IQSS · pdurbin · Sep 21, 2022 · Aug 31, 2022 · Aug 31, 2022 · Sep 12, 2022
diff --git a/conf/docker-aio/0prep_deps.sh b/conf/docker-aio/0prep_deps.sh
@@ -4,9 +4,9 @@ if [ ! -d dv/deps ]; then
 fi
 wdir=`pwd`
 
-if [ ! -e dv/deps/payara-5.2021.6.zip ]; then
+if [ ! -e dv/deps/payara-5.2022.3.zip ]; then
 	echo "payara dependency prep"
-	wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.6/payara-5.2021.6.zip  -O dv/deps/payara-5.2021.6.zip
+	wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip  -O dv/deps/payara-5.2022.3.zip
 fi
 
 if [ ! -e dv/deps/solr-8.11.1dv.tgz ]; then

diff --git a/conf/docker-aio/c8.dockerfile b/conf/docker-aio/c8.dockerfile
@@ -24,7 +24,7 @@ COPY disableipv6.conf /etc/sysctl.d/
 RUN rm /etc/httpd/conf/*
 COPY httpd.conf /etc/httpd/conf 
 RUN cd /opt ; tar zxf /tmp/dv/deps/solr-8.11.1dv.tgz
-RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2021.6.zip ; ln -s /opt/payara5 /opt/glassfish4
+RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2022.3.zip ; ln -s /opt/payara5 /opt/glassfish4
 
 # this copy of domain.xml is the result of running `asadmin set server.monitoring-service.module-monitoring-levels.jvm=LOW` on a default glassfish installation (aka - enable the glassfish REST monitir endpoint for the jvm`
 # this dies under Java 11, do we keep it?

diff --git a/doc/release-notes/8947-payara-update.md b/doc/release-notes/8947-payara-update.md
@@ -0,0 +1,76 @@
+# Update to Payara 5.2022.3 highly recommended
+
+*NOTE: this might be rephrased to "required" depending on https://github.com/IQSS/dataverse/pull/8915 being merged.*
+
+With lots of bug and security fixes included, we encourage everyone to update to Payara 5.2022.3 as soon as possible.
+
+**Note:** with the approaching EOL for the Payara 5 Community release train it's likely we will switch to a
+yet-to-be-released Payara 6 in the not-so-far-away future.
+
+We recommend you ensure you followed all update instructions from the past releases regarding Payara.
+(latest Payara update was for [v5.6](https://github.com/IQSS/dataverse/releases/tag/v5.6))
+
+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%205.2022.3.html)
+
+If you are running Payara as a non-root user (and you should be!), remember not to execute the commands below as root.
+Use `sudo` to change to that user first. For example, `sudo -i -u dataverse` if `dataverse` is your dedicated
+application user.
+
+In the following commands we assume that Payara 5 is installed in `/usr/local/payara5`. If not, adjust as needed.
+
+Please note that the deletion of the `lib/databases` directory below is only required once, for this upgrade (see Issue #8230 for details).
+
+```shell
+export PAYARA=/usr/local/payara5
+```
+
+(or `setenv PAYARA /usr/local/payara5` 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 (5.2022.3), and unzip it in its place
+
+5. Replace the brand new payara/glassfish/domains/domain1 with your old, preserved domain1
+
+6. Start Payara
+
+```shell
+    service payara start
+```
+
+7. Deploy this version.
+
+```shell
+    $PAYARA/bin/asadmin deploy dataverse-5.12.war
+```
+
+8. Restart payara
+
+```shell
+    service payara stop
+    service payara start
+```
diff --git a/doc/sphinx-guides/source/admin/troubleshooting.rst b/doc/sphinx-guides/source/admin/troubleshooting.rst
@@ -96,10 +96,8 @@ Sometimes your Dataverse installation fails to deploy, or Payara fails to restar
 
 We don't know what's causing this issue, but here's a known workaround: 
 
-- Stop Payara; 
-
-- Remove the ``generated`` and ``osgi-cache`` directories;
-
+- Stop Payara;
+- Remove the ``generated`` and ``osgi-cache`` directories from the ``domain1`` directory;
 - Start Payara
 
