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package ca.uhn.fhir.cql.r4;
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import ca.uhn.fhir.cql.BaseCqlR4Test;
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import ca.uhn.fhir.cql.r4.provider.MeasureOperationsProvider;
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import ca.uhn.fhir.util.BundleUtil;
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import org.apache.commons.collections.map.HashedMap;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.r4.model.Base64BinaryType;
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import org.hl7.fhir.r4.model.Bundle;
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import org.hl7.fhir.r4.model.DateTimeType;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Library;
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import org.hl7.fhir.r4.model.Measure;
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import org.hl7.fhir.r4.model.MeasureReport;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.Base64;
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import java.util.Date;
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import java.util.List;
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import java.util.Map;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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/**
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* This testing class and the used resources are work in progress and will likely be subject to change.
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*/
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public class CqlMeasureEvaluationR4ImmunizationTest extends BaseCqlR4Test {
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Logger ourLog = LoggerFactory.getLogger(CqlMeasureEvaluationR4ImmunizationTest.class);
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@Autowired
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MeasureOperationsProvider myMeasureOperationsProvider;
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private static final String MY_TESTBUNDLE_MMR_SIMPLE = "r4/immunization/testdata-bundles/Testbundle_3Patients_1MMRVaccinated_1PVaccinated_1NoVaccination.json";
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private static final String MY_TESTBUNDLE_MMR_INCL_PRACTITIONER = "r4/immunization/testdata-bundles/Testbundle_Patients_By_Practitioner.json";
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//overall testing function including bundle manipulation and evaluation and assertion
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protected void testMeasureScoresByBundleAndCQLLocation(String theBundleLocation, String theCQLMeasureLocation, String thePractitionerRef, Map<String, Double> theExpectedScores) throws IOException {
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//load provided bundle and replace placeholder CQL content of Library with CQL content of provided file location
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Bundle bundle = loadBundleFromFileLocationAndManipulate(theBundleLocation, theCQLMeasureLocation);
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//we require at least one MeasureReport in the bundle
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List<MeasureReport> measureReports = findMeasureReportsOrThrowException(bundle);
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//evaluate each measure report of the provided bundle
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for (MeasureReport report : measureReports) {
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double expectedScore = theExpectedScores.get(report.getIdentifierFirstRep().getValue());
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evaluateSingleReport(report, thePractitionerRef, expectedScore);
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}
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}
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//overall testing function including bundle manipulation and evaluation and assertion
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protected void testMeasureScoresByBundleAndCQLLocation(String theBundleLocation, String theCQLMeasureLocation, String thePractitionerRef, double theExpectedScore) throws IOException {
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//load provided bundle and replace placeholder CQL content of Library with CQL content of provided file location
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Bundle bundle = loadBundleFromFileLocationAndManipulate(theBundleLocation, theCQLMeasureLocation);
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//we require at least one MeasureReport in the bundle
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List<MeasureReport> measureReports = findMeasureReportsOrThrowException(bundle);
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//evaluate each measure report of the provided bundle
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for (MeasureReport report : measureReports) {
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evaluateSingleReport(report, thePractitionerRef, theExpectedScore);
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}
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}
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protected void evaluateSingleReport (MeasureReport theReport, String thePractitionerRef, double theExpectedScore) {
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MeasureReport actualEvaluatedReport = this.evaluateMeasure(theReport, thePractitionerRef);
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ourLog.info("Score of evaluation: {}", actualEvaluatedReport.getGroupFirstRep().getMeasureScore().getValue());
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assertMeasureScore(actualEvaluatedReport, theExpectedScore);
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}
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//double compare to assert no difference between expected and actual measure score
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protected void assertMeasureScore(MeasureReport theReport, double theExpectedScore) {
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//find the predefined expected score by looking up the report identifier
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double epsilon = 0.000001d;
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double actualScore = theReport.getGroupFirstRep().getMeasureScore().getValue().doubleValue();
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assertEquals(theExpectedScore, actualScore, epsilon);
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}
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//evaluates a Measure to produce one certain MeasureReport
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protected MeasureReport evaluateMeasure(MeasureReport theMeasureReport, String thePractitionerRef) {
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String measureId = this.getMeasureId(theMeasureReport);
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String patientId = null;
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//only when the type of the MeasureReport is set to 'individual', there is a patient required as a subject (i.e. not for a 'summary' report)
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if (theMeasureReport.getSubject().getReference() != null) {
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patientId = this.getPatientId(theMeasureReport);
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}
