Ensure local Ids for all ELM Elements

Src/java/.vscode/settings.json

@@ -10,7 +10,11 @@
         "fhirpath",
         "hamcrest",
         "Inferencing",
+        "opdef",
+        "Instancio",
+        "Objenesis",
         "qicore",
+        "Randomizer",
         "testng",
         "tngtech",
         "trackback"

Src/java/buildSrc/src/main/groovy/cql.java-conventions.gradle

@@ -29,7 +29,7 @@ dependencies {
     testImplementation 'org.testng:testng:7.4.0'
     testImplementation 'org.hamcrest:hamcrest-all:1.3'
     testImplementation 'uk.co.datumedge:hamcrest-json:0.2'
-    testImplementation 'junit:junit:4.12'
+    testImplementation 'junit:junit:4.13.2'
     testImplementation 'org.slf4j:slf4j-simple:1.7.36'
 
     // These are JAXB dependencies excluded because the libraries need to work

Src/java/buildSrc/src/main/groovy/cql.xjc-conventions.gradle

@@ -24,7 +24,7 @@ dependencies {
 
 ext.xjc = [
     destDir: "${buildDir}/generated/sources/$name/main/java",
-    args: '-disableXmlSecurity -Xfluent-api -Xequals -XhashCode -XtoString'
+    args: '-disableXmlSecurity -Xfluent-api -Xequals -XhashCode -XtoString -Xsetters -Xsetters-mode=direct'
 ]
 
 

Src/java/cql-to-elm/build.gradle

@@ -21,4 +21,5 @@ dependencies {
     testImplementation project(':qdm')
     testImplementation 'com.github.reinert:jjschema:1.16'
     testImplementation 'com.tngtech.archunit:archunit:1.2.1'
+    testImplementation 'org.skyscreamer:jsonassert:1.5.1'
 }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/CqlCompiler.java

@@ -1,17 +1,26 @@
 package org.cqframework.cql.cql2elm;
 
+import static org.cqframework.cql.cql2elm.CqlCompilerOptions.Options.EnableAnnotations;
+import static org.cqframework.cql.cql2elm.CqlCompilerOptions.Options.EnableLocators;
+import static org.cqframework.cql.cql2elm.CqlCompilerOptions.Options.EnableResultTypes;
+
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 import org.antlr.v4.runtime.*;
 import org.antlr.v4.runtime.tree.ParseTree;
+import org.cqframework.cql.cql2elm.elm.ElmEdit;
+import org.cqframework.cql.cql2elm.elm.ElmEditor;
 import org.cqframework.cql.cql2elm.model.CompiledLibrary;
-import org.cqframework.cql.cql2elm.preprocessor.CqlPreprocessorVisitor;
+import org.cqframework.cql.cql2elm.preprocessor.CqlPreprocessor;
+import org.cqframework.cql.elm.IdObjectFactory;
 import org.cqframework.cql.elm.tracking.TrackBack;
 import org.cqframework.cql.gen.cqlLexer;
 import org.cqframework.cql.gen.cqlParser;
@@ -190,34 +199,45 @@ public Library run(CharStream is) {
         warnings = new ArrayList<>();
         messages = new ArrayList<>();
 
-        LibraryBuilder builder = new LibraryBuilder(namespaceInfo, libraryManager);
-        builder.setCompilerOptions(libraryManager.getCqlCompilerOptions());
-        Cql2ElmVisitor visitor = new Cql2ElmVisitor(builder);
-        builder.setVisitor(visitor);
-        visitor.setTranslatorOptions(libraryManager.getCqlCompilerOptions());
+        var options = libraryManager.getCqlCompilerOptions().getOptions();
 
-        CqlCompiler.CqlErrorListener errorListener =
-                new CqlCompiler.CqlErrorListener(builder, visitor.isDetailedErrorsEnabled());
+        LibraryBuilder builder = new LibraryBuilder(namespaceInfo, libraryManager, new IdObjectFactory());
+        CqlCompiler.CqlErrorListener errorListener = new CqlCompiler.CqlErrorListener(
+                builder, options.contains(CqlCompilerOptions.Options.EnableDetailedErrors));
 
