ELM JSON reader and writer (Kotlin feature branch) (#1489)

* JSON serializers for QName and BigDecimal. Initial cleanup. * Fix Sonar warnings --------- Co-authored-by: Jonathan Percival <[email protected]>
cqframework · Jan 16, 2025 · 4479b47 · 4479b47
1 parent b5a62e8
commit 4479b47
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Showing 20 changed files with 141 additions and 98 deletions.
diff --git a/Src/java/elm-test/src/test/java/org/cqframework/cql/elm/ElmDeserializeTests.java b/Src/java/elm-test/src/test/java/org/cqframework/cql/elm/ElmDeserializeTests.java
@@ -30,7 +30,7 @@ void elmTests() {
     }
 
     @Test
-    @Disabled("TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented")
+    @Disabled("TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented for annotations")
     void jsonANCFHIRDummyLibraryLoad() {
         try {
             final Library library = deserializeJsonLibrary("ElmDeserialize/ANCFHIRDummy.json");
@@ -65,7 +65,6 @@ void jsonANCFHIRDummyLibraryLoad() {
     }
 
     @Test
-    @Disabled("TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented")
     void jsonAdultOutpatientEncountersFHIR4LibraryLoad() {
         try {
             final Library library =
@@ -145,7 +144,7 @@ void xmlLibraryLoad() {
     }
 
     @Test
-    @Disabled("TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented")
+    @Disabled("TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented for annotations")
     void jsonTerminologyLibraryLoad() {
         try {
             final Library library = deserializeJsonLibrary("ElmDeserialize/ANCFHIRTerminologyDummy.json");
@@ -328,12 +327,10 @@ void emptyStringsTest() throws IOException {
                 new org.cqframework.cql.elm.serializing.xmlutil.ElmXmlLibraryReader().read(new StringReader(xml));
         validateEmptyStringsTest(xmlLibrary);
 
-        // TODO: Re-enable once XmlUtil-based ELM JSON deserialization is implemented
-        //        String json = toJson(translator.toELM());
-        //        Library jsonLibrary =
-        //                new org.cqframework.cql.elm.serializing.xmlutil.ElmJsonLibraryReader().read(new
-        // StringReader(json));
-        //        validateEmptyStringsTest(jsonLibrary);
+        String json = toJson(translator.toELM());
+        Library jsonLibrary =
+                new org.cqframework.cql.elm.serializing.xmlutil.ElmJsonLibraryReader().read(new StringReader(json));
+        validateEmptyStringsTest(jsonLibrary);
     }
 
     private static Library deserializeJsonLibrary(String filePath) throws IOException {

diff --git a/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryCommon.kt b/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryCommon.kt
@@ -0,0 +1,15 @@
+package org.cqframework.cql.elm.serializing.xmlutil
+
+import kotlinx.serialization.json.Json
+import kotlinx.serialization.modules.plus
+import kotlinx.serialization.modules.serializersModuleOf
+import org.hl7.elm_modelinfo.r1.serializing.BigDecimalJsonSerializer
+
+val json = Json {
+    serializersModule =
+        serializersModuleOf(BigDecimalJsonSerializer) +
+            org.hl7.elm.r1.serializersModule +
+            org.hl7.cql_annotations.r1.serializersModule
+    explicitNulls = false
+    ignoreUnknownKeys = true
+}
diff --git a/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryReader.kt b/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryReader.kt
@@ -8,22 +8,11 @@ import java.io.Reader
 import java.net.URI
 import java.net.URL
 import kotlinx.serialization.ExperimentalSerializationApi
-import kotlinx.serialization.json.Json
 import kotlinx.serialization.json.decodeFromStream
-import kotlinx.serialization.modules.plus
 import org.cqframework.cql.elm.serializing.ElmLibraryReader
 import org.hl7.elm.r1.Library
 
 class ElmJsonLibraryReader : ElmLibraryReader {
-    val module =
-        org.hl7.elm.r1.Serializer.createSerializer() +
-            org.hl7.cql_annotations.r1.Serializer.createSerializer()
-    val json = Json {
-        serializersModule = module
-        explicitNulls = false
-        ignoreUnknownKeys = true
-    }
-
     override fun read(file: File): Library {
         file.inputStream().use {
             return read(it)

diff --git a/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryWriter.kt b/...xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmJsonLibraryWriter.kt
@@ -1,8 +1,6 @@
 package org.cqframework.cql.elm.serializing.xmlutil
 
 import java.io.Writer
-import kotlinx.serialization.json.Json
-import kotlinx.serialization.modules.plus
 import org.cqframework.cql.elm.serializing.ElmLibraryWriter
 import org.hl7.elm.r1.Library
 
