Examples with CanonicalType org.hl7.fhir.r4.model.CanonicalType used on opensource projects

Example 6 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType 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 CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project cqf-ruler by DBCG.

the class CdsHooksServlet method doPost.

@Override
@SuppressWarnings("deprecation")
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
    logger.info(request.getRequestURI());
    try {
        // validate that we are dealing with JSON
        if (request.getContentType() == null || !request.getContentType().startsWith("application/json")) {
            throw new ServletException(String.format("Invalid content type %s. Please use application/json.", request.getContentType()));
        }
        String baseUrl = this.myAppProperties.getServer_address();
        String service = request.getPathInfo().replace("/", "");
        JsonParser parser = new JsonParser();
        Request cdsHooksRequest = new Request(service, parser.parse(request.getReader()).getAsJsonObject(), JsonHelper.getObjectRequired(getService(service), "prefetch"));
        logger.info(cdsHooksRequest.getRequestJson().toString());
        Hook hook = HookFactory.createHook(cdsHooksRequest);
        String hookName = hook.getRequest().getHook();
        logger.info("cds-hooks hook: {}", hookName);
        logger.info("cds-hooks hook instance: {}", hook.getRequest().getHookInstance());
        logger.info("cds-hooks maxCodesPerQuery: {}", this.getProviderConfiguration().getMaxCodesPerQuery());
        logger.info("cds-hooks expandValueSets: {}", this.getProviderConfiguration().getExpandValueSets());
        logger.info("cds-hooks searchStyle: {}", this.getProviderConfiguration().getSearchStyle());
        logger.info("cds-hooks prefetch maxUriLength: {}", this.getProviderConfiguration().getMaxUriLength());
        logger.info("cds-hooks local server address: {}", baseUrl);
        logger.info("cds-hooks fhir server address: {}", hook.getRequest().getFhirServerUrl());
        logger.info("cds-hooks cql_logging_enabled: {}", this.getProviderConfiguration().getCqlLoggingEnabled());
        PlanDefinition planDefinition = read(Ids.newId(PlanDefinition.class, hook.getRequest().getServiceName()));
        AtomicBoolean planDefinitionHookMatchesRequestHook = new AtomicBoolean(false);
        planDefinition.getAction().forEach(action -> {
            action.getTrigger().forEach(trigger -> {
                if (hookName.equals(trigger.getName())) {
                    planDefinitionHookMatchesRequestHook.set(true);
                    return;
                }
            });
            if (planDefinitionHookMatchesRequestHook.get()) {
                return;
            }
        });
        if (!planDefinitionHookMatchesRequestHook.get()) {
            throw new ServletException("ERROR: Request hook does not match the service called.");
        }
        // No tenant information available, so create local system request
        RequestDetails requestDetails = new SystemRequestDetails();
        LibraryLoader libraryLoader = libraryLoaderFactory.create(Lists.newArrayList(jpaLibraryContentProviderFactory.create(requestDetails)));
        CanonicalType canonical = planDefinition.getLibrary().get(0);
        Library library = search(Library.class, Searches.byCanonical(canonical)).single();
        org.cqframework.cql.elm.execution.Library elm = libraryLoader.load(new VersionedIdentifier().withId(library.getName()).withVersion(library.getVersion()));
        Context context = new Context(elm);
        context.setDebugMap(this.getDebugMap());
        // provider case
        // No tenant information available for cds-hooks
        TerminologyProvider serverTerminologyProvider = myJpaTerminologyProviderFactory.create(requestDetails);
        context.registerDataProvider("http://hl7.org/fhir", // TODO make sure tooling
        fhirRetrieveProviderFactory.create(requestDetails, serverTerminologyProvider));
        // handles remote
        context.registerTerminologyProvider(serverTerminologyProvider);
        context.registerLibraryLoader(libraryLoader);
        context.setContextValue("Patient", hook.getRequest().getContext().getPatientId().replace("Patient/", ""));
        context.setExpressionCaching(true);
        EvaluationContext<PlanDefinition> evaluationContext = new R4EvaluationContext(hook, FhirContext.forCached(FhirVersionEnum.R4).newRestfulGenericClient(baseUrl), context, elm, planDefinition, this.getProviderConfiguration(), this.modelResolver);
        this.setAccessControlHeaders(response);
        response.setHeader("Content-Type", ContentType.APPLICATION_JSON.getMimeType());
        R4HookEvaluator evaluator = new R4HookEvaluator(this.modelResolver);
        String jsonResponse = toJsonResponse(evaluator.evaluate(evaluationContext));
        logger.info(jsonResponse);
        response.getWriter().println(jsonResponse);
    } catch (BaseServerResponseException e) {
        this.setAccessControlHeaders(response);
        // This will be overwritten with the correct status code downstream if needed.
        response.setStatus(500);
        response.getWriter().println("ERROR: Exception connecting to remote server.");
        this.printMessageAndCause(e, response);
        this.handleServerResponseException(e, response);
        this.printStackTrack(e, response);
        logger.error(e.toString());
    } catch (DataProviderException e) {
        this.setAccessControlHeaders(response);
        // This will be overwritten with the correct status code downstream if needed.
        response.setStatus(500);
        response.getWriter().println("ERROR: Exception in DataProvider.");
        this.printMessageAndCause(e, response);
        if (e.getCause() != null && (e.getCause() instanceof BaseServerResponseException)) {
            this.handleServerResponseException((BaseServerResponseException) e.getCause(), response);
        }
        this.printStackTrack(e, response);
        logger.error(e.toString());
    } catch (CqlException e) {
        this.setAccessControlHeaders(response);
        // This will be overwritten with the correct status code downstream if needed.
        response.setStatus(500);
        response.getWriter().println("ERROR: Exception in CQL Execution.");
        this.printMessageAndCause(e, response);
        if (e.getCause() != null && (e.getCause() instanceof BaseServerResponseException)) {
            this.handleServerResponseException((BaseServerResponseException) e.getCause(), response);
        }
        this.printStackTrack(e, response);
        logger.error(e.toString());
    } catch (Exception e) {
        logger.error(e.toString());
        throw new ServletException("ERROR: Exception in cds-hooks processing.", e);
    }
}

