Merge branch 'master' into 863-date-time-interval-inclusion

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

@@ -10,6 +10,7 @@ ext {
 dependencies {
     api platform("ca.uhn.hapi.fhir:hapi-fhir-bom:${hapiVersion}") {
         exclude group: 'org.eclipse.jetty'
+        exclude group: 'xpp3'
     }
 
     implementation "ca.uhn.hapi.fhir:org.hl7.fhir.r5:${coreVersion}"
@@ -23,4 +24,12 @@ dependencies {
     implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-dstu3"
     implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r4"
     implementation "ca.uhn.hapi.fhir:hapi-fhir-structures-r5"
+
+    // This is to align with the FHIR core dependencies
+    // Note that this dependency hasn't been updated since 2013
+    // we probably need to standardize on a fork up the dependency chain
+    implementation ('org.ogce:xpp3:1.1.6') {
+        exclude group: 'junit'
+        exclude group: 'org.hamcrest'
+    }
 }

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

@@ -33,8 +33,8 @@ dependencies {
 
     // These are JAXB dependencies excluded because the libraries need to work
     // on Android. But for test purposes we use them pretty much everywhere.
-    testRuntimeOnly 'org.eclipse.persistence:org.eclipse.persistence.moxy:2.7.7'
-    testRuntimeOnly 'xpp3:xpp3:1.1.4c'
+    testRuntimeOnly 'org.eclipse.persistence:org.eclipse.persistence.moxy:4.0.2'
+    testRuntimeOnly 'org.eclipse.parsson:parsson:1.1.5'
 }
 
 jar {

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

@@ -7,19 +7,19 @@ configurations {
 }
 
 dependencies {
-    xjc 'org.jvnet.jaxb2_commons:jaxb2-basics-ant:0.13.1'
-    xjc 'org.jvnet.jaxb2_commons:jaxb2-basics:0.13.1'
-    xjc 'org.jvnet.jaxb2_commons:jaxb2-fluent-api:3.0'
+    xjc 'codes.rafael.jaxb2_commons:jaxb2-basics-ant:3.0.0'
+    xjc 'codes.rafael.jaxb2_commons:jaxb2-basics:3.0.0'
+    xjc 'codes.rafael.jaxb2_commons:jaxb2-fluent-api:3.0.0'
     // Eclipse has taken over all Java EE reference components
     // https://www.infoworld.com/article/3310042/eclipse-takes-over-all-java-ee-reference-components.html
     // https://wiki.eclipse.org/Jakarta_EE_Maven_Coordinates
-    xjc 'jakarta.xml.bind:jakarta.xml.bind-api:2.3.3'
-    xjc 'org.glassfish.jaxb:jaxb-xjc:2.4.0-b180830.0438'
-    xjc 'org.eclipse.persistence:org.eclipse.persistence.moxy:2.7.7'
+    xjc 'jakarta.xml.bind:jakarta.xml.bind-api:4.0.1'
+    xjc 'org.glassfish.jaxb:jaxb-xjc:3.0.2'
+    xjc 'org.glassfish.jaxb:jaxb-runtime:4.0.3'
+    xjc 'org.eclipse.persistence:org.eclipse.persistence.moxy:4.0.2'
     xjc 'org.slf4j:slf4j-simple:1.7.36'
-
-    api 'org.jvnet.jaxb2_commons:jaxb2-basics-runtime:0.13.1'
-    api 'jakarta.xml.bind:jakarta.xml.bind-api:2.3.3'
+    api 'jakarta.xml.bind:jakarta.xml.bind-api:4.0.1'
+    api 'codes.rafael.jaxb2_commons:jaxb2-basics-runtime:3.0.0'
 }
 
 ext.xjc = [
@@ -66,4 +66,4 @@ sourceSets {
 
 clean {
     delete xjc.destDir
-}
+}

Src/java/cqf-fhir-npm/src/main/java/org/cqframework/fhir/npm/NpmModelInfoProvider.java

@@ -1,18 +1,17 @@
 package org.cqframework.fhir.npm;
 
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
-
+import jakarta.xml.bind.JAXB;
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
 import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.model.Library;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
-import javax.xml.bind.JAXB;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
 
 /**
  * Provides a model info provider that can resolve CQL model info from an Npm package

