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

Example 6 with DataType

use of org.hl7.fhir.r5.model.DataType in project kindling by HL7.

the class DictHTMLGenerator method encodeValue.

private String encodeValue(DataType value) throws Exception {
    if (value == null || value.isEmpty())
        return null;
    if (value instanceof PrimitiveType)
        return Utilities.escapeXml(((PrimitiveType) value).asStringValue());
    ByteArrayOutputStream bs = new ByteArrayOutputStream();
    XmlParser parser = new XmlParser();
    parser.setOutputStyle(OutputStyle.PRETTY);
    parser.compose(bs, null, value);
    String[] lines = bs.toString().split("\\r?\\n");
    StringBuilder b = new StringBuilder();
    for (String s : lines) {
        if (!Utilities.noString(s) && !s.startsWith("<?")) {
            // eliminate the xml header
            b.append(Utilities.escapeXml(s).replace(" ", "&nbsp;") + "<br/>");
        }
    }
    return b.toString();
}

Example 7 with DataType

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

the class CohortEngineRestHandler method evaluateMeasure.

@POST
@Path("/evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a measure bundle for a single patient", notes = EVALUATION_API_NOTES, response = String.class, tags = { "Measure Evaluation" }, nickname = "evaluate_measure", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), // These are necessary to create a proper view of the request body that is all wrapped up in the Liberty IMultipartBody parameter
@ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_REQUEST_DATA_JSON, dataTypeClass = MeasureEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = MEASURE_PART, value = EXAMPLE_MEASURE_ZIP, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation: This API returns the JSON representation of a FHIR MeasureReport. A full example can be found at https://www.hl7.org/fhir/measurereport-cms146-cat1-example.html"), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateMeasure(@Context HttpServletRequest request, @ApiParam(value = ServiceBaseConstants.MINOR_VERSION_DESCRIPTION, required = true, defaultValue = ServiceBuildConstants.DATE) @QueryParam(CohortEngineRestHandler.VERSION) String version, @ApiParam(hidden = true, type = "file", required = true) IMultipartBody multipartBody) {
    final String methodName = MethodNames.EVALUATE_MEASURE.getName();
    Response response = null;
    // Error out if feature is not enabled
    ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION);
    try {
        // Perform api setup
        Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
        if (errorResponse != null) {
            return errorResponse;
        }
        if (multipartBody == null) {
            throw new IllegalArgumentException("A multipart/form-data body is required");
        }
        IAttachment metadataAttachment = multipartBody.getAttachment(REQUEST_DATA_PART);
        if (metadataAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", REQUEST_DATA_PART));
        }
        IAttachment measureAttachment = multipartBody.getAttachment(MEASURE_PART);
        if (measureAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", MEASURE_PART));
        }
        // deserialize the MeasuresEvaluation request
        ObjectMapper om = new ObjectMapper();
        MeasureEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), MeasureEvaluation.class);
        // validate the contents of the evaluationRequest
        validateBean(evaluationRequest);
        FhirContext fhirContext = FhirContext.forR4();
        try (InputStream is = measureAttachment.getDataHandler().getInputStream();
            RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
            MeasureEvaluator evaluator = createMeasureEvaluator(is, evaluationRequest.getDataServerConfig(), evaluationRequest.getTerminologyServerConfig(), evaluationRequest.isExpandValueSets(), evaluationRequest.getSearchPageSize(), retrieveCacheContext, fhirContext);
            MeasureReport report = evaluator.evaluatePatientMeasure(evaluationRequest.getPatientId(), evaluationRequest.getMeasureContext(), evaluationRequest.getEvidenceOptions());
            // The default serializer gets into an infinite loop when trying to serialize MeasureReport, so we use the
            // HAPI encoder instead.
            IParser parser = fhirContext.newJsonParser();
            ResponseBuilder responseBuilder = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(parser.encodeResourceToString(report));
            response = responseBuilder.build();
        }
    } catch (Throwable e) {
        // map any exceptions caught into the proper REST error response objects
        response = new CohortServiceExceptionMapper().toResponse(e);
    } finally {
        // Perform api cleanup
        Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
        if (errorResponse != null) {
            response = errorResponse;
        }
    }
    return response;
}

Example 8 with DataType

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

the class SparkCqlEvaluator method createDataTypeAliases.

