Experimental changes for issues 600, 601, and 602.

cqf-fhir-cr/pom.xml

@@ -76,6 +76,16 @@
         <artifactId>slf4j-test</artifactId>
         <scope>test</scope>
     </dependency>
+    <!--
+    Needed to support @Language annotation for JDK 17 multi-line strings and syntax highlighting.
+    This supports SQL, JSON, etc, but unfortunately, not CQL (yet).
+    -->
+    <dependency>
+        <groupId>org.jetbrains</groupId>
+        <artifactId>annotations</artifactId>
+        <version>23.0.0</version>
+        <scope>test</scope>
+    </dependency>
   </dependencies>
 
   <build>

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/common/MeasureEvaluator.java

@@ -19,6 +19,8 @@
 import java.time.ZonedDateTime;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.Set;
@@ -303,6 +305,8 @@ protected MeasureDef evaluate(
             EvaluationResult result =
                     libraryEngine.getEvaluationResult(id, subjectId, null, null, null, null, zonedDateTime, context);
 
+            someEvaluationValidationStuff(measureDef, result);
+
             evaluateSubject(measureDef, subjectTypePart, subjectIdPart, subjectSize, type, result);
         }
 
@@ -565,6 +569,7 @@ protected void evaluateGroup(
             int populationSize,
             MeasureReportType reportType,
             EvaluationResult evaluationResult) {
+
         evaluateStratifiers(subjectId, groupDef.stratifiers(), evaluationResult);
 
         var scoring = groupDef.measureScoring();
@@ -582,6 +587,29 @@ protected void evaluateGroup(
         }
     }
 
+    private void someEvaluationValidationStuff(MeasureDef measureDef, EvaluationResult evaluationResult) {
+        measureDef.groups().forEach(groupDef -> someEvaluationValidationStuff(groupDef, evaluationResult));
+    }
+
+    private void someEvaluationValidationStuff(GroupDef groupDef, EvaluationResult evaluationResult) {
+        final Map<String, ExpressionResult> expressionResults = evaluationResult.expressionResults;
+        final CodeDef groupDefPopulationBasis = groupDef.getPopulationBasis();
+        final List<StratifierDef> stratifiers = groupDef.stratifiers();
+        final List<Map<String, CriteriaResult>> criteriaResults =
+                stratifiers.stream().map(StratifierDef::getResults).collect(Collectors.toList());
+
+        // LUKETODO:  600 LEFT side of the comparison is the groupDefPopulationBasis
+        logger.info("expressionResults: {}, groupDefPopulationBasis: {}", expressionResults, groupDefPopulationBasis);
+
+        for (Map<String, CriteriaResult> criteriaResult : criteriaResults) {
+            logger.info("criteriaResult: {}", criteriaResult);
+
+            for (Entry<String, CriteriaResult> criteriaResultEntry : criteriaResult.entrySet()) {
+                logger.info("criteriaResultEntry: {}", criteriaResultEntry);
+            }
+        }
+    }
+
     protected Object evaluateDateOfCompliance(PopulationDef populationDef) {
         var ref = Libraries.resolveExpressionRef(
                 populationDef.expression(), this.context.getState().getCurrentLibrary());

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/constant/MeasureConstants.java

@@ -43,8 +43,12 @@ private MeasureConstants() {}
     public static final String FHIR_ALL_TYPES_SYSTEM_URL = "http://hl7.org/fhir/fhir-types";
     public static final String POPULATION_BASIS_URL =
             "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-populationBasis";
+    // LUKETODO: 602  get rid of this:
+    @Deprecated
     public static final String EXT_TOTAL_DENOMINATOR_URL =
             "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-cqfm-denominator-membership";
+    // LUKETODO: 602 get rid of this:
+    @Deprecated
     public static final String EXT_TOTAL_NUMERATOR_URL =
             "http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-cqfm-numerator-membership";
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4MeasureReportBuilder.java

