#4259 support Java 11

doc/release-notes/4259-java-11.md

@@ -0,0 +1,91 @@
+## Release Highlights
+
+### Java 11
+
+The Dataverse software now runs and requires Java 11. This will provide performance and security enhancements, allows developers to take advantage of new and updated Java features, and moves the project to a platform with better longer term support. This upgrade requires a few extra steps in the release process, outlined below.
+
+## Notes to Admins
+
+### Java 11
+
+There are some things to note and keep in mind regarding the move to Java 11:
+
+- You should install the JDK/JRE following your usual methods, depending on your operating system.
+- We targeted and tested Java 11, but 11+ will likely work. Java 11 was targeted because of its long term support.
+- You will need to adjust some JVM options in domain.xml as part of the upgrade process. We've provided these steps below.
+
+### New JVM and DB Options
+
+#### New JVM Options
+
+The following JVM Options have been added in support of Java 11:
+
+<jvm-options>[9|]--add-opens=java.base/jdk.internal.loader=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=jdk.management/com.sun.management.internal=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-exports=java.base/jdk.internal.ref=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/java.lang=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/java.net=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/java.nio=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/java.util=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/sun.nio.ch=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.management/sun.management=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/sun.net.www.protocol.jrt=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.base/sun.net.www.protocol.jar=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED</jvm-options>
+<jvm-options>[9|]--add-opens=java.logging/java.util.logging=ALL-UNNAMED</jvm-options>
+
+## Upgrade Instructions
+
+0\. These instructions assume that you've already successfully upgraded from Dataverse 4.x to  Dataverse 5 following the instructions in the [Dataverse 5 Release Notes](https://github.com/IQSS/dataverse/releases/tag/v5.0).
+
+1\. Undeploy the previous version.
+
+- `<payara install path>/bin/asadmin list-applications`
+- `<payara install path>/bin/asadmin undeploy dataverse<-version>`
+
+(where `<payara install path>` is where Payara 5 is installed, for example: `/usr/local/payara5`)
+
+2\. Stop Payara and remove the generated directory
+
+- `service payara stop`
+- remove the generated directory: 
+`rm -rf <payara install path>/payara/domains/domain1/generated`
+
+3\. In domain.xml:
+
+Remove the following JVM options from the domain><configs><config name-"server-config"><java-config> element::
+
+  <jvm-options>-Djava.endorsed.dirs=/usr/local/payara5/glassfish/modules/endorsed:/usr/local/payara5/glassfish/lib/endorsed</jvm-options>
+  459a448
+  <jvm-options>-Djava.ext.dirs=${com.sun.aas.javaRoot}/lib/ext${path.separator}${com.sun.aas.javaRoot}/jre/lib/ext${path.separator}${com.sun.aas.instanceRoot}/lib/ext</jvm-options>
+
+Add the following JVM options to the domain><configs><config name-"server-config"><java-config> element:  
+
+  <jvm-options>[9|]--add-opens=java.base/jdk.internal.loader=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=jdk.management/com.sun.management.internal=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-exports=java.base/jdk.internal.ref=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/java.lang=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/java.net=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/java.nio=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/java.util=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/sun.nio.ch=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.management/sun.management=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/sun.net.www.protocol.jrt=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.base/sun.net.www.protocol.jar=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED</jvm-options>
+  <jvm-options>[9|]--add-opens=java.logging/java.util.logging=ALL-UNNAMED</jvm-options>
+
+4\. Start Payara
+
+- `service payara start`
+
+5\. Deploy this version.
+
+- `<payara install path>/bin/asadmin deploy dataverse-5.4.war`
+
+6\. Restart payara
+
+- `service payara stop`
+- `service payara start`

pom.xml

@@ -39,11 +39,7 @@
         <mockito.version>2.28.2</mockito.version>
         <flyway.version>5.2.4</flyway.version>
         <jhove.version>1.20.1</jhove.version>
-        <!--
-        Jacoco 0.8.2 seems to break Netbeans code coverage integration so we'll use 0.8.1 instead.
-        See https://github.com/jacoco/jacoco/issues/772 for discussion of how the XML changed.
-        -->
-        <jacoco.version>0.8.1</jacoco.version>
+        <jacoco.version>0.8.6</jacoco.version>
     </properties>
     <pluginRepositories>
         <pluginRepository>
@@ -816,27 +812,6 @@
             <id>all-unit-tests</id>
         </profile>
         <!-- TODO: Add a profile to run API tests (integration tests that end in IT.java. See conf/docker-aio/run-test-suite.sh -->
-      <profile>
-        <id>Java8</id>
-        <activation>
-          <jdk>1.8</jdk>
-        </activation>
-        <build>
-          <plugins>
-            <plugin>
-              <groupId>org.apache.maven.plugins</groupId>
-              <artifactId>maven-compiler-plugin</artifactId>
-              <version>3.8.0</version>
-              <configuration>
-                <source>1.8</source>
-                <target>1.8</target>
-                <!-- for use with `mvn -DcompilerArgument=-Xlint:unchecked compile` -->
-                <compilerArgument>${compilerArgument}</compilerArgument>
-              </configuration>
-            </plugin>
-          </plugins>
-        </build>
-      </profile>
       <profile>
         <id>Java9Plus</id>
         <activation>
@@ -849,7 +824,7 @@
               <artifactId>maven-compiler-plugin</artifactId>
               <version>3.8.0</version>
               <configuration>
-                <release>8</release>
+                <release>11</release>
                 <!-- for use with `mvn -DcompilerArgument=-Xlint:unchecked compile` -->
                 <compilerArgument>${compilerArgument}</compilerArgument>
               </configuration>

