Measure scoring specified at group level (#391)

* allow setting measureScorer on group level or Measurelevel

* spotless apply edits

* group scoring logic

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

@@ -1,6 +1,7 @@
 package org.opencds.cqf.fhir.cr.measure.common;
 
 import java.util.List;
+import java.util.Map;
 import org.opencds.cqf.cql.engine.runtime.Interval;
 
 public class MeasureDef {
@@ -9,18 +10,23 @@ public class MeasureDef {
     private final String url;
     private final String version;
     private Interval defaultMeasurementPeriod;
-    private final MeasureScoring scoring;
+    private final Map<GroupDef, MeasureScoring> scoring;
     private final List<GroupDef> groups;
     private final List<SdeDef> sdes;
 
     public MeasureDef(
-            String id, String url, String version, MeasureScoring scoring, List<GroupDef> groups, List<SdeDef> sdes) {
+            String id,
+            String url,
+            String version,
+            Map<GroupDef, MeasureScoring> scoring,
+            List<GroupDef> groups,
+            List<SdeDef> sdes) {
         this.id = id;
         this.url = url;
         this.version = version;
-        this.scoring = scoring;
         this.groups = groups;
         this.sdes = sdes;
+        this.scoring = scoring;
     }
 
     public String id() {
@@ -35,10 +41,6 @@ public String version() {
         return this.version;
     }
 
-    public MeasureScoring scoring() {
-        return this.scoring;
-    }
-
     public Interval getDefaultMeasurementPeriod() {
         return defaultMeasurementPeriod;
     }
@@ -54,4 +56,8 @@ public List<SdeDef> sdes() {
     public List<GroupDef> groups() {
         return this.groups;
     }
+
+    public Map<GroupDef, MeasureScoring> scoring() {
+        return this.scoring;
+    }
 }

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

@@ -13,6 +13,7 @@
 import java.time.OffsetDateTime;
 import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
 import org.apache.commons.lang3.tuple.Pair;
@@ -31,11 +32,16 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * This class implements the core Measure evaluation logic that's defined in the Quality Measure
- * implementation guide and HQMF specifications. There are a number of model-independent concepts
- * such as "groups", "populations", and "stratifiers" that can be used across a number of different
- * data models including FHIR, QDM, and QICore. To the extent feasible, this class is intended to be
- * model-independent so that it can be used in any Java-based implementation of Quality Measure
+ * This class implements the core Measure evaluation logic that's defined in the
+ * Quality Measure
+ * implementation guide and HQMF specifications. There are a number of
+ * model-independent concepts
+ * such as "groups", "populations", and "stratifiers" that can be used across a
+ * number of different
+ * data models including FHIR, QDM, and QICore. To the extent feasible, this
+ * class is intended to be
+ * model-independent so that it can be used in any Java-based implementation of
+ * Quality Measure
  * evaluation.
  *
  * @see <a href=
@@ -209,10 +215,7 @@ protected MeasureDef evaluate(MeasureDef measureDef, MeasureReportType type, Lis
                 type.toCode(),
                 subjectIds.size());
 
-        MeasureScoring scoring = measureDef.scoring();
-        if (scoring == null) {
-            throw new RuntimeException("MeasureScoring type is required in order to calculate.");
-        }
+        Map<GroupDef, MeasureScoring> scoring = measureDef.scoring();
 
         for (String subjectId : subjectIds) {
             if (subjectId == null) {
@@ -229,7 +232,7 @@ protected MeasureDef evaluate(MeasureDef measureDef, MeasureReportType type, Lis
     }
 
     protected void evaluateSubject(
-            MeasureDef measureDef, MeasureScoring scoring, String subjectType, String subjectId) {
+            MeasureDef measureDef, Map<GroupDef, MeasureScoring> scoring, String subjectType, String subjectId) {
         evaluateSdes(subjectId, measureDef.sdes());
         for (GroupDef groupDef : measureDef.groups()) {
             evaluateGroup(scoring, groupDef, subjectType, subjectId);
@@ -399,9 +402,11 @@ protected void evaluateCohort(GroupDef groupDef, String subjectType, String subj
     }
 
     protected void evaluateGroup(
-            MeasureScoring measureScoring, GroupDef groupDef, String subjectType, String subjectId) {
+            Map<GroupDef, MeasureScoring> measureScoring, GroupDef groupDef, String subjectType, String subjectId) {
         evaluateStratifiers(subjectId, groupDef.stratifiers());
-        switch (measureScoring) {
+
+        var scoring = measureScoring.get(groupDef);
+        switch (scoring) {
             case PROPORTION:
             case RATIO:
                 evaluateProportion(groupDef, subjectType, subjectId);

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

@@ -1,5 +1,7 @@
 package org.opencds.cqf.fhir.cr.measure.common;
 
+import java.util.Map;
+
 public interface MeasureReportScorer<MeasureReportT> {
-    public void score(MeasureScoring measureScoring, MeasureReportT measureReport);
+    public void score(Map<GroupDef, MeasureScoring> measureScoring, MeasureReportT measureReport);
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/dstu3/Dstu3MeasureDefBuilder.java