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String periodStart = this.getPeriodStart(theMeasureReport);
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String periodEnd = this.getPeriodEnd(theMeasureReport);
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String measureReportIdentifier = theMeasureReport.getIdentifierFirstRep().getValue();
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String measureReportType = theMeasureReport.getTypeElement().getValueAsString();
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//only when the type of the MeasureReport is set to 'individual', there is a patient required as a subject (i.e. not for a 'summary' report)
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if (patientId == null) {
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ourLog.info("Evaluating Measure '{}' for MeasureReport '{}' of type '{}': [{} - {}]", measureId, measureReportIdentifier, measureReportType, periodStart, periodEnd);
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} else {
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ourLog.info("Evaluating Measure '{}' for MeasureReport '{}' of type '{}' for Patient '{}' [{} - {}]", measureId, measureReportIdentifier, measureReportType, patientId, periodStart, periodEnd);
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}
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return this.myMeasureOperationsProvider.evaluateMeasure(new IdType("Measure", measureId),
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periodStart, periodEnd, null,
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"patient", patientId,
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null, thePractitionerRef, null, null, null, null, myRequestDetails);
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}
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//helper function to manipulate a test bundle
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//loads a bundle from theBundleLocation: requirement: containing 1 exact FHIR Measure
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//finds the relevant measure, determines the related Library and replaces the CQL content of that Library with a separate CQL file
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//the CQL file defined by theCQLLocation contains regular CQL text and is automatically transformed into base64 content and automatically replaces the Library content
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//this process keeps manual testing simple, as the only place to change the CQL logic is by adding a new CQL file (containing no test resources and no other content) and writing a unit test with that CQL file path
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protected Bundle loadBundleFromFileLocationAndManipulate(String theBundleLocation, String theCQLLocation) throws IOException {
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Bundle bundle = parseBundle(theBundleLocation);
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//manipulate Bundle
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Measure measure = findExactlyOneMeasuresOrThrowException(bundle);
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Library libraryToManipulate = findLibraryById(bundle, measure.getLibrary().get(0).getValue());
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replaceCQLOfLibrary(libraryToManipulate, theCQLLocation);
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loadBundle(bundle, myRequestDetails);
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return bundle;
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}
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//requirement: test bundle must contain exactly one Measure resource
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protected Measure findExactlyOneMeasuresOrThrowException(Bundle theBundle) {
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List<Measure> measures = BundleUtil.toListOfResourcesOfType(myFhirContext, theBundle, Measure.class);
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if (measures == null || measures.isEmpty()) {
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throw new IllegalArgumentException(String.format("No measures found for Bundle %s", theBundle.getId()));
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} else if (measures.size() > 1) {
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throw new IllegalArgumentException(String.format("Too many measures found for Bundle %s. Only one measure is allowed for this automated testing setup.", theBundle.getId()));
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}
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return measures.get(0);
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}
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//requirement: test bundle must contain at least one MeasureReport resource
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protected List<MeasureReport> findMeasureReportsOrThrowException(Bundle theBundle) {
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List<MeasureReport> reports = BundleUtil.toListOfResourcesOfType(myFhirContext, theBundle, MeasureReport.class);
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if (reports == null || reports.isEmpty()) {
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throw new IllegalArgumentException(String.format("No measure reports found for Bundle %s", theBundle.getId()));
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}
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return reports;
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}
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//returns a Library resource of a bundle by a given ID
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protected Library findLibraryById(Bundle theBundle, String theLibraryId) {
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List<Library> libraries = BundleUtil.toListOfResourcesOfType(myFhirContext, theBundle, Library.class);
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return libraries.stream().filter(lib -> lib.getId().equals(theLibraryId)).findFirst().orElse(null);
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}
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//the provided Library resource only contains a placeholder CQL
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//this function replaces this placeholder CQL with the content of a specified file
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protected Library replaceCQLOfLibrary(Library theLibrary, String theCQLFileLocation) throws IOException {
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String decodedCQLString = stringFromResource(theCQLFileLocation);
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//replace cql in library
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String encodedCQLString = Base64.getEncoder().encodeToString(decodedCQLString.getBytes(StandardCharsets.UTF_8));
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Base64BinaryType encodedCQLBinary = new Base64BinaryType();
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encodedCQLBinary.setValueAsString(encodedCQLString);
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theLibrary.getContentFirstRep().setDataElement(encodedCQLBinary);
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return theLibrary;
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}
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// TODO: In R4 the Subject will not necessarily be a Patient.
