Examples with Attachment org.hl7.fhir.r4b.model.Attachment used on opensource projects

Example 66 with Attachment

use of org.hl7.fhir.r4b.model.Attachment in project Gravity-SDOH-Exchange-RI by FHIR.

the class CreateConsentFactory method createConsent.

public Consent createConsent() {
    Consent consent = new Consent();
    consent.getSourceAttachment().setTitle(name);
    try {
        consent.getSourceAttachment().setData(attachment.getBytes());
    } catch (IOException e) {
        throw new ConsentCreateException("Consent attachment cannot be read.");
    }
    consent.getSourceAttachment().setContentType(MediaType.APPLICATION_PDF_VALUE);
    consent.setId(IdType.newRandomUuid());
    consent.setStatus(Consent.ConsentState.ACTIVE);
    consent.setDateTimeElement(DateTimeType.now());
    consent.getMeta().addProfile(SDOHProfiles.CONSENT);
    ConsentScope consentScope = ConsentScope.PATIENTPRIVACY;
    consent.getScope().addCoding(new Coding(consentScope.getSystem(), consentScope.toCode(), consentScope.getDisplay()));
    V3ActCode actCode = V3ActCode.IDSCL;
    consent.addCategory(new CodeableConcept().addCoding(new Coding(actCode.getSystem(), actCode.toCode(), actCode.getDisplay())));
    consent.setPatient(patient);
    ConsentPolicy consentPolicy = ConsentPolicy.HIPAAAUTH;
    consent.getPolicyRule().addCoding(new Coding(consentPolicy.getSystem(), consentPolicy.toCode(), consentPolicy.getDisplay()));
    V3RoleClass roleClass = V3RoleClass.PAT;
    consent.getProvision().addActor().setReference(patient).getRole().addCoding(new Coding(roleClass.getSystem(), roleClass.toCode(), roleClass.getDisplay()));
    ConsentAction consentAction = ConsentAction.DISCLOSE;
    consent.getProvision().addAction().getCoding().add(new Coding(consentAction.getSystem(), consentAction.toCode(), consentAction.getDisplay()));
    consent.getOrganization().add(organization);
    return consent;
}

Example 67 with Attachment

use of org.hl7.fhir.r4b.model.Attachment in project geoprism-registry by terraframe.

the class AbstractFhirResourceProcessor method getGeometry.

protected Geometry getGeometry(Location location, ServerGeoObjectType type) {
    Extension extension = location.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/location-boundary-geojson");
    if (extension != null) {
        Attachment value = (Attachment) extension.getValue();
        if (value.hasData()) {
            Decoder decoder = Base64.getDecoder();
            byte[] binary = decoder.decode(value.getDataElement().getValueAsString());
            String geojson = new String(binary);
            GeoJsonReader reader = new GeoJsonReader();
            try {
                return reader.read(geojson);
            } catch (ParseException e) {
                e.printStackTrace();
            }
        }
    }
    return null;
}

Example 68 with Attachment

use of org.hl7.fhir.r4b.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 69 with Attachment

use of org.hl7.fhir.r4b.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 70 with Attachment

use of org.hl7.fhir.r4b.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;
}