Merge pull request #1083 from hkir-dev/jre_11

Java 11 upgrade
protegeproject · Nov 28, 2022 · 3db25ed · 3db25ed
2 parents 6c6fe76 + 8a148f2
commit 3db25ed
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Showing 14 changed files with 154 additions and 54 deletions.
diff --git a/pom.xml b/pom.xml
@@ -138,13 +138,13 @@
 			<dependency>
 				<groupId>net.sourceforge.owlapi</groupId>
 				<artifactId>owlapi-osgidistribution</artifactId>
-				<version>4.5.19</version>
+				<version>4.5.22</version>
 			</dependency>
 
 			<dependency>
 				<groupId>org.apache.felix</groupId>
 				<artifactId>org.apache.felix.main</artifactId>
-				<version>5.4.0</version>
+				<version>7.0.5</version>
 			</dependency>
 
 			<dependency>
@@ -313,6 +313,37 @@
 				<version>1.6.3rc1</version>
 				<scope>provided</scope>
 			</dependency>
+
+			<dependency>	
+			  	<groupId>javax.xml.bind</groupId>	
+			  	<artifactId>jaxb-api</artifactId>	
+			  	<version>2.3.0</version>	
+			</dependency>	
+
+			<dependency>	
+			  	<groupId>com.sun.xml.bind</groupId>	
+			  	<artifactId>jaxb-core</artifactId>	
+			  	<version>2.3.0</version>	
+			</dependency>	
+
+			<dependency>	
+			  	<groupId>com.sun.xml.bind</groupId>	
+			  	<artifactId>jaxb-impl</artifactId>	
+			  	<version>2.3.0</version>	
+			</dependency>	
+
+			<dependency>	
+			    	<groupId>com.sun.activation</groupId>	
+			    	<artifactId>javax.activation</artifactId>	
+			    	<version>1.2.0</version>	
+			</dependency>
+
+			<!-- swrltab plugin requires -->
+			<dependency>
+			    <groupId>org.glassfish.corba</groupId>
+			    <artifactId>glassfish-corba-orb</artifactId>
+			    <version>4.2.4</version>
+			</dependency>
 
 		</dependencies>
 	</dependencyManagement>
@@ -325,8 +356,7 @@
 					<artifactId>maven-compiler-plugin</artifactId>
 					<version>3.8.0</version>
 					<configuration>
-						<source>1.8</source>
-						<target>1.8</target>
+						<release>11</release>
 					</configuration>
 				</plugin>
 
@@ -371,6 +401,11 @@
 						</instructions>
 					</configuration>
 				</plugin>
+
+				<plugin>	
+				   	 <artifactId>maven-surefire-plugin</artifactId>	
+				   	 <version>3.0.0-M3</version>	
+				</plugin>
 
 			</plugins>
 		</pluginManagement>

diff --git a/protege-desktop/pom.xml b/protege-desktop/pom.xml
@@ -68,21 +68,21 @@
 		<dependency>
 			<groupId>edu.stanford.protege</groupId>
 			<artifactId>jre.os-x</artifactId>
-			<version>1.8.0_121</version>
+			<version>11.0.17_8</version>
 			<scope>runtime</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>edu.stanford.protege</groupId>
 			<artifactId>jre.win</artifactId>
-			<version>1.8.0_121</version>
+			<version>11.0.17_8</version>
 			<scope>runtime</scope>
 		</dependency>
 
 		<dependency>
 			<groupId>edu.stanford.protege</groupId>
 			<artifactId>jre.linux</artifactId>
-			<version>1.8.0_121</version>
+			<version>11.0.17_8</version>
 			<scope>runtime</scope>
 		</dependency>
 
