Examples with CapabilityStatement org.hl7.fhir.r5.model.CapabilityStatement used on opensource projects

Example 81 with CapabilityStatement

use of org.hl7.fhir.r5.model.CapabilityStatement in project pathling by aehrc.

the class DockerImageTest method importDataAndQuery.

@Test
void importDataAndQuery() throws JSONException {
    try {
        // Get the token endpoint from the CapabilityStatement.
        final CapabilityStatement capabilities = getCapabilityStatement();
        final String tokenUrl = capabilities.getRest().stream().findFirst().map(rest -> ((UriType) rest.getSecurity().getExtensionByUrl("http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris").getExtensionByUrl("token").getValue()).asStringValue()).orElseThrow();
        // Get an access token from the token endpoint.
        final HttpPost clientCredentialsGrant = new HttpPost(tokenUrl);
        final List<? extends NameValuePair> nameValuePairs = Arrays.asList(new BasicNameValuePair("grant_type", "client_credentials"), new BasicNameValuePair("client_id", CLIENT_ID), new BasicNameValuePair("client_secret", CLIENT_SECRET), new BasicNameValuePair("scope", REQUESTED_SCOPE));
        clientCredentialsGrant.setEntity(new UrlEncodedFormEntity(nameValuePairs));
        log.info("Requesting client credentials grant");
        final String accessToken;
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(clientCredentialsGrant)) {
            assertThat(response.getStatusLine().getStatusCode()).withFailMessage("Client credentials grant did not succeed").isEqualTo(200);
            final InputStream clientCredentialsStream = response.getEntity().getContent();
            final Gson gson = new GsonBuilder().setFieldNamingPolicy(FieldNamingPolicy.LOWER_CASE_WITH_UNDERSCORES).create();
            final ClientCredentialsResponse ccResponse = gson.fromJson(new InputStreamReader(clientCredentialsStream), ClientCredentialsResponse.class);
            accessToken = ccResponse.getAccessToken();
        }
        // Create a request to the $import operation, referencing the NDJSON files we have loaded into
        // the staging area.
        final InputStream requestStream = Thread.currentThread().getContextClassLoader().getResourceAsStream("import/SystemTest/request.Parameters.json");
        assertThat(requestStream).isNotNull();
        final HttpPost importRequest = new HttpPost("http://localhost:8091/fhir/$import");
        importRequest.setEntity(new InputStreamEntity(requestStream));
        importRequest.addHeader("Content-Type", "application/json");
        importRequest.addHeader("Accept", "application/fhir+json");
        importRequest.addHeader("Authorization", "Bearer " + accessToken);
        log.info("Sending import request");
        final OperationOutcome importOutcome;
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(importRequest)) {
            final InputStream importResponseStream = response.getEntity().getContent();
            importOutcome = (OperationOutcome) jsonParser.parseResource(importResponseStream);
            assertThat(response.getStatusLine().getStatusCode()).withFailMessage(importOutcome.getIssueFirstRep().getDiagnostics()).isEqualTo(200);
        }
        assertThat(importOutcome.getIssueFirstRep().getDiagnostics()).isEqualTo("Data import completed successfully");
        log.info("Import completed successfully");
        final Parameters inParams = new Parameters();
        // Set subject resource parameter.
        final ParametersParameterComponent subjectResourceParam = new ParametersParameterComponent();
        subjectResourceParam.setName("subjectResource");
        subjectResourceParam.setValue(new CodeType("Patient"));
        // Add aggregation, number of patients.
        final ParametersParameterComponent aggregationParam = new ParametersParameterComponent();
        aggregationParam.setName("aggregation");
        aggregationParam.setValue(new StringType("count()"));
        // Add grouping, has the patient been diagnosed with a chronic disease?
        final ParametersParameterComponent groupingParam = new ParametersParameterComponent();
        groupingParam.setName("grouping");
        groupingParam.setValue(new StringType("reverseResolve(Condition.subject)" + ".code" + ".memberOf('http://snomed.info/sct?fhir_vs=ecl/" + "^ 32570581000036105 : " + "<< 263502005 = << 90734009')"));
        // Add filter, females only.
        final ParametersParameterComponent filterParam = new ParametersParameterComponent();
        filterParam.setName("filter");
        filterParam.setValue(new StringType("gender = 'female'"));
        inParams.getParameter().add(subjectResourceParam);
        inParams.getParameter().add(aggregationParam);
        inParams.getParameter().add(groupingParam);
        inParams.getParameter().add(filterParam);
        // Send a request to the `$aggregate` operation on the FHIR server.
        final String requestString = jsonParser.encodeResourceToString(inParams);
        final HttpPost queryRequest = new HttpPost("http://localhost:8091/fhir/Patient/$aggregate");
        queryRequest.setEntity(new StringEntity(requestString));
        queryRequest.addHeader("Content-Type", "application/fhir+json");
        queryRequest.addHeader("Accept", "application/fhir+json");
        queryRequest.addHeader("Authorization", "Bearer " + accessToken);
        log.info("Sending query request");
        try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(queryRequest)) {
            final int statusCode = response.getStatusLine().getStatusCode();
            final InputStream queryResponseStream = response.getEntity().getContent();
            if (statusCode == 200) {
                final StringWriter writer = new StringWriter();
                IOUtils.copy(queryResponseStream, writer, StandardCharsets.UTF_8);
                assertJson("responses/DockerImageTest/importDataAndQuery.Parameters.json", writer.toString());
            } else {
                captureLogs();
                final OperationOutcome opOutcome = (OperationOutcome) jsonParser.parseResource(queryResponseStream);
                assertEquals(200, statusCode, opOutcome.getIssueFirstRep().getDiagnostics());
            }
        }
    } catch (final Exception e) {
        captureLogs();
    } finally {
        stopContainer(dockerClient, fhirServerContainerId);
        fhirServerContainerId = null;
        getRuntime().removeShutdownHook(shutdownHook);
    }
}