@@ -1,7 +1,9 @@
 package org.opencds.cqf.fhir.cr.measure.dstu3;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.dstu3.model.CodeableConcept;
 import org.hl7.fhir.dstu3.model.Coding;
@@ -51,7 +53,12 @@ public MeasureDef build(Measure measure) {
         }
 
         // Groups
+        MeasureScoring groupMeasureScoringCode = getMeasureScoring(measure);
+        if (groupMeasureScoringCode == null) {
+            throw new IllegalStateException("MeasureScoring must be specified on Measure");
+        }
         List<GroupDef> groups = new ArrayList<>();
+        Map<GroupDef, MeasureScoring> groupMeasureScoring = new HashMap<>();
         for (MeasureGroupComponent group : measure.getGroup()) {
             checkId(group);
 
@@ -78,21 +85,17 @@ public MeasureDef build(Measure measure) {
 
                 stratifiers.add(stratifierDef);
             }
-
-            groups.add(new GroupDef(
+            var groupDef = new GroupDef(
                     group.getId(),
                     null, // No code on group in dstu3
                     stratifiers,
-                    populations));
+                    populations);
+            groups.add(groupDef);
+            groupMeasureScoring.put(groupDef, groupMeasureScoringCode);
         }
 
         return new MeasureDef(
-                measure.getId(),
-                measure.getUrl(),
-                measure.getVersion(),
-                MeasureScoring.fromCode(measure.getScoring().getCodingFirstRep().getCode()),
-                groups,
-                sdes);
+                measure.getId(), measure.getUrl(), measure.getVersion(), groupMeasureScoring, groups, sdes);
     }
 
     private ConceptDef conceptToConceptDef(CodeableConcept codeable) {
@@ -123,4 +126,8 @@ private void checkId(Resource r) {
             throw new NullPointerException("id is required on all Resources of type: " + r.fhirType());
         }
     }
+
+    private MeasureScoring getMeasureScoring(Measure measure) {
+        return MeasureScoring.fromCode(measure.getScoring().getCodingFirstRep().getCode());
+    }
 }

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/dstu3/Dstu3MeasureReportScorer.java

@@ -1,5 +1,6 @@
 package org.opencds.cqf.fhir.cr.measure.dstu3;
 
+import java.util.Map;
 import java.util.Optional;
 import org.hl7.fhir.dstu3.model.MeasureReport;
 import org.hl7.fhir.dstu3.model.MeasureReport.MeasureReportGroupComponent;
@@ -8,15 +9,19 @@
 import org.hl7.fhir.dstu3.model.MeasureReport.StratifierGroupComponent;
 import org.hl7.fhir.dstu3.model.MeasureReport.StratifierGroupPopulationComponent;
 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.MeasurePopulationType;
 import org.opencds.cqf.fhir.cr.measure.common.MeasureScoring;
 
 public class Dstu3MeasureReportScorer extends BaseMeasureReportScorer<MeasureReport> {
 
     @Override
-    public void score(MeasureScoring measureScoring, MeasureReport measureReport) {
+    public void score(Map<GroupDef, MeasureScoring> measureScoring, MeasureReport measureReport) {
+        // Dstu3 only has MeasureScoring defined on Measure level,
+        // use that for all groups
+        var scoring = measureScoring.entrySet().stream().findFirst().get().getValue();
         for (MeasureReportGroupComponent mrgc : measureReport.getGroup()) {
-            scoreGroup(measureScoring, mrgc);
+            scoreGroup(scoring, mrgc);
         }
     }
 

cqf-fhir-cr/src/main/java/org/opencds/cqf/fhir/cr/measure/r4/R4MeasureDefBuilder.java

@@ -1,7 +1,9 @@
 package org.opencds.cqf.fhir.cr.measure.r4;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import org.apache.commons.lang3.StringUtils;
 import org.hl7.fhir.r4.model.CodeableConcept;
 import org.hl7.fhir.r4.model.Coding;
@@ -37,6 +39,8 @@ public R4MeasureDefBuilder(boolean enforceIds) {
         this.enforceIds = enforceIds;
     }
 
+    public final String CQFM_SCORING_EXT_URL = "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/cqfm-scoring";
+
     @Override
     public MeasureDef build(Measure measure) {
         checkId(measure);
@@ -51,10 +55,27 @@ public MeasureDef build(Measure measure) {
         }
 
         // Groups
+        var measureLevelMeasureScoring = getMeasureScoring(measure);
         List<GroupDef> groups = new ArrayList<>();
+        Map<GroupDef, MeasureScoring> groupMeasureScoring = new HashMap<>();
         for (MeasureGroupComponent group : measure.getGroup()) {
             checkId(group);
 