@@ -148,7 +148,7 @@
 					<plugin>
 						<groupId>com.akathist.maven.plugins.launch4j</groupId>
 						<artifactId>launch4j-maven-plugin</artifactId>
-						<version>1.7.10</version>
+						<version>2.1.3</version>
 						<executions>
 							<execution>
 								<configuration>
@@ -163,20 +163,22 @@
 									<classPath>
 										<mainClass>org.protege.osgi.framework.Launcher</mainClass>
 										<addDependencies>false</addDependencies>
-										<preCp>bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar</preCp>
+										<preCp>bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bundles/glassfish-corba-orb.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar</preCp>
 									</classPath>
 									<jre>
 										<path>jre</path>
-										<minVersion>1.8.0</minVersion>
+										<minVersion>11.0.1</minVersion>
 										<bundledJreAsFallback>false</bundledJreAsFallback>
 										<bundledJre64Bit>true</bundledJre64Bit>
-										<initialHeapSize>${conf.mem.xms}</initialHeapSize>
-										<maxHeapSize>${conf.mem.xmx}</maxHeapSize>
+<!-- 										<initialHeapSize>${conf.mem.xms}</initialHeapSize> -->
+<!-- 										<maxHeapSize>${conf.mem.xmx}</maxHeapSize> -->
 										<opts>
-											<opt>-Xss${conf.mem.xss}M</opt>
+<!-- 											<opt>-Xss${conf.mem.xss}M</opt> -->
+											<opt>${conf.extra.args}</opt>
 											<opt>-DentityExpansionLimit=100000000</opt>
 											<opt>-Dlogback.configurationFile=conf/logback-win.xml</opt>
 											<opt>-Dfile.encoding=utf-8</opt>
+											<opt>-Dorg.protege.plugin.dir=plugins</opt>
 										</opts>
 									</jre>
 									<versionInfo>

diff --git a/protege-desktop/src/main/assembly/dependency-sets.xml b/protege-desktop/src/main/assembly/dependency-sets.xml
@@ -34,6 +34,23 @@
                 <include>org.apache.servicemix.bundles:org.apache.servicemix.bundles.aopalliance:jar</include>
                 <include>org.eclipse.jgit:org.eclipse.jgit:jar</include>
                 <include>com.googlecode.javaewah:JavaEWAH:jar</include>
+                <include>javax.xml.bind:jaxb-api:jar</include>	
+                <include>com.sun.xml.bind:jaxb-core:jar</include>	
+                <include>com.sun.xml.bind:jaxb-impl:jar</include>	
+                <include>com.sun.activation:javax.activation</include>
+                <!-- CORBA dependencies -->
+                <include>org.glassfish.corba:glassfish-corba-orb:jar</include>
+                <include>org.glassfish.corba:glassfish-corba-internal-api:jar</include>
+                <include>org.glassfish.corba:glassfish-corba-omgapi:jar</include>
+                <include>org.glassfish.gmbal:gmbal:jar</include>
+                <include>org.glassfish.external:management-api:jar</include>
+                <include>org.glassfish.pfl:pfl-basic:jar</include>
+                <include>org.glassfish.pfl:pfl-tf:jar</include>
+                <include>org.glassfish.pfl:pfl-dynamic:jar</include>
+                <include>org.ow2.asm:asm:jar</include>
+                <include>org.ow2.asm:asm-util:jar</include>
+                <include>org.ow2.asm:asm-tree:jar</include>
+                <include>org.ow2.asm:asm-analysis:jar</include>
             </includes>
             <useStrictFiltering>true</useStrictFiltering>
             <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}</outputFileNameMapping>

diff --git a/protege-desktop/src/main/assembly/protege-os-x.xml b/protege-desktop/src/main/assembly/protege-os-x.xml
@@ -45,6 +45,23 @@
                 <include>org.apache.servicemix.bundles:org.apache.servicemix.bundles.aopalliance:jar</include>
                 <include>org.eclipse.jgit:org.eclipse.jgit:jar</include>
                 <include>com.googlecode.javaewah:JavaEWAH:jar</include>
+                <include>javax.xml.bind:jaxb-api:jar</include>
+                <include>com.sun.xml.bind:jaxb-core:jar</include>
+                <include>com.sun.xml.bind:jaxb-impl:jar</include>
+                <include>com.sun.activation:javax.activation</include>
+                <!-- CORBA dependencies -->
+                <include>org.glassfish.corba:glassfish-corba-orb:jar</include>
+                <include>org.glassfish.corba:glassfish-corba-internal-api:jar</include>
+                <include>org.glassfish.corba:glassfish-corba-omgapi:jar</include>
+                <include>org.glassfish.gmbal:gmbal:jar</include>
+                <include>org.glassfish.external:management-api:jar</include>
+                <include>org.glassfish.pfl:pfl-basic:jar</include>
+                <include>org.glassfish.pfl:pfl-tf:jar</include>
+                <include>org.glassfish.pfl:pfl-dynamic:jar</include>
+                <include>org.ow2.asm:asm:jar</include>
+                <include>org.ow2.asm:asm-util:jar</include>
+                <include>org.ow2.asm:asm-tree:jar</include>
+                <include>org.ow2.asm:asm-analysis:jar</include>
             </includes>
             <useStrictFiltering>true</useStrictFiltering>
             <outputFileNameMapping>${artifact.artifactId}.${artifact.extension}</outputFileNameMapping>

