTest method ensurePractitionersExist.

@Test
void ensurePractitionersExist() throws IOException, URISyntaxException, GeneralSecurityException {
    final IParser parser = ctx.newJsonParser();
    final IGenericClient attrClient = APITestHelpers.buildAttributionClient(ctx);
    IGenericClient client = APIAuthHelpers.buildAuthenticatedClient(ctx, getBaseURL(), ORGANIZATION_TOKEN, PUBLIC_KEY_ID, PRIVATE_KEY);
    APITestHelpers.setupPractitionerTest(client, parser);
    // Find everything attributed
    final Bundle practitioners = client.search().forResource(Practitioner.class).returnBundle(Bundle.class).encodedJson().execute();
    assertEquals(4, practitioners.getTotal(), "Should have all the providers");
    final Bundle specificSearch = client.search().forResource(Practitioner.class).where(Practitioner.IDENTIFIER.exactly().code("1232131239")).returnBundle(Bundle.class).encodedJson().execute();
    assertEquals(1, specificSearch.getTotal(), "Should have a specific provider");
    // Fetch the provider directly
    final Practitioner foundProvider = (Practitioner) specificSearch.getEntryFirstRep().getResource();
    final IReadExecutable<Practitioner> clientQuery = client.read().resource(Practitioner.class).withId(foundProvider.getIdElement()).encodedJson();
    final Practitioner queriedProvider = clientQuery.execute();
    assertTrue(foundProvider.equalsDeep(queriedProvider), "Search and GET should be identical");
    // Try to delete the practitioner
    client.delete().resourceById(queriedProvider.getIdElement()).encodedJson().execute();
    // Try again, should be not found
    assertThrows(AuthenticationException.class, clientQuery::execute, "Should not have practitioner");
    // Create a new org and make sure it has no providers
    final String m2 = FHIRHelpers.registerOrganization(attrClient, parser, OTHER_ORG_ID, "1112111111", getAdminURL());
    // Submit a new public key to use for JWT flow
    final String keyLabel = "new-key";
    final Pair<UUID, PrivateKey> uuidPrivateKeyPair = APIAuthHelpers.generateAndUploadKey(keyLabel, OTHER_ORG_ID, GOLDEN_MACAROON, getBaseURL());
    // Update the authenticated client to use the new organization
    client = APIAuthHelpers.buildAuthenticatedClient(ctx, getBaseURL(), m2, uuidPrivateKeyPair.getLeft(), uuidPrivateKeyPair.getRight());
    final Bundle otherPractitioners = client.search().forResource(Practitioner.class).returnBundle(Bundle.class).encodedJson().execute();
    assertEquals(0, otherPractitioners.getTotal(), "Should not have any practitioners");
    // Try to look for one of the other practitioners
    final Bundle otherSpecificSearch = client.search().forResource(Practitioner.class).where(Practitioner.IDENTIFIER.exactly().identifier(foundProvider.getIdentifierFirstRep().getValue())).returnBundle(Bundle.class).encodedJson().execute();
    assertEquals(0, otherSpecificSearch.getTotal(), "Should not have a specific provider");
// Try to search for our fund provider
}