private Map<String, String> createDataTypeAliases(List<ContextDefinition> filteredContexts, CqlToElmTranslator translator) {
    Set<String> dataTypes = filteredContexts.stream().map(ContextDefinition::getPrimaryDataType).collect(Collectors.toSet());
    Collection<ModelInfo> modelInfos = translator.getRegisteredModelInfos().values();
    Map<String, String> dataTypeAliases = new HashMap<>();
    for (ModelInfo modelInfo : modelInfos) {
        modelInfo.getTypeInfo().stream().filter(ClassInfo.class::isInstance).map(ClassInfo.class::cast).filter(classInfo -> dataTypes.contains(classInfo.getName())).forEach(info -> {
            String dataType = info.getName();
            QName baseType = ModelUtils.getBaseTypeName(modelInfo, info);
            if (baseType != null) {
                // for inheritance types
                dataTypeAliases.put(dataType, baseType.getLocalPart());
            }
            Collection<String> choiceTypes = ModelUtils.getChoiceTypeNames(info);
            // for choice types
            choiceTypes.forEach(choiceType -> dataTypeAliases.put(dataType, choiceType));
        });
    }
    return dataTypeAliases;
}

Example 9 with DataType

use of org.hl7.fhir.r5.model.DataType in project drug-formulary-ri by HL7-DaVinci.

the class PatientAuthorizationInterceptor method verify.

/**
 * Helper method to verify and decode the access token
 *
 * @param token       - the access token
 * @param fhirBaseUrl - the base url of this FHIR server
 * @return the base interface Patient ID datatype if the jwt token is verified
 *         and contains a patient ID in it claim, otherwise null.
 * @throws SignatureVerificationException
 * @throws TokenExpiredException
 * @throws JWTVerificationException
 */
private IIdType verify(String token, String fhirBaseUrl) throws SignatureVerificationException, TokenExpiredException, JWTVerificationException {
    Algorithm algorithm = Algorithm.RSA256(OauthEndpointController.getPublicKey(), null);
    logger.fine("Verifying JWT token iss and aud is " + fhirBaseUrl);
    JWTVerifier verifier = JWT.require(algorithm).withIssuer(fhirBaseUrl).withAudience(fhirBaseUrl).build();
    DecodedJWT jwt = verifier.verify(token);
    String patientId = jwt.getClaim("patient_id").asString();
    if (patientId != null)
        return new IdType("Patient", patientId);
    return null;
}

Example 10 with DataType

use of org.hl7.fhir.r5.model.DataType in project org.hl7.fhir.core by hapifhir.

the class ElementDefinition30_50 method convertElementDefinitionBindingComponent.

public static ElementDefinition.ElementDefinitionBindingComponent convertElementDefinitionBindingComponent(org.hl7.fhir.dstu3.model.ElementDefinition.ElementDefinitionBindingComponent src) throws FHIRException {
    if (src == null)
        return null;
    ElementDefinition.ElementDefinitionBindingComponent tgt = new ElementDefinition.ElementDefinitionBindingComponent();
    ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().copyElement(src, tgt, VersionConvertor_30_50.EXT_SRC_TYPE);
    if (src.hasStrength())
        tgt.setStrengthElement(Enumerations30_50.convertBindingStrength(src.getStrengthElement()));
    if (src.hasDescription())
        tgt.setDescriptionElement(String30_50.convertString(src.getDescriptionElement()));
    if (src.hasValueSet()) {
        DataType t = ConversionContext30_50.INSTANCE.getVersionConvertor_30_50().convertType(src.getValueSet());
        if (t instanceof org.hl7.fhir.r5.model.Reference) {
            tgt.setValueSet(((org.hl7.fhir.r5.model.Reference) t).getReference());
            tgt.getValueSetElement().addExtension(VersionConvertor_30_50.EXT_SRC_TYPE, new org.hl7.fhir.r5.model.UrlType("Reference"));
        } else {
            tgt.setValueSet(t.primitiveValue());
            tgt.getValueSetElement().addExtension(VersionConvertor_30_50.EXT_SRC_TYPE, new org.hl7.fhir.r5.model.UrlType("uri"));
        }
        tgt.setValueSet(VersionConvertorConstants.refToVS(tgt.getValueSet()));
    }
    return tgt;
}