@@ -12,14 +10,6 @@ class ElmJsonLibraryWriter : ElmLibraryWriter {
     }
 
     override fun writeAsString(library: Library): String {
-        val module =
-            org.hl7.elm.r1.Serializer.createSerializer() +
-                org.hl7.cql_annotations.r1.Serializer.createSerializer()
-        val json = Json {
-            serializersModule = module
-            explicitNulls = false
-        }
-
         return json.encodeToString(LibraryWrapper.serializer(), LibraryWrapper(library))
     }
 }
diff --git a/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryCommon.kt b/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryCommon.kt
@@ -0,0 +1,20 @@
+package org.cqframework.cql.elm.serializing.xmlutil
+
+import kotlinx.serialization.modules.plus
+import kotlinx.serialization.modules.serializersModuleOf
+import nl.adaptivity.xmlutil.QName
+import nl.adaptivity.xmlutil.serialization.XML
+import org.hl7.elm_modelinfo.r1.serializing.BigDecimalXmlSerializer
+
+val xml =
+    XML(
+        serializersModuleOf(BigDecimalXmlSerializer) +
+            org.hl7.elm.r1.serializersModule +
+            org.hl7.cql_annotations.r1.serializersModule
+    ) {
+        xmlDeclMode = nl.adaptivity.xmlutil.XmlDeclMode.Charset
+        defaultPolicy {
+            typeDiscriminatorName =
+                QName("http://www.w3.org/2001/XMLSchema-instance", "type", "xsi")
+        }
+    }
diff --git a/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryReader.kt b/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryReader.kt
@@ -7,8 +7,6 @@ import java.io.InputStream
 import java.io.Reader
 import java.net.URI
 import java.net.URL
-import kotlinx.serialization.modules.plus
-import nl.adaptivity.xmlutil.serialization.XML
 import nl.adaptivity.xmlutil.xmlStreaming
 import org.cqframework.cql.elm.serializing.ElmLibraryReader
 import org.hl7.elm.r1.Library
@@ -45,11 +43,6 @@ class ElmXmlLibraryReader : ElmLibraryReader {
     }
 
     override fun read(reader: Reader): Library {
-        val serializersModule =
-            org.hl7.elm.r1.Serializer.createSerializer() +
-                org.hl7.cql_annotations.r1.Serializer.createSerializer()
-        val xml = XML(serializersModule)
-
         return xml.decodeFromReader(Library.serializer(), xmlStreaming.newReader(reader))
     }
 }
diff --git a/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryWriter.kt b/...-xmlutil/src/main/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlLibraryWriter.kt
@@ -1,9 +1,6 @@
 package org.cqframework.cql.elm.serializing.xmlutil
 
 import java.io.Writer
-import kotlinx.serialization.modules.plus
-import nl.adaptivity.xmlutil.QName
-import nl.adaptivity.xmlutil.serialization.XML
 import org.cqframework.cql.elm.serializing.ElmLibraryWriter
 import org.hl7.elm.r1.Library
 
@@ -13,18 +10,6 @@ class ElmXmlLibraryWriter : ElmLibraryWriter {
     }
 
     override fun writeAsString(library: Library): String {
-        val serializersModule =
-            org.hl7.elm.r1.Serializer.createSerializer() +
-                org.hl7.cql_annotations.r1.Serializer.createSerializer()
-
-        val xml =
-            XML(serializersModule) {
-                xmlDeclMode = nl.adaptivity.xmlutil.XmlDeclMode.Charset
-                defaultPolicy {
-                    typeDiscriminatorName =
-                        QName("http://www.w3.org/2001/XMLSchema-instance", "type", "xsi")
-                }
-            }
 
         return xml.encodeToString(Library.serializer(), library)
     }

diff --git a/...elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/CMS146JsonTest.java b/...elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/CMS146JsonTest.java
@@ -13,16 +13,10 @@
 import org.cqframework.cql.cql2elm.LibraryManager;
 import org.cqframework.cql.cql2elm.ModelManager;
 import org.json.JSONException;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
 import org.skyscreamer.jsonassert.JSONAssert;
 
