Examples with Section org.hl7.fhir.r4.utils.formats.Turtle.Section used on opensource projects

Example 6 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project cqf-ruler by DBCG.

the class CqlExecutionProvider method evaluate.

/**
 * Evaluates a CQL expression and returns the results as a Parameters resource.
 *
 * @param theRequestDetails   the {@link RequestDetails RequestDetails}
 * @param subject             Subject for which the expression will be
 *                            evaluated. This corresponds to the context in
 *                            which the expression will be evaluated and is
 *                            represented as a relative FHIR id (e.g.
 *                            Patient/123), which establishes both the context
 *                            and context value for the evaluation
 * @param expression          Expression to be evaluated. Note that this is an
 *                            expression of CQL, not the text of a library with
 *                            definition statements.
 * @param parameters          Any input parameters for the expression.
 *                            {@link Parameters} Parameters defined in this
 *                            input will be made available by name to the CQL
 *                            expression. Parameter types are mapped to CQL as
 *                            specified in the Using CQL section of the CPG
 *                            Implementation guide. If a parameter appears more
 *                            than once in the input Parameters resource, it is
 *                            represented with a List in the input CQL. If a
 *                            parameter has parts, it is represented as a Tuple
 *                            in the input CQL.
 * @param library             A library to be included. The {@link Library}
 *                            library is resolved by url and made available by
 *                            name within the expression to be evaluated.
 * @param useServerData       Whether to use data from the server performing the
 *                            evaluation. If this parameter is true (the
 *                            default), then the operation will use data first
 *                            from any bundles provided as parameters (through
 *                            the data and prefetch parameters), second data
 *                            from the server performing the operation, and
 *                            third, data from the dataEndpoint parameter (if
 *                            provided). If this parameter is false, the
 *                            operation will use data first from the bundles
 *                            provided in the data or prefetch parameters, and
 *                            second from the dataEndpoint parameter (if
 *                            provided).
 * @param data                Data to be made available to the library
 *                            evaluation. This parameter is exclusive with the
 *                            prefetchData parameter (i.e. either provide all
 *                            data as a single bundle, or provide data using
 *                            multiple bundles with prefetch descriptions).
 * @param prefetchData        ***Not Yet Implemented***
 * @param dataEndpoint        An {@link Endpoint} endpoint to use to access data
 *                            referenced by retrieve operations in the library.
 *                            If provided, this endpoint is used after the data
 *                            or prefetchData bundles, and the server, if the
 *                            useServerData parameter is true.
 * @param contentEndpoint     An {@link Endpoint} endpoint to use to access
 *                            content (i.e. libraries) referenced by the
 *                            library. If no content endpoint is supplied, the
 *                            evaluation will attempt to retrieve content from
 *                            the server on which the operation is being
 *                            performed.
 * @param terminologyEndpoint An {@link Endpoint} endpoint to use to access
 *                            terminology (i.e. valuesets, codesystems, and
 *                            membership testing) referenced by the library. If
 *                            no terminology endpoint is supplied, the
 *                            evaluation will attempt to use the server on which
 *                            the operation is being performed as the
 *                            terminology server.
 * @return The result of evaluating the given expression, returned as a FHIR
 *         type, either a {@link Resource} resource, or a FHIR-defined type
 *         corresponding to the CQL return type, as defined in the Using CQL
 *         section of the CPG Implementation guide. If the result is a List of
 *         resources, the result will be a {@link Bundle} Bundle . If the result
 *         is a CQL system-defined or FHIR-defined type, the result is returned
 *         as a {@link Parameters} Parameters resource
 */
@Operation(name = "$cql")
@Description(shortDefinition = "$cql", value = "Evaluates a CQL expression and returns the results as a Parameters resource. Defined: http://build.fhir.org/ig/HL7/cqf-recommendations/OperationDefinition-cpg-cql.html", example = "$cql?expression=5*5")
public Parameters evaluate(RequestDetails theRequestDetails, @OperationParam(name = "subject", max = 1) String subject, @OperationParam(name = "expression", min = 1, max = 1) String expression, @OperationParam(name = "parameters", max = 1) Parameters parameters, @OperationParam(name = "library") List<Parameters> library, @OperationParam(name = "useServerData", max = 1) BooleanType useServerData, @OperationParam(name = "data", max = 1) Bundle data, @OperationParam(name = "prefetchData") List<Parameters> prefetchData, @OperationParam(name = "dataEndpoint", max = 1) Endpoint dataEndpoint, @OperationParam(name = "contentEndpoint", max = 1) Endpoint contentEndpoint, @OperationParam(name = "terminologyEndpoint", max = 1) Endpoint terminologyEndpoint) {
    if (prefetchData != null) {
        throw new NotImplementedException("prefetchData is not yet supported.");
    }
    if (useServerData == null) {
        useServerData = new BooleanType(true);
    }
    List<LibraryParameter> libraryParameters = new ArrayList<>();
    if (library != null) {
        for (Parameters libraryParameter : library) {
            CanonicalType url = null;
            String name = null;
            for (ParametersParameterComponent param : libraryParameter.getParameter()) {
                switch(param.getName()) {
                    case "url":
                        url = ((CanonicalType) param.getValue());
                        break;
                    case "name":
                        name = ((StringType) param.getValue()).asStringValue();
                        break;
                    default:
                        throw new IllegalArgumentException("Only url and name parts are allowed for Parameter: library");
                }
            }
            if (url == null) {
                throw new IllegalArgumentException("If library parameter must provide a url parameter part.");
            }
            libraryParameters.add(new LibraryParameter().withUrl(url).withName(name));
        }
    // Remove LocalLibrary from cache first...
    }
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary").withVersion("1.0.0");
    globalLibraryCache.remove(localLibraryIdentifier);
    CqlEngine engine = setupEngine(localLibraryIdentifier, expression, libraryParameters, subject, parameters, contentEndpoint, dataEndpoint, terminologyEndpoint, data, useServerData.booleanValue(), theRequestDetails);
    Map<String, Object> resolvedParameters = new HashMap<>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    String contextType = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    String subjectId = subject != null ? subject.substring(0, subject.lastIndexOf("/") - 1) : null;
    EvaluationResult evalResult = engine.evaluate(localLibraryIdentifier, null, Pair.of(contextType != null ? contextType : "Unspecified", subjectId == null ? "null" : subject), resolvedParameters, this.getDebugMap());
    if (evalResult != null && evalResult.expressionResults != null) {
        if (evalResult.expressionResults.size() > 1) {
            logger.debug("Evaluation resulted in more than one expression result.  ");
        }
        Parameters result = new Parameters();
        resolveResult(theRequestDetails, evalResult, result);
        return result;
    }
    return null;
}

