Deduplicate logicDefinition extensions on the moduleDefinitionLibrary

tooling/src/main/java/org/opencds/cqf/tooling/measure/MeasureRefreshProcessor.java

@@ -20,6 +20,7 @@
 import org.hl7.fhir.r5.model.RelatedArtifact;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.r5.model.StringType;
+import org.opencds.cqf.tooling.utilities.LogicDefinitionUtils;
 import org.opencds.cqf.tooling.utilities.constants.CrmiConstants;
 
 public class MeasureRefreshProcessor {
@@ -39,6 +40,7 @@ public Measure refreshMeasure(Measure measureToUse, LibraryManager libraryManage
 
     	Library moduleDefinitionLibrary = getModuleDefinitionLibrary(measureToUse, libraryManager, compiledLibrary, options);
         removeModelInfoDependencies(moduleDefinitionLibrary);
+        LogicDefinitionUtils.deduplicate(moduleDefinitionLibrary.getExtension());
         measureToUse.setDate(new Date());
         // http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/measure-cqfm
         setMeta(measureToUse, moduleDefinitionLibrary);

tooling/src/main/java/org/opencds/cqf/tooling/operation/ig/Refresh.java

@@ -9,6 +9,7 @@
 import org.hl7.fhir.r5.model.*;
 import org.opencds.cqf.tooling.parameter.RefreshIGParameters;
 import org.opencds.cqf.tooling.utilities.BundleUtils;
+import org.opencds.cqf.tooling.utilities.LogicDefinitionUtils;
 import org.opencds.cqf.tooling.utilities.constants.CqfmConstants;
 import org.opencds.cqf.tooling.utilities.constants.CrmiConstants;
 import org.opencds.cqf.tooling.utilities.converters.ResourceAndTypeConverter;
@@ -66,10 +67,17 @@ public void refreshCqfmExtensions(MetadataResource resource, Library moduleDefin
       resource.getExtension().removeAll(resource.getExtensionsByUrl(CqfmConstants.LOGIC_DEFINITION_EXT_URL));
       resource.getExtension().removeAll(resource.getExtensionsByUrl(CqfmConstants.EFFECTIVE_DATA_REQS_EXT_URL));
 
+      Set<String> logicDefinitionKeys = new HashSet<>();
       for (Extension extension : moduleDefinitionLibrary.getExtension()) {
          if (extension.hasUrl() && extension.getUrl().equals(CqfmConstants.DIRECT_REF_CODE_EXT_URL)) {
             continue;
          }
+         if (LogicDefinitionUtils.isLogicDefinition(extension)) {
+            String key = LogicDefinitionUtils.getLogicDefinitionKey(extension);
+            if (key != null && !logicDefinitionKeys.add(key)) {
+               continue;
+            }
+         }
          resource.addExtension(extension);
       }
    }

tooling/src/main/java/org/opencds/cqf/tooling/plandefinition/PlanDefinitionRefreshProcessor.java

@@ -5,6 +5,7 @@
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
 import org.cqframework.cql.elm.requirements.fhir.DataRequirementsProcessor;
 import org.hl7.fhir.r5.model.*;
+import org.opencds.cqf.tooling.utilities.LogicDefinitionUtils;
 import org.opencds.cqf.tooling.utilities.constants.CqfConstants;
 import org.opencds.cqf.tooling.utilities.constants.CqfmConstants;
 import org.opencds.cqf.tooling.utilities.constants.CrmiConstants;
@@ -23,6 +24,7 @@ public PlanDefinition refreshPlanDefinition(PlanDefinition planToUse, LibraryMan
         var dqReqTrans = new DataRequirementsProcessor();
         var moduleDefinitionLibrary = dqReqTrans.gatherDataRequirements(libraryManager, compiledLibrary,
                 options, expressions, true);
+        LogicDefinitionUtils.deduplicate(moduleDefinitionLibrary.getExtension());
 
         // Clear all existing CQFM extensions
         // These extensions are now deprecated, but may be in use for older artifacts

tooling/src/main/java/org/opencds/cqf/tooling/utilities/LogicDefinitionUtils.java

@@ -0,0 +1,45 @@
+package org.opencds.cqf.tooling.utilities;
+
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.hl7.fhir.r5.model.Extension;
+import org.opencds.cqf.tooling.utilities.constants.CqfConstants;
+import org.opencds.cqf.tooling.utilities.constants.CqfmConstants;
+
+public class LogicDefinitionUtils {
+
+    private LogicDefinitionUtils() {
+    }
+
+    public static String getLogicDefinitionKey(Extension logicDefinition) {
+        String libraryName = null;
+        String name = null;
+        for (Extension sub : logicDefinition.getExtension()) {
+            if ("libraryName".equals(sub.getUrl()) && sub.hasValue()) {
+                libraryName = sub.getValue().primitiveValue();
+            } else if ("name".equals(sub.getUrl()) && sub.hasValue()) {
+                name = sub.getValue().primitiveValue();
+            }
+        }
+        return (libraryName != null && name != null) ? libraryName + "|" + name : null;
+    }
+
+    public static boolean isLogicDefinition(Extension extension) {
+        return extension.hasUrl()
+                && (CqfmConstants.LOGIC_DEFINITION_EXT_URL.equals(extension.getUrl())
+                        || CqfConstants.LOGIC_DEFINITION_EXT_URL.equals(extension.getUrl()));
+    }
+
+    public static void deduplicate(List<Extension> extensions) {
+        Set<String> seen = new HashSet<>();
+        extensions.removeIf(ext -> {
+            if (isLogicDefinition(ext)) {
+                String key = getLogicDefinitionKey(ext);
+                return key != null && !seen.add(key);
+            }
+            return false;
+        });
+    }
+}

tooling/src/test/java/org/opencds/cqf/tooling/utilities/LogicDefinitionUtilsTests.java

