Using Jackson's XML reader instead of JAXB.unmarshal for ModelInfo files

Src/java/build.gradle

@@ -127,7 +127,10 @@ configure(subprojects.findAll {it.name in ['model', 'elm', 'quick', 'qdm', 'cql-
         xjc group: 'org.slf4j', name: 'slf4j-simple', version: '1.7.30'
         compile group: 'org.jvnet.jaxb2_commons', name: 'jaxb2-basics', version: '0.12.0'
         compile group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.3'
+        compile group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.13.2'
+        compile group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-xml', version: '2.13.2'
         compile group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.13.2'
+        compile group: 'com.fasterxml.jackson.module', name: 'jackson-module-jaxb-annotations', version: '2.13.2'
         compile group: 'org.eclipse.persistence', name: 'org.eclipse.persistence.moxy', version: '2.7.7'
     }
 

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

@@ -25,6 +25,7 @@
 import org.hl7.elm.r1.Retrieve;
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
+import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 
 import javax.xml.bind.*;
 import java.io.*;
@@ -668,12 +669,17 @@ public static String convertToJxson(Library library) throws JsonProcessingExcept
         return getJxsonMapper().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());
-        final ModelInfoProvider modelProvider = (VersionedIdentifier modelIdentifier) -> modelInfo;
-        final ModelInfoLoader modelInfoLoader = new ModelInfoLoader();
-        modelInfoLoader.registerModelInfoProvider(modelProvider);
+    public static void loadModelInfo(File modelInfoXML)  {
+        try {
+            final ModelInfo modelInfo = JacksonXML.readValue(modelInfoXML, ModelInfo.class);
+            final VersionedIdentifier modelId = new VersionedIdentifier().withId(modelInfo.getName()).withVersion(modelInfo.getVersion());
+            final ModelInfoProvider modelProvider = (VersionedIdentifier modelIdentifier) -> modelInfo;
+            final ModelInfoLoader modelInfoLoader = new ModelInfoLoader();
+            modelInfoLoader.registerModelInfoProvider(modelProvider);
+        } catch (IOException e) {
+            e.printStackTrace();
+            return;
+        }
     }
 
     private static void outputExceptions(Iterable<CqlTranslatorException> exceptions) {

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

@@ -4,7 +4,6 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 
-import javax.xml.bind.JAXB;
 import java.io.*;
 import java.nio.file.Path;
 
@@ -81,11 +80,13 @@ public boolean accept(File path, String name) {
         try {
             if (modelFile != null) {
                 InputStream is = new FileInputStream(modelFile);
-                return JAXB.unmarshal(is, ModelInfo.class);
+
+                return JacksonXML.readValue(is, ModelInfo.class);
             }
-        } catch (FileNotFoundException e) {
+        } catch (IOException e) {
+            e.printStackTrace();
             throw new IllegalArgumentException(String.format("Could not load definition for model info %s.", modelIdentifier.getId()), e);
-        }
+        } 
 
         return null;
     }

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

@@ -3,7 +3,7 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 
-import javax.xml.bind.JAXB;
+import java.io.IOException;
 
 /**
  * Created by Bryn on 4/15/2016.
@@ -27,47 +27,53 @@ private boolean isFHIRModelIdentifier(VersionedIdentifier modelIdentifier) {
     public ModelInfo load(VersionedIdentifier modelIdentifier) {
         if (isFHIRModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
-            switch (localVersion) {
-                case "1.0.2":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.0.2.xml"),
-                            ModelInfo.class);
-
-                case "1.4":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.4.xml"),
-                            ModelInfo.class);
-
-                case "1.6":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.6.xml"),
-                            ModelInfo.class);
-
-                case "1.8":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.8.xml"),
-                            ModelInfo.class);
-
-                case "3.0.0":
-                case "":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.0.0.xml"),
-                            ModelInfo.class);
-
-                case "3.0.1":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.0.1.xml"),
-                            ModelInfo.class);
-
-                case "3.2.0":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.2.0.xml"),
-                            ModelInfo.class);
-
-                case "4.0.0":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-4.0.0.xml"),
-                            ModelInfo.class);
-
-                case "4.0.1":
-                    return JAXB.unmarshal(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-4.0.1.xml"),
-                            ModelInfo.class);
-
-                // Do not throw, allow other providers to return the model if known
-                //default:
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the FHIR model.", localVersion));
+            try { 
+                switch (localVersion) {
+                    case "1.0.2":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.0.2.xml"),
+                                ModelInfo.class);
+
+                    case "1.4":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.4.xml"),
+                                ModelInfo.class);
+
+                    case "1.6":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.6.xml"),
+                                ModelInfo.class);
+
+                    case "1.8":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-1.8.xml"),
+                                ModelInfo.class);
+
+                    case "3.0.0":
+                    case "":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.0.0.xml"),
+                                ModelInfo.class);
+
+                    case "3.0.1":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.0.1.xml"),
+                                ModelInfo.class);
+
+                    case "3.2.0":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-3.2.0.xml"),
+                                ModelInfo.class);
+
+                    case "4.0.0":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-4.0.0.xml"),
+                                ModelInfo.class);
+
+                    case "4.0.1":
+                        return JacksonXML.readValue(FhirModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/fhir-modelinfo-4.0.1.xml"),
+                                ModelInfo.class);
+
+                    // Do not throw, allow other providers to return the model if known
+                    //default:
+                    //    throw new IllegalArgumentException(String.format("Unknown version %s of the FHIR model.", localVersion));
+                }
+            } catch (IOException e) {
+                e.printStackTrace();
+                // Do not throw, allow other providers to resolve
+                //    throw new IllegalArgumentException(String.format("Unknown version %s of the Fhir model.", localVersion));
             }
         }
 