Example 7 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project summary-care-record-api by NHSDigital.

the class GpSummaryMapper method map.

@SneakyThrows
public List<Resource> map(Node document) {
    var gpSummaryId = xmlUtils.getValueByXPath(document, GP_SUMMARY_ID_XPATH);
    var gpSummaryCodeCode = xmlUtils.getValueByXPath(document, GP_SUMMARY_CODE_CODE_XPATH);
    var gpSummaryCodeDisplayName = xmlUtils.getValueByXPath(document, GP_SUMMARY_CODE_DISPLAY_NAME_XPATH);
    var gpSummaryStatusCode = xmlUtils.getValueByXPath(document, GP_SUMMARY_STATUS_CODE_XPATH);
    var gpSummaryEffectiveTime = parseDate(xmlUtils.getValueByXPath(document, GP_SUMMARY_EFFECTIVE_TIME_XPATH), InstantType.class);
    var authorTime = parseDate(xmlUtils.getValueByXPath(document, GP_SUMMARY_AUTHOR_TIME_XPATH), DateTimeType.class);
    var replacementOfPriorMessageRefIdRoot = xmlUtils.getOptionalValueByXPath(document, REPLACEMENT_OF_PRIOR_MESSAGE_REF_ID_ROOT_XPATH);
    var pertinentRootCreTypeCodeCode = xmlUtils.getValueByXPath(document, PERTINENT_ROOT_CRE_TYPE_CODE_CODE_XPATH);
    var pertinentRootCreTypeCodeDisplayName = xmlUtils.getValueByXPath(document, PERTINENT_ROOT_CRE_TYPE_CODE_DISPLAY_NAME_XPATH);
    var presentationTextValue = xmlUtils.detachOptionalNodeByXPath(document, PRESENTATION_TEXT_VALUE);
    var eventId = xmlUtils.getValueByXPath(document, EVENT_ID_XPATH);
    List<Resource> resources = new ArrayList<>();
    var composition = new Composition();
    composition.setId(eventId);
    composition.setIdentifier(new Identifier().setValue(gpSummaryId).setSystem("https://tools.ietf.org/html/rfc4122"));
    composition.setType(new CodeableConcept().addCoding(new Coding().setCode(gpSummaryCodeCode).setSystem(SNOMED_SYSTEM).setDisplay(gpSummaryCodeDisplayName)));
    composition.setMeta(new Meta().setLastUpdatedElement(gpSummaryEffectiveTime));
    composition.setStatus(mapCompositionStatus(gpSummaryStatusCode));
    composition.setDateElement(authorTime);
    replacementOfPriorMessageRefIdRoot.ifPresent(val -> composition.addRelatesTo(new Composition.CompositionRelatesToComponent().setTarget(new Identifier().setValue(val)).setCode(REPLACES)));
    composition.addCategory(new CodeableConcept().addCoding(new Coding().setCode(pertinentRootCreTypeCodeCode).setSystem(SNOMED_SYSTEM).setDisplay(pertinentRootCreTypeCodeDisplayName)));
    Map<String, List<String>> references = sectionReferences(document);
    presentationTextValue.map(htmlParser::parse).map(Collection::stream).ifPresent(it -> it.forEach(section -> {
        if (section.getTitle() != null && CODED_ENTRY_RESOURCE_MAP.keySet().contains(section.getTitle()) && references.containsKey(section.getTitle())) {
            for (String codedEntryId : references.get(section.getTitle())) {
                section.addEntry(new Reference(CODED_ENTRY_RESOURCE_MAP.get(section.getTitle()) + "/" + codedEntryId));
            }
        }
        composition.addSection(section);
    }));
    resources.add(composition);
    addAuthor(document, resources, composition);
    return resources;
}

