Rev to 3.0.0, Javax -> Jakarta (#504)

* Rev to 3.0.0, Javax -> Jakarta * Update to CQL 3.5.1
cqframework · Dec 8, 2023 · 99641bf · 99641bf
1 parent a324934
commit 99641bf
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Showing 17 changed files with 134 additions and 98 deletions.
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -9,9 +9,5 @@
         "pagecontent",
         "plandefinition",
         "testng"
-    ],
-    "editor.codeActionsOnSave": {
-		"source.organizeImports": true,
-		"editor.formatOnSave": true
-	},
+    ]
 }
diff --git a/pom.xml b/pom.xml
@@ -5,16 +5,16 @@
 
     <groupId>org.opencds.cqf</groupId>
     <artifactId>tooling-parent</artifactId>
-    <version>3.0.0-SNAPSHOT</version>
+    <version>3.0.0</version>
 
     <packaging>pom</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <cql.version>3.3.2</cql.version>
-        <hapi.version>6.8.5</hapi.version>
-        <core.version>6.0.22.2</core.version>
+        <cql.version>3.5.1</cql.version>
+        <hapi.version>6.10.0</hapi.version>
+        <core.version>6.1.2.2</core.version>
         <spring-boot.version>2.1.5.RELEASE</spring-boot.version>
         <slf4j.version>2.0.5</slf4j.version>
     </properties>
@@ -106,6 +106,13 @@
 
     <dependencyManagement>
         <dependencies>
+            <dependency>
+                <groupId>jakarta.platform</groupId>
+                <artifactId>jakarta.jakartaee-bom</artifactId>
+                <version>10.0.0</version>
+                <type>pom</type>
+                <scope>import</scope>
+            </dependency>
             <dependency>
                 <groupId>info.cqframework</groupId>
                 <artifactId>engine</artifactId>
@@ -188,6 +195,30 @@
                 <version>${cql.version}</version>
             </dependency>
 
+            <dependency>
+                <groupId>jakarta.xml.bind</groupId>
+                <artifactId>jakarta.xml.bind-api</artifactId>
+                <version>4.0.1</version>
+            </dependency>
+
+            <dependency>
+                <groupId>jakarta.activation</groupId>
+                <artifactId>jakarta.activation-api</artifactId>
+                <version>2.1.2</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.glassfish.jaxb</groupId>
+                <artifactId>jaxb-runtime</artifactId>
+                <version>4.0.4</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.eclipse.persistence</groupId>
+                <artifactId>org.eclipse.persistence.moxy</artifactId>
+                <version>4.0.2</version>
+            </dependency>
+
             <dependency>
                 <groupId>com.sun.istack</groupId>
                 <artifactId>istack-commons-runtime</artifactId>
@@ -230,7 +261,6 @@
                 <artifactId>jul-to-slf4j</artifactId>
                 <version>${slf4j.version}</version>
             </dependency>
-
         </dependencies>
     </dependencyManagement>
 

diff --git a/tooling-cli/pom.xml b/tooling-cli/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.0.0-SNAPSHOT</version>
+        <version>3.0.0</version>
     </parent>
 
     <artifactId>tooling-cli</artifactId>
-    <version>3.0.0-SNAPSHOT</version>
+    <version>3.0.0</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling CLI</description>
@@ -19,7 +19,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>3.0.0-SNAPSHOT</version>
+            <version>3.0.0</version>
         </dependency>
 
         <dependency>

diff --git a/tooling-ui/pom.xml b/tooling-ui/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.0.0-SNAPSHOT</version>
+        <version>3.0.0</version>
     </parent>
 
     <artifactId>tooling-ui</artifactId>
-    <version>3.0.0-SNAPSHOT</version>
+    <version>3.0.0</version>
     <packaging>jar</packaging>
 
     <description>CQF Tooling UI</description>
@@ -19,7 +19,7 @@
         <dependency>
             <groupId>org.opencds.cqf</groupId>
             <artifactId>tooling</artifactId>
-            <version>3.0.0-SNAPSHOT</version>
+            <version>3.0.0</version>
         </dependency>
         <dependency>
             <groupId>org.openjfx</groupId>

diff --git a/tooling/pom.xml b/tooling/pom.xml
@@ -6,11 +6,11 @@
     <parent>
         <groupId>org.opencds.cqf</groupId>
         <artifactId>tooling-parent</artifactId>
-        <version>3.0.0-SNAPSHOT</version>
+        <version>3.0.0</version>
     </parent>
 