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public String getPatientId(MeasureReport measureReport) {
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String[] subjectRefParts = measureReport.getSubject().getReference().split("/");
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String patientId = subjectRefParts[subjectRefParts.length - 1];
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return patientId;
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}
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public String getMeasureId(MeasureReport measureReport) {
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String[] measureRefParts = measureReport.getMeasure().split("/");
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String measureId = measureRefParts[measureRefParts.length - 1];
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return measureId;
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}
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public String getPeriodStart(MeasureReport measureReport) {
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Date periodStart = measureReport.getPeriod().getStart();
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if (periodStart != null) {
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return toDateString(periodStart);
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}
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return null;
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}
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public String getPeriodEnd(MeasureReport measureReport) {
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Date periodEnd = measureReport.getPeriod().getEnd();
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if (periodEnd != null) {
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return toDateString(periodEnd);
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}
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return null;
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}
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public String toDateString(Date date) {
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return new DateTimeType(date).getValueAsString();
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}
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@Test
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public void test_Immunization_MMR_Individual_Vaccinated() throws IOException {
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Map<String, Double> expectedScoresByIdentifier = new HashedMap();
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//expected result: individual should be in numerator because Patient is MMR vaccinated
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expectedScoresByIdentifier.put("measureReportIndividualVaccinatedPatient", 1.0);
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//expected result: individual should not be in numerator because Patient is not MMR vaccinated (only Pertussis)
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expectedScoresByIdentifier.put("measureReportIndividualNotMMRVaccinatedPatient", 0.0);
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//expected result: individual should not be in numerator because Patient is not at all vaccinated (no associated Immmunization resource)
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expectedScoresByIdentifier.put("measureReportIndividualNotAtAllVaccinatedPatient", 0.0);
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//expected result: summary confirms that 1 out of all 3 patients are MMR immunized
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expectedScoresByIdentifier.put("measureReportSummary", 1.0 / 3.0);
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//note: all those CQL files specified as the second parameter produce the exact same outcome with the given test resources provided by the first parameter.
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//TODO: tests are dependent and will fail if the order is incorrect. --> clean up tests
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_SIMPLE, "r4/immunization/cqls/3-Vaccine-Codes-Defined-By-ValueSet-MMR-Vaccine-Codes.cql", null, expectedScoresByIdentifier);
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_SIMPLE, "r4/immunization/cqls/1-Explicit-Vaccine-Codes-From-Any-System.cql", null, expectedScoresByIdentifier);
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_SIMPLE, "r4/immunization/cqls/2-Explicit-Vaccine-Codes-And-Systems.cql", null, expectedScoresByIdentifier);
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}
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@Test
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public void test_Immunization_ByPractitioner_MMR_Summary() throws IOException {
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//half of dreric' s patients (total of 2) are vaccinated, so 1/2 is vaccinated.
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_INCL_PRACTITIONER, "r4/immunization/cqls/3-Vaccine-Codes-Defined-By-ValueSet-MMR-Vaccine-Codes.cql", "Practitioner/dreric", 1.0/2.0);
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//of drfrank's patients (total of 1), none are vaccinated
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_INCL_PRACTITIONER, "r4/immunization/cqls/3-Vaccine-Codes-Defined-By-ValueSet-MMR-Vaccine-Codes.cql", "Practitioner/drfrank", 0.0/1.0);
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}
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@Test
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public void test_Immunization_ByAge() throws IOException {
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//be aware that this test will fail eventually, because this patient will at some point become one years old (today - birthdate > 1 year)
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//this patient is not yet immunized, because too young. so it won't be counted as a denominator patient and therefore the measure score is corrected to have a higher percentage
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//of dreric' s patients, all are vaccinated, because the second patient who is not vaccinated yet doesn't meet the age criteria (denominator), so 1/1 is vaccinated.
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this.testMeasureScoresByBundleAndCQLLocation(MY_TESTBUNDLE_MMR_INCL_PRACTITIONER, "r4/immunization/cqls/4-Patients-ByAge.cql", "Practitioner/dreric", 1.0/1.0);
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}
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}
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alackerbauer
GitHub