revert jakarta migration due to AA failure

ebi-uniprot · Apr 24, 2024 · 789da77 · 789da77
1 parent a8324b8
commit 789da77
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Showing 8 changed files with 45 additions and 55 deletions.
diff --git a/xml-parser/pom.xml b/xml-parser/pom.xml
@@ -26,9 +26,6 @@
 		<uniparc-xsd-pojo-package>org.uniprot.core.xml.jaxb.uniparc</uniparc-xsd-pojo-package>
 		<unirule-xsd-pojo-package>org.uniprot.core.xml.jaxb.unirule</unirule-xsd-pojo-package>
 		<feature-xsd-pojo-package>org.uniprot.core.xml.jaxb.feature</feature-xsd-pojo-package>
-		<jakarta-xml-bind.version>4.0.0</jakarta-xml-bind.version>
-		<jvnet.hisrc.jaxb>2.1.1</jvnet.hisrc.jaxb>
-		<jakarta-activation.version>2.0.1</jakarta-activation.version>
 	</properties>
 
 	<dependencies>
@@ -43,21 +40,19 @@
 			<version>${project.parent.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>jakarta.xml.bind</groupId>
-			<artifactId>jakarta.xml.bind-api</artifactId>
-			<version>${jakarta-xml-bind.version}</version>
+			<groupId>org.jvnet.jaxb2_commons</groupId>
+			<artifactId>jaxb2-basics</artifactId>
+			<version>${jvnet.jaxb2.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>com.sun.xml.bind</groupId>
-			<artifactId>jaxb-impl</artifactId>
-			<version>${jakarta-xml-bind.version}</version>
-			<scope>runtime</scope>
+			<groupId>org.jvnet.jaxb2_commons</groupId>
+			<artifactId>jaxb2-basics-runtime</artifactId>
+			<version>${jvnet.jaxb2.version}</version>
 		</dependency>
-
 		<dependency>
-			<groupId>org.patrodyne.jvnet</groupId>
-			<artifactId>hisrc-basicjaxb-plugins</artifactId>
-			<version>${jvnet.hisrc.jaxb}</version>
+			<groupId>javax.xml.bind</groupId>
+			<artifactId>jaxb-api</artifactId>
+			<version>${jaxb.version}</version><!--$NO-MVN-MAN-VER$ -->
 		</dependency>
 
 		<dependency>
@@ -66,9 +61,9 @@
 			<version>${jaxb.version}</version>
 		</dependency>
 		<dependency>
-			<groupId>jakarta.activation</groupId>
-			<artifactId>jakarta.activation-api</artifactId>
-			<version>${jakarta-activation.version}</version>
+			<groupId>javax.activation</groupId>
+			<artifactId>javax.activation-api</artifactId>
+			<version>1.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>com.beust</groupId>
@@ -126,11 +121,10 @@
 			<plugin>
 				<groupId>org.apache.cxf</groupId>
 				<artifactId>cxf-xjc-plugin</artifactId>
-				<version>4.0.0</version>
+				<version>3.3.0</version>
 				<configuration>
 					<extensions>
-						<extension>org.apache.cxf.xjcplugins:cxf-xjc-dv:4.0.0</extension>
-						<extension>org.patrodyne.jvnet:hisrc-basicjaxb-plugins:2.1.1</extension>
+						<extension>org.apache.cxf.xjcplugins:cxf-xjc-dv:3.2.1</extension>
 					</extensions>
 				</configuration>
 				<executions>

diff --git a/xml-parser/src/main/java/org/uniprot/core/xml/XmlChainIterator.java b/xml-parser/src/main/java/org/uniprot/core/xml/XmlChainIterator.java
@@ -9,13 +9,12 @@
 import java.util.function.Function;
 import java.util.zip.GZIPInputStream;
 
+import javax.xml.bind.JAXBException;
+import javax.xml.stream.XMLStreamException;
 
-import jakarta.xml.bind.JAXBException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.stream.XMLStreamException;
-
 public class XmlChainIterator<T, R> implements Iterator<R> {
     private static final Logger logger = LoggerFactory.getLogger(XmlChainIterator.class);
     private final Iterator<InputStream> inputStreamIterator;

diff --git a/xml-parser/src/main/java/org/uniprot/core/xml/XmlIterator.java b/xml-parser/src/main/java/org/uniprot/core/xml/XmlIterator.java
@@ -5,15 +5,15 @@
 import java.util.NoSuchElementException;
 import java.util.function.Function;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBElement;
-import jakarta.xml.bind.Unmarshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamConstants;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 
-import jakarta.xml.bind.JAXBException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

diff --git a/xml-parser/src/main/java/org/uniprot/core/xml/uniprot/unload/UniProtFFToXmlBuilder.java b/xml-parser/src/main/java/org/uniprot/core/xml/uniprot/unload/UniProtFFToXmlBuilder.java
@@ -15,10 +15,9 @@
 import java.util.stream.Collectors;
 import java.util.stream.IntStream;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.Marshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
 