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

@@ -0,0 +1,64 @@
+package org.cqframework.cql.cql2elm;
+
+import com.fasterxml.jackson.annotation.JsonSubTypes;
+import com.fasterxml.jackson.annotation.JsonTypeInfo;
+import com.fasterxml.jackson.dataformat.xml.XmlMapper;
+import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
+import org.hl7.elm_modelinfo.r1.*;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+
+@JsonTypeInfo(
+        use = JsonTypeInfo.Id.NAME,
+        include = JsonTypeInfo.As.PROPERTY,
+        property = "type")
+@JsonSubTypes({
+        @JsonSubTypes.Type(value = SimpleTypeInfo.class, name = "ns4:SimpleTypeInfo"),
+        @JsonSubTypes.Type(value = ClassInfo.class, name = "ns4:ClassInfo"),
+        @JsonSubTypes.Type(value = ChoiceTypeInfo.class, name = "ns4:ChoiceTypeInfo"),
+        @JsonSubTypes.Type(value = IntervalTypeInfo.class, name = "ns4:IntervalTypeInfo"),
+        @JsonSubTypes.Type(value = ListTypeInfo.class, name = "ns4:ListTypeInfo"),
+        @JsonSubTypes.Type(value = ProfileInfo.class, name = "ns4:ProfileInfo"),
+        @JsonSubTypes.Type(value = TupleTypeInfo.class, name = "ns4:TupleTypeInfo")
+})
+interface TypeInfoMixIn {}
+
+@JsonTypeInfo(
+        use = JsonTypeInfo.Id.NAME,
+        include = JsonTypeInfo.As.PROPERTY,
+        property = "type")
+@JsonSubTypes({
+        @JsonSubTypes.Type(value = NamedTypeSpecifier.class, name = "ns4:NamedTypeSpecifier"),
+        @JsonSubTypes.Type(value = ListTypeSpecifier.class, name = "ns4:ListTypeSpecifier"),
+        @JsonSubTypes.Type(value = IntervalTypeSpecifier.class, name = "ns4:IntervalTypeSpecifier"),
+        @JsonSubTypes.Type(value = ChoiceTypeSpecifier.class, name = "ns4:ChoiceTypeSpecifier"),
+        @JsonSubTypes.Type(value = ParameterTypeSpecifier.class, name = "ns4:ParameterTypeSpecifier"),
+        @JsonSubTypes.Type(value = BoundParameterTypeSpecifier.class, name = "ns4:BoundParameterTypeSpecifier"),
+        @JsonSubTypes.Type(value = TupleTypeSpecifier.class, name = "ns4:TupleTypeSpecifier")
+})
+interface TypeSpecifierMixIn {}
+
+@JsonTypeInfo(
+        use = JsonTypeInfo.Id.NAME,
+        defaultImpl = NamedTypeSpecifier.class)
+interface NamedTypeSpecifierMixIn {}
+
+public class JacksonXML {
+    static XmlMapper mapper = new XmlMapper().builder()
+            .defaultUseWrapper(false)
+            .addMixIn(TypeInfo.class, TypeInfoMixIn.class)
+            .addMixIn(TypeSpecifier.class, TypeSpecifierMixIn.class)
+            .addMixIn(NamedTypeSpecifier.class, NamedTypeSpecifierMixIn.class)
+            .addModule(new JaxbAnnotationModule())
+            .build();
+
+    public static <T> T readValue(File src, Class<T> valueType) throws IOException {
+        return mapper.readValue(src, valueType);
+    }
+
+    public static <T> T readValue(InputStream src, Class<T> valueType) throws IOException {
+        return mapper.readValue(src, valueType);
+    }
+}

