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Example 1 with LibraryContentProvider

use of org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider in project cqf-ruler by DBCG.

the class CqlExecutionProvider method setupEngine.

private CqlEngine setupEngine(VersionedIdentifier localLibraryIdentifier, String expression, List<LibraryParameter> library, String subject, Parameters parameters, Endpoint contentEndpoint, Endpoint dataEndpoint, Endpoint terminologyEndpoint, Bundle data, boolean useServerData, RequestDetails theRequestDetails) {
    JpaFhirDal jpaFhirDal = jpaFhirDalFactory.create(theRequestDetails);
    // temporary LibraryLoader to resolve library dependencies when building
    // includes
    List<LibraryContentProvider> libraryProviders = new ArrayList<>();
    libraryProviders.add(jpaLibraryContentProviderFactory.create(theRequestDetails));
    if (contentEndpoint != null) {
        libraryProviders.add(fhirRestLibraryContentProviderFactory.create(contentEndpoint.getAddress(), contentEndpoint.getHeader().stream().map(PrimitiveType::asStringValue).collect(Collectors.toList())));
    }
    LibraryLoader tempLibraryLoader = libraryLoaderFactory.create(new ArrayList<>(libraryProviders));
    String cql = buildCqlLibrary(library, jpaFhirDal, tempLibraryLoader, expression, parameters, theRequestDetails);
    libraryProviders.add(new InMemoryLibraryContentProvider(Arrays.asList(cql)));
    LibraryLoader libraryLoader = libraryLoaderFactory.create(new ArrayList<>(libraryProviders));
    return setupEngine(subject, parameters, dataEndpoint, terminologyEndpoint, data, useServerData, libraryLoader, localLibraryIdentifier, theRequestDetails);
}
Also used : LibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider) InMemoryLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.InMemoryLibraryContentProvider) InMemoryLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.InMemoryLibraryContentProvider) ArrayList(java.util.ArrayList) JpaFhirDal(org.opencds.cqf.ruler.cql.JpaFhirDal) LibraryLoader(org.opencds.cqf.cql.engine.execution.LibraryLoader)

Example 2 with LibraryContentProvider

use of org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider in project cqf-ruler by DBCG.

the class LibraryEvaluationProvider method evaluate.