Example 8 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project cqf-ruler by DBCG.

the class ExpressionEvaluation method setupContext.

private Context setupContext(DomainResource instance, String cql, String patientId, Boolean aliasedExpression, RequestDetails theRequest) {
    JpaFhirDal jpaFhirDal = jpaFhirDalFactory.create(theRequest);
    List<CanonicalType> libraries = getLibraryReferences(instance, theRequest);
    String fhirVersion = this.fhirContext.getVersion().getVersion().getFhirVersionString();
    // Remove LocalLibrary from cache first...
    VersionedIdentifier localLibraryIdentifier = new VersionedIdentifier().withId("LocalLibrary");
    globalLibraryCache.remove(localLibraryIdentifier);
    // temporary LibraryLoader to resolve library dependencies when building
    // includes
    LibraryLoader tempLibraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest))));
    String source = "";
    if (aliasedExpression) {
        if (libraries.size() != 1) {
            throw new RuntimeException("If an aliased expression is provided, there must be exactly one primary Library");
        }
        VersionedIdentifier vi = getVersionedIdentifierFromCanonical(libraries.get(0));
        // Still not the best way to build include, but at least checks dal for an
        // existing library
        // Check if id works for LibraryRetrieval
        org.cqframework.cql.elm.execution.Library executionLibrary = null;
        try {
            executionLibrary = tempLibraryLoader.load(vi);
        } catch (Exception e) {
        // log error
        }
        if (executionLibrary == null) {
            Library library = (Library) jpaFhirDal.read(new IdType("Library", Canonicals.getIdPart(libraries.get(0))));
            vi.setId(library.getName());
            if (library.getVersion() != null) {
                vi.setVersion(library.getVersion());
            }
        }
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), vi.getId() + ".\"" + cql + "\"");
    } else {
        source = String.format("library LocalLibrary using FHIR version '" + fhirVersion + "' include FHIRHelpers version '" + fhirVersion + "' called FHIRHelpers %s parameter %s %s parameter \"%%context\" %s define Expression: %s", buildIncludes(tempLibraryLoader, jpaFhirDal, libraries, theRequest), instance.fhirType(), instance.fhirType(), instance.fhirType(), cql);
    }
    LibraryLoader libraryLoader = libraryLoaderFactory.create(new ArrayList<LibraryContentProvider>(Arrays.asList(jpaLibraryContentProviderFactory.create(theRequest), new InMemoryLibraryContentProvider(Arrays.asList(source)))));
    // resolve execution context
    return setupContext(instance, patientId, libraryLoader, theRequest);
}