@@ -346,11 +346,15 @@ protected void buildGroup(
             }
 
             if (groupDef.isBooleanBasis()) {
+                // LUKETODO: 602 why doesn't this consider exclusions?
+                // LUKETODO: 602 do we add this WITH or WITHOUT exclusions? my guess is WITHOUT
                 addExtension(
                         reportGroup, EXT_TOTAL_DENOMINATOR_URL, getReportPopulation(groupDef, TOTALDENOMINATOR), true);
                 addExtension(reportGroup, EXT_TOTAL_NUMERATOR_URL, getReportPopulation(groupDef, TOTALNUMERATOR), true);
 
             } else {
+                // LUKETODO: 602 why doesn't this consider exclusions?
+                // LUKETODO: 602 do we add this WITH or WITHOUT exclusions? my guess is WITHOUT
                 addExtension(
                         reportGroup, EXT_TOTAL_DENOMINATOR_URL, getReportPopulation(groupDef, TOTALDENOMINATOR), false);
                 addExtension(
@@ -377,6 +381,8 @@ protected void addExtension(
         group.addExtension().setUrl(extUrl).setValue(new StringType(Integer.toString(count)));
     }
 
+    // LUKETODO: 602 is there such a thing as validation for group population basis?
+
     /**
      *
      * Resource result --> Patient Key, Resource result --> can intersect on patient for Boolean basis, can't for Resource
@@ -390,6 +396,7 @@ protected void validateStratifierBasisType(Map<String, CriteriaResult> subjectVa
                     .filter(x -> x.rawValue() instanceof Resource)
                     .collect(Collectors.toList());
             if (list.size() != subjectValues.values().size()) {
+                // LUKETODO:  602 this is the stratifier case
                 throw new IllegalArgumentException(
                         "stratifier expression criteria results must match the same type as population.");
             }
@@ -497,6 +504,7 @@ protected void buildStratum(
         }
 
         // add totalDenominator and totalNumerator extensions
+        // LUKETODO: 602
         buildStratumExtPopulation(groupDef, TOTALDENOMINATOR, subjectIds, stratum, EXT_TOTAL_DENOMINATOR_URL);
         buildStratumExtPopulation(groupDef, TOTALNUMERATOR, subjectIds, stratum, EXT_TOTAL_NUMERATOR_URL);
     }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4MeasureReportScorer.java

@@ -3,15 +3,21 @@
 import static org.opencds.cqf.fhir.cr.measure.constant.MeasureConstants.EXT_TOTAL_DENOMINATOR_URL;
 import static org.opencds.cqf.fhir.cr.measure.constant.MeasureConstants.EXT_TOTAL_NUMERATOR_URL;
 
+import java.util.List;
+import java.util.stream.Collectors;
 import org.hl7.fhir.r4.model.MeasureReport;
 import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupComponent;
+import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupPopulationComponent;
 import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupStratifierComponent;
 import org.hl7.fhir.r4.model.MeasureReport.StratifierGroupComponent;
+import org.hl7.fhir.r4.model.MeasureReport.StratifierGroupPopulationComponent;
 import org.hl7.fhir.r4.model.Quantity;
 import org.opencds.cqf.fhir.cr.measure.common.BaseMeasureReportScorer;
 import org.opencds.cqf.fhir.cr.measure.common.GroupDef;
 import org.opencds.cqf.fhir.cr.measure.common.MeasureDef;
 import org.opencds.cqf.fhir.cr.measure.common.MeasureScoring;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * <p>The R4 MeasureScorer takes population components from MeasureReport resources and scores each group population
@@ -36,6 +42,8 @@
  */
 public class R4MeasureReportScorer extends BaseMeasureReportScorer<MeasureReport> {
 
+    private static final Logger logger = LoggerFactory.getLogger(R4MeasureReportScorer.class);
+
     @Override
     public void score(MeasureDef measureDef, MeasureReport measureReport) {
         // Measure Def Check
@@ -48,6 +56,7 @@ public void score(MeasureDef measureDef, MeasureReport measureReport) {
         }
 
         for (MeasureReportGroupComponent mrgc : measureReport.getGroup()) {
+
             scoreGroup(
                     getGroupMeasureScoring(mrgc, measureDef),
                     mrgc,
@@ -106,12 +115,70 @@ protected MeasureScoring getGroupMeasureScoring(MeasureReportGroupComponent mrgc
 