@SuppressWarnings({ "unchecked" })
@Operation(name = "$evaluate", idempotent = true, type = Library.class)
public Bundle evaluate(@IdParam IdType theId, @OperationParam(name = "patientId") String patientId, @OperationParam(name = "periodStart") String periodStart, @OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "productLine") String productLine, @OperationParam(name = "terminologyEndpoint") Endpoint terminologyEndpoint, @OperationParam(name = "dataEndpoint") Endpoint dataEndpoint, @OperationParam(name = "context") String contextParam, @OperationParam(name = "executionResults") String executionResults, @OperationParam(name = "parameters") Parameters parameters, @OperationParam(name = "additionalData") Bundle additionalData, RequestDetails theRequestDetails) {
    log.info("Library evaluation started..");
    if (patientId == null && contextParam != null && contextParam.equals("Patient")) {
        log.error("Patient id null");
        throw new IllegalArgumentException("Must specify a patientId when executing in Patient context.");
    }
    Bundle libraryBundle = new Bundle();
    Library theResource = null;
    if (additionalData != null) {
        for (Bundle.BundleEntryComponent entry : additionalData.getEntry()) {
            if (entry.getResource().fhirType().equals("Library")) {
                libraryBundle.addEntry(entry);
                if (entry.getResource().getIdElement().equals(theId)) {
                    theResource = (Library) entry.getResource();
                }
            }
        }
    }
    if (theResource == null) {
        theResource = read(theId, theRequestDetails);
    }
    VersionedIdentifier libraryIdentifier = new VersionedIdentifier().withId(theResource.getName()).withVersion(theResource.getVersion());
    TerminologyProvider terminologyProvider;
    if (terminologyEndpoint != null) {
        IGenericClient client = Clients.forEndpoint(getFhirContext(), terminologyEndpoint);
        terminologyProvider = new R4FhirTerminologyProvider(client);
    } else {
        terminologyProvider = myJpaTerminologyProviderFactory.create(new SystemRequestDetails());
    }
    DataProvider dataProvider;
    if (dataEndpoint != null) {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        IGenericClient client = Clients.forEndpoint(dataEndpoint);
        RestFhirRetrieveProvider retriever = new RestFhirRetrieveProvider(new SearchParameterResolver(getFhirContext()), client);
        retriever.setTerminologyProvider(terminologyProvider);
        if (terminologyEndpoint == null || (terminologyEndpoint != null && !terminologyEndpoint.getAddress().equals(dataEndpoint.getAddress()))) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    } else {
        List<RetrieveProvider> retrieveProviderList = new ArrayList<>();
        JpaFhirRetrieveProvider retriever = new JpaFhirRetrieveProvider(getDaoRegistry(), new SearchParameterResolver(getFhirContext()));
        retriever.setTerminologyProvider(terminologyProvider);
        // Assume it's a different server, therefore need to expand.
        if (terminologyEndpoint != null) {
            retriever.setExpandValueSets(true);
        }
        retrieveProviderList.add(retriever);
        if (additionalData != null) {
            BundleRetrieveProvider bundleProvider = new BundleRetrieveProvider(getFhirContext(), additionalData);
            bundleProvider.setTerminologyProvider(terminologyProvider);
            retrieveProviderList.add(bundleProvider);
            PriorityRetrieveProvider priorityProvider = new PriorityRetrieveProvider(retrieveProviderList);
            dataProvider = new CompositeDataProvider(myModelResolver, priorityProvider);
        } else {
            dataProvider = new CompositeDataProvider(myModelResolver, retriever);
        }
    }
    LibraryContentProvider bundleLibraryProvider = new BundleFhirLibraryContentProvider(this.getFhirContext(), libraryBundle, adapterFactory, libraryVersionSelector);
    LibraryContentProvider jpaLibraryContentProvider = this.myJpaLibraryContentProviderFactory.create(theRequestDetails);
    List<LibraryContentProvider> sourceProviders = new ArrayList<LibraryContentProvider>(Arrays.asList(bundleLibraryProvider, jpaLibraryContentProvider));
    LibraryLoader libraryLoader = this.myLibraryLoaderFactory.create(sourceProviders);
    CqlEngine engine = new CqlEngine(libraryLoader, Collections.singletonMap("http://hl7.org/fhir", dataProvider), terminologyProvider);
    Map<String, Object> resolvedParameters = new HashMap<>();
    if (parameters != null) {
        for (Parameters.ParametersParameterComponent pc : parameters.getParameter()) {
            resolvedParameters.put(pc.getName(), pc.getValue());
        }
    }
    if (periodStart != null && periodEnd != null) {
        // resolve the measurement period
        Interval measurementPeriod = new Interval(Operations.resolveRequestDate(periodStart, true), true, Operations.resolveRequestDate(periodEnd, false), true);
        resolvedParameters.put("Measurement Period", new Interval(DateTime.fromJavaDate((Date) measurementPeriod.getStart()), true, DateTime.fromJavaDate((Date) measurementPeriod.getEnd()), true));
    }
    if (productLine != null) {
        resolvedParameters.put("Product Line", productLine);
    }
    EvaluationResult evalResult = engine.evaluate(libraryIdentifier, null, Pair.of(contextParam != null ? contextParam : "Unspecified", patientId == null ? "null" : patientId), resolvedParameters, this.getDebugMap());