+            // Group MeasureScoring
+            if (measureLevelMeasureScoring == null && group.getExtensionByUrl(CQFM_SCORING_EXT_URL) == null) {
+                throw new IllegalStateException("MeasureScoring must be specified on Group or Measure");
+            }
+            MeasureScoring groupMeasureScoringCode = null;
+            if (group.getExtensionByUrl(CQFM_SCORING_EXT_URL) != null) {
+                CodeableConcept coding = (CodeableConcept)
+                        group.getExtensionByUrl(CQFM_SCORING_EXT_URL).getValue();
+                groupMeasureScoringCode =
+                        getGroupMeasureScoring(coding.getCodingFirstRep().getCode());
+            }
+            if (group.getExtensionByUrl(CQFM_SCORING_EXT_URL) == null && measureLevelMeasureScoring != null) {
+                groupMeasureScoringCode = measureLevelMeasureScoring;
+            }
+
             // Populations
             List<PopulationDef> populations = new ArrayList<>();
             for (MeasureGroupPopulationComponent pop : group.getPopulation()) {
@@ -94,17 +115,13 @@ public MeasureDef build(Measure measure) {
 
                 stratifiers.add(stratifierDef);
             }
-
-            groups.add(new GroupDef(group.getId(), conceptToConceptDef(group.getCode()), stratifiers, populations));
+            var groupDef = new GroupDef(group.getId(), conceptToConceptDef(group.getCode()), stratifiers, populations);
+            groups.add(groupDef);
+            groupMeasureScoring.put(groupDef, groupMeasureScoringCode);
         }
 
         return new MeasureDef(
-                measure.getId(),
-                measure.getUrl(),
-                measure.getVersion(),
-                MeasureScoring.fromCode(measure.getScoring().getCodingFirstRep().getCode()),
-                groups,
-                sdes);
+                measure.getId(), measure.getUrl(), measure.getVersion(), groupMeasureScoring, groups, sdes);
     }
 
     private ConceptDef conceptToConceptDef(CodeableConcept codeable) {
@@ -135,4 +152,12 @@ private void checkId(Resource r) {
             throw new NullPointerException("id is required on all Resources of type: " + r.fhirType());
         }
     }
+
+    private MeasureScoring getMeasureScoring(Measure measure) {
+        return MeasureScoring.fromCode(measure.getScoring().getCodingFirstRep().getCode());
+    }
+
+    private MeasureScoring getGroupMeasureScoring(String scoringCode) {
+        return MeasureScoring.fromCode(scoringCode);
+    }
 }

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

@@ -1,5 +1,6 @@
 package org.opencds.cqf.fhir.cr.measure.r4;
 
+import java.util.Map;
 import java.util.Optional;
 import org.hl7.fhir.r4.model.MeasureReport;
 import org.hl7.fhir.r4.model.MeasureReport.MeasureReportGroupComponent;
@@ -9,18 +10,60 @@
 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.MeasurePopulationType;
 import org.opencds.cqf.fhir.cr.measure.common.MeasureScoring;
+import org.opencds.cqf.fhir.cr.measure.common.PopulationDef;
 
 public class R4MeasureReportScorer extends BaseMeasureReportScorer<MeasureReport> {
 
     @Override
-    public void score(MeasureScoring measureScoring, MeasureReport measureReport) {
+    public void score(Map<GroupDef, MeasureScoring> measureScoring, MeasureReport measureReport) {
         for (MeasureReportGroupComponent mrgc : measureReport.getGroup()) {
-            scoreGroup(measureScoring, mrgc);
+            scoreGroup(getGroupMeasureScoring(mrgc, measureScoring), mrgc);
         }
     }
 
+    protected MeasureScoring getGroupMeasureScoring(
+            MeasureReportGroupComponent mrgc, Map<GroupDef, MeasureScoring> measureScoring) {
+        MeasureScoring measureScoringFromGroup = null;
+        // cycle through available Group Definitions to retrieve appropriate MeasureScoring
+        for (Map.Entry<GroupDef, MeasureScoring> entry : measureScoring.entrySet()) {
+            // Take only MeasureScoring available
+            if (measureScoring.size() == 1) {
+                measureScoringFromGroup = entry.getValue();
+                break;
+            }
+            // Match by group id if available
+            if (mrgc.getId() != null && entry.getKey().id() != null) {
+                if (entry.getKey().id().equals(mrgc.getId())) {
+                    measureScoringFromGroup = entry.getValue();
+                    break;
+                }
+            }
+            // Match by group's population id
+            if (mrgc.getPopulation().size() == entry.getKey().populations().size()) {
+                int i = 0;
+                for (MeasureReportGroupPopulationComponent popId : mrgc.getPopulation()) {
+                    for (PopulationDef popDefEntry : entry.getKey().populations()) {
+                        if (popId.getId().equals(popDefEntry.id())) {
+                            i++;
+                            break;
+                        }
+                    }
+                }
+                // Check all populations found a match
+                if (i == mrgc.getPopulation().size()) {
+                    measureScoringFromGroup = entry.getValue();
+                }
+            }
+        }
+        if (measureScoringFromGroup == null) {
+            throw new IllegalStateException("No MeasureScoring value set");
+        }
+        return measureScoringFromGroup;
+    }
+
     protected void scoreGroup(MeasureScoring measureScoring, MeasureReportGroupComponent mrgc) {
         switch (measureScoring) {
             case PROPORTION: