Merge pull request #21 from MeasureAuthoringTool/MAT-7897_FhirOrderin…

…gDuplicates

MAT-7897: Fixing equals check so that libraries aren't discarded when…

pom.xml

@@ -1,6 +1,7 @@
 <project
 	xmlns="http://maven.apache.org/POM/4.0.0"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>gov.cms.madie</groupId>
 	<artifactId>madie-translator-commons</artifactId>
@@ -25,12 +26,13 @@
 		<com.jayway.jsonpath.version>2.9.0</com.jayway.jsonpath.version>
 	</properties>
 	<distributionManagement>
-        <repository>
-            <id>github</id>
-            <name>MeasureAuthoringTool madie translator commons Package</name>
-            <url>https://maven.pkg.github.com/measureauthoringtool/madie-translator-commons</url>
-        </repository>
-    </distributionManagement>
+		<repository>
+			<id>github</id>
+			<name>MeasureAuthoringTool madie translator commons Package</name>
+			<url>
+				https://maven.pkg.github.com/measureauthoringtool/madie-translator-commons</url>
+		</repository>
+	</distributionManagement>
 	<dependencies>
 		<dependency>
 			<groupId>org.projectlombok</groupId>
@@ -78,7 +80,14 @@
 			<artifactId>javax.ws.rs-api</artifactId>
 			<version>2.1.1</version>
 		</dependency>
-		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
+		<dependency>
+			<groupId>org.eclipse.persistence</groupId>
+			<artifactId>org.eclipse.persistence.moxy</artifactId>
+			<version>4.0.2</version>
+			<scope>test</scope>
+		</dependency>
+		<!--
+		https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>
 			<groupId>org.junit.jupiter</groupId>
 			<artifactId>junit-jupiter-api</artifactId>
@@ -99,14 +108,16 @@
 			<version>${mockito.version}</version>
 			<scope>test</scope>
 		</dependency>
-		<!-- https://mvnrepository.com/artifact/org.mockito/mockito-junit-jupiter -->
+		<!--
+		https://mvnrepository.com/artifact/org.mockito/mockito-junit-jupiter -->
 		<dependency>
 			<groupId>org.mockito</groupId>
 			<artifactId>mockito-junit-jupiter</artifactId>
 			<version>${mockito.version}</version>
 			<scope>test</scope>
 		</dependency>
-		<!-- https://mvnrepository.com/artifact/jakarta.xml.bind/jakarta.xml.bind-api -->
+		<!--
+		https://mvnrepository.com/artifact/jakarta.xml.bind/jakarta.xml.bind-api -->
 		<dependency>
 			<groupId>jakarta.xml.bind</groupId>
 			<artifactId>jakarta.xml.bind-api</artifactId>
@@ -119,12 +130,12 @@
 			<version>${jaxb.api.version}</version>
 		</dependency>
 		<!-- JAXB RI -->
-	    <dependency>
-	    	<groupId>com.sun.xml.bind</groupId>
-	    	<artifactId>jaxb-impl</artifactId>
-	    	<version>4.0.4</version>
-	    	<scope>runtime</scope>
-	    </dependency>
+		<dependency>
+			<groupId>com.sun.xml.bind</groupId>
+			<artifactId>jaxb-impl</artifactId>
+			<version>4.0.4</version>
+			<scope>runtime</scope>
+		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.springframework/spring-test -->
 		<dependency>
 			<groupId>org.springframework</groupId>
@@ -133,29 +144,29 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-	      <groupId>gov.cms.madie</groupId>
-	      	<artifactId>madie-java-models</artifactId>
-	      	<version>${gov.cms.madie.models.version}</version>
-	      	<exclusions>
-	        	<exclusion>
-	          		<artifactId>jackson-core</artifactId>
-	          		<groupId>com.fasterxml.jackson.core</groupId>
-	        	</exclusion>
-	        	<exclusion>
-	          		<artifactId>jackson-databind</artifactId>
-	          		<groupId>com.fasterxml.jackson.core</groupId>
-	        	</exclusion>
-	        	<exclusion>
-	          		<artifactId>jackson-annotations</artifactId>
-	          		<groupId>com.fasterxml.jackson.core</groupId>
-	        	</exclusion>
-	      	</exclusions>
-	    </dependency>
-	    <dependency>
-      		<groupId>com.jayway.jsonpath</groupId>
-      		<artifactId>json-path</artifactId>
-      		<version>${com.jayway.jsonpath.version}</version>
-    	</dependency>
+			<groupId>gov.cms.madie</groupId>
+			<artifactId>madie-java-models</artifactId>
+			<version>${gov.cms.madie.models.version}</version>
+			<exclusions>
+				<exclusion>
+					<artifactId>jackson-core</artifactId>
+					<groupId>com.fasterxml.jackson.core</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>jackson-databind</artifactId>
+					<groupId>com.fasterxml.jackson.core</groupId>
+				</exclusion>
+				<exclusion>
+					<artifactId>jackson-annotations</artifactId>
+					<groupId>com.fasterxml.jackson.core</groupId>
+				</exclusion>
+			</exclusions>
+		</dependency>
+		<dependency>
+			<groupId>com.jayway.jsonpath</groupId>
+			<artifactId>json-path</artifactId>
+			<version>${com.jayway.jsonpath.version}</version>
+		</dependency>
 	</dependencies>
 	<!--    Required to fetch artifacts from repositories other than maven central -->
 	<repositories>
@@ -165,7 +176,8 @@
 			</releases>
 			<id>github</id>
 			<name>Github madie rest commons</name>
-			<url>https://maven.pkg.github.com/MeasureAuthoringTool/madie-rest-commons</url>
+			<url>
+				https://maven.pkg.github.com/MeasureAuthoringTool/madie-rest-commons</url>
 		</repository>
 	</repositories>
 	<build>

src/main/java/gov/cms/madie/cql_elm_translator/dto/CqlBuilderLookup.java

@@ -5,6 +5,8 @@
 
 import java.util.Set;
 
+import org.apache.commons.lang3.StringUtils;
+
 @Data
 @Builder
 public class CqlBuilderLookup {
@@ -20,5 +22,21 @@ public static class Lookup {
     private String libraryName;
     private String libraryAlias;
     private String logic;
+    private int startLine;
+
+    @Override
+    public boolean equals(Object o) {
+      if (o == this) {
+        return true;
+      }
+      CqlBuilderLookup.Lookup lookup = (CqlBuilderLookup.Lookup) o;
+
+      if (StringUtils.equals(lookup.getName(), this.getName())
+          && StringUtils.equals(lookup.getLibraryAlias(), this.getLibraryAlias())
+          && lookup.getLibraryName().equals(this.getLibraryName())) {
+        return true;
+      }
+      return false;
+    }
   }
 }

src/main/java/gov/cms/madie/cql_elm_translator/dto/CqlBuilderLookupComparator.java

@@ -0,0 +1,32 @@
+package gov.cms.madie.cql_elm_translator.dto;
+
+import java.util.Comparator;
+
+import org.apache.commons.lang3.StringUtils;
+
+import lombok.extern.slf4j.Slf4j;
+
+@Slf4j
+public class CqlBuilderLookupComparator<T> implements Comparator<CqlBuilderLookup.Lookup> {
+
+  /***
+   * This is required because the name/line numbers can conflict between line
+   * numbers
+   */
+  public int compare(CqlBuilderLookup.Lookup lookup1, CqlBuilderLookup.Lookup lookup2) {
+
+    int result;
+
+    if (StringUtils.equalsIgnoreCase(lookup1.getName(), lookup2.getName())
+        && StringUtils.equalsIgnoreCase(lookup1.getLibraryAlias(), lookup2.getLibraryAlias())) {
+      result = 0;
+    } else if (lookup1.getStartLine() == lookup2.getStartLine()) {
+      // if the names are different but the lines are the same
+      result = lookup1.getStartLine() - lookup2.getStartLine() + 1;
+    } else {
+      result = lookup1.getStartLine() - lookup2.getStartLine();
+    }
+
+    return result;
+  }
+}

src/main/java/gov/cms/madie/cql_elm_translator/utils/cql/CQLTools.java

@@ -7,6 +7,7 @@
 import java.util.*;
 
 import lombok.Getter;
+
 import org.antlr.v4.runtime.CharStreams;
 import org.antlr.v4.runtime.CommonTokenStream;
 import org.antlr.v4.runtime.tree.ParseTree;
@@ -131,9 +132,10 @@ public void generate() throws IOException {
 
     TranslationResource translationResource =
         TranslationResource.getInstance(
-            usingProperties.getLibraryType() == "FHIR"
-                || usingProperties.getLibraryType()
-                    == "QICore"); // <-- BADDDDD!!!! Defaults to fhir
+            usingProperties.getLibraryType().equals("FHIR")
+                || usingProperties
+                    .getLibraryType()
+                    .equals("QICore")); // <-- BADDDDD!!!! Defaults to fhir
 
     CqlPreprocessorElmCommonVisitor preprocessor =
         new CqlPreprocessorElmCommonVisitor(
@@ -143,8 +145,8 @@ public void generate() throws IOException {
     preprocessor.visit(tree);
     ParseTreeWalker walker = new ParseTreeWalker();
     walker.walk(listener, tree);
-
     definitionContents.addAll(listener.getDefinitionContents());
+
     allParameters.addAll(listener.getParameters()); // MAT-7450
     callstack = graph.getAdjacencyList();
 

src/main/java/gov/cms/madie/cql_elm_translator/utils/cql/parsing/Cql2ElmListener.java

@@ -278,7 +278,11 @@ public void enterExpressionDefinition(@NotNull cqlParser.ExpressionDefinitionCon
             .getInputStream()
             .getText(new Interval(ctx.getStart().getStartIndex(), ctx.getStop().getStopIndex()));
     definitionContents.add(
-        DefinitionContent.builder().name(currentContext).content(content).build());
+        DefinitionContent.builder()
+            .startLine(ctx.getStart().getLine())
+            .name(currentContext)
+            .content(content)
+            .build());
     graph.addNode(currentContext);
   }
 

src/main/java/gov/cms/madie/cql_elm_translator/utils/cql/parsing/model/CQLDefinition.java

@@ -4,10 +4,12 @@
 import lombok.Builder;
 import lombok.Data;
 import lombok.NoArgsConstructor;
+import lombok.extern.slf4j.Slf4j;
 
 import java.util.List;
 import java.util.Objects;
 
+@Slf4j
 @Data
 @Builder(toBuilder = true)
 @AllArgsConstructor
@@ -17,15 +19,16 @@ public class CQLDefinition implements CQLExpression {
   private String uuid;
   private String definitionName;
   private String definitionLogic;
-  private String context = "Patient";
+  @Builder.Default private String context = "Patient";
   private boolean supplDataElement;
   private boolean popDefinition;
-  private String commentString = "";
+  @Builder.Default private String commentString = "";
   private String returnType;
   private String parentLibrary;
   private String libraryDisplayName;
   private String libraryVersion;
   private boolean isFunction;
+  private int startLine;
   private List<CQLFunctionArgument> functionArguments;
 
   public static class Comparator implements java.util.Comparator<CQLDefinition> {
@@ -83,6 +86,15 @@ public boolean equals(Object o) {
       return false;
     }
     CQLDefinition that = (CQLDefinition) o;
-    return Objects.equals(definitionName, that.definitionName);
+    boolean result =
+        Objects.equals(definitionName, that.definitionName)
+            && Objects.equals(libraryDisplayName, that.libraryDisplayName);
+
+    return result;
+  }
+
+  @Override
+  public int hashCode() {
+    return Objects.hash(uuid);
   }
 }

src/main/java/gov/cms/madie/cql_elm_translator/utils/cql/parsing/model/DefinitionContent.java

@@ -12,4 +12,5 @@ public class DefinitionContent {
   private String content;
   private List<CQLFunctionArgument> functionArguments;
   private boolean function; // MAT-7450
+  private int startLine; // MAT-7897
 }

src/test/java/gov/cms/madie/cql_elm_translator/dto/CqlBuilderLookupComparatorTest.java

@@ -0,0 +1,85 @@
+package gov.cms.madie.cql_elm_translator.dto;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.util.Set;
+import java.util.TreeSet;
+
+import org.junit.jupiter.api.Test;
+
+class CqlBuilderLookupComparatorTest {
+
+  @Test
+  void testAddOne() {
+
+    CqlBuilderLookup.Lookup lookup =
+        CqlBuilderLookup.Lookup.builder()
+            .name("SDE Race")
+            .libraryAlias("SDE")
+            .libraryName("Supplemental Data")
+            .startLine(11)
+            .build();
+
+    Set<CqlBuilderLookup.Lookup> definitions =
+        new TreeSet<CqlBuilderLookup.Lookup>(
+            new CqlBuilderLookupComparator<CqlBuilderLookup.Lookup>());
+
+    definitions.add(lookup);
+    assertEquals(definitions.size(), 1);
+  }
+
+  @Test
+  void testAddTwoIdentical() {
+
+    CqlBuilderLookup.Lookup lookup =
+        CqlBuilderLookup.Lookup.builder()
+            .name("SDE Race")
+            .libraryAlias("SDE")
+            .libraryName("Supplemental Data")
+            .startLine(11)
+            .build();
+
+    CqlBuilderLookup.Lookup lookup2 =
+        CqlBuilderLookup.Lookup.builder()
+            .name("SDE Race")
+            .libraryAlias("SDE")
+            .libraryName("Supplemental Data")
+            .startLine(11)
+            .build();
+
+    Set<CqlBuilderLookup.Lookup> definitions =
+        new TreeSet<CqlBuilderLookup.Lookup>(
+            new CqlBuilderLookupComparator<CqlBuilderLookup.Lookup>());
+
+    definitions.add(lookup);
+    definitions.add(lookup2);
+    assertEquals(definitions.size(), 1);
+  }
+
+  @Test
+  void testSameNameDifferentAlias() {
+
+    CqlBuilderLookup.Lookup lookup =
+        CqlBuilderLookup.Lookup.builder()
+            .name("SDE Race")
+            .libraryAlias("SDE")
+            .libraryName("Supplemental Data")
+            .startLine(11)
+            .build();
+
+    CqlBuilderLookup.Lookup lookup2 =
+        CqlBuilderLookup.Lookup.builder()
+            .name("SDE Race")
+            .libraryName("Supplemental Data")
+            .startLine(11)
+            .build();
+
+    Set<CqlBuilderLookup.Lookup> definitions =
+        new TreeSet<CqlBuilderLookup.Lookup>(
+            new CqlBuilderLookupComparator<CqlBuilderLookup.Lookup>());
+
+    definitions.add(lookup);
+    definitions.add(lookup2);
+    assertEquals(2, definitions.size());
+  }
+}