src/main/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApi.java

@@ -250,11 +250,12 @@ public Response loadDatasetFields(File file) {
         int lineNumber = 0;
         HeaderType header = null;
         JsonArrayBuilder responseArr = Json.createArrayBuilder();
+        String[] values = null;
         try {
             br = new BufferedReader(new FileReader("/" + file));
             while ((line = br.readLine()) != null) {
                 lineNumber++;
-                String[] values = line.split(splitBy);
+                values = line.split(splitBy);
                 if (values[0].startsWith("#")) { // Header row
                     switch (values[0]) {
                         case "#metadataBlock":
@@ -301,7 +302,7 @@ public Response loadDatasetFields(File file) {
             return error(Status.EXPECTATION_FAILED, "File not found");
 
         } catch (ArrayIndexOutOfBoundsException e) {
-            String message = getArrayIndexOutOfBoundMessage(header, lineNumber, e);
+            String message = getArrayIndexOutOfBoundMessage(header, lineNumber, values.length);
             logger.log(Level.WARNING, message, e);
             alr.setActionResult(ActionLogRecord.Result.InternalError);
             alr.setInfo(alr.getInfo() + "// " + message);
@@ -352,10 +353,9 @@ public String getGeneralErrorMessage(HeaderType header, int lineNumber, String m
      */
     public String getArrayIndexOutOfBoundMessage(HeaderType header,
                                                  int lineNumber,
-                                                 ArrayIndexOutOfBoundsException e) {
+                                                 int wrongIndex) {
 
         List<String> columns = getColumnsByHeader(header);
-        int wrongIndex = Integer.parseInt(e.getMessage());
 
         String column = columns.get(wrongIndex - 1);
         List<String> arguments = new ArrayList<>();

src/test/java/edu/harvard/iq/dataverse/api/DatasetFieldServiceApiTest.java

@@ -43,7 +43,7 @@ public void testGeneralErrorMessageBundle() {
     @Test
     public void testGetArrayIndexOutOfBoundMessage() {
         DatasetFieldServiceApi api = new DatasetFieldServiceApi();
-        String message = api.getArrayIndexOutOfBoundMessage(DatasetFieldServiceApi.HeaderType.DATASETFIELD, 5, new ArrayIndexOutOfBoundsException("4"));
+        String message = api.getArrayIndexOutOfBoundMessage(DatasetFieldServiceApi.HeaderType.DATASETFIELD, 5, 4);
         assertEquals(
             "Error parsing metadata block in DATASETFIELD part, line #5: missing 'watermark' column (#5)",
             message

src/test/java/edu/harvard/iq/dataverse/dataaccess/StorageIOTest.java

@@ -62,24 +62,26 @@ public void testGetReadChannel() throws Exception {
     @Test
     public void testGetDvObject() {
         assertEquals(null, instance.getDvObject());
-        instance.setDvObject(new Dataset());
-        assertEquals(new Dataset(), instance.getDataset());
-
-        try {
+        Dataset d= new Dataset();
+        instance.setDvObject(d);
+        //assertSame uses == rather than the .equals() method which would (currently) be true for any two Datasets 
+        assertSame(d, instance.getDataset());        try {
             instance.getDataFile();
             fail("This should have thrown");
         } catch (ClassCastException ex) {
-            assertEquals(ex.getMessage(), "edu.harvard.iq.dataverse.Dataset cannot be cast to edu.harvard.iq.dataverse.DataFile");
+            //Test succeeds
         }
         try {
             instance.getDataverse();
             fail("This should have thrown");
         } catch (ClassCastException ex) {
-            assertEquals(ex.getMessage(), "edu.harvard.iq.dataverse.Dataset cannot be cast to edu.harvard.iq.dataverse.Dataverse");
+            //Test succeeds
         }
         // null driver defaults to 'file'
-        assertEquals(new DataFile(), new FileAccessIO<>(new DataFile(), null, null).getDataFile());
-        assertEquals(new Dataverse(), new FileAccessIO<>(new Dataverse(), null, null).getDataverse());
+        DataFile f= new DataFile();
+        Dataverse dv = new Dataverse();
+        assertSame(f, new FileAccessIO<>(f, null, null).getDataFile());
+        assertSame(dv, new FileAccessIO<>(dv, null, null).getDataverse());
     }
 
     @Test