Example 9 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project quality-measure-and-cohort-service by Alvearie.

the class MeasureSupplementalDataEvaluationTest method testProcessAccumulators.

@Test
public void testProcessAccumulators() {
    Map<String, Map<String, Integer>> sdeAccumulators = getSexSDEAccumulators();
    MeasureReport report = new MeasureReport();
    MeasureSupplementalDataEvaluation.processAccumulators(report, sdeAccumulators, true, new ArrayList<>());
    assertNotNull(report);
    // EvaluatedResource should contain a reference to an observation record created for supplemental data
    assertEquals(1, report.getEvaluatedResource().size());
    // The observation record mentioned previously should exist within the contained resources of the measure report
    assertEquals(1, report.getContained().size());
    assertTrue(report.getContained().get(0) instanceof Observation);
    Observation obs = (Observation) report.getContained().get(0);
    // For a single patient, the code of the observation should be the supplemental data text
    assertEquals(MeasureSupplementalDataEvaluation.SDE_SEX, obs.getCode().getText());
    // For a single patient, the value of the observation should be the result of the appropriate define
    assertTrue(obs.getValue() instanceof CodeableConcept);
    assertEquals(MALE_CODE, ((CodeableConcept) obs.getValue()).getCoding().get(0).getCode());
    // Within the observation, there should be 1 extension, with two further nested extensions
    Extension obsExt = obs.getExtensionByUrl(MeasureSupplementalDataEvaluation.CQF_MEASUREINFO_URL);
    assertNotNull(obsExt);
    assertEquals(2, obsExt.getExtension().size());
    Extension measureNestedExt = obsExt.getExtensionByUrl(MeasureSupplementalDataEvaluation.MEASURE);
    assertTrue(measureNestedExt.getValue() instanceof CanonicalType);
    assertEquals(MeasureSupplementalDataEvaluation.CQFMEASURES_URL + report.getMeasure(), ((CanonicalType) measureNestedExt.getValue()).asStringValue());
    Extension populationNestedExt = obsExt.getExtensionByUrl(MeasureSupplementalDataEvaluation.POPULATION_ID);
    assertEquals(MeasureSupplementalDataEvaluation.SDE_SEX, ((StringType) populationNestedExt.getValue()).asStringValue());
}

Example 10 with CanonicalType

use of org.hl7.fhir.r4.model.CanonicalType in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluatorTest method id_based_library_link___successfully_loaded_and_evaluated.

@Test
public void id_based_library_link___successfully_loaded_and_evaluated() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("TestDummyPopulations", DEFAULT_VERSION, "cql/fhir-measure/test-dummy-populations.cql");
    Measure measure = getCareGapMeasure("IDBasedLibraryMeasure", library, expressionsByPopulationType, "CareGap1", "CareGap2");
    measure.setLibrary(Arrays.asList(new CanonicalType("Library/" + library.getId())));
    mockFhirResourceRetrieval(measure);
    Map<String, Parameter> passingParameters = new HashMap<>();
    passingParameters.put("InInitialPopulation", new BooleanParameter(true));
    List<MeasureContext> measureContexts = new ArrayList<>();
    measureContexts.add(new MeasureContext(measure.getId(), passingParameters));
    List<MeasureReport> reports = evaluator.evaluatePatientMeasures(patient.getId(), measureContexts);
    assertEquals(1, reports.size());
    MeasureReport report = reports.get(0);
    verifyStandardPopulationCounts(report);
    verify(1, getRequestedFor(urlEqualTo("/Library/" + library.getId() + "?_format=json")));
}