Ensure date basis merges do not de-duplicate dates in population counts

PRPs/integrate-measure-def-scorer-part1-foundation.md

@@ -258,7 +258,7 @@ These bugs are **hidden during Part 1** because old scorers are still active and
 
 **Source of Fixes:**
 All implementations verified in cr1 codebase at:
-- `/Users/lukedegruchy/development/smilecdr/git/clinical-reasoning-repos/clinical-reasoning-only/cr1`
+- `{clinical-reasoning git repo directory}`
 
 ## Implementation Plan
 

PRPs/version-agnostic-def-capture-framework.md

@@ -219,7 +219,7 @@ callback.onDefCaptured(measureDef.createSnapshot());
 **Files to Create:**
 - `common/DefCaptureCallback.java` - Callback interface
 
-**Detailed Implementation:** See cr5 PRP: `/Users/lukedegruchy/development/smilecdr/git/clinical-reasoning-repos/clinical-reasoning-only/cr5/prp-def-snapshot-api.md`
+**Detailed Implementation:** See cr5 PRP: `{clinical-reasoning git repo directory}/prp-def-snapshot-api.md`
 
 **Status:** ✅ COMPLETE
 

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

@@ -78,15 +78,11 @@ public boolean add(T newElement) {
             }
         }
 
-        final CqlType newElementCqlType = FhirResourceAndCqlTypeUtils.castToCqlTypeIfApplicable(newElement);
-
-        if (newElementCqlType != null) {
-            if (this.contains(newElementCqlType)) {
-                return false;
-            } else {
-                return super.add(newElement);
-            }
-        }
+        // CDO-714 tactical fix: the CqlType dedup branch is disabled so distinct runtime.Date
+        // (and other no-equals-override CqlType) instances survive default HashSet identity
+        // semantics. The holistic, basis-aware design is captured in
+        // PRPs/prp-population-basis-primitive-duplicate-counting.md and is sequenced after the
+        // CQL 5.0 (cql1) ExpressionResult type changes land.
 
         return super.add(newElement);
     }
@@ -116,17 +112,8 @@ public boolean remove(Object removalCandidate) {
             return false;
         }
 
-        final CqlType removalCandidateCqlType = FhirResourceAndCqlTypeUtils.castToCqlTypeIfApplicable(removalCandidate);
-
-        if (removalCandidateCqlType != null) {
-            for (T next : this) {
-                if (next instanceof CqlType nextCqlType
-                        && FhirResourceAndCqlTypeUtils.areEqualCqlTypes(nextCqlType, removalCandidateCqlType)) {
-                    return super.remove(nextCqlType);
-                }
-            }
-            return false;
-        }
+        // CDO-714 tactical fix: matching CqlType remove path disabled. See add() above and
+        // PRPs/prp-population-basis-primitive-duplicate-counting.md.
 
         return super.remove(removalCandidate);
     }
@@ -165,10 +152,11 @@ public boolean retainAll(@Nonnull Collection<?> otherCollection) {
 
     private static boolean contains(Collection<?> collection, Object obj) {
         final IBaseResource otherResource = FhirResourceAndCqlTypeUtils.castToResourceIfApplicable(obj);
-        final CqlType otherCqlType = FhirResourceAndCqlTypeUtils.castToCqlTypeIfApplicable(obj);
+        // CDO-714 tactical fix: CqlType detection disabled here too. See add() above and
+        // PRPs/prp-population-basis-primitive-duplicate-counting.md.
 
         // prevent infinite recursion
-        if (otherResource != null || otherCqlType != null || collection instanceof HashSetForFhirResourcesAndCqlTypes) {
+        if (otherResource != null || collection instanceof HashSetForFhirResourcesAndCqlTypes) {
             return containsInner(collection, obj);
         }
 

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/common/HashSetForFhirResourcesAndCqlTypesTest.java

@@ -10,6 +10,7 @@
 import org.hl7.fhir.instance.model.api.IBaseResource;
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
+import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.opencds.cqf.cql.engine.runtime.Date;
 import org.opencds.cqf.cql.engine.runtime.Precision;
@@ -56,6 +57,7 @@ void removeFhirResourceByIdRemovesCorrectResource() {
         assertFalse(set.contains(patient2));
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void removeCqlDateRemovesCorrectCqlDate() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -88,6 +90,7 @@ void retainAllKeepsOnlyMatchingFhirResourcesById() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void retainAllKeepsOnlyMatchingCqlDate() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -104,6 +107,7 @@ void retainAllKeepsOnlyMatchingCqlDate() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void retainAllKeepsOnlyMatchingCqlDateWithMatchingPrecision() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -120,6 +124,7 @@ void retainAllKeepsOnlyMatchingCqlDateWithMatchingPrecision() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void retainAllKeepsOnlyMatchingCqlDateWithPrecisionMismatch() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -153,6 +158,7 @@ void removeAllRemovesMatchingFhirResourcesById() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void removeAllRemovesMatchingCqlDate() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -169,6 +175,7 @@ void removeAllRemovesMatchingCqlDate() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void removeAllRemovesMatchingCqlDateWithPrecision() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -185,6 +192,7 @@ void removeAllRemovesMatchingCqlDateWithPrecision() {
         assertEquals(1, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void removeAllRemovesMatchingCqlDateMismatchPrecision() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();
@@ -218,6 +226,7 @@ void addAllAddsOnlyNonDuplicateFhirResourcesById() {
         assertEquals(2, set.size());
     }
 