 The shell script below performs the steps above. 

diff --git a/doc/sphinx-guides/source/developers/dev-environment.rst b/doc/sphinx-guides/source/developers/dev-environment.rst
@@ -79,15 +79,15 @@ On Linux, install ``jq`` from your package manager or download a binary from htt
 Install Payara
 ~~~~~~~~~~~~~~
 
-Payara 5.2021.6 or higher is required.
+Payara 5.2022.3 or higher is required.
 
 To install Payara, run the following commands:
 
 ``cd /usr/local``
 
-``sudo curl -O -L https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.6/payara-5.2021.6.zip``
+``sudo curl -O -L https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip``
 
-``sudo unzip payara-5.2021.6.zip``
+``sudo unzip payara-5.2022.3.zip``
 
 ``sudo chown -R $USER /usr/local/payara5``
 

diff --git a/doc/sphinx-guides/source/installation/installation-main.rst b/doc/sphinx-guides/source/installation/installation-main.rst
@@ -207,7 +207,7 @@ Fresh Reinstall
 Early on when you're installing the Dataverse Software, you may think, "I just want to blow away what I've installed and start over." That's fine. You don't have to uninstall the various components like Payara, PostgreSQL and Solr, but you should be conscious of how to clear out their data. For Payara, a common helpful process is to:
 
 - Stop Payara; 
-- Remove the ``generated`` and ``osgi-cache`` directories;
+- Remove the ``generated``, ``lib/databases`` and ``osgi-cache`` directories from the ``domain1`` directory;
 - Start Payara
 
 Drop database

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 11 the default with the ``alternatives`` co
 Payara
 ------
 
-Payara 5.2021.6 is recommended. Newer versions might work fine, regular updates are recommended.
+Payara 5.2022.3 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/payara5`` in the example commands below)::
 
-	# wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.6/payara-5.2021.6.zip
-	# unzip payara-5.2021.6.zip
+	# wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip
+	# unzip payara-5.2022.3.zip
 	# mv payara5 /usr/local
 
 If you intend to install and run Payara under a service account (and we hope you do), chown -R the Payara hierarchy to root to protect it but give the service account access to the below directories:

diff --git a/downloads/download.sh b/downloads/download.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
-curl -L -O https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.6/payara-5.2021.6.zip
+curl -L -O https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip
 curl -L -O https://archive.apache.org/dist/lucene/solr/8.11.1/solr-8.11.1.tgz
 curl -L -O https://search.maven.org/remotecontent?filepath=org/jboss/weld/weld-osgi-bundle/2.2.10.Final/weld-osgi-bundle-2.2.10.Final-glassfish4.jar
 curl -s -L http://sourceforge.net/projects/schemaspy/files/schemaspy/SchemaSpy%205.0.0/schemaSpy_5.0.0.jar/download > schemaSpy_5.0.0.jar
diff --git a/modules/dataverse-parent/pom.xml b/modules/dataverse-parent/pom.xml
@@ -146,7 +146,7 @@
         <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>5.2021.6</payara.version>
+        <payara.version>5.2022.3</payara.version>
         <postgresql.version>42.3.5</postgresql.version>
         <solr.version>8.11.1</solr.version>
         <aws.version>1.11.762</aws.version>

diff --git a/scripts/vagrant/setup.sh b/scripts/vagrant/setup.sh
@@ -51,7 +51,7 @@ SOLR_USER=solr
 echo "Ensuring Unix user '$SOLR_USER' exists"
 useradd $SOLR_USER || :
 DOWNLOAD_DIR='/dataverse/downloads'
-PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2021.6.zip"
+PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2022.3.zip"
 SOLR_TGZ="$DOWNLOAD_DIR/solr-8.11.1.tgz"
 if [ ! -f $PAYARA_ZIP ] || [ ! -f $SOLR_TGZ ]; then
     echo "Couldn't find $PAYARA_ZIP or $SOLR_TGZ! Running download script...."