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

@@ -14,10 +14,6 @@ dependencies {
     implementation project(':model-jaxb')
     implementation project(':elm-jaxb')
     implementation 'net.sf.jopt-simple:jopt-simple:4.7'
-    runtimeOnly 'org.eclipse.persistence:org.eclipse.persistence.moxy:2.7.7'
-    runtimeOnly 'xpp3:xpp3_min:1.1.4c'
-    runtimeOnly 'xmlpull:xmlpull:1.1.3.1'
-
     testImplementation project(':model-jaxb')
     testImplementation project(':model-jackson')
     testImplementation project(':elm-jaxb')

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

@@ -1,27 +1,20 @@
 plugins {
     id 'cql.library-conventions'
+    id 'cql.xjc-conventions'
 }
 
 dependencies {
     api project(':cql')
     api project(':model')
     api project(':elm')
+    api 'org.fhir:ucum:1.0.8'
+    api 'org.apache.commons:commons-text:1.10.0'
 
-    // The FHIR ucum service depends on an
-    // XML pull-parser being present on the classpath, and have a compile-time reference to xpp3.
-    // However, some platfoms such as Android provide their own pull-parser implementations.
-    // Additionally, The xpp3.xpp3 dependency includes the javax.xml packagename, which is invalid in
-    // Java 9+ because split packages (i.e. the same packagename being available in multipe jar) are
-    // disallowed. For those reasons xpp3 is excluded here, and included as a runtime dependency for
-    // tests. Users of the CQL translator will need to supply their own implementation or add xpp3
-    // at runtime.
-    api ('org.fhir:ucum:1.0.3') {
-        exclude group: 'xpp3'
-    }
-
-    implementation 'org.apache.commons:commons-text:1.10.0'
-    implementation 'com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.15.2'
-
+    // TODO: This dependencies are required due the the fact that the CqlTranslatorOptionsMapper lives
+    // in the cql-to-elm project. Ideally, we'd factor out all serialization depedencies into common
+    // libraries such that we could swap out jackson for something else. In the meantime, these are
+    // "implementation" dependencies so that they are not exported downstream.
+    implementation 'com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations:2.15.2'
     testImplementation project(':elm-jackson')
     testImplementation project(':model-jackson')
     testImplementation project(':quick')

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

@@ -19,14 +19,13 @@
 import org.hl7.cql_annotations.r1.Tag;
 import org.hl7.elm.r1.*;
 
-import javax.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBElement;
 import javax.xml.namespace.QName;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Stack;
-import java.util.stream.Collectors;
 
 /**
  * Common functionality used by {@link CqlPreprocessorVisitor} and {@link Cql2ElmVisitor}

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/CommentTests.java

@@ -10,7 +10,7 @@
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import javax.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBElement;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;

Src/java/cql-to-elm/src/test/java/org/cqframework/cql/cql2elm/TranslationTests.java

@@ -7,7 +7,7 @@
 import org.testng.annotations.Ignore;
 import org.testng.annotations.Test;
 
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;

Src/java/elm-fhir/build.gradle

@@ -8,10 +8,9 @@ ext {
 }
 
 dependencies {
-    implementation project(':cql-to-elm')
-    implementation project(':engine')
-    implementation project(":engine-fhir")
-    implementation "org.mapstruct:mapstruct:${mapstructVersion}"
+    api project(':cql-to-elm')
+    api project(':engine')
+    api project(":engine-fhir")
 
     testImplementation project(':quick')
     testImplementation "org.reflections:reflections:0.10.2"

Src/java/elm-fhir/src/main/java/org/cqframework/cql/elm/requirements/fhir/DataRequirementsProcessor.java

@@ -30,8 +30,7 @@
 import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverter;
 import org.opencds.cqf.cql.engine.fhir.converter.FhirTypeConverterFactory;
 
-import javax.xml.bind.JAXBElement;
-import javax.xml.namespace.QName;
+import jakarta.xml.bind.JAXBElement;
 import java.io.Serializable;
 import java.math.BigDecimal;
 import java.time.ZonedDateTime;

Src/java/elm-jackson/build.gradle

@@ -7,7 +7,5 @@ dependencies {
     api project(':elm')
     implementation 'org.apache.commons:commons-text:1.10.0'
     implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.15.2'
-    implementation 'com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.15.2'
-    // needs javax.json.JsonException when using SAXUnmarshaller.getNewXMLReader
-    implementation 'org.glassfish:javax.json:1.0.4'
+    implementation 'com.fasterxml.jackson.module:jackson-module-jakarta-xmlbind-annotations:2.15.2'
 }

