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

Example 76 with Attachment

use of org.hl7.fhir.r5.model.Attachment in project geoprism-registry by terraframe.

the class ListTypeFhirExporter method createFacility.

private Facility createFacility(Business row, Identifier identifier) {
    String code = row.getValue(DefaultAttribute.CODE.getName());
    Organization org = new Organization();
    org.setId(new IdType(org.getResourceType().name(), code));
    org.setName(row.getValue(DefaultAttribute.DISPLAY_LABEL.getName() + ListTypeVersion.DEFAULT_LOCALE));
    org.addIdentifier(identifier);
    Location location = new Location();
    location.setId(new IdType(location.getResourceType().name(), code));
    location.setName(row.getValue(DefaultAttribute.DISPLAY_LABEL.getName() + ListTypeVersion.DEFAULT_LOCALE));
    location.setManagingOrganization(new Reference(org.getIdElement()));
    location.addIdentifier(identifier);
    Geometry geometry = row.getObjectValue(RegistryConstants.GEOMETRY_ATTRIBUTE_NAME);
    if (geometry != null) {
        Point centroid = geometry.getCentroid();
        GeoJsonWriter writer = new GeoJsonWriter();
        String geojson = writer.write(geometry);
        Encoder encoder = Base64.getEncoder();
        // Create a location
        Attachment attachment = new Attachment();
        attachment.setContentType("application/json");
        attachment.setDataElement(new Base64BinaryType(encoder.encodeToString(geojson.getBytes())));
        attachment.setTitle("Geojson");
        Extension extension = new Extension("http://hl7.org/fhir/StructureDefinition/location-boundary-geojson");
        extension.setValue(attachment);
        location.setPosition(new LocationPositionComponent(new DecimalType(centroid.getX()), new DecimalType(centroid.getY())));
        location.addExtension(extension);
    }
    return new Facility(org, location);
}

Example 77 with Attachment

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

the class CohortCLI method toCqlLibraryMap.

private Map<CqlLibraryDescriptor, CqlLibrary> toCqlLibraryMap(List<Library> libraries) {
    Map<CqlLibraryDescriptor, CqlLibrary> retVal = new HashMap<>();
    for (Library library : libraries) {
        String libraryId = library.getName();
        String version = library.getVersion();
        for (Attachment attachment : library.getContent()) {
            Format libraryFormat = Format.lookupByName(attachment.getContentType());
            if (libraryFormat != null) {
                CqlLibraryDescriptor key = new CqlLibraryDescriptor().setLibraryId(libraryId).setVersion(version).setFormat(libraryFormat);
                CqlLibrary value = new CqlLibrary().setContent(new String(attachment.getData())).setDescriptor(key);
                retVal.put(key, value);
            }
        }
    }
    return retVal;
}

Example 78 with Attachment

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

the class CohortEngineRestHandler method evaluatePatientListMeasure.

@POST
@Path("/evaluation-patient-list")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a measure bundle for a list of patients", notes = EVALUATION_API_NOTES, response = String.class, tags = { "Measure Evaluation" }, extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_PATIENT_LIST_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_PATIENT_LIST_MEASURE_REQUEST_DATA_JSON, dataTypeClass = PatientListMeasureEvaluation.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-cat2-example.html"), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluatePatientListMeasure(@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_PATIENT_LIST_MEASURE.getName();
    Response response = null;
    // Error out if feature is not enabled
    ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_PATIENT_LIST_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 PatientListMeasureEvaluation request
        ObjectMapper om = new ObjectMapper();
        PatientListMeasureEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), PatientListMeasureEvaluation.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.evaluatePatientListMeasure(evaluationRequest.getPatientIds(), 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 79 with Attachment

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

the class R4LibraryDependencyGathererTest method withContent.

private void withContent(Library library, String contentType) {
    Attachment attachment = new Attachment();
    attachment.setContentType(contentType);
    library.addContent(attachment);
}

Example 80 with Attachment

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

the class R4TranslatingLibraryLoaderTest method load_invalidCqlContent.

@Test
public void load_invalidCqlContent() throws IOException {
    Library library = new Library();
    withIdentifiers(library, NAME, VERSION);
    withContent(library, "/cql/basic/Test-1.0.0.xml", "text/cql");
    R4TranslatingLibraryLoader loader = getLoader(getLibraryResolver(NAME, VERSION, library));
    VersionedIdentifier identifier = new VersionedIdentifier().withId(NAME).withVersion(VERSION);
    String expectedPrefix = String.format("Library %s-%s cql attachment", NAME, VERSION);
    assertIllegalArgumentException(() -> loader.load(identifier), expectedPrefix);
}