-import org.glassfish.jaxb.core.marshaller.DataWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.uniprot.core.flatfile.parser.impl.EntryBufferedReader2;
@@ -29,6 +28,7 @@
 import org.uniprot.core.xml.jaxb.uniprot.Entry;
 
 import com.codahale.metrics.Timer;
+import com.sun.xml.bind.marshaller.DataWriter;
 
 public class UniProtFFToXmlBuilder implements XmlBuilder {
     private static final Logger LOGGER = LoggerFactory.getLogger(UniProtFFToXmlBuilder.class);

diff --git a/xml-parser/src/main/java/org/uniprot/core/xml/writer/DefaultXmlWriter.java b/xml-parser/src/main/java/org/uniprot/core/xml/writer/DefaultXmlWriter.java
@@ -5,8 +5,8 @@
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Stream;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.Marshaller;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Marshaller;
 
 import org.uniprot.core.xml.XmlWriter;
 import org.uniprot.core.xml.XmlWriterException;

diff --git a/xml-parser/src/main/resources/xsd/uniprot.episode b/xml-parser/src/main/resources/xsd/uniprot.episode
@@ -1,11 +1,12 @@
 <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<bindings version="3.0" xmlns="https://jakarta.ee/xml/ns/jaxb">
+<bindings version="2.1" xmlns="http://java.sun.com/xml/ns/jaxb">
   <!--
 
-This file was generated by the Eclipse Implementation of JAXB, v4.0.3 
-See https://eclipse-ee4j.github.io/jaxb-ri 
+This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.3.2 
+See <a href="https://javaee.github.io/jaxb-v2/">https://javaee.github.io/jaxb-v2/</a> 
 Any modifications to this file will be lost upon recompilation of the source schema. 
-Generated on: 2024.02.06 at 01:05:02 PM GMT
+Generated on: 2020.04.04 at 07:45:45 PM BST 
+
   -->
   <bindings scd="x-schema::tns" xmlns:tns="http://uniprot.org/uniprot">
     <schemaBindings map="false">
@@ -107,12 +108,6 @@ Generated on: 2024.02.06 at 01:05:02 PM GMT
     <bindings scd="~tns:positionType">
       <class ref="org.uniprot.core.xml.jaxb.uniprot.PositionType"/>
     </bindings>
-    <bindings scd="~tns:ligandType">
-      <class ref="org.uniprot.core.xml.jaxb.uniprot.LigandType"/>
-    </bindings>
-    <bindings scd="~tns:ligandPartType">
-      <class ref="org.uniprot.core.xml.jaxb.uniprot.LigandPartType"/>
-    </bindings>
     <bindings scd="~tns:moleculeType">
       <class ref="org.uniprot.core.xml.jaxb.uniprot.MoleculeType"/>
     </bindings>
@@ -125,6 +120,11 @@ Generated on: 2024.02.06 at 01:05:02 PM GMT
     <bindings scd="~tns:evidencedStringType">
       <class ref="org.uniprot.core.xml.jaxb.uniprot.EvidencedStringType"/>
     </bindings>
+     <bindings scd="~tns:ligandType">
+      <class ref="org.uniprot.core.xml.jaxb.uniprot.LigandType"/>
+    </bindings>
+     <bindings scd="~tns:ligandPartType">
+      <class ref="org.uniprot.core.xml.jaxb.uniprot.LigandPartType"/>
+    </bindings>
   </bindings>
-</bindings>
-
+</bindings>
diff --git a/xml-parser/src/test/java/org/uniprot/core/xml/uniparc/UniParcXmlTestHelper.java b/xml-parser/src/test/java/org/uniprot/core/xml/uniparc/UniParcXmlTestHelper.java
@@ -1,12 +1,11 @@
 package org.uniprot.core.xml.uniparc;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBElement;
-import jakarta.xml.bind.Marshaller;
-
-import javax.xml.namespace.QName;
 import java.io.StringWriter;
 
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.namespace.QName;
 
 /**
  * @author jluo
@@ -16,8 +15,7 @@ class UniParcXmlTestHelper {
     private static final String TARGET_PACKAGE = "org.uniprot.core.xml.jaxb.uniparc";
 
     @SuppressWarnings("unchecked")
-    static <T> String
-    toXmlString(T obj, Class<T> clazz, String element) {
+    static <T> String toXmlString(T obj, Class<T> clazz, String element) {
         try {
             StringWriter stringWriter = new StringWriter();
             JAXBContext jc = JAXBContext.newInstance(TARGET_PACKAGE);

diff --git a/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtXmlTestHelper.java b/xml-parser/src/test/java/org/uniprot/core/xml/uniprot/UniProtXmlTestHelper.java
@@ -1,11 +1,10 @@
 package org.uniprot.core.xml.uniprot;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBElement;
-import jakarta.xml.bind.Marshaller;
-
 import java.io.StringWriter;
 
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
 import javax.xml.namespace.QName;
 
 public class UniProtXmlTestHelper {