-@Disabled(
-        """
-        Currently failing due to differences in QName serialization.
-        The default QName serializer expects a structured object, not a string
-        Possible fix: Custom serializer for QName.""")
 class CMS146JsonTest {
 
     private static Object[][] sigFileAndSigLevel() {
@@ -47,7 +41,17 @@ void cms146SignatureLevels(String fileName, SignatureLevel expectedSignatureLeve
                 new LibraryManager(
                         modelManager, new CqlCompilerOptions(ErrorSeverity.Warning, expectedSignatureLevel)));
         final String jsonWithVersion = translator.toJson();
-        final String actualJson = jsonWithVersion.replaceAll("\"translatorVersion\":\"[^\"]*\",", "");
+        final String actualJson = jsonWithVersion
+                .replaceAll("\"translatorVersion\":\"[^\"]*\",", "")
+                // The original JSON marshaller (JAXB + MOXy) does not output
+                // accessLevel if it is null. (It always emits it otherwise,
+                // even when it's set to the default value.) The new JSON
+                // serializer always emits accessLevel.
+                // We do not set accessLevel in the translator on the
+                // model/context def node, thus the difference in JSON output.
+                .replace(
+                        "\"name\":\"Patient\",\"context\":\"Patient\",\"accessLevel\":\"Public\"",
+                        "\"name\":\"Patient\",\"context\":\"Patient\"");
         JSONAssert.assertEquals(expectedJson, actualJson, true);
     }
 

diff --git a/.../elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/CMS146XmlTest.java b/.../elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/CMS146XmlTest.java
@@ -53,8 +53,13 @@ void cms146SignatureLevels(String fileName, SignatureLevel expectedSignatureLeve
                 // temporary fix for namespace prefix differences
                 //                .replaceAll("xmlns:n1=\"urn:hl7-org:elm:r1\"", "")
                 //                .replaceAll("n1:", "")
-                // Possible bug in original XML, no access modifier on when name and context are both Patient?
-                // Maybe it's not emitting default access modifiers?
+
+                // The original XML marshaller (JAXB) does not output
+                // accessLevel if it is null. (It always emits it otherwise,
+                // even when it's set to the default value.) The new XML
+                // serializer (XmlUtil) always emits accessLevel.
+                // We do not set accessLevel in the translator on the
+                // model/context def node, thus the difference in XML output.
                 .replace(
                         "name=\"Patient\" context=\"Patient\" accessLevel=\"Public\"",
                         "name=\"Patient\" context=\"Patient\"");

diff --git a/...elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlutilTest.java b/...elm-xmlutil/src/test/java/org/cqframework/cql/elm/serializing/xmlutil/ElmXmlutilTest.java
@@ -2,7 +2,6 @@
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
 
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 public class ElmXmlutilTest {
@@ -18,8 +17,6 @@ void deserializeReserializeElmJson() {
     }
 
     @Test
-    @Disabled(
-            "TODO: Polymorphic serializer for class org.hl7.elm.r1.ChoiceTypeSpecifier (Kotlin reflection is not available) has property 'type' that conflicts with JSON class discriminator. You can either change class discriminator in JsonConfiguration, rename property with @SerialName annotation or fall back to array polymorphism")
     void deserializeBigElmJson() {
         var lib = new ElmJsonLibraryReader()
                 .read(

diff --git a/...-xmlutil/src/main/java/org/hl7/elm_modelinfo/r1/serializing/xmlutil/XmlModelInfoReader.kt b/...-xmlutil/src/main/java/org/hl7/elm_modelinfo/r1/serializing/xmlutil/XmlModelInfoReader.kt
@@ -12,10 +12,10 @@ import org.hl7.elm_modelinfo.r1.*
 import org.hl7.elm_modelinfo.r1.ModelInfo
 import org.hl7.elm_modelinfo.r1.serializing.ModelInfoReader
 
+val xml = XML(org.hl7.elm_modelinfo.r1.serializersModule)
+
 class XmlModelInfoReader : ModelInfoReader {
     override fun read(source: Source): ModelInfo {
-        val serializersModule = Serializer.createSerializer()
-        val xml = XML(serializersModule)
         val modelInfo =
             xml.decodeFromReader(
                 ModelInfo.serializer(),

diff --git a/...ava/model/src/jvmMain/kotlin/org/hl7/elm_modelinfo/r1/serializing/BigDecimalSerializer.kt b/...ava/model/src/jvmMain/kotlin/org/hl7/elm_modelinfo/r1/serializing/BigDecimalSerializer.kt
@@ -5,15 +5,29 @@ import kotlinx.serialization.*
 import kotlinx.serialization.descriptors.*
 import kotlinx.serialization.encoding.*
 