+    @Disabled("CDO-714 — CqlType dedup branch disabled; see PRPs/prp-population-basis-primitive-duplicate-counting.md")
     @Test
     void addAllAddsNoDuplicateCqlDates() {
         var set = new HashSetForFhirResourcesAndCqlTypes<Date>();

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/DuplicateTypeIntraSubjectTest.java

@@ -0,0 +1,115 @@
+package org.opencds.cqf.fhir.cr.measure.r4;
+
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import org.opencds.cqf.fhir.cr.measure.common.MeasurePopulationType;
+import org.opencds.cqf.fhir.cr.measure.r4.Measure.Given;
+
+/**
+ * Integration test pinning the expected behaviour for CDO-714.
+ *
+ * <p>When a Measure has a non-boolean population basis and a CQL expression for a population
+ * yields duplicate values within a single subject, each occurrence is a discrete data point and
+ * the population count must include the duplicates.
+ *
+ * <p>This test covers three flavours of "primitive" basis that the evaluator must handle:
+ * <ul>
+ *   <li><b>CQL Date</b> ({@code System.Date} → {@code runtime.Date}) yielded by a literal list
+ *       expression. The tactical CDO-714 fix disables the {@code CqlType} dedup branches in
+ *       {@code HashSetForFhirResourcesAndCqlTypes} so distinct {@code runtime.Date} instances
+ *       survive default {@link java.util.HashSet} identity semantics and the count reflects every
+ *       yielded date.
+ *   <li><b>CQL Integer</b> ({@code System.Integer} → {@code java.lang.Integer}) yielded by a
+ *       literal list expression. <b>Deferred to the holistic fix</b>: {@code Integer} is neither
+ *       {@code IBaseResource} nor {@code CqlType}, and {@code Integer}'s value-based
+ *       {@code equals}/{@code hashCode} still dedups in the default {@link java.util.HashSet}
+ *       path. See {@code PRPs/prp-population-basis-primitive-duplicate-counting.md}.
+ *   <li><b>FHIR primitive</b> ({@link org.hl7.fhir.instance.model.api.IPrimitiveType}) yielded by
+ *       walking {@code Patient.address[0].line}. Regression guard: HAPI FHIR primitive instances
+ *       are neither {@code IBaseResource} nor {@code CqlType}, and {@code Base.equals} is not
+ *       overridden, so default {@link java.util.HashSet} identity semantics keep distinct
+ *       instances. The tactical fix must (and does) preserve this.
+ * </ul>
+ *
+ * @see <a href="https://simpaticois.atlassian.net/browse/CDO-714">CDO-714</a>
+ */
+@SuppressWarnings("squid:S2699")
+class DuplicateTypeIntraSubjectTest {
+
+    private static final Given GIVEN = Measure.given().repositoryFor("DuplicateTypeIntraSubject");
+
+    @Test
+    void cqlDateBasis_intraSubjectDuplicates_populationReport_includesDuplicates() {
+        GIVEN.when()
+                .measureId("DuplicateTypeIntraSubjectDateBasisMeasure")
+                .periodStart("2025-01-01")
+                .periodEnd("2025-12-31")
+                .reportType("population")
+                .evaluate()
+                .then()
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .report();
+    }
+
+    @Test
+    void cqlDateBasis_intraSubjectDuplicates_subjectReport_includesDuplicates() {
+        GIVEN.when()
+                .measureId("DuplicateTypeIntraSubjectDateBasisMeasure")
+                .subject("Patient/patient-a")
+                .periodStart("2025-01-01")
+                .periodEnd("2025-12-31")
+                .evaluate()
+                .then()
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .report();
+    }
+
+    // Deferred: the CQL engine returns java.lang.Integer for CQL Integer literals, which has
+    // value-based equals/hashCode and dedups via default HashSet semantics. The tactical
+    // CDO-714 fix (disabling CqlType branches in HashSetForFhirResourcesAndCqlTypes) does not
+    // reach the java.lang.Integer path. The holistic fix is captured in
+    // PRPs/prp-population-basis-primitive-duplicate-counting.md and is sequenced after the
+    // CQL 5.0 (cql1) ExpressionResult type changes land.
+    @Disabled("CDO-714 — deferred to PRPs/prp-population-basis-primitive-duplicate-counting.md")
+    @Test
+    void cqlIntegerBasis_intraSubjectDuplicates_populationReport_includesDuplicates() {
+        GIVEN.when()
+                .measureId("DuplicateTypeIntraSubjectIntegerBasisMeasure")
+                .periodStart("2025-01-01")
+                .periodEnd("2025-12-31")
+                .reportType("population")
+                .evaluate()
+                .then()
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .report();
+    }
+
+    @Test
+    void fhirStringBasis_intraSubjectDuplicates_populationReport_includesDuplicates() {
+        GIVEN.when()
+                .measureId("DuplicateTypeIntraSubjectFhirStringBasisMeasure")
+                .periodStart("2025-01-01")
+                .periodEnd("2025-12-31")
+                .reportType("population")
+                .evaluate()
+                .then()
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .report();
+    }
+}