     <artifactId>tooling</artifactId>
-    <version>3.0.0-SNAPSHOT</version>
+    <version>3.0.0</version>
     <packaging>jar</packaging>
 
     <dependencies>
@@ -19,18 +19,12 @@
             <artifactId>jaxb2-basics</artifactId>
             <version>0.13.1</version>
         </dependency>
-        <dependency>
-            <groupId>javax.xml.stream</groupId>
-            <artifactId>stax-api</artifactId>
-            <version>1.0-2</version>
-        </dependency>
 
         <!-- RCKMS Data Objects -->
         <dependency>
             <groupId>org.cdsframework.rckms</groupId>
             <artifactId>mts-support-rckms</artifactId>
             <version>2.0.0</version>
-            <!-- excludes log4j dependencies -->
             <exclusions>
                 <exclusion>
                     <groupId>log4j</groupId>
@@ -42,6 +36,17 @@
                 </exclusion>
             </exclusions>
         </dependency>
+        <!-- Needed for RCKMS -->
+        <dependency>
+            <groupId>javax.xml.bind</groupId>
+            <artifactId>jaxb-api</artifactId>
+            <version>2.1</version>
+        </dependency>
+        <dependency>
+            <groupId>javax.validation</groupId>
+            <artifactId>validation-api</artifactId>
+            <version>2.0.1.Final</version>
+        </dependency>
 
         <!-- WikiMedia to HTML conversion library (-QdmToQiCore) -->
         <dependency>
@@ -220,22 +225,31 @@
             <version>2.14.2</version>
             <scope>compile</scope>
         </dependency>
+
+
         <dependency>
             <groupId>jakarta.xml.bind</groupId>
             <artifactId>jakarta.xml.bind-api</artifactId>
-            <version>2.3.3</version>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.servlet</groupId>
+            <artifactId>jakarta.servlet-api</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>jakarta.annotation</groupId>
+            <artifactId>jakarta.annotation-api</artifactId>
         </dependency>
 
         <dependency>
             <groupId>org.glassfish.jaxb</groupId>
             <artifactId>jaxb-runtime</artifactId>
-            <version>2.3.3</version>
         </dependency>
 
         <dependency>
             <groupId>org.eclipse.persistence</groupId>
             <artifactId>org.eclipse.persistence.moxy</artifactId>
-            <version>2.5.0</version>
         </dependency>
 
         <dependency>

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java b/tooling/src/main/java/org/opencds/cqf/tooling/acceleratorkit/Processor.java
@@ -13,7 +13,7 @@
 import java.util.Map;
 import java.util.NoSuchElementException;
 
-import javax.annotation.Nonnull;
+import jakarta.annotation.Nonnull;
 
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/DroolCqlGenerator.java b/tooling/src/main/java/org/opencds/cqf/tooling/cql_generation/drool/DroolCqlGenerator.java
@@ -6,8 +6,6 @@
 import java.util.List;
 import java.util.Map;
 
-import javax.xml.bind.JAXBException;
-
 import org.cdsframework.dto.ConditionDTO;
 import org.hl7.elm.r1.Library;
 import org.hl7.elm.r1.VersionedIdentifier;
@@ -28,13 +26,15 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import jakarta.xml.bind.JAXBException;
+
 /**
  * Implements the {@link CqlGenerator CqlGenerator} Interface, {@link Deserializer Deserializes} the {@link ConditionDTO ConditionDTO}
  * objects and Traverses the object graph by setting up the {@link VmrToModelElmBuilder ModelElmBuilder},
  * {@link Visitor Visitor}, and {@link DroolTraverser DroolTraverser}
  * May toggle Elm Library granularity with {@link CQLTYPES CQLTYPES}
  * @author  Joshua Reynolds
- * @since   2021-02-24 
+ * @since   2021-02-24
  */
 public class DroolCqlGenerator implements CqlGenerator {
     private static final Logger logger = LoggerFactory.getLogger(DroolCqlGenerator.class);
@@ -75,7 +75,7 @@ public void generateAndWriteToFile(URI inputURI, URI outputURI, String fhirVersi
         cqlOutput.mkdirs();
         VmrToModelElmBuilder modelBuilder = resolveModel(fhirVersion);
         ElmContext context = readAndGenerateCQL(file, modelBuilder);
-        writeElm(context, modelBuilder, output);  
+        writeElm(context, modelBuilder, output);
     }
 