    List<Resource> results = new ArrayList<>();
    FhirMeasureBundler bundler = new FhirMeasureBundler();
    if (evalResult != null && evalResult.expressionResults != null) {
        for (Map.Entry<String, Object> def : evalResult.expressionResults.entrySet()) {
            Parameters result = new Parameters();
            try {
                result.setId(def.getKey());
                Object res = def.getValue();
                if (res == null) {
                    result.addParameter().setName("value").setValue(new StringType("null"));
                } else if (res instanceof List<?>) {
                    if (((List<?>) res).size() > 0 && ((List<?>) res).get(0) instanceof Resource) {
                        if (executionResults != null && executionResults.equals("Summary")) {
                            result.addParameter().setName("value").setValue(new StringType(((Resource) ((List<?>) res).get(0)).getIdElement().getResourceType() + "/" + ((Resource) ((List<?>) res).get(0)).getIdElement().getIdPart()));
                        } else {
                            result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                        }
                    } else {
                        result.addParameter().setName("value").setValue(new StringType(res.toString()));
                    }
                } else if (res instanceof Iterable) {
                    result.addParameter().setName("value").setResource(bundler.bundle((Iterable<Resource>) res, theRequestDetails.getFhirServerBase()));
                } else if (res instanceof Resource) {
                    if (executionResults != null && executionResults.equals("Summary")) {
                        result.addParameter().setName("value").setValue(new StringType(((Resource) res).getIdElement().getResourceType() + "/" + ((Resource) res).getIdElement().getIdPart()));
                    } else {
                        result.addParameter().setName("value").setResource((Resource) res);
                    }
                } else if (res instanceof Type) {
                    result.addParameter().setName("value").setValue((Type) res);
                } else {
                    result.addParameter().setName("value").setValue(new StringType(res.toString()));
                }
                result.addParameter().setName("resultType").setValue(new StringType(resolveType(res)));
            } catch (RuntimeException re) {
                re.printStackTrace();
                String message = re.getMessage() != null ? re.getMessage() : re.getClass().getName();
                result.addParameter().setName("error").setValue(new StringType(message));
            }
            results.add(result);
        }
    }
    return bundler.bundle(results, theRequestDetails.getFhirServerBase());
}
Also used : HashMap(java.util.HashMap) StringType(org.hl7.fhir.r4.model.StringType) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) ArrayList(java.util.ArrayList) LibraryLoader(org.opencds.cqf.cql.engine.execution.LibraryLoader) CompositeDataProvider(org.opencds.cqf.cql.engine.data.CompositeDataProvider) DataProvider(org.opencds.cqf.cql.engine.data.DataProvider) VersionedIdentifier(org.cqframework.cql.elm.execution.VersionedIdentifier) BundleRetrieveProvider(org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider) RestFhirRetrieveProvider(org.opencds.cqf.cql.engine.fhir.retrieve.RestFhirRetrieveProvider) SystemRequestDetails(ca.uhn.fhir.jpa.partition.SystemRequestDetails) PriorityRetrieveProvider(org.opencds.cqf.cql.evaluator.engine.retrieve.PriorityRetrieveProvider) List(java.util.List) ArrayList(java.util.ArrayList) R4FhirTerminologyProvider(org.opencds.cqf.cql.engine.fhir.terminology.R4FhirTerminologyProvider) FhirMeasureBundler(org.opencds.cqf.ruler.cpg.r4.util.FhirMeasureBundler) JpaFhirRetrieveProvider(org.opencds.cqf.ruler.cql.JpaFhirRetrieveProvider) LibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider) BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) Parameters(org.hl7.fhir.r4.model.Parameters) BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) Bundle(org.hl7.fhir.r4.model.Bundle) Resource(org.hl7.fhir.r4.model.Resource) CqlEngine(org.opencds.cqf.cql.engine.execution.CqlEngine) EvaluationResult(org.opencds.cqf.cql.engine.execution.EvaluationResult) StringType(org.hl7.fhir.r4.model.StringType) Type(org.hl7.fhir.r4.model.Type) IdType(org.hl7.fhir.r4.model.IdType) SearchParameterResolver(org.opencds.cqf.cql.engine.fhir.searchparam.SearchParameterResolver) TerminologyProvider(org.opencds.cqf.cql.engine.terminology.TerminologyProvider) R4FhirTerminologyProvider(org.opencds.cqf.cql.engine.fhir.terminology.R4FhirTerminologyProvider) CompositeDataProvider(org.opencds.cqf.cql.engine.data.CompositeDataProvider) Library(org.hl7.fhir.r4.model.Library) RestFhirRetrieveProvider(org.opencds.cqf.cql.engine.fhir.retrieve.RestFhirRetrieveProvider) JpaFhirRetrieveProvider(org.opencds.cqf.ruler.cql.JpaFhirRetrieveProvider) RetrieveProvider(org.opencds.cqf.cql.engine.retrieve.RetrieveProvider) BundleRetrieveProvider(org.opencds.cqf.cql.evaluator.engine.retrieve.BundleRetrieveProvider) PriorityRetrieveProvider(org.opencds.cqf.cql.evaluator.engine.retrieve.PriorityRetrieveProvider) Map(java.util.Map) DebugMap(org.opencds.cqf.cql.engine.debug.DebugMap) HashMap(java.util.HashMap) Interval(org.opencds.cqf.cql.engine.runtime.Interval) Operation(ca.uhn.fhir.rest.annotation.Operation)

