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Deduplicate logicDefinition extensions on the moduleDefinitionLibrary (#594)
* Deduplicate logicDefinition extensions on the moduleDefinitionLibrary * Created util for common code and added focused unit testing for new utility
1 parent 1524d69 commit 11b055c

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

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

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

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

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

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

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

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

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

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

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