IQSS · landreev · Jun 27, 2024 · Apr 15, 2024 · Apr 15, 2024 · Apr 15, 2024
diff --git a/doc/release-notes/10494-payara-upgrade.md b/doc/release-notes/10494-payara-upgrade.md
@@ -0,0 +1,119 @@
+# Upgrade Payara to v6.2024.6
+
+With this version of Dataverse, we encourage you to upgrade to version 6.2024.6.
+This will address security issues accumulated since the release of 6.2023.8, which was required since Dataverse release 6.0.
+
+## Instructions for Upgrading
+
+If you are using GDCC containers, this upgrade is included when pulling new release images.
+No manual intervention is necessary.
+
+We recommend you ensure you followed all update instructions from the past releases regarding Payara.
+(Latest Payara update was for [v6.0](https://github.com/IQSS/dataverse/releases/tag/v6.0))
+
+Upgrading requires a maintenance window and downtime. Please plan ahead, create backups of your database, etc.
+
+The steps below are a simple matter of reusing your existing domain directory with the new distribution.
+But we also recommend that you review the Payara upgrade instructions as it could be helpful during any troubleshooting:
+[Payara Release Notes](https://docs.payara.fish/community/docs/Release%20Notes/Release%20Notes%206.2024.6.html)
+We assume you are already on a Dataverse 6.x installation, using a Payara 6.x release.
+
+```shell
+export PAYARA=/usr/local/payara6
+```
+
+(or `setenv PAYARA /usr/local/payara6` if you are using a `csh`-like shell)
+
+1\. Undeploy the previous version
+
+```shell
+    $PAYARA/bin/asadmin list-applications
+    $PAYARA/bin/asadmin undeploy dataverse<-version>
+```
+
+2\. Stop Payara
+
+```shell
+    service payara stop
+    rm -rf $PAYARA/glassfish/domains/domain1/generated
+    rm -rf $PAYARA/glassfish/domains/domain1/osgi-cache
+    rm -rf $PAYARA/glassfish/domains/domain1/lib/databases
+```
+
+3\. Move the current Payara directory out of the way
+
+```shell
+    mv $PAYARA $PAYARA.MOVED
+```
+
+4\. Download the new Payara version (6.2024.6), and unzip it in its place
+
+5\. Replace the brand new payara/glassfish/domains/domain1 with your old, preserved domain1
+
+6\. Make sure that you have the following `--add-opens` options in your domain.xml. If not present, add them:
+
+```diff
+--- payara-6.2023.8/glassfish/domains/domain1/config/domain.xml
++++ payara-6.2024.6/glassfish/domains/domain1/config/domain.xml
+@@ -212,12 +212,16 @@
+                 <jvm-options>--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED</jvm-options>
+                 <jvm-options>--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED</jvm-options>
+                 <jvm-options>--add-opens=java.logging/java.util.logging=ALL-UNNAMED</jvm-options>
++                <jvm-options>--add-opens=java.management/javax.management=ALL-UNNAMED</jvm-options>
++                <jvm-options>--add-opens=java.management/javax.management.openmbean=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.base/sun.net.www=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.base/sun.security.util=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-opens=java.base/java.lang.invoke=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-opens=java.desktop/java.beans=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=jdk.naming.dns/com.sun.jndi.dns=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.naming/com.sun.jndi.ldap=ALL-UNNAMED</jvm-options>
++                <jvm-options>[17|]--add-opens=java.base/java.io=ALL-UNNAMED</jvm-options>
++                <jvm-options>[21|]--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED</jvm-options>
+                 <jvm-options>-Xmx512m</jvm-options>
+                 <jvm-options>-XX:NewRatio=2</jvm-options>
+                 <jvm-options>-XX:+UnlockDiagnosticVMOptions</jvm-options>
+@@ -447,12 +451,16 @@
+                 <jvm-options>--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED</jvm-options>
+                 <jvm-options>--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED</jvm-options>
+                 <jvm-options>--add-opens=java.logging/java.util.logging=ALL-UNNAMED</jvm-options>
++                <jvm-options>--add-opens=java.management/javax.management=ALL-UNNAMED</jvm-options>
++                <jvm-options>--add-opens=java.management/javax.management.openmbean=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.base/sun.net.www=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.base/sun.security.util=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-opens=java.base/java.lang.invoke=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-opens=java.desktop/java.beans=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=jdk.naming.dns/com.sun.jndi.dns=ALL-UNNAMED</jvm-options>
+                 <jvm-options>[17|]--add-exports=java.naming/com.sun.jndi.ldap=ALL-UNNAMED</jvm-options>
++                <jvm-options>[17|]--add-opens=java.base/java.io=ALL-UNNAMED</jvm-options>
++                <jvm-options>[21|]--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED</jvm-options>
+                 <jvm-options>-Xmx512m</jvm-options>
+                 <jvm-options>-XX:NewRatio=2</jvm-options>
+                 <jvm-options>-XX:+UnlockDiagnosticVMOptions</jvm-options>
+```
+(You can also save this as a patch file and try to apply it.)
