Fixes Jackson's XML QName parser to the correct namespace (#605)

* Mapping QName to the correct namespace.

* Import cleanup

engine.jackson/src/main/java/org/opencds/cqf/cql/engine/serializing/jackson/XmlCqlMapper.java

@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.SerializationFeature;
+import com.fasterxml.jackson.databind.module.SimpleModule;
 import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import com.fasterxml.jackson.dataformat.xml.ser.ToXmlGenerator;
 import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
@@ -15,6 +16,7 @@
 import org.cqframework.cql.elm.execution.TypeSpecifier;
 import org.opencds.cqf.cql.engine.elm.execution.Executable;
 import org.opencds.cqf.cql.engine.serializing.jackson.mixins.*;
+import org.opencds.cqf.cql.engine.serializing.jackson.modules.QNameFixerXMLMapperModifier;
 
 public class XmlCqlMapper {
     private static final XmlMapper mapper = XmlMapper.builder()
@@ -27,6 +29,8 @@ public class XmlCqlMapper {
             .enable(MapperFeature.USE_BASE_TYPE_AS_DEFAULT_IMPL)
             .defaultPropertyInclusion(JsonInclude.Value.construct(JsonInclude.Include.NON_NULL, JsonInclude.Include.NON_NULL))
             .addModule(new JaxbAnnotationModule())
+            // Jackson's base QName deserializer does not unpack the namespace. This Modifier fixes it.
+            .addModule(new SimpleModule().setDeserializerModifier(new QNameFixerXMLMapperModifier()))
             //.addMixIn(Library.class, LibraryMixin.class) // Some case sensitivity issue in the name [L]ibrary
             // The ordering here of the mix ins for
             // ExpressionDef -> CodeSystemRef ->  Expression -> Element matters,

engine.jackson/src/main/java/org/opencds/cqf/cql/engine/serializing/jackson/modules/QNameFixerXMLMapperDeserializer.java

@@ -0,0 +1,33 @@
+package org.opencds.cqf.cql.engine.serializing.jackson.modules;
+
+import javax.xml.namespace.QName;
+
+import java.io.IOException;
+
+import com.fasterxml.jackson.core.JacksonException;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.databind.DeserializationContext;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.dataformat.xml.deser.FromXmlParser;
+
+public class QNameFixerXMLMapperDeserializer extends JsonDeserializer<QName> {
+    JsonDeserializer<?> originalDeserializer;
+    public QNameFixerXMLMapperDeserializer(JsonDeserializer<?> deserializer) {
+        originalDeserializer = deserializer;
+    }
+
+    @Override
+    public QName deserialize(JsonParser jsonParser, DeserializationContext deserializationContext) throws IOException, JacksonException {
+        var qName = (QName) originalDeserializer.deserialize(jsonParser, deserializationContext);
+
+        if (qName.getLocalPart().indexOf(":") > 0) {
+            var prefix = qName.getLocalPart().split(":")[0];
+            var localPart = qName.getLocalPart().split(":")[1];
+            var namespace = ((FromXmlParser)deserializationContext.getParser()).getStaxReader().getNamespaceContext().getNamespaceURI(prefix);
+
+            return new QName(namespace, localPart, prefix);
+        }
+
+        return qName;
+    }
+}

engine.jackson/src/main/java/org/opencds/cqf/cql/engine/serializing/jackson/modules/QNameFixerXMLMapperModifier.java

@@ -0,0 +1,17 @@
+package org.opencds.cqf.cql.engine.serializing.jackson.modules;
+
+import javax.xml.namespace.QName;
+
+import com.fasterxml.jackson.databind.BeanDescription;
+import com.fasterxml.jackson.databind.DeserializationConfig;
+import com.fasterxml.jackson.databind.JsonDeserializer;
+import com.fasterxml.jackson.databind.deser.BeanDeserializerModifier;
+
+public class QNameFixerXMLMapperModifier extends BeanDeserializerModifier {
+    public JsonDeserializer<?> modifyDeserializer(DeserializationConfig config, BeanDescription beanDesc, JsonDeserializer<?> deserializer) {
+        if (beanDesc.getBeanClass() == QName.class) {
+            return new QNameFixerXMLMapperDeserializer(deserializer);
+        }
+        return super.modifyDeserializer(config, beanDesc, deserializer);
+    }
+}

engine.jackson/src/test/java/org/opencds/cqf/cql/engine/serializing/QNameIssueJacksonTest.java