-object BigDecimalSerializer : KSerializer<BigDecimal?> {
+object BigDecimalXmlSerializer : KSerializer<BigDecimal> {
     override val descriptor: SerialDescriptor =
         PrimitiveSerialDescriptor("BigDecimal", PrimitiveKind.STRING)
 
-    override fun serialize(encoder: Encoder, value: BigDecimal?) {
-        encoder.encodeString(value?.toPlainString() ?: "")
+    override fun serialize(encoder: Encoder, value: BigDecimal) {
+        encoder.encodeString(value.toPlainString())
     }
 
     override fun deserialize(decoder: Decoder): BigDecimal {
-        return BigDecimal(decoder.decodeString())
+        return decoder.decodeString().toBigDecimal()
     }
 }
+
+// We use JSON numbers, not strings to serialize BigDecimals in JSON.
+object BigDecimalJsonSerializer : KSerializer<BigDecimal> {
+    override val descriptor: SerialDescriptor =
+        PrimitiveSerialDescriptor("BigDecimal", PrimitiveKind.DOUBLE)
+
+    override fun serialize(encoder: Encoder, value: BigDecimal) {
+        encoder.encodeDouble(value.toDouble())
+    }
+
+    override fun deserialize(decoder: Decoder): BigDecimal {
+        return decoder.decodeDouble().toBigDecimal()
+    }
+}
diff --git a/...java/model/src/jvmMain/kotlin/org/hl7/elm_modelinfo/r1/serializing/QNameJsonSerializer.kt b/...java/model/src/jvmMain/kotlin/org/hl7/elm_modelinfo/r1/serializing/QNameJsonSerializer.kt
@@ -0,0 +1,27 @@
+package org.hl7.elm_modelinfo.r1.serializing
+
+import kotlinx.serialization.descriptors.*
+import kotlinx.serialization.encoding.*
+import nl.adaptivity.xmlutil.*
+
+
+@OptIn(ExperimentalXmlUtilApi::class)
+object QNameJsonSerializer : XmlSerializer<QName> by QNameSerializer {
+    @OptIn(XmlUtilInternal::class)
+    override val descriptor: SerialDescriptor =
+        PrimitiveSerialDescriptor("javax.xml.namespace.QName", PrimitiveKind.STRING).xml(
+            PrimitiveSerialDescriptor("javax.xml.namespace.QName", PrimitiveKind.STRING),
+            QName(XMLConstants.XSD_NS_URI, "QName", XMLConstants.XSD_PREFIX)
+        )
+
+    override fun serialize(encoder: Encoder, value: QName) {
+        encoder.encodeString(
+            value.toString()
+        )
+    }
+
+    override fun deserialize(decoder: Decoder): QName {
+        return QName.valueOf(decoder.decodeString())
+    }
+}
+
diff --git a/Src/java/qdm/src/main/java/org/cqframework/cql/cql2elm/qdm/QdmModelInfoProvider.java b/Src/java/qdm/src/main/java/org/cqframework/cql/cql2elm/qdm/QdmModelInfoProvider.java
@@ -35,7 +35,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isQDMModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getQdmResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;

diff --git a/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/FhirModelInfoProvider.java b/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/FhirModelInfoProvider.java
@@ -35,7 +35,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isFHIRModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;

diff --git a/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QICoreModelInfoProvider.java b/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QICoreModelInfoProvider.java
@@ -31,7 +31,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isQICoreModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;

diff --git a/...ava/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QuickFhirModelInfoProvider.java b/...ava/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QuickFhirModelInfoProvider.java
@@ -34,7 +34,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isQuickFhirModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;

diff --git a/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QuickModelInfoProvider.java b/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/QuickModelInfoProvider.java
@@ -31,7 +31,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isQuickModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;

diff --git a/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/UsCoreModelInfoProvider.java b/Src/java/quick/src/main/java/org/cqframework/cql/cql2elm/quick/UsCoreModelInfoProvider.java
@@ -31,7 +31,11 @@ public ModelInfo load(ModelIdentifier modelIdentifier) {
         if (isUSCoreModelIdentifier(modelIdentifier)) {
             String localVersion = modelIdentifier.getVersion() == null ? "" : modelIdentifier.getVersion();
             var stream = getResource(localVersion);
-            return ModelInfoReaderFactory.INSTANCE.getReader("application/xml").read(buffered(asSource(stream)));
+            if (stream != null) {
+                return ModelInfoReaderFactory.INSTANCE
+                        .getReader("application/xml")
+                        .read(buffered(asSource(stream)));
+            }
         }
 
         return null;