+
+TODO: For the combined 6.3 release note, I would consider replacing the patch format above with just the 4 specific options, for clarity etc. (L.A.) As in: 
+```
+         <jvm-options>--add-opens=java.management/javax.management=ALL-UNNAMED</jvm-options>
+         <jvm-options>--add-opens=java.management/javax.management.openmbean=ALL-UNNAMED</jvm-options>
+         <jvm-options>[17|]--add-opens=java.base/java.io=ALL-UNNAMED</jvm-options>
+         <jvm-options>[21|]--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED</jvm-options>
+```
+
+7\. Start Payara
+
+```shell
+    service payara start
+```
+
+8\. Deploy this version.
+
+```shell
+    $PAYARA/bin/asadmin deploy dataverse-6.3.war
+```
+
+9\. Restart payara
+
+```shell
+    service payara stop
+    service payara start
diff --git a/doc/sphinx-guides/source/admin/monitoring.rst b/doc/sphinx-guides/source/admin/monitoring.rst
@@ -154,7 +154,7 @@ Tips:
 MicroProfile Metrics endpoint
 -----------------------------
 
-Payara provides the metrics endpoint: <https://docs.payara.fish/community/docs/6.2023.9/Technical%20Documentation/MicroProfile/Metrics/Metrics%20Rest%20Endpoint.html>_
+Payara provides the metrics endpoint: <https://docs.payara.fish/community/docs/Technical%20Documentation/MicroProfile/Metrics/Metrics%20Rest%20Endpoint.html>_
 The metrics you can retrieve that way:
 - `index_permit_wait_time_seconds_mean` displays how long does it take to receive a permit to index a dataset.
 - `index_time_seconds` displays how long does it take to index a dataset.
diff --git a/doc/sphinx-guides/source/developers/classic-dev-env.rst b/doc/sphinx-guides/source/developers/classic-dev-env.rst
@@ -93,15 +93,15 @@ On Linux, install ``jq`` from your package manager or download a binary from htt
 Install Payara
 ~~~~~~~~~~~~~~
 
-Payara 6.2023.8 or higher is required.
+Payara 6.2024.6 or higher is required.
 
 To install Payara, run the following commands:
 
 ``cd /usr/local``
 
-``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip``
+``sudo curl -O -L https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.6/payara-6.2024.6.zip``
 
-``sudo unzip payara-6.2023.8.zip``
+``sudo unzip payara-6.2024.6.zip``
 
 ``sudo chown -R $USER /usr/local/payara6``
 

diff --git a/doc/sphinx-guides/source/installation/prerequisites.rst b/doc/sphinx-guides/source/installation/prerequisites.rst
@@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 17 the default with the ``alternatives`` co
 Payara
 ------
 
-Payara 6.2023.8 is recommended. Newer versions might work fine. Regular updates are recommended.
+Payara 6.2024.6 is recommended. Newer versions might work fine. Regular updates are recommended.