+        // Phase 1: Lexing
         cqlLexer lexer = new cqlLexer(is);
         lexer.removeErrorListeners();
         lexer.addErrorListener(errorListener);
         CommonTokenStream tokens = new CommonTokenStream(lexer);
+
+        // Phase 2: Parsing (the lexer is actually streaming, so Phase 1 and 2 happen together)
         cqlParser parser = new cqlParser(tokens);
         parser.setBuildParseTree(true);
-
         parser.removeErrorListeners(); // Clear the default console listener
         parser.addErrorListener(errorListener);
         ParseTree tree = parser.library();
 
-        CqlPreprocessorVisitor preprocessor = new CqlPreprocessorVisitor(builder, tokens);
+        // Phase 3: preprocess the parse tree (generates the LibraryInfo with
+        // header information for definitions)
+        CqlPreprocessor preprocessor = new CqlPreprocessor(builder, tokens);
         preprocessor.visit(tree);
 
-        visitor.setTokenStream(tokens);
-        visitor.setLibraryInfo(preprocessor.getLibraryInfo());
-
+        // Phase 4: generate the ELM (the ELM is generated with full type information that can be used
+        // for validation, optimization, rewriting, debugging, etc.)
+        ElmGenerator visitor = new ElmGenerator(builder, tokens, preprocessor.getLibraryInfo());
         visitResult = visitor.visit(tree);
         library = builder.getLibrary();
+
+        // Phase 5: ELM optimization/reduction (this is where result types, annotations, etc. are removed
+        // and there will probably be a lot of other optimizations that happen here in the future)
+        var edits = coalesceAll(
+                nullIfFalse(options.contains(EnableAnnotations), ElmEdit.REMOVE_ANNOTATION),
+                nullIfFalse(options.contains(EnableResultTypes), ElmEdit.REMOVE_RESULT_TYPE),
+                nullIfFalse(options.contains(EnableLocators), ElmEdit.REMOVE_LOCATOR));
+
+        new ElmEditor(edits).edit(library);
+
         compiledLibrary = builder.getCompiledLibrary();
         retrieves = visitor.getRetrieves();
         exceptions.addAll(builder.getExceptions());
@@ -227,4 +247,12 @@ public Library run(CharStream is) {
 
         return library;
     }
+
+    private static <T> T nullIfFalse(boolean b, T t) {
+        return !b ? t : null;
+    }
+
+    private static List<ElmEdit> coalesceAll(ElmEdit... ts) {
+        return Arrays.stream(ts).filter(t -> t != null).collect(Collectors.toList());
+    }
 }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/Cql2ElmVisitor.java → Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/ElmGenerator.java

@@ -6,6 +6,7 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import org.antlr.v4.runtime.ParserRuleContext;
+import org.antlr.v4.runtime.TokenStream;
 import org.antlr.v4.runtime.tree.ParseTree;
 import org.antlr.v4.runtime.tree.TerminalNode;
 import org.cqframework.cql.cql2elm.model.*;
@@ -17,23 +18,14 @@
 import org.cqframework.cql.gen.cqlParser;
 import org.hl7.cql.model.*;
 import org.hl7.elm.r1.*;
-import org.hl7.elm.r1.Element;
-import org.hl7.elm.r1.Interval;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class Cql2ElmVisitor extends CqlPreprocessorElmCommonVisitor {
-    private static final Logger logger = LoggerFactory.getLogger(Cql2ElmVisitor.class);
+public class ElmGenerator extends CqlPreprocessorElmCommonVisitor {
+    private static final Logger logger = LoggerFactory.getLogger(ElmGenerator.class);
     private final SystemMethodResolver systemMethodResolver;
 
-    public void setLibraryInfo(LibraryInfo libraryInfo) {
-        if (libraryInfo == null) {
-            throw new IllegalArgumentException("libraryInfo is null");
-        }
-        this.libraryInfo = libraryInfo;
-    }
-
     private final Set<String> definedExpressionDefinitions = new HashSet<>();
     private final Stack<ExpressionDefinitionInfo> forwards = new Stack<>();
     private final Map<cqlParser.FunctionDefinitionContext, FunctionHeader> functionHeaders = new HashMap<>();
@@ -45,13 +37,9 @@ public void setLibraryInfo(LibraryInfo libraryInfo) {
     private final List<Expression> expressions = new ArrayList<>();
     private final Map<String, Element> contextDefinitions = new HashMap<>();
 