Example 3 with LibraryContentProvider

use of org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider in project cqf-ruler by DBCG.

the class DataOperationsProvider method createLibraryManager.

private LibraryManager createLibraryManager(Library library, RequestDetails theRequestDetails) {
    JpaLibraryContentProvider jpaLibraryContentProvider = jpaLibraryContentProviderFactory.create(theRequestDetails);
    Bundle libraryBundle = new Bundle();
    List<Library> listLib = fetchDependencyLibraries(library, theRequestDetails);
    listLib.add(library);
    listLib.forEach(lib -> {
        Bundle.BundleEntryComponent component = new Bundle.BundleEntryComponent();
        component.setResource(lib);
        libraryBundle.addEntry(component);
    });
    LibraryContentProvider bundleLibraryProvider = new BundleFhirLibraryContentProvider(this.getFhirContext(), libraryBundle, adapterFactory, libraryVersionSelector);
    List<LibraryContentProvider> sourceProviders = new ArrayList<>(Arrays.asList(bundleLibraryProvider, jpaLibraryContentProvider));
    return libraryManagerFactory.create(sourceProviders);
}
Also used : BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) LibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider) JpaLibraryContentProvider(org.opencds.cqf.ruler.cql.JpaLibraryContentProvider) BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) Bundle(org.hl7.fhir.r4.model.Bundle) JpaLibraryContentProvider(org.opencds.cqf.ruler.cql.JpaLibraryContentProvider) ArrayList(java.util.ArrayList) Library(org.hl7.fhir.r4.model.Library)

Example 4 with LibraryContentProvider

use of org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider in project cqf-ruler by DBCG.

the class MeasureEvaluateProvider method evaluateMeasure.

/**
 * Implements the <a href=
 * "https://www.hl7.org/fhir/operation-measure-evaluate-measure.html">$evaluate-measure</a>
 * operation found in the
 * <a href="http://www.hl7.org/fhir/clinicalreasoning-module.html">FHIR Clinical
 * Reasoning Module</a>. This implementation aims to be compatible with the CQF
 * IG.
 *
 * @param requestDetails The details (such as tenant) of this request. Usually
 *                       auto-populated HAPI.
 * @param theId          the Id of the Measure to evaluate
 * @param periodStart    The start of the reporting period
 * @param periodEnd      The end of the reporting period
 * @param reportType     The type of MeasureReport to generate
 * @param subject        the subject to use for the evaluation
 * @param practitioner   the practitioner to use for the evaluation
 * @param lastReceivedOn the date the results of this measure were last
 *                       received.
 * @param productLine    the productLine (e.g. Medicare, Medicaid, etc) to use
 *                       for the evaluation. This is a non-standard parameter.
 * @param additionalData the data bundle containing additional data
 * @return the calculated MeasureReport
 */
// warning for greater than 7 parameters
@SuppressWarnings("squid:S00107")
@Description(shortDefinition = "$evaluate-measure", value = "Implements the <a href=\"https://www.hl7.org/fhir/operation-measure-evaluate-measure.html\">$evaluate-measure</a> operation found in the <a href=\"http://www.hl7.org/fhir/clinicalreasoning-module.html\">FHIR Clinical Reasoning Module</a>. This implementation aims to be compatible with the CQF IG.", example = "Measure/example/$evaluate-measure?subject=Patient/123&periodStart=2019&periodEnd=2020")
@Operation(name = "$evaluate-measure", idempotent = true, type = Measure.class)
public MeasureReport evaluateMeasure(RequestDetails requestDetails, @IdParam IdType theId, @OperationParam(name = "periodStart") String periodStart, @OperationParam(name = "periodEnd") String periodEnd, @OperationParam(name = "reportType") String reportType, @OperationParam(name = "subject") String subject, @OperationParam(name = "practitioner") String practitioner, @OperationParam(name = "lastReceivedOn") String lastReceivedOn, @OperationParam(name = "productLine") String productLine, @OperationParam(name = "additionalData") Bundle additionalData) {
    Measure measure = read(theId);
    TerminologyProvider terminologyProvider = this.jpaTerminologyProviderFactory.create(requestDetails);
    DataProvider dataProvider = this.jpaDataProviderFactory.create(requestDetails, terminologyProvider);
    LibraryContentProvider libraryContentProvider = this.libraryContentProviderFactory.create(requestDetails);
    FhirDal fhirDal = this.fhirDalFactory.create(requestDetails);
    org.opencds.cqf.cql.evaluator.measure.r4.R4MeasureProcessor measureProcessor = new org.opencds.cqf.cql.evaluator.measure.r4.R4MeasureProcessor(null, this.dataProviderFactory, null, null, null, terminologyProvider, libraryContentProvider, dataProvider, fhirDal, null, this.globalLibraryCache);
    MeasureReport report = measureProcessor.evaluateMeasure(measure.getUrl(), periodStart, periodEnd, reportType, subject, null, lastReceivedOn, null, null, null, additionalData);
    if (productLine != null) {
        Extension ext = new Extension();
        ext.setUrl("http://hl7.org/fhir/us/cqframework/cqfmeasures/StructureDefinition/cqfm-productLine");
        ext.setValue(new StringType(productLine));
        report.addExtension(ext);
    }
    return report;
}
Also used : LibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider) StringType(org.hl7.fhir.r4.model.StringType) MeasureReport(org.hl7.fhir.r4.model.MeasureReport) FhirDal(org.opencds.cqf.cql.evaluator.fhir.dal.FhirDal) DataProvider(org.opencds.cqf.cql.engine.data.DataProvider) Extension(org.hl7.fhir.r4.model.Extension) TerminologyProvider(org.opencds.cqf.cql.engine.terminology.TerminologyProvider) Measure(org.hl7.fhir.r4.model.Measure) Description(ca.uhn.fhir.model.api.annotation.Description) Operation(ca.uhn.fhir.rest.annotation.Operation)