     protected void scoreGroup(
             MeasureScoring measureScoring, MeasureReportGroupComponent mrgc, boolean isIncreaseImprovementNotation) {
+        // LUKETODO: 602  should this be from the MeasureReportGroupComponent  or the GroupDef?
+                /*
+                   MeasureScorer should now look for Numerator/Denominator values to make the calculation instead of the extension values.
+                   Any code that sets or maintains these populations can be removed
+                   Testing classes that have assertions for these values should be deprecated
+                */
+        final List<MeasureReportGroupPopulationComponent> populations = mrgc.getPopulation();
+
+        // LUKETODO:  602 I think we need to do the populations.stream()
+        final List<MeasureReportGroupPopulationComponent> numerators = populations.stream()
+            .filter(population -> "numerator"
+                .equals(population.getCode().getCodingFirstRep().getCode()))
+            .collect(Collectors.toList());
+
+        final List<MeasureReportGroupPopulationComponent> denominators = populations.stream()
+            .filter(population -> "numerator"
+                .equals(population.getCode().getCodingFirstRep().getCode()))
+            .collect(Collectors.toList());
+
+        final Integer populationNumeratorCount = populations.stream()
+            .filter(population -> "numerator"
+                .equals(population.getCode().getCodingFirstRep().getCode()))
+            .map(MeasureReportGroupPopulationComponent::getCount)
+            .findAny()
+            .orElse(0);
+
+        final Integer populationDenominatorCount = populations.stream()
+            .filter(population -> "denominator"
+                .equals(population.getCode().getCodingFirstRep().getCode()))
+            .map(MeasureReportGroupPopulationComponent::getCount)
+            .findAny()
+            .orElse(0);
+        logger.info(
+            "populationNumeratorCount: {}, populationDenominatorCount: {}",
+            populationNumeratorCount,
+            populationDenominatorCount);
+        System.out.println("populationNumeratorCount = " + populationNumeratorCount);
+        System.out.println("populationDenominatorCount = " + populationDenominatorCount);
+
+        final Integer extNumeratorCount = getGroupExtensionCount(mrgc, EXT_TOTAL_NUMERATOR_URL);
+        final Integer extDenominatorCount = getGroupExtensionCount(mrgc, EXT_TOTAL_DENOMINATOR_URL);
+
+        logger.info("extNumeratorCount: {}, extDenominatorCount: {}", extNumeratorCount, extDenominatorCount);
+        System.out.println("extNumeratorCount= " + populationNumeratorCount);
+        System.out.println("extDenominatorCount= " + extDenominatorCount);
+
+        // LUKETODO:  602
+        //                if (!Objects.equals(extNumeratorCount, populationNumeratorCount)) {
+        //                    throw new IllegalStateException("numerator counts don't match: ext:" +
+        // extNumeratorCount + " != population:" + populationNumeratorCount);
+        //                }
+        //
+        //                if (!Objects.equals(extDenominatorCount, populationDenominatorCount)) {
+        //                    throw new IllegalStateException("denominator counts don't match: ext:" +
+        // extDenominatorCount + " != population:" + populationDenominatorCount);
+        //                }
         switch (measureScoring) {
             case PROPORTION:
             case RATIO:
-                Double score = this.calcProportionScore(
-                        getGroupExtensionCount(mrgc, EXT_TOTAL_NUMERATOR_URL),
-                        getGroupExtensionCount(mrgc, EXT_TOTAL_DENOMINATOR_URL));
+
+                // LUKETODO: 602:  do we need a fix for the PRODUCTION WRITE????
+                // LUKETODO: 602:  this is the actual fix for the READ
+//                Double score = this.calcProportionScore(extNumeratorCount, extDenominatorCount);
+                Double score = this.calcProportionScore(populationNumeratorCount, populationDenominatorCount);
                 if (score != null) {
                     if (isIncreaseImprovementNotation) {
                         mrgc.setMeasureScore(new Quantity(score));
@@ -124,6 +191,7 @@ protected void scoreGroup(
                 break;
         }
 