-    public Cql2ElmVisitor(LibraryBuilder libraryBuilder) {
-        super(libraryBuilder);
-
-        if (libraryBuilder == null) {
-            throw new IllegalArgumentException("libraryBuilder is null");
-        }
-
+    public ElmGenerator(LibraryBuilder libraryBuilder, TokenStream tokenStream, LibraryInfo libraryInfo) {
+        super(libraryBuilder, tokenStream);
+        this.libraryInfo = Objects.requireNonNull(libraryInfo, "libraryInfo required");
         this.systemMethodResolver = new SystemMethodResolver(this, libraryBuilder);
     }
 
@@ -1624,10 +1612,6 @@ public Expression visitEqualityExpression(cqlParser.EqualityExpressionContext ct
 
             libraryBuilder.resolveBinaryCall("System", "Equivalent", equivalent);
 
-            if (isAnnotationEnabled()) {
-                equivalent.setLocalId(Integer.toString(getNextLocalId()));
-            }
-
             if (!"~".equals(parseString(ctx.getChild(1)))) {
                 track(equivalent, ctx);
                 Not not = of.createNot().withOperand(equivalent);

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/LibraryBuilder.java

@@ -19,7 +19,7 @@
 /**
  * Created by Bryn on 12/29/2016.
  */
-public class LibraryBuilder implements ModelResolver {
+public class LibraryBuilder {
     public static enum SignatureLevel {
         /*
         Indicates signatures will never be included in operator invocations
@@ -42,19 +42,17 @@ public static enum SignatureLevel {
         All
     }
 
-    public LibraryBuilder(LibraryManager libraryManager) {
-        this(null, libraryManager);
+    public LibraryBuilder(LibraryManager libraryManager, ObjectFactory objectFactory) {
+        this(null, libraryManager, objectFactory);
     }
 
-    public LibraryBuilder(NamespaceInfo namespaceInfo, LibraryManager libraryManager) {
-        if (libraryManager == null) {
-            throw new IllegalArgumentException("libraryManager is null");
-        }
+    public LibraryBuilder(NamespaceInfo namespaceInfo, LibraryManager libraryManager, ObjectFactory objectFactory) {
+        this.libraryManager = Objects.requireNonNull(libraryManager);
+        this.of = Objects.requireNonNull(objectFactory);
 
         this.namespaceInfo = namespaceInfo; // Note: allowed to be null, implies global namespace
         this.modelManager = libraryManager.getModelManager();
-        this.libraryManager = libraryManager;
-        this.typeBuilder = new TypeBuilder(of, this);
+        this.typeBuilder = new TypeBuilder(of, this.modelManager);
 
         this.library = of.createLibrary()
                 .withSchemaIdentifier(of.createVersionedIdentifier()
@@ -63,8 +61,13 @@ public LibraryBuilder(NamespaceInfo namespaceInfo, LibraryManager libraryManager
 
         this.cqlToElmInfo = af.createCqlToElmInfo();
         this.cqlToElmInfo.setTranslatorVersion(LibraryBuilder.class.getPackage().getImplementationVersion());
+
         this.library.getAnnotation().add(this.cqlToElmInfo);
 
+        this.options = Objects.requireNonNull(
+                libraryManager.getCqlCompilerOptions(), "libraryManager compilerOptions can not be null.");
+
+        this.setCompilerOptions(this.options);
         compiledLibrary = new CompiledLibrary();
         compiledLibrary.setLibrary(library);
     }
@@ -97,6 +100,14 @@ public List<CqlCompilerException> getExceptions() {
         return exceptions;
     }
 
+    public ObjectFactory getObjectFactory() {
+        return of;
+    }
+
+    public LibraryManager getLibraryManager() {
+        return libraryManager;
+    }
+
     private final Map<String, Model> models = new LinkedHashMap<>();
 
     private final Map<String, ResultWithPossibleError<NamedTypeSpecifier>> nameTypeSpecifiers = new HashMap<>();
@@ -108,10 +119,10 @@ public List<CqlCompilerException> getExceptions() {
     private final Deque<HidingIdentifierContext> hidingIdentifiersContexts = new ArrayDeque<>();
     private int literalContext = 0;
     private int typeSpecifierContext = 0;
-    private NamespaceInfo namespaceInfo = null;
-    private ModelManager modelManager = null;
+    private final NamespaceInfo namespaceInfo;
+    private final ModelManager modelManager;
     private Model defaultModel = null;
-    private LibraryManager libraryManager = null;
+    private final LibraryManager libraryManager;
     private Library library = null;
 
     public Library getLibrary() {
@@ -130,24 +141,18 @@ public ConversionMap getConversionMap() {
         return conversionMap;
     }
 