Src/java/elm-jackson/src/main/java/org/cqframework/cql/elm/serializing/jackson/ElmJsonLibraryReader.java

@@ -1,17 +1,8 @@
 package org.cqframework.cql.elm.serializing.jackson;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.MapperFeature;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.databind.json.JsonMapper;
-import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
 import org.cqframework.cql.elm.serializing.ElmLibraryReader;
 import org.cqframework.cql.elm.serializing.LibraryWrapper;
-import org.cqframework.cql.elm.serializing.jackson.mixins.CqlToElmBaseMixIn;
-import org.cqframework.cql.elm.serializing.jackson.mixins.TypeSpecifierMixIn;
-import org.hl7.cql_annotations.r1.CqlToElmBase;
 import org.hl7.elm.r1.Library;
-import org.hl7.elm.r1.TypeSpecifier;
 
 import java.io.File;
 import java.io.IOException;

Src/java/elm-jackson/src/main/java/org/cqframework/cql/elm/serializing/jackson/ElmJsonMapper.java

@@ -5,7 +5,7 @@
 import com.fasterxml.jackson.databind.MapperFeature;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.databind.json.JsonMapper;
-import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
+import com.fasterxml.jackson.module.jakarta.xmlbind.JakartaXmlBindAnnotationModule;
 import org.cqframework.cql.elm.serializing.jackson.mixins.CqlToElmBaseMixIn;
 import org.cqframework.cql.elm.serializing.jackson.mixins.TrackableMixIn;
 import org.cqframework.cql.elm.serializing.jackson.mixins.TypeSpecifierMixIn;
@@ -20,7 +20,7 @@ public class ElmJsonMapper {
             .enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
             .enable(MapperFeature.USE_BASE_TYPE_AS_DEFAULT_IMPL)
             .defaultPropertyInclusion(JsonInclude.Value.construct(JsonInclude.Include.NON_NULL, JsonInclude.Include.NON_NULL))
-            .addModule(new JaxbAnnotationModule())
+            .addModule(new JakartaXmlBindAnnotationModule())
             .addMixIn(Trackable.class, TrackableMixIn.class)
             .addMixIn(TypeSpecifier.class, TypeSpecifierMixIn.class)
             .addMixIn(CqlToElmBase.class, CqlToElmBaseMixIn.class)

Src/java/elm-jackson/src/main/java/org/cqframework/cql/elm/serializing/jackson/ElmXmlLibraryReader.java

@@ -1,17 +1,7 @@
 package org.cqframework.cql.elm.serializing.jackson;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.MapperFeature;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.dataformat.xml.XmlMapper;
-import com.fasterxml.jackson.dataformat.xml.ser.ToXmlGenerator;
-import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
 import org.cqframework.cql.elm.serializing.ElmLibraryReader;
-import org.cqframework.cql.elm.serializing.jackson.mixins.CqlToElmBaseMixIn;
-import org.cqframework.cql.elm.serializing.jackson.mixins.TypeSpecifierMixIn;
-import org.hl7.cql_annotations.r1.CqlToElmBase;
 import org.hl7.elm.r1.Library;
-import org.hl7.elm.r1.TypeSpecifier;
 
 import java.io.File;
 import java.io.IOException;

Src/java/elm-jackson/src/main/java/org/cqframework/cql/elm/serializing/jackson/ElmXmlMapper.java

@@ -9,7 +9,7 @@
 import com.fasterxml.jackson.dataformat.xml.XmlFactory;
 import com.fasterxml.jackson.dataformat.xml.XmlMapper;
 import com.fasterxml.jackson.dataformat.xml.ser.ToXmlGenerator;
-import com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule;
+import com.fasterxml.jackson.module.jakarta.xmlbind.JakartaXmlBindAnnotationModule;
 import org.cqframework.cql.elm.serializing.jackson.mixins.CqlToElmBaseMixIn;
 import org.cqframework.cql.elm.serializing.jackson.mixins.TrackableMixIn;
 import org.cqframework.cql.elm.serializing.jackson.mixins.TypeSpecifierMixIn;
@@ -31,7 +31,7 @@ public class ElmXmlMapper {
             .enable(DeserializationFeature.ACCEPT_SINGLE_VALUE_AS_ARRAY)
             .enable(MapperFeature.USE_BASE_TYPE_AS_DEFAULT_IMPL)
             .defaultPropertyInclusion(JsonInclude.Value.construct(JsonInclude.Include.NON_NULL, JsonInclude.Include.NON_NULL))
-            .addModule(new JaxbAnnotationModule())
+            .addModule(new JakartaXmlBindAnnotationModule())
             .addMixIn(Trackable.class, TrackableMixIn.class)
             .addMixIn(TypeSpecifier.class, TypeSpecifierMixIn.class)
             .addMixIn(CqlToElmBase.class, CqlToElmBaseMixIn.class)

