#513: Added a JXSON format option to support using the Jackson serial…

…izer to produce JSON output.

Src/java/build.gradle

@@ -116,6 +116,10 @@ configure(subprojects.findAll {it.name in ['model', 'elm', 'quick', 'qdm']}) {
         runtime group: 'com.sun.xml.bind', name: 'jaxb-impl', version: '2.4.0-b180830.0438'
         runtime group: 'javax.xml.bind', name: 'jaxb-api', version: '2.3.1'
         runtime group: 'com.sun.activation', name: 'javax.activation', version: '1.2.0'
+        runtime group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.10.1'
+        runtime group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.10.1'
+        runtime group: 'com.fasterxml.jackson.core', name: 'jackson-core', version: '2.10.1'
+        runtime group: 'com.fasterxml.jackson.module', name: 'jackson-module-jaxb-annotations', version: '2.10.1'
     }
 
     ext.xjc = [

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

@@ -1,12 +1,18 @@
 package org.cqframework.cql.cql2elm;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
 import joptsimple.OptionParser;
 import joptsimple.OptionSet;
 import joptsimple.OptionSpec;
 import org.antlr.v4.runtime.*;
 import org.antlr.v4.runtime.misc.NotNull;
 import org.antlr.v4.runtime.tree.ParseTree;
 import org.cqframework.cql.cql2elm.model.TranslatedLibrary;
+import org.cqframework.cql.cql2elm.model.serialization.LibraryWrapper;
 import org.cqframework.cql.cql2elm.preprocessor.CqlPreprocessorVisitor;
 import org.cqframework.cql.elm.tracking.TrackBack;
 import org.cqframework.cql.gen.cqlLexer;
@@ -44,7 +50,7 @@ public static enum Options {
         DisableMethodInvocation,
         RequireFromKeyword
     }
-    public static enum Format { XML, JSON, COFFEE }
+    public static enum Format { XML, JSON, JXSON, COFFEE }
     private static JAXBContext jaxbContext;
 
     private Library library = null;
@@ -325,10 +331,23 @@ private String toJson(Library library) {
             return convertToJson(library);
         }
         catch (JAXBException e) {
-            throw new IllegalArgumentException("Could not convert library to JSON.", e);
+            throw new IllegalArgumentException("Could not convert library to JSON using JAXB serializer.", e);
         }
     }
 
+    private String toJxson(Library library) {
+        try {
+            return convertToJxson(library);
+        }
+        catch (JsonProcessingException e) {
+            throw new IllegalArgumentException("Could not convert library to JSON using Jackson serializer.", e);
+        }
+    }
+
+    public String toJxson() {
+        return toJxson(library);
+    }
+
     public String toJson() {
         return toJson(library);
     }
@@ -377,6 +396,14 @@ public Map<String, String> getLibrariesAsJSON() {
         return result;
     }
 
+    public Map<String, String> getLibrariesAsJXSON() {
+        Map<String, String> result = new HashMap();
+        for (Map.Entry<String, TranslatedLibrary> entry : libraryManager.getTranslatedLibraries().entrySet()) {
+            result.put(entry.getKey(), toJxson(entry.getValue().getLibrary()));
+        }
+        return result;
+    }
+
     public List<CqlTranslatorException> getExceptions() { return exceptions; }
 
     public List<CqlTranslatorException> getErrors() { return errors; }
@@ -410,7 +437,6 @@ public CqlErrorListener(LibraryBuilder builder, boolean detailedErrors) {
         @Override
         public void syntaxError(@NotNull Recognizer<?, ?> recognizer, Object offendingSymbol, int line, int charPositionInLine, @NotNull String msg, RecognitionException e) {
             TrackBack trackback = new TrackBack(new VersionedIdentifier().withId("unknown"), line, charPositionInLine, line, charPositionInLine);
-//            CqlTranslator.this.errors.add(new CqlTranslatorException(msg, trackback, e));
 
             if (detailedErrors) {
                 builder.recordParsingException(new CqlSyntaxException(msg, trackback, e));
@@ -519,6 +545,17 @@ public String convertToJson(Library library) throws JAXBException {
         return writer.getBuffer().toString();
     }
 
+    public String convertToJxson(Library library) throws JsonProcessingException {
+        ObjectMapper mapper = new ObjectMapper();
+        mapper.setDefaultPropertyInclusion(JsonInclude.Include.NON_DEFAULT);
+        mapper.configure(SerializationFeature.INDENT_OUTPUT, true);
+        JaxbAnnotationModule annotationModule = new JaxbAnnotationModule();
+        mapper.registerModule(annotationModule);
+        LibraryWrapper wrapper = new LibraryWrapper();
+        wrapper.setLibrary(library);
+        return mapper.writeValueAsString(wrapper);
+    }
+
     public static void loadModelInfo(File modelInfoXML) {
         final ModelInfo modelInfo = JAXB.unmarshal(modelInfoXML, ModelInfo.class);
         final VersionedIdentifier modelId = new VersionedIdentifier().withId(modelInfo.getName()).withVersion(modelInfo.getVersion());
@@ -616,6 +653,9 @@ private static void writeELM(Path inPath, Path outPath, CqlTranslator.Format for
                         pw.print("module.exports = ");
                         pw.println(translator.toJson());
                         break;
+                    case JXSON:
+                        pw.println(translator.toJxson());
+                        break;
                     case JSON:
                         pw.println(translator.toJson());
                         break;
@@ -700,6 +740,7 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
                 }
                 switch (outputFormat) {
                     case JSON:
+                    case JXSON:
                         name += ".json";
                         break;
                     case COFFEE:

Src/java/cql-to-elm/src/main/java/org/cqframework/cql/cql2elm/model/serialization/LibraryWrapper.java

@@ -0,0 +1,14 @@
+package org.cqframework.cql.cql2elm.model.serialization;
+
+import org.hl7.elm.r1.Library;
+
+public class LibraryWrapper {
+    private Library library;
+    public Library getLibrary() {
+        return this.library;
+    }
+
+    public void setLibrary(Library library) {
+        this.library = library;
+    }
+}

Src/java/elm/src/main/java/org/cqframework/cql/elm/tracking/Trackable.java

@@ -1,12 +1,16 @@
 package org.cqframework.cql.elm.tracking;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
 import org.hl7.cql.model.DataType;
 
 import javax.xml.bind.annotation.XmlTransient;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
+@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
 public class Trackable {
     private final UUID trackerId;
     private final List<TrackBack> trackbacks;
@@ -18,15 +22,20 @@ public Trackable() {
         this.trackbacks = new ArrayList<>();
     }
 
+    @XmlTransient
+    @JsonIgnore
     public UUID getTrackerId() {
         return trackerId;
     }
 
+    @XmlTransient
+    @JsonIgnore
     public List<TrackBack> getTrackbacks() {
         return trackbacks;
     }
 
     @XmlTransient
+    @JsonIgnore
     public DataType getResultType() {
         return resultType;
     }