Example 8 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project summary-care-record-api by NHSDigital.

the class CompositionMapper method setPresentation.

private static void setPresentation(GpSummary gpSummary, Composition composition) throws FhirMappingException {
    if (!composition.hasSection()) {
        throw new FhirMappingException("Missing mandatory Composition.section");
    }
    Presentation presentation = new Presentation();
    var htmlDocument = createNewDocument("html", "xhtml:NPfIT:PresentationText");
    var bodyNode = htmlDocument.createElement("body");
    htmlDocument.getDocumentElement().appendChild(bodyNode);
    for (Composition.SectionComponent section : composition.getSection()) {
        var h2Node = htmlDocument.createElement("h2");
        h2Node.setAttribute("id", section.getCode().getCodingFirstRep().getCode());
        h2Node.appendChild(htmlDocument.createTextNode(section.getTitle()));
        bodyNode.appendChild(h2Node);
        var divDocument = parseDocument(section.getText().getDiv().getValueAsString());
        removeEmptyNodes(divDocument);
        var divChildNodes = divDocument.getDocumentElement().getChildNodes();
        for (int i = 0; i < divChildNodes.getLength(); i++) {
            bodyNode.appendChild(htmlDocument.importNode(divChildNodes.item(i), true));
        }
    }
    presentation.setPresentationId(randomUUID());
    presentation.setPresentationText(serialize(htmlDocument));
    gpSummary.setPresentation(presentation);
}

Example 9 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project integration-adaptor-111 by nhsconnect.

the class AppointmentServiceTest method setUp.

@BeforeEach
public void setUp() {
    clinicalDocument1 = mock(POCDMT000002UK01ClinicalDocument1.class);
    POCDMT000002UK01Component2 component2 = mock(POCDMT000002UK01Component2.class);
    POCDMT000002UK01StructuredBody structuredBody = mock(POCDMT000002UK01StructuredBody.class);
    POCDMT000002UK01Component3 component3 = mock(POCDMT000002UK01Component3.class);
    section = mock(POCDMT000002UK01Section.class);
    patient = mock(Reference.class);
    when(clinicalDocument1.getComponent()).thenReturn(component2);
    when(component2.getStructuredBody()).thenReturn(structuredBody);
    when(structuredBody.getComponentArray()).thenReturn(new POCDMT000002UK01Component3[] { component3 });
    when(component3.getSection()).thenReturn(section);
}

Example 10 with Section

use of org.hl7.fhir.r4.utils.formats.Turtle.Section in project integration-adaptor-111 by nhsconnect.

the class ConsentMapper method extractTextBody.

private void extractTextBody(Consent consent, POCDMT000002UK01StructuredBody structuredBody) {
    List<POCDMT000002UK01Section> sections = getSectionsOfType(structuredBody);
    for (POCDMT000002UK01Section section : sections) {
        Narrative narrative = new Narrative();
        narrative.setStatus(GENERATED);
        if (section.isSetText()) {
            narrative.setDivAsString(Arrays.asList(DIV_START, section.getText().xmlText(), DIV_END).stream().collect(Collectors.joining()));
            consent.setText(narrative);
        }
    }
}