Example 82 with CapabilityStatement

use of org.hl7.fhir.r5.model.CapabilityStatement in project pathling by aehrc.

the class DockerImageTest method getCapabilityStatement.

CapabilityStatement getCapabilityStatement() throws IOException {
    final HttpUriRequest capabilitiesRequest = new HttpGet("http://localhost:8091/fhir/metadata");
    capabilitiesRequest.addHeader("Accept", "application/fhir+json");
    log.info("Sending capabilities request");
    final CapabilityStatement capabilities;
    try (final CloseableHttpResponse response = (CloseableHttpResponse) httpClient.execute(capabilitiesRequest)) {
        final InputStream capabilitiesStream = response.getEntity().getContent();
        capabilities = (CapabilityStatement) jsonParser.parseResource(capabilitiesStream);
        assertThat(response.getStatusLine().getStatusCode()).withFailMessage("Capabilities operation did not succeed").isEqualTo(200);
    }
    return capabilities;
}

Example 83 with CapabilityStatement

use of org.hl7.fhir.r5.model.CapabilityStatement in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestStatusHandlerTest method testEnhancedHealthCheckFailNoTermServer.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class, DefaultFhirClientBuilder.class })
@Test
public /**
 * Test a failure connecting to data server and no terminology server provided
 */
void testEnhancedHealthCheckFailNoTermServer() throws Exception {
    prepMocks(false);
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, CohortEngineRestStatusHandler.GET_HEALTH_CHECK_ENCHANCED)).thenReturn(null);
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    mockFhirResourceRetrieval("/Patient?_format=json", null);
    Response response = cerSH.getHealthCheckEnhanced(VERSION, getEnhancedHealthCheckInputConfigFileBody(false));
    assertEquals(Status.OK.getStatusCode(), response.getStatus());
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getDataServerConnectionResults().getConnectionResults(), FhirConnectionStatus.failure);
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getTerminologyServerConnectionResults().getConnectionResults(), FhirConnectionStatus.notAttempted);
}

Example 84 with CapabilityStatement

use of org.hl7.fhir.r5.model.CapabilityStatement in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestStatusHandlerTest method testEnhancedHealthCheckOK.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class, DefaultFhirClientBuilder.class })
@Test
public /**
 * Test the setting of service status to OK.
 */
void testEnhancedHealthCheckOK() throws Exception {
    prepMocks(false);
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, CohortEngineRestStatusHandler.GET_HEALTH_CHECK_ENCHANCED)).thenReturn(null);
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval("/Patient?_format=json", patient);
    // don't need to return a valueset since we only care that the call returns something
    mockFhirResourceRetrieval("/ValueSet?_format=json", patient);
    Response response = cerSH.getHealthCheckEnhanced(VERSION, getEnhancedHealthCheckInputConfigFileBody(true));
    assertEquals(Status.OK.getStatusCode(), response.getStatus());
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getDataServerConnectionResults().getConnectionResults(), FhirConnectionStatus.success);
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getTerminologyServerConnectionResults().getConnectionResults(), FhirConnectionStatus.success);
}

Example 85 with CapabilityStatement

use of org.hl7.fhir.r5.model.CapabilityStatement in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestStatusHandlerTest method testEnhancedHealthCheckOKNoTermServer.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class, DefaultFhirClientBuilder.class })
@Test
public void testEnhancedHealthCheckOKNoTermServer() throws Exception {
    prepMocks(false);
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, CohortEngineRestStatusHandler.GET_HEALTH_CHECK_ENCHANCED)).thenReturn(null);
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval("/Patient?_format=json", patient);
    Response response = cerSH.getHealthCheckEnhanced(VERSION, getEnhancedHealthCheckInputConfigFileBody(false));
    assertEquals(Status.OK.getStatusCode(), response.getStatus());
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getDataServerConnectionResults().getConnectionResults(), FhirConnectionStatus.success);
    assertEquals(((EnhancedHealthCheckResults) response.getEntity()).getTerminologyServerConnectionResults().getConnectionResults(), FhirConnectionStatus.notAttempted);
}