@@ -0,0 +1,90 @@
+package org.opencds.cqf.tooling.utilities;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.IntegerType;
+import org.hl7.fhir.r5.model.StringType;
+import org.opencds.cqf.tooling.utilities.constants.CqfConstants;
+import org.opencds.cqf.tooling.utilities.constants.CqfmConstants;
+import org.testng.annotations.Test;
+
+public class LogicDefinitionUtilsTests {
+
+    private static Extension logicDefinition(String url, String libraryName, String name, int displaySequence) {
+        Extension ext = new Extension().setUrl(url);
+        ext.addExtension(new Extension().setUrl("libraryName").setValue(new StringType(libraryName)));
+        ext.addExtension(new Extension().setUrl("name").setValue(new StringType(name)));
+        ext.addExtension(new Extension().setUrl("displaySequence").setValue(new IntegerType(displaySequence)));
+        return ext;
+    }
+
+    @Test
+    public void TestKeyUsesLibraryNameAndName() {
+        Extension ext = logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "HRDMeasure", "Inpatient Beds Initial Population", 38);
+        assertEquals(LogicDefinitionUtils.getLogicDefinitionKey(ext), "HRDMeasure|Inpatient Beds Initial Population");
+    }
+
+    @Test
+    public void TestKeyIsNullWhenLibraryNameMissing() {
+        Extension ext = new Extension().setUrl(CqfConstants.LOGIC_DEFINITION_EXT_URL);
+        ext.addExtension(new Extension().setUrl("name").setValue(new StringType("X")));
+        assertNull(LogicDefinitionUtils.getLogicDefinitionKey(ext));
+    }
+
+    @Test
+    public void TestIsLogicDefinitionRecognizesBothUrls() {
+        Extension cqf = new Extension().setUrl(CqfConstants.LOGIC_DEFINITION_EXT_URL);
+        Extension cqfm = new Extension().setUrl(CqfmConstants.LOGIC_DEFINITION_EXT_URL);
+        Extension other = new Extension().setUrl("http://example.org/other");
+        assertEquals(LogicDefinitionUtils.isLogicDefinition(cqf), true);
+        assertEquals(LogicDefinitionUtils.isLogicDefinition(cqfm), true);
+        assertEquals(LogicDefinitionUtils.isLogicDefinition(other), false);
+    }
+
+    @Test
+    public void TestDeduplicateRemovesDuplicatesKeepingFirst() {
+        List<Extension> extensions = new ArrayList<>();
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "HRDMeasure", "Inpatient Beds Initial Population", 38));
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "HRDMeasure", "Adult Inpatient Beds Initial Population", 40));
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "HRDMeasure", "Inpatient Beds Initial Population", 82));
+
+        LogicDefinitionUtils.deduplicate(extensions);
+
+        assertEquals(extensions.size(), 2);
+        assertEquals(LogicDefinitionUtils.getLogicDefinitionKey(extensions.get(0)), "HRDMeasure|Inpatient Beds Initial Population");
+        // The first-encountered entry is kept, so the displaySequence of the survivor is 38, not 82.
+        Extension kept = extensions.get(0);
+        int displaySequence = ((IntegerType) kept.getExtensionByUrl("displaySequence").getValue()).getValue();
+        assertEquals(displaySequence, 38);
+    }
+
+    @Test
+    public void TestDeduplicatePreservesNonLogicDefinitionExtensions() {
+        List<Extension> extensions = new ArrayList<>();
+        extensions.add(new Extension().setUrl("http://example.org/other").setValue(new StringType("a")));
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "Lib", "Def", 1));
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "Lib", "Def", 2));
+        extensions.add(new Extension().setUrl("http://example.org/other").setValue(new StringType("b")));
+
+        LogicDefinitionUtils.deduplicate(extensions);
+
+        // One logicDefinition removed; both unrelated extensions retained.
+        assertEquals(extensions.size(), 3);
+    }
+
+    @Test
+    public void TestDeduplicateDedupesAcrossCqfmAndCqfUrls() {
+        List<Extension> extensions = new ArrayList<>();
+        extensions.add(logicDefinition(CqfmConstants.LOGIC_DEFINITION_EXT_URL, "Lib", "Def", 1));
+        extensions.add(logicDefinition(CqfConstants.LOGIC_DEFINITION_EXT_URL, "Lib", "Def", 2));
+
+        LogicDefinitionUtils.deduplicate(extensions);
+
+        assertEquals(extensions.size(), 1);
+    }
+}