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

@@ -3,7 +3,7 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 
-import javax.xml.bind.JAXB;
+import java.io.IOException;
 
 public class QICoreModelInfoProvider implements ModelInfoProvider {
     private NamespaceManager namespaceManager;
@@ -24,17 +24,23 @@ private boolean isQICoreModelIdentifier(VersionedIdentifier modelIdentifier) {
     public ModelInfo load(VersionedIdentifier modelIdentifier) {
         if (isQICoreModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
-            switch (localVersion) {
-                case "4.0.0":
-                    return JAXB.unmarshal(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.0.0.xml"),
-                            ModelInfo.class);
-                case "4.1.0":
-                    return JAXB.unmarshal(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.1.0.xml"),
-                            ModelInfo.class);
-                case "4.1.1":
-                default:
-                    return JAXB.unmarshal(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.1.1.xml"),
-                            ModelInfo.class);
+            try {
+                switch (localVersion) {
+                    case "4.0.0":
+                        return JacksonXML.readValue(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.0.0.xml"),
+                                ModelInfo.class);
+                    case "4.1.0":
+                        return JacksonXML.readValue(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.1.0.xml"),
+                                ModelInfo.class);
+                    case "4.1.1":
+                    default:
+                        return JacksonXML.readValue(QICoreModelInfoProvider.class.getResourceAsStream("/org/hl7/fhir/qicore-modelinfo-4.1.1.xml"),
+                                ModelInfo.class);
+                }
+            } catch (IOException e) {
+                e.printStackTrace();
+                // Do not throw, allow other providers to resolve
+                //    throw new IllegalArgumentException(String.format("Unknown version %s of the QI model.", localVersion));
             }
         }
 

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

@@ -3,7 +3,7 @@
 import org.hl7.elm.r1.VersionedIdentifier;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 
-import javax.xml.bind.JAXB;
+import java.io.IOException;
 
 /**
  * Created by Bryn on 2/3/2016.
@@ -27,42 +27,44 @@ private boolean isQDMModelIdentifier(VersionedIdentifier modelIdentifier) {
     public ModelInfo load(VersionedIdentifier modelIdentifier) {
         if (isQDMModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
-            switch (localVersion) {
-                case "4.1.2":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo.xml"),
-                            ModelInfo.class);
-                case "4.2":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-4.2.xml"),
-                            ModelInfo.class);
-                case "4.3":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-4.3.xml"),
-                            ModelInfo.class);
-                case "5.0":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.xml"),
-                            ModelInfo.class);
-                case "5.0.1":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.1.xml"),
-                            ModelInfo.class);
-                case "5.0.2":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.2.xml"),
-                            ModelInfo.class);
-                case "5.3":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.3.xml"),
-                            ModelInfo.class);
-                case "5.4":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.4.xml"),
-                            ModelInfo.class);
-                case "5.5":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.5.xml"),
-                            ModelInfo.class);
-                case "5.6":
-                case "":
-                    return JAXB.unmarshal(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.6.xml"),
-                            ModelInfo.class);
-
-                // Do not throw, allow other providers to resolve
-                //default:
-                //    throw new IllegalArgumentException(String.format("Unknown version %s of the QDM model.", localVersion));
+            try {
+                switch (localVersion) {
+                    case "4.1.2":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo.xml"),
+                                ModelInfo.class);
+                    case "4.2":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-4.2.xml"),
+                                ModelInfo.class);
+                    case "4.3":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-4.3.xml"),
+                                ModelInfo.class);
+                    case "5.0":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.xml"),
+                                ModelInfo.class);
+                    case "5.0.1":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.1.xml"),
+                                ModelInfo.class);
+                    case "5.0.2":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.0.2.xml"),
+                                ModelInfo.class);
+                    case "5.3":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.3.xml"),
+                                ModelInfo.class);
+                    case "5.4":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.4.xml"),
+                                ModelInfo.class);
+                    case "5.5":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.5.xml"),
+                                ModelInfo.class);
+                    case "5.6":
+                    case "":
+                        return JacksonXML.readValue(QdmModelInfoProvider.class.getResourceAsStream("/gov/healthit/qdm/qdm-modelinfo-5.6.xml"),
+                                ModelInfo.class);
+                }
+            } catch (IOException e) {
+                e.printStackTrace();
+            // Do not throw, allow other providers to resolve
+            //    throw new IllegalArgumentException(String.format("Unknown version %s of the QDM model.", localVersion));
             }
         }