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

Example 21 with IParser

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

the class CohortEngineRestHandlerTest method testEvaluatePatientListMeasureMissingPatient.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluatePatientListMeasureMissingPatient() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_PATIENT_LIST_MEASURE.getName())).thenReturn(null);
    mockResponseClasses();
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    Patient patient = getPatient("patientId", AdministrativeGender.MALE, 40);
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    mockNotFound("/Patient/" + patient.getId() + "\\?_format=json");
    FhirServerConfig clientConfig = getFhirServerConfig();
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureContext measureContext = new MeasureContext(measure.getId(), parameterOverrides);
    PatientListMeasureEvaluation request = new PatientListMeasureEvaluation();
    request.setDataServerConfig(clientConfig);
    request.setPatientIds(Collections.singletonList(patient.getId()));
    request.setMeasureContext(measureContext);
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    // Create the metadata part of the request
    ObjectMapper om = new ObjectMapper();
    String json = om.writeValueAsString(request);
    ByteArrayInputStream jsonIs = new ByteArrayInputStream(json.getBytes());
    IAttachment rootPart = mockAttachment(jsonIs);
    // Create the ZIP part of the request
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
    IAttachment measurePart = mockAttachment(zipIs);
    // Assemble them together into a reasonable facsimile of the real request
    IMultipartBody body = mock(IMultipartBody.class);
    when(body.getAttachment(CohortEngineRestHandler.REQUEST_DATA_PART)).thenReturn(rootPart);
    when(body.getAttachment(CohortEngineRestHandler.MEASURE_PART)).thenReturn(measurePart);
    Response loadResponse = restHandler.evaluatePatientListMeasure(mockRequestContext, VERSION, body);
    assertNotNull(loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(400);
}

Example 22 with IParser

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

the class CohortEngineRestHandlerTest method testEvaluateMeasureSuccess.

/**
 * Test the successful building of a response.
 */
@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluateMeasureSuccess() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_MEASURE.getName())).thenReturn(null);
    mockResponseClasses();
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    Patient patient = getPatient("patientId", AdministrativeGender.MALE, 40);
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    mockFhirResourceRetrieval(patient);
    FhirServerConfig clientConfig = getFhirServerConfig();
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureContext measureContext = new MeasureContext(measure.getId(), parameterOverrides);
    MeasureEvaluation evaluationRequest = new MeasureEvaluation();
    evaluationRequest.setDataServerConfig(clientConfig);
    evaluationRequest.setPatientId(patient.getId());
    evaluationRequest.setMeasureContext(measureContext);
    // evaluationRequest.setEvidenceOptions(evidenceOptions);
    evaluationRequest.setExpandValueSets(true);
    evaluationRequest.setSearchPageSize(500);
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    // Create the metadata part of the request
    ObjectMapper om = new ObjectMapper();
    String json = om.writeValueAsString(evaluationRequest);
    ByteArrayInputStream jsonIs = new ByteArrayInputStream(json.getBytes());
    IAttachment rootPart = mockAttachment(jsonIs);
    // Create the ZIP part of the request
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
    IAttachment measurePart = mockAttachment(zipIs);
    // Assemble them together into a reasonable facsimile of the real request
    IMultipartBody body = mock(IMultipartBody.class);
    when(body.getAttachment(CohortEngineRestHandler.REQUEST_DATA_PART)).thenReturn(rootPart);
    when(body.getAttachment(CohortEngineRestHandler.MEASURE_PART)).thenReturn(measurePart);
    Response loadResponse = restHandler.evaluateMeasure(mockRequestContext, VERSION, body);
    assertEquals(mockResponse, loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(Response.Status.OK);
}

Example 23 with IParser

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

the class DefaultVT method testMeasureEvaluationByMeasureIdentifier.

// to tag a specific test to be part of DVT (deployment verification test)
@Category(DVT.class)
@Test
public /**
 * Test a successful measure evaluation using identifier and version as the lookup key
 */
void testMeasureEvaluationByMeasureIdentifier() throws Exception {
    // You want -Denabled.dark.features=all in your Liberty jvm.options
    Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION));
    final String RESOURCE = getUrlBase() + CohortServiceAPISpec.CREATE_DELETE_EVALUATION_PATH;
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    Library library = TestHelper.getTemplateLibrary();
    Identifier identifier = new Identifier().setValue("measure-identifier").setSystem("http://ibm.com/health/test");
    Measure measure = TestHelper.getTemplateMeasure(library);
    measure.setIdentifier(Arrays.asList(identifier));
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    // Files.write( baos.toByteArray(), new File("target/test_measure_v1_0_0.zip"));
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureEvaluation requestData = new MeasureEvaluation();
    requestData.setDataServerConfig(dataServerConfig);
    requestData.setTerminologyServerConfig(termServerConfig);
    // This is a patient ID that is assumed to exist in the target FHIR server
    requestData.setPatientId(VALID_PATIENT_ID);
    requestData.setMeasureContext(new MeasureContext(null, parameterOverrides, new com.ibm.cohort.engine.measure.Identifier(identifier.getSystem(), identifier.getValue()), measure.getVersion()));
    requestData.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.NONE));
    ObjectMapper om = new ObjectMapper();
    System.out.println(om.writeValueAsString(requestData));
    RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.MEASURE_PART, "test_measure_v1_0_0.zip", new ByteArrayInputStream(baos.toByteArray()));
    ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
    ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
    String expected = getJsonFromFile(ServiceAPIGlobalSpec.EXP_FOLDER_TYPE, "measure_evaluation_exp.json");
    String actual = vr.extract().asString();
    assertMeasureReportEquals(parser, expected, actual, false);
}

Example 24 with IParser

use of org.hl7.fhir.r5.formats.IParser in project openmrs-module-fhir2 by openmrs.

the class FhirImmunizationServiceImplTest method updateImmunization_shouldUpdateImmunizationAccordingly.