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/MultiMeasure.java

@@ -55,6 +55,8 @@
 import org.opencds.cqf.fhir.utility.BundleHelper;
 import org.opencds.cqf.fhir.utility.repository.ig.IgRepository;
 import org.opencds.cqf.fhir.utility.search.Searches.SearchBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 @SuppressWarnings("squid:S1135")
 class MultiMeasure {
@@ -475,6 +477,10 @@ public MeasureReport resourceToMeasureReport(
     }
 
     public static class SelectedMeasureReport extends MultiMeasure.Selected<MeasureReport, SelectedReport> {
+        private static final Logger logger = LoggerFactory.getLogger(SelectedMeasureReport.class);
+        private static final IParser JSON_PARSER =
+                FhirContext.forR4Cached().newJsonParser().setPrettyPrint(true);
+
         public MeasureReport report() {
             return this.value();
         }
@@ -627,6 +633,13 @@ public SelectedMeasureReport hasPeriodEnd(Date periodEnd) {
             assertEquals(periodEnd, period.getEnd());
             return this;
         }
+
+        // Log the JSON corresponding to the report at this point:
+        public SelectedMeasureReport logReportJson() {
+            logger.info(JSON_PARSER.encodeResourceToString(report()));
+
+            return this;
+        }
     }
 
     public static class SelectedGroup

cqf-fhir-cr/src/test/java/org/opencds/cqf/fhir/cr/measure/r4/MultiMeasureDuplicateTypeIntraSubjectTest.java

@@ -0,0 +1,71 @@
+package org.opencds.cqf.fhir.cr.measure.r4;
+
+import org.junit.jupiter.api.Test;
+import org.opencds.cqf.fhir.cr.measure.common.MeasurePopulationType;
+import org.opencds.cqf.fhir.cr.measure.r4.MultiMeasure.Given;
+
+/**
+ * MultiMeasure integration test pinning CDO-714 behaviour across the {@link R4MultiMeasureService}
+ * orchestration path.
+ *
+ * <p>Runs three Measures in the same evaluation call against a single patient: a CQL-Date-basis
+ * Measure with intra-subject duplicate dates, a FHIR-string-basis Measure with intra-subject
+ * duplicate {@link org.hl7.fhir.instance.model.api.IPrimitiveType} strings, and a boolean-basis
+ * Measure used as an unaffected baseline.
+ *
+ * <p>The date-basis Measure reports a population count of {@code 3} (each duplicate counted) under
+ * the tactical CDO-714 fix; the FHIR-string-basis Measure also reports {@code 3}; and the
+ * boolean-basis Measure stays at {@code 1}.
+ *
+ * <p>The CQL-Integer-basis Measure is deliberately excluded from this chain — the tactical fix
+ * does not reach the {@code java.lang.Integer} dedup path. The full multi-basis assertion
+ * (date / integer / FHIR string / boolean) will be restored when the holistic fix lands; see
+ * {@code PRPs/prp-population-basis-primitive-duplicate-counting.md}.
+ *
+ * @see <a href="https://simpaticois.atlassian.net/browse/CDO-714">CDO-714</a>
+ */
+@SuppressWarnings("squid:S2699")
+class MultiMeasureDuplicateTypeIntraSubjectTest {
+
+    private static final Given GIVEN = MultiMeasure.given().repositoryFor("DuplicateTypeIntraSubject");
+
+    @Test
+    void multiMeasure_dateBasis_fhirStringBasis_booleanBasis_countsAreBasisAware() {
+        // CQL-Integer-basis Measure intentionally omitted from this chain; see class JavaDoc and
+        // PRPs/prp-population-basis-primitive-duplicate-counting.md for the deferred coverage.
+        var when = GIVEN.when()
+                .measureId("DuplicateTypeIntraSubjectDateBasisMeasure")
+                .measureId("DuplicateTypeIntraSubjectFhirStringBasisMeasure")
+                .measureId("DuplicateTypeIntraSubjectBooleanBasisMeasure")
+                .periodStart("2025-01-01")
+                .periodEnd("2025-12-31")
+                .reportType("population")
+                .evaluate();
+
+        when.then()
+                .hasBundleCount(1)
+                .hasMeasureReportCount(3)
+                .measureReport("http://example.com/Measure/DuplicateTypeIntraSubjectDateBasisMeasure")
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .up()
+                .measureReport("http://example.com/Measure/DuplicateTypeIntraSubjectFhirStringBasisMeasure")
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(3)
+                .up()
+                .up()
+                .up()
+                .measureReport("http://example.com/Measure/DuplicateTypeIntraSubjectBooleanBasisMeasure")
+                .firstGroup()
+                .population(MeasurePopulationType.INITIALPOPULATION)
+                .hasCount(1)
+                .up()
+                .up()
+                .up()
+                .report();
+    }
+}