Example 5 with LibraryContentProvider

use of org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider in project cqf-ruler by DBCG.

the class DataOperationsProvider method createLibraryManager.

private LibraryManager createLibraryManager(Library library, RequestDetails theRequestDetails) {
    JpaLibraryContentProvider jpaLibraryContentProvider = jpaLibraryContentProviderFactory.create(theRequestDetails);
    Bundle libraryBundle = new Bundle();
    List<Library> listLib = fetchDependencyLibraries(library, theRequestDetails);
    listLib.add(library);
    listLib.forEach(lib -> {
        Bundle.BundleEntryComponent component = new Bundle.BundleEntryComponent();
        component.setResource(lib);
        libraryBundle.addEntry(component);
    });
    LibraryContentProvider bundleLibraryProvider = new BundleFhirLibraryContentProvider(this.getFhirContext(), libraryBundle, adapterFactory, libraryVersionSelector);
    List<LibraryContentProvider> sourceProviders = Lists.newArrayList(bundleLibraryProvider, jpaLibraryContentProvider);
    return libraryManagerFactory.create(sourceProviders);
}
Also used : BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) LibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider) JpaLibraryContentProvider(org.opencds.cqf.ruler.cql.JpaLibraryContentProvider) BundleFhirLibraryContentProvider(org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider) Bundle(org.hl7.fhir.dstu3.model.Bundle) JpaLibraryContentProvider(org.opencds.cqf.ruler.cql.JpaLibraryContentProvider) Library(org.hl7.fhir.dstu3.model.Library)

Aggregations

LibraryContentProvider (org.opencds.cqf.cql.evaluator.cql2elm.content.LibraryContentProvider)9 LibraryLoader (org.opencds.cqf.cql.engine.execution.LibraryLoader)5 ArrayList (java.util.ArrayList)4 DataProvider (org.opencds.cqf.cql.engine.data.DataProvider)4 TerminologyProvider (org.opencds.cqf.cql.engine.terminology.TerminologyProvider)4 InMemoryLibraryContentProvider (org.opencds.cqf.cql.evaluator.cql2elm.content.InMemoryLibraryContentProvider)4 JpaFhirDal (org.opencds.cqf.ruler.cql.JpaFhirDal)4 Operation (ca.uhn.fhir.rest.annotation.Operation)3 VersionedIdentifier (org.cqframework.cql.elm.execution.VersionedIdentifier)3 Library (org.hl7.fhir.r4.model.Library)3 BundleFhirLibraryContentProvider (org.opencds.cqf.cql.evaluator.cql2elm.content.fhir.BundleFhirLibraryContentProvider)3 Description (ca.uhn.fhir.model.api.annotation.Description)2 Library (org.hl7.fhir.dstu3.model.Library)2 Bundle (org.hl7.fhir.r4.model.Bundle)2 IdType (org.hl7.fhir.r4.model.IdType)2 StringType (org.hl7.fhir.r4.model.StringType)2 JpaLibraryContentProvider (org.opencds.cqf.ruler.cql.JpaLibraryContentProvider)2 SystemRequestDetails (ca.uhn.fhir.jpa.partition.SystemRequestDetails)1 IGenericClient (ca.uhn.fhir.rest.client.api.IGenericClient)1 HashMap (java.util.HashMap)1