 
 Installing Payara
 =================
@@ -55,8 +55,8 @@ Installing Payara
 
 - Download and install Payara (installed in ``/usr/local/payara6`` in the example commands below)::
 
-	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip
-	# unzip payara-6.2023.8.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.6/payara-6.2024.6.zip
+	# unzip payara-6.2024.6.zip
 	# mv payara6 /usr/local
 
 If nexus.payara.fish is ever down for maintenance, Payara distributions are also available from https://repo1.maven.org/maven2/fish/payara/distributions/payara/

diff --git a/doc/sphinx-guides/source/qa/test-automation.md b/doc/sphinx-guides/source/qa/test-automation.md
@@ -52,7 +52,7 @@ Go to the end of the log and then scroll up, looking for the failure. A failed A
 
 ```
 TASK [dataverse : download payara zip] *****************************************
-fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.8/payara-6.2023.8.zip"}
+fatal: [localhost]: FAILED! => {"changed": false, "dest": "/tmp/payara.zip", "elapsed": 10, "msg": "Request failed: <urlopen error timed out>", "url": "https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2024.6/payara-6.2024.6.zip"}
 ```
 
 In the example above, if Payara can't be downloaded, we're obviously going to have problems deploying Dataverse to it!

diff --git a/modules/container-base/src/main/docker/Dockerfile b/modules/container-base/src/main/docker/Dockerfile
@@ -166,8 +166,6 @@ RUN <<EOF
     ${ASADMIN} create-jvm-options '-XX\:MetaspaceSize=${ENV=MEM_METASPACE_SIZE}'
     ${ASADMIN} create-jvm-options '-XX\:MaxMetaspaceSize=${ENV=MEM_MAX_METASPACE_SIZE}'
     ${ASADMIN} create-jvm-options '-XX\:+IgnoreUnrecognizedVMOptions'
-    # Workaround for FISH-7722: Failed to deploy war with @Stateless https://github.com/payara/Payara/issues/6337
-    ${ASADMIN} create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED
     # Disable autodeploy and hot reload
     ${ASADMIN} set configs.config.server-config.admin-service.das-config.dynamic-reload-enabled="false"
     ${ASADMIN} set configs.config.server-config.admin-service.das-config.autodeploy-enabled="false"

diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
@@ -148,14 +148,13 @@
         <argLine>-Duser.timezone=${project.timezone} -Dfile.encoding=${project.build.sourceEncoding} -Duser.language=${project.language} -Duser.region=${project.region}</argLine>
 
         <!-- Major system components and dependencies -->
-        <payara.version>6.2023.8</payara.version>
+        <payara.version>6.2024.6</payara.version>
         <postgresql.version>42.7.2</postgresql.version>
         <solr.version>9.4.1</solr.version>
         <aws.version>1.12.290</aws.version>
         <google.library.version>26.30.0</google.library.version>
 
         <!-- Basic libs, logging -->
-        <jakartaee-api.version>8.0.0</jakartaee-api.version>
         <slf4j.version>1.7.35</slf4j.version>
         <commons.io.version>2.15.1</commons.io.version>
         <commons.logging.version>1.2</commons.logging.version>
@@ -386,18 +385,6 @@
                 <enabled>false</enabled>
             </snapshots>
         </repository>
-        <!-- This repository is about to being phased out. See https://github.com/payara/Payara_PatchedProjects/issues/366 -->
-        <repository>
-            <id>payara-patched-externals</id>
-            <name>Payara Patched Externals</name>
-            <url>https://raw.github.com/payara/Payara_PatchedProjects/master</url>
-            <releases>
-                <enabled>true</enabled>
-            </releases>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-        </repository>
         <repository>
             <id>central-repo</id>
             <name>Central Repository</name>

diff --git a/pom.xml b/pom.xml
@@ -224,9 +224,6 @@
             <groupId>fish.payara.api</groupId>
             <artifactId>payara-api</artifactId>
             <scope>provided</scope>
-            <!-- Note: The version was provided by Payara BOM till 6.2023.7, when they removed the Core BOM from it as
-                       meant for internal use only. Simply referencing the version property here solves the problem. -->
-            <version>${payara.version}</version>
         </dependency>
 
         <!-- JSON-P -->

diff --git a/scripts/installer/as-setup.sh b/scripts/installer/as-setup.sh
@@ -117,9 +117,6 @@ function preliminary_setup()
 
   ./asadmin $ASADMIN_OPTS create-jvm-options "-Ddataverse.timerServer=true"
 
-  # Workaround for FISH-7722: Failed to deploy war with @Stateless https://github.com/payara/Payara/issues/6337
-  ./asadmin $ASADMIN_OPTS create-jvm-options --add-opens=java.base/java.io=ALL-UNNAMED
-
   # enable comet support
   ./asadmin $ASADMIN_OPTS set server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled="true"