@@ -0,0 +1,26 @@
+package org.opencds.cqf.cql.engine.serializing;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.io.IOException;
+
+import org.cqframework.cql.cql2elm.LibraryContentType;
+import org.cqframework.cql.elm.execution.IntervalTypeSpecifier;
+import org.cqframework.cql.elm.execution.NamedTypeSpecifier;
+import org.testng.annotations.Test;
+
+public class QNameIssueJacksonTest {
+    @Test
+    void loaderIsAvailable() throws IOException {
+        var lib =
+            CqlLibraryReaderFactory.getReader(LibraryContentType.XML.mimeType())
+                .read(QNameIssueJacksonTest.class.getResourceAsStream("QNameIssue.xml"));
+
+        var actual = ((NamedTypeSpecifier)
+            ((IntervalTypeSpecifier) lib.getParameters().getDef().get(0).getParameterTypeSpecifier()).getPointType()
+        ).getName();
+
+        assertEquals("{urn:hl7-org:elm-types:r1}DateTime", actual.toString());
+    }
+
+}

engine.jackson/src/test/resources/org/opencds/cqf/cql/engine/serializing/QNameIssue.xml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<library
+    xmlns="urn:hl7-org:elm:r1"
+    xmlns:t="urn:hl7-org:elm-types:r1"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <parameters>
+        <def localId="25" locator="25:1-26:66" name="Measurement Period" accessLevel="Public">
+            <parameterTypeSpecifier localId="24" locator="25:32-25:49" xsi:type="IntervalTypeSpecifier">
+                <pointType localId="23" locator="25:41-25:48" name="t:DateTime" xsi:type="NamedTypeSpecifier"/>
+            </parameterTypeSpecifier>
+        </def>
+    </parameters>
+</library>

engine.jaxb/src/test/java/org/opencds/cqf/cql/engine/serializing/QNameIssueJaxbTest.java

@@ -0,0 +1,26 @@
+package org.opencds.cqf.cql.engine.serializing;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.io.IOException;
+
+import org.cqframework.cql.cql2elm.LibraryContentType;
+import org.cqframework.cql.elm.execution.IntervalTypeSpecifier;
+import org.cqframework.cql.elm.execution.NamedTypeSpecifier;
+import org.testng.annotations.Test;
+
+public class QNameIssueJaxbTest {
+    @Test
+    void loaderIsAvailable() throws IOException {
+        var lib =
+            CqlLibraryReaderFactory.getReader(LibraryContentType.XML.mimeType())
+                .read(QNameIssueJaxbTest.class.getResourceAsStream("QNameIssue.xml"));
+
+        var actual = ((NamedTypeSpecifier)
+            ((IntervalTypeSpecifier) lib.getParameters().getDef().get(0).getParameterTypeSpecifier()).getPointType()
+        ).getName();
+
+        assertEquals("{urn:hl7-org:elm-types:r1}DateTime", actual.toString());
+    }
+
+}

engine.jaxb/src/test/resources/org/opencds/cqf/cql/engine/serializing/QNameIssue.xml

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<library
+    xmlns="urn:hl7-org:elm:r1"
+    xmlns:t="urn:hl7-org:elm-types:r1"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+    <parameters>
+        <def localId="25" locator="25:1-26:66" name="Measurement Period" accessLevel="Public">
+            <parameterTypeSpecifier localId="24" locator="25:32-25:49" xsi:type="IntervalTypeSpecifier">
+                <pointType localId="23" locator="25:41-25:48" name="t:DateTime" xsi:type="NamedTypeSpecifier"/>
+            </parameterTypeSpecifier>
+        </def>
+    </parameters>
+</library>