+        // LUKETODO: 602:  pass down populationNumerator and denominator to scoreStratifier() ???
         for (MeasureReportGroupStratifierComponent stratifierComponent : mrgc.getStratifier()) {
             scoreStratifier(measureScoring, stratifierComponent);
         }
@@ -133,6 +201,29 @@ protected void scoreStratum(MeasureScoring measureScoring, StratifierGroupCompon
         switch (measureScoring) {
             case PROPORTION:
             case RATIO:
+                // LUKETODO: 602:  use this instead of the MeasureGroup Population????????
+                final List<StratifierGroupPopulationComponent> populations = stratum.getPopulation();
+
+                final Integer stratumPopulationNumeratorCount = populations.stream()
+                    .filter(population -> "numerator"
+                        .equals(population.getCode().getCodingFirstRep().getCode()))
+                    .map(StratifierGroupPopulationComponent::getCount)
+                    .findAny()
+                    .orElse(0);
+
+                final Integer stratumPopulationDenominatorCount = populations.stream()
+                    .filter(population -> "denominator"
+                        .equals(population.getCode().getCodingFirstRep().getCode()))
+                    .map(StratifierGroupPopulationComponent::getCount)
+                    .findAny()
+                    .orElse(0);
+                logger.info(
+                    "stratumPopulationNumeratorCount: {}, stratumPopulationDenominatorCount: {}",
+                    stratumPopulationNumeratorCount,
+                    stratumPopulationDenominatorCount);
+                System.out.println("stratumPopulationNumeratorCount = " + stratumPopulationNumeratorCount);
+                System.out.println("stratumPopulationDenominatorCount = " + stratumPopulationDenominatorCount);
+
                 Double score = this.calcProportionScore(
                         getStratumPopulationCount(stratum, EXT_TOTAL_NUMERATOR_URL),
                         getStratumPopulationCount(stratum, EXT_TOTAL_DENOMINATOR_URL));

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4SubmitDataService.java

@@ -4,7 +4,9 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.IdType;
+import org.hl7.fhir.r4.model.Measure;
 import org.hl7.fhir.r4.model.MeasureReport;
+import org.hl7.fhir.r4.model.Period;
 import org.hl7.fhir.r4.model.Resource;
 import org.opencds.cqf.fhir.api.Repository;
 
@@ -19,16 +21,24 @@ public R4SubmitDataService(Repository repository) {
     /**
      * Save measure report and resources to the local repository
      *
-     * @param id
-     * @param report
-     * @param resources
+     * @param measureId ???
+     * @param report The measure report being submitted
+     * @param resources The individual resources that make up the data-of-interest being submitted
      * @return Bundle transaction result
      */
-    public Bundle submitData(IdType id, MeasureReport report, List<IBaseResource> resources) {
+    public Bundle submitData(IdType measureId, MeasureReport report, List<IBaseResource> resources) {
         /*
-         * TODO - resource validation using $data-requirements operation (params are the provided id and
+         * TODO - resource validation using $data-requirements operation (params are the provided measureId and
          * the measurement period from the MeasureReport)
-         *
+         */
+
+        var measureFromDb = repository.read(Measure.class, measureId);
+        var measureReportPeriod = report.getPeriod();
+
+        validateResource(measureFromDb, measureReportPeriod);
+
+        // LUKETODO: 601
+        /*
          * TODO - profile validation ... not sure how that would work ... (get StructureDefinition from
          * URL or must it be stored in Ruler?)
          */
@@ -39,6 +49,7 @@ public Bundle submitData(IdType id, MeasureReport report, List<IBaseResource> re
         if (resources != null) {
             for (IBaseResource res : resources) {
                 // Unpack nested Bundles
+                // TODO: LD: replace with pattern variable once animal sniffer allows it
                 if (res instanceof Bundle) {
                     Bundle nestedBundle = (Bundle) res;
                     for (Bundle.BundleEntryComponent entry : nestedBundle.getEntry()) {
@@ -52,6 +63,11 @@ public Bundle submitData(IdType id, MeasureReport report, List<IBaseResource> re
         return repository.transaction(transactionBundle);
     }
 
+    private void validateResource(Measure measureFromDb, Period measureReportPeriod) {
+        // LUKETODO: 601 ???
+        // LUKETODO: 601 unit tests for any cases that fail validation
+    }
+
     private Bundle.BundleEntryComponent createEntry(IBaseResource resource) {
         return new Bundle.BundleEntryComponent()
                 .setResource((Resource) resource)