diff --git a/protege-desktop/src/main/env/linux/run.sh b/protege-desktop/src/main/env/linux/run.sh
@@ -13,7 +13,7 @@ jre/bin/java \
      -Dlogback.configurationFile=conf/logback.xml \
      -Dfile.encoding=UTF-8 \
      ${conf.extra.args} \
-     -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
+     -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bundles/glassfish-corba-orb.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
      $CMD_OPTIONS org.protege.osgi.framework.Launcher $1
 
 

diff --git a/protege-desktop/src/main/env/os-x/bundle-info/Info.plist b/protege-desktop/src/main/env/os-x/bundle-info/Info.plist
@@ -73,34 +73,7 @@
         <true/>
         <key>NSSupportsAutomaticGraphicsSwitching</key>
         <true/>
-        <key>JVMRuntime</key>
-        <string>JRE</string>
-        <key>JVMMainClassName</key>
-        <string>org.protege.osgi.framework.Launcher</string>
-        <key>JVMClassPaths</key>
-        <array>
-            <string>bundles/guava.jar</string>
-            <string>bundles/logback-classic.jar</string>
-            <string>bundles/logback-core.jar</string>
-            <string>bundles/slf4j-api.jar</string>
-            <string>bin/org.apache.felix.main.jar</string>
-            <string>bin/protege-launcher.jar</string>
-            <string>bin/maven-artifact.jar</string>
-        </array>
-        <key>JVMVersion</key>
-        <string>1.8+</string>
-        <key>JVMOptions</key>
-        <array>
-            <string>-Dapple.laf.useScreenMenuBar=true</string>
-            <string>-Xdock:name=Protégé</string>
-            <string>-DentityExpansionLimit=100000000</string>
-            <string>-Dlogback.configurationFile=conf/logback.xml</string>
-            <string>-Dfile.encoding=UTF-8</string>
-            <string>-XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot</string>
-        </array>
-        <key>JVMArguments</key>
-        <array/>
-        <key>LauncherWorkingDirectory</key>
-        <string>$APP_ROOT/Contents/Java</string>
+        <key>LSRequiresNativeExecution</key>
+        <true/>
     </dict>
 </plist>
diff --git a/protege-desktop/src/main/env/os-x/bundle-resources/MacOS/JavaAppLauncher b/protege-desktop/src/main/env/os-x/bundle-resources/MacOS/JavaAppLauncher
diff --git a/protege-desktop/src/main/env/os-x/bundle-resources/run.sh b/protege-desktop/src/main/env/os-x/bundle-resources/run.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+cd "$(dirname "$0")/Java"
+
+../Plugins/JRE/Contents/Home/jre/bin/java \
+     -Dlogback.configurationFile=conf/logback.xml \
+     -DentityExpansionLimit=100000000 \
+     -Dfile.encoding=UTF-8 \
+     -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot \
+     -Dapple.laf.useScreenMenuBar=true \
+     -Dcom.apple.mrj.application.apple.menu.about.name=Protege \
+     -Xdock:name=Protege \
+     -Xdock:icon=app/Protege.icns \
+     -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bundles/glassfish-corba-orb.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
+     org.protege.osgi.framework.Launcher $1
diff --git a/protege-desktop/src/main/env/platform-independent/run.bat b/protege-desktop/src/main/env/platform-independent/run.bat
@@ -1,3 +1,3 @@
 setlocal
 cd /d %~dp0
-java ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1
+java ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bundles/glassfish-corba-orb.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1
diff --git a/protege-desktop/src/main/env/platform-independent/run.sh b/protege-desktop/src/main/env/platform-independent/run.sh
@@ -12,7 +12,7 @@ java -Dlogback.configurationFile=conf/logback.xml \
      -DentityExpansionLimit=100000000 \
      -Dfile.encoding=UTF-8 \
      ${conf.extra.args} \
-     -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
+     -classpath bundles/guava.jar:bundles/logback-classic.jar:bundles/logback-core.jar:bundles/slf4j-api.jar:bundles/glassfish-corba-orb.jar:bin/org.apache.felix.main.jar:bin/maven-artifact.jar:bin/protege-launcher.jar \
      $CMD_OPTIONS org.protege.osgi.framework.Launcher $1
 