-    private final ObjectFactory of = new ObjectFactory();
+    private final ObjectFactory of;
     private final org.hl7.cql_annotations.r1.ObjectFactory af = new org.hl7.cql_annotations.r1.ObjectFactory();
     private boolean listTraversal = true;
-    private CqlCompilerOptions options;
-    private CqlToElmInfo cqlToElmInfo = null;
-    private TypeBuilder typeBuilder = null;
-    private Cql2ElmVisitor visitor = null;
+    private final CqlCompilerOptions options;
+    private final CqlToElmInfo cqlToElmInfo;
+    private final TypeBuilder typeBuilder;
 
     public void enableListTraversal() {
         listTraversal = true;
     }
 
-    public void setCompilerOptions(CqlCompilerOptions options) {
-        if (options == null) {
-            throw new IllegalArgumentException("Options cannot be null");
-        }
-
-        this.options = options;
+    private void setCompilerOptions(CqlCompilerOptions options) {
         if (options.getOptions().contains(CqlCompilerOptions.Options.DisableListTraversal)) {
             this.listTraversal = false;
         }
@@ -168,10 +173,6 @@ public void setCompilerOptions(CqlCompilerOptions options) {
         this.cqlToElmInfo.setSignatureLevel(options.getSignatureLevel().name());
     }
 
-    public void setVisitor(Cql2ElmVisitor visitor) {
-        this.visitor = visitor;
-    }
-
     private String compatibilityLevel = null;
 
     public boolean isCompatibilityLevel3() {
@@ -964,11 +965,6 @@ public Expression resolveUnion(Expression left, Expression right) {
         // TODO: Take advantage of nary unions
         BinaryWrapper wrapper = normalizeListTypes(left, right);
         Union union = of.createUnion().withOperand(wrapper.left, wrapper.right);
-
-        if (visitor != null && visitor.isAnnotationEnabled()) {
-            union.setLocalId(Integer.toString(visitor.getNextLocalId()));
-        }
-
         resolveNaryCall("System", "Union", union);
         return union;
     }

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/SystemMethodResolver.java

@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
+import java.util.Objects;
 import java.util.Set;
 import org.cqframework.cql.cql2elm.model.QueryContext;
 import org.cqframework.cql.gen.cqlParser;
@@ -13,21 +14,14 @@
  * Created by Bryn on 12/27/2016.
  */
 public class SystemMethodResolver {
-    private final ObjectFactory of = new ObjectFactory();
-    private final Cql2ElmVisitor visitor;
+    private final ObjectFactory of;
+    private final ElmGenerator visitor;
     private final LibraryBuilder builder;
 
-    public SystemMethodResolver(Cql2ElmVisitor visitor, LibraryBuilder builder) {
-        if (visitor == null) {
-            throw new IllegalArgumentException("visitor is null");
-        }
-
-        if (builder == null) {
-            throw new IllegalArgumentException("builder is null");
-        }
-
-        this.visitor = visitor;
-        this.builder = builder;
+    public SystemMethodResolver(ElmGenerator visitor, LibraryBuilder builder) {
+        this.visitor = Objects.requireNonNull(visitor, "visitor required");
+        this.builder = Objects.requireNonNull(builder, "builder required");
+        this.of = Objects.requireNonNull(builder.getObjectFactory(), "builder must have an object factory");
     }
 
     private List<Expression> getParams(Expression target, cqlParser.ParamListContext ctx) {

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/TypeBuilder.java

@@ -16,7 +16,7 @@ public class TypeBuilder {
     private ObjectFactory of;
     private ModelResolver mr;
 
-    public class InternalModelResolver implements ModelResolver {
+    public static class InternalModelResolver implements ModelResolver {
         private ModelManager modelManager;
 
         public InternalModelResolver(ModelManager modelManager) {
@@ -33,9 +33,8 @@ public TypeBuilder(ObjectFactory of, ModelResolver mr) {
         this.mr = mr;
     }
 
-    public TypeBuilder(ModelManager modelManager) {
-        this.of = new ObjectFactory();
-        this.mr = new InternalModelResolver(modelManager);
+    public TypeBuilder(ObjectFactory of, ModelManager modelManager) {
+        this(of, new InternalModelResolver(modelManager));
     }
 
     public QName dataTypeToQName(DataType type) {