     @Override

diff --git a/.../src/main/java/org/opencds/cqf/tooling/cql_generation/drool/serialization/Serializer.java b/.../src/main/java/org/opencds/cqf/tooling/cql_generation/drool/serialization/Serializer.java
@@ -2,12 +2,12 @@
 
 import java.io.StringWriter;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-
 import org.hl7.cql_annotations.r1.Annotation;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 /**
  * Serializes Objects to xml
  * @author Joshua Reynolds
@@ -28,7 +28,7 @@ public String convertToXml(Object object, JAXBContext context) throws JAXBExcept
         marshaller.marshal(object, writer);
         return writer.getBuffer().toString().replace("<xml version=\"1.0\"", "<xml version=\"1.1\"").replace("\f", "&#xc;");
     }
-    
+
     public JAXBContext getJaxbContext() {
         JAXBContext jaxbContext;
         try {

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/modelinfo/StructureDefinitionToModelInfo.java b/tooling/src/main/java/org/opencds/cqf/tooling/modelinfo/StructureDefinitionToModelInfo.java
@@ -7,11 +7,13 @@
 import java.nio.file.Paths;
 import java.util.Map;
 
-// import javax.xml.bind.JAXBContext;
-// import javax.xml.bind.JAXBElement;
-// import javax.xml.bind.Marshaller;
 import javax.xml.namespace.QName;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBElement;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+
 import org.hl7.elm_modelinfo.r1.ClassInfo;
 import org.hl7.elm_modelinfo.r1.ConversionInfo;
 import org.hl7.elm_modelinfo.r1.ModelInfo;
@@ -29,10 +31,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.Marshaller;
-
 public class StructureDefinitionToModelInfo extends Operation {
 
     private static final Logger logger = LoggerFactory.getLogger(StructureDefinitionToModelInfo.class);
@@ -248,7 +246,7 @@ private void writeOutput(String fileName, String content) throws IOException {
             writer.flush();
         }
     }
-    
+
     public static void main(String[] args) {
         Operation op = new StructureDefinitionToModelInfo();
         op.execute(args);

diff --git a/tooling/src/main/java/org/opencds/cqf/tooling/npm/NpmModelInfoProvider.java b/tooling/src/main/java/org/opencds/cqf/tooling/npm/NpmModelInfoProvider.java
@@ -5,8 +5,6 @@
 import java.io.InputStream;
 import java.util.List;
 
-import javax.xml.bind.JAXB;
-
 import org.hl7.cql.model.ModelIdentifier;
 import org.hl7.cql.model.ModelInfoProvider;
 import org.hl7.elm.r1.VersionedIdentifier;
@@ -15,6 +13,8 @@
 import org.hl7.fhir.r5.model.Library;
 import org.hl7.fhir.utilities.npm.NpmPackage;
 
+import jakarta.xml.bind.JAXB;
+
 /**
  * Provides a model info provider that can resolve CQL model info from an Npm package
  */

diff --git a/...rc/main/java/org/opencds/cqf/tooling/operations/acceleratorkit/ProcessAcceleratorKit.java b/...rc/main/java/org/opencds/cqf/tooling/operations/acceleratorkit/ProcessAcceleratorKit.java
@@ -1,6 +1,19 @@
 package org.opencds.cqf.tooling.operations.acceleratorkit;
 
-import ca.uhn.fhir.context.FhirContext;
+import static org.opencds.cqf.tooling.utilities.IOUtils.ensurePath;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.NoSuchElementException;
+
 import org.apache.poi.ss.usermodel.Cell;
 import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.ss.usermodel.Sheet;
@@ -39,20 +52,8 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.annotation.Nonnull;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.time.Instant;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.NoSuchElementException;
-
-import static org.opencds.cqf.tooling.utilities.IOUtils.ensurePath;
+import ca.uhn.fhir.context.FhirContext;
+import jakarta.annotation.Nonnull;
 
 @Operation(name = "ProcessAcceleratorKit")
 public class ProcessAcceleratorKit implements ExecutableOperation {