 

diff --git a/protege-desktop/src/main/env/win/run.bat b/protege-desktop/src/main/env/win/run.bat
@@ -1,3 +1,3 @@
 setlocal
 cd /d %~dp0
-jre\bin\java ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1
+jre\bin\java ${conf.extra.args} -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bundles/glassfish-corba-orb.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher %1
diff --git a/...or-core/src/main/java/org/protege/editor/core/platform/apple/ProtegeAppleApplication.java b/...or-core/src/main/java/org/protege/editor/core/platform/apple/ProtegeAppleApplication.java
@@ -8,9 +8,10 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.swing.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
+//import javax.swing.*;
+//import java.awt.event.ActionEvent;
+//import java.awt.event.ActionListener;
+import java.awt.*;
 import java.io.File;
 /*
 * Copyright (C) 2007, University of Manchester
@@ -26,7 +27,7 @@
  * Bio Health Informatics Group<br>
  * Date: Sep 19, 2008<br><br>
  */
-public class ProtegeAppleApplication extends AbstractAppleApplicationWrapper {
+public class ProtegeAppleApplication { //extends AbstractAppleApplicationWrapper {
 
     private static final Logger logger = LoggerFactory.getLogger(ProtegeAppleApplication.class);
 
@@ -43,16 +44,29 @@ public static ProtegeAppleApplication getInstance(){
     }
 
 
+//    private ProtegeAppleApplication() {
+//    }
     private ProtegeAppleApplication() {
+        Desktop application = Desktop.getDesktop();
+        application.setPreferencesHandler(event -> handlePreferencesRequest());
+        application.setAboutHandler(event -> handleAboutRequest());
+        application.setOpenFileHandler(event -> {
+            File file = event.getFiles().get(0);
+            try {
+                editFile(file.getAbsolutePath());
+            } catch (Exception e) {
+                logger.error("invalid file: {}", file);
+            }
+        });
+        application.setQuitHandler((event, response) -> handleQuitRequest());
     }
 
-
     public void setEditorKit(EditorKit eKit){
         this.eKit = eKit;
-        setEnabledPreferencesMenu(eKit != null);
+        //setEnabledPreferencesMenu(eKit != null);
     }
 
-    @Override
+    //@Override
     protected void editFile(String fileName) throws Exception {
         ProtegeManager.getInstance().getApplication().editURI(new File(fileName).toURI());
     }

diff --git a/protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewsPane.java b/protege-editor-core/src/main/java/org/protege/editor/core/ui/view/ViewsPane.java
@@ -9,6 +9,7 @@
 
 import javax.swing.*;
 import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.TransformerFactoryConfigurationError;
 import java.awt.*;
 import java.io.*;
 import java.util.Collections;
@@ -121,7 +122,7 @@ public void saveViews(Writer writer) {
             nodeSerialiser.serialise();
             writer.flush();
         }
-        catch (ParserConfigurationException | IOException e) {
+        catch (ParserConfigurationException | IOException | TransformerFactoryConfigurationError e) {
             logger.error("An error occurred whilst saving a views configuration file: {}", e);
         }
     }

diff --git a/protege-launcher/pom.xml b/protege-launcher/pom.xml
@@ -109,6 +109,32 @@
 			<artifactId>mockito-all</artifactId>
 			<scope>test</scope>
 		</dependency>
+
+		<dependency>	
+		  	<groupId>javax.xml.bind</groupId>	
+		  	<artifactId>jaxb-api</artifactId>	
+		</dependency>	
+
+		<dependency>	
+		  	<groupId>com.sun.xml.bind</groupId>	
+		 	 <artifactId>jaxb-core</artifactId>	
+		</dependency>	
+
+		<dependency>	
+		 	 <groupId>com.sun.xml.bind</groupId>	
+		 	 <artifactId>jaxb-impl</artifactId>	
+		</dependency>	
+
+		<dependency>	
+			<groupId>com.sun.activation</groupId>	
+		   	<artifactId>javax.activation</artifactId>		    	
+		</dependency>
+
+		<!-- swrltab plugin requires -->
+		<dependency>
+		    <groupId>org.glassfish.corba</groupId>
+		    <artifactId>glassfish-corba-orb</artifactId>
+		</dependency>		
 
 	</dependencies>
 </project>