@Test
public void updateImmunization_shouldUpdateImmunizationAccordingly() {
    // setup
    FhirContext ctx = FhirContext.forR4();
    IParser parser = ctx.newJsonParser();
    Immunization updatedImmunization = parser.parseResource(Immunization.class, "{\n" + "  \"resourceType\": \"Immunization\",\n" + "  \"id\": \"9353776b-dead-4588-8723-d687197d8438\",\n" + "  \"status\": \"completed\",\n" + "  \"vaccineCode\": {\n" + "    \"coding\": [\n" + "      {\n" + "        \"code\": \"d144d24f-6913-4b63-9660-a9108c2bebef\",\n" + "        \"display\": \"STAVUDINE LAMIVUDINE AND NEVIRAPINE\"\n" + "      }\n" + "    ]\n" + "  },\n" + "  \"patient\": {\n" + "    \"reference\": \"Patient/a7e04421-525f-442f-8138-05b619d16def\",\n" + "    \"type\": \"Patient\"\n" + "  },\n" + "  \"encounter\": {\n" + "    \"reference\": \"Encounter/7d8c1980-6b78-11e0-93c3-18a905e044dc\",\n" + "    \"type\": \"Encounter\"\n" + "  },\n" + "  \"occurrenceDateTime\": \"2020-07-08T20:30:00+02:00\",\n" + "  \"manufacturer\": {\n" + "    \"display\": \"Pharma Inc.\"\n" + "  },\n" + "  \"lotNumber\": \"YU765YT-1\",\n" + "  \"expirationDate\": \"2020-10-08\",\n" + "  \"performer\": [\n" + "    {\n" + "      \"actor\": {\n" + "        \"reference\": \"Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66\",\n" + "        \"type\": \"Practitioner\"\n" + "      }\n" + "    }\n" + "  ],\n" + "  \"protocolApplied\": [\n" + "    {\n" + "      \"doseNumberPositiveInt\": 4\n" + "    }\n" + "  ]\n" + "}");
    // replay
    Immunization savedImmunization = service.update("9353776b-dead-4588-8723-d687197d8438", updatedImmunization);
    Obs obs = obsService.getObsByUuid(savedImmunization.getId());
    // verify
    helper.validateImmunizationObsGroup(obs);
    assertObsCommons(obs, "a7e04421-525f-442f-8138-05b619d16def", "7d8c1980-6b78-11e0-93c3-18a905e044dc", "f9badd80-ab76-11e2-9e96-0800200c9a66");
    obs.getGroupMembers().forEach(o -> {
        assertObsCommons(o, "a7e04421-525f-442f-8138-05b619d16def", "7d8c1980-6b78-11e0-93c3-18a905e044dc", "f9badd80-ab76-11e2-9e96-0800200c9a66");
    });
    Map<String, Obs> members = helper.getObsMembersMap(obs);
    assertThat(members.get(CIEL_984).getValueCoded().getUuid(), is("d144d24f-6913-4b63-9660-a9108c2bebef"));
    assertThat(members.get(CIEL_1410).getValueDatetime(), equalTo(new DateTimeType("2020-07-08T20:30:00+02:00").getValue()));
    assertThat(members.get(CIEL_1418).getValueNumeric(), equalTo(4.0));
    assertThat(members.get(CIEL_1419).getValueText(), is("Pharma Inc."));
    assertThat(members.get(CIEL_1420).getValueText(), is("YU765YT-1"));
    assertThat(members.get(CIEL_165907).getValueDate(), equalTo(new DateType("2020-10-08").getValue()));
}

Example 25 with IParser

use of org.hl7.fhir.r5.formats.IParser in project ab2d by CMSgov.

the class CapabilityAPIV2 method capabilityStatement.

@Operation(summary = CAP_REQ)
@ApiResponses(value = { @ApiResponse(responseCode = "200", description = CAP_DESC + " http://hl7.org/fhir/capabilitystatement.html") })
@ResponseStatus(value = HttpStatus.OK)
@GetMapping(value = "/metadata")
public ResponseEntity<String> capabilityStatement(HttpServletRequest request) {
    IParser parser = R4.getJsonParser();
    eventLogger.log(new ApiResponseEvent(MDC.get(ORGANIZATION), null, HttpStatus.OK, CAP_STMT, CAP_RET, (String) request.getAttribute(REQUEST_ID)));
    String server = common.getCurrentUrl(request).replace("/metadata", "");
    CapabilityStatement capabilityStatement = CapabilityStatementR4.populateCS(server);
    return new ResponseEntity<>(parser.encodeResourceToString(capabilityStatement), null, HttpStatus.OK);
}