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmJsonLibraryReader.java

@@ -1,18 +1,18 @@
 package org.cqframework.cql.elm.serializing.jaxb;
 
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.PropertyException;
+import jakarta.xml.bind.Unmarshaller;
+import jakarta.xml.bind.ValidationEvent;
+import jakarta.xml.bind.ValidationEventHandler;
 import org.cqframework.cql.elm.serializing.ElmLibraryReader;
 import org.hl7.elm.r1.Library;
 
-import javax.xml.bind.*;
-import javax.xml.transform.Source;
-import javax.xml.transform.stream.StreamSource;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.Reader;
-import java.net.MalformedURLException;
 import java.net.URI;
-import java.net.URISyntaxException;
 import java.net.URL;
 
 public class ElmJsonLibraryReader implements ElmLibraryReader {

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmJsonLibraryWriter.java

@@ -4,9 +4,9 @@
 import org.hl7.elm.r1.Library;
 import org.hl7.elm.r1.ObjectFactory;
 
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.PropertyException;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+import jakarta.xml.bind.PropertyException;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.io.Writer;

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmJsonMapper.java

@@ -3,8 +3,8 @@
 import org.hl7.cql_annotations.r1.CqlToElmBase;
 import org.hl7.elm.r1.Library;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
 
 public class ElmJsonMapper {
 

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmXmlLibraryReader.java

@@ -3,9 +3,9 @@
 import org.cqframework.cql.elm.serializing.ElmLibraryReader;
 import org.hl7.elm.r1.Library;
 
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
 import javax.xml.transform.Source;
 import java.io.File;
 import java.io.IOException;

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmXmlLibraryWriter.java

@@ -4,9 +4,9 @@
 import org.hl7.elm.r1.Library;
 import org.hl7.elm.r1.ObjectFactory;
 
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.PropertyException;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+import jakarta.xml.bind.PropertyException;
 import java.io.*;
 
 public class ElmXmlLibraryWriter implements ElmLibraryWriter {

Src/java/elm-jaxb/src/main/java/org/cqframework/cql/elm/serializing/jaxb/ElmXmlMapper.java

@@ -3,8 +3,8 @@
 import org.hl7.cql_annotations.r1.CqlToElmBase;
 import org.hl7.elm.r1.Library;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
 
 public class ElmXmlMapper {
 

Src/java/elm-jaxb/src/main/resources/org/cqframework/cql/elm/serializing/jaxb/jaxb.properties

@@ -1 +1 @@
-javax.xml.bind.context.factory=org.eclipse.persistence.jaxb.JAXBContextFactory
+jakarta.xml.bind.context.factory=org.eclipse.persistence.jaxb.JAXBContextFactory

Src/java/elm-test/build.gradle

@@ -4,7 +4,8 @@ plugins {
 
 dependencies {
     implementation project(':cql-to-elm')
-    implementation project(':model-jaxb')
-    implementation project(':elm-jackson')
+    // implementation project(':model-jaxb')
     implementation project(':elm-jaxb')
+    implementation project(':model-jackson')
+    implementation project(':elm-jackson')
 }

Src/java/elm-test/src/test/java/org/cqframework/cql/elm/ElmDeserializeTests.java

@@ -7,7 +7,7 @@
 import java.util.List;
 import java.util.stream.Collectors;
 
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
 
 import org.cqframework.cql.cql2elm.CqlTranslator;
 import org.cqframework.cql.cql2elm.CqlCompilerOptions;

Src/java/elm/build.gradle

@@ -4,7 +4,7 @@ plugins {
 }
 
 dependencies {
-    implementation project(':model')
+    api project(':model')
 }
 
 generateSources {