IQSS/12715 payara 7.2026.9 update

doc/release-notes/21715-Payara-7.2026.9-update.md

@@ -0,0 +1,85 @@
+This PR updates Dataverse to be compatible with Payara version 7.2026.9 which includes breaking changes for our code.
+
+## Upgrade Instructions
+
+Upgrading requires a maintenance window and downtime. Please plan accordingly, create backups of your database, etc.
+
+Note: These instructions assume that you are upgrading from the immediate previous version. That is to say, you've already upgraded through all the 6.x releases and are now running Dataverse 6.12. See [tags on GitHub](https://github.com/IQSS/dataverse/tags) for a list of versions. If you are running an earlier version, the only supported way to upgrade is to progress through the upgrades to all the releases in between before attempting the upgrade to this version.
+
+If you are running Payara as a non-root user (and you should be!), **remember not to execute the commands below as root**. By default, Payara runs as the `dataverse` user. In the commands below, we use sudo to run the commands as a non-root user.
+
+Also, we assume that Payara is installed in `/usr/local/payara7`. If not, adjust as needed.
+
+The instructions below describe the upgrade procedure based on moving your existing Payara 7.2026.8 domain directory into the new Payara 7.2026.9 distribution. We recommend this method because it is the easiest way to recreate your current configuration and preserve your data.
+
+1. Undeploy Dataverse, if deployed, using the unprivileged service account ("dataverse", by default).
+
+   The new version of Payara is not compatible with previous versions of Dataverse, so you should undeploy the running Dataverse 6.12 war file first.
+
+   ```shell
+   sudo -u dataverse /usr/local/payara7/bin/asadmin list-applications
+
+   sudo -u dataverse /usr/local/payara7/bin/asadmin undeploy dataverse-6.12
+   ```
+
+1. Stop Payara.
+
+   ```shell
+   sudo systemctl stop payara
+   ```
+
+1. Move the current Payara directory out of the way. Version 7.2026.8 is used in the examples below. Adjust accordingly if you are upgrading from a different version. 
+
+   ```shell
+   sudo mv /usr/local/payara7 /usr/local/payara7-2026.8
+   ```
+
+1. Download the new Payara version 7.2026.9, and unzip it.
+
+   ```shell
+   curl -L -O https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.9/payara-7.2026.9.zip
+
+   sudo unzip payara-7.2026.9.zip -d /usr/local/
+   ```
+1. Set ownership of the payara distribution to root, making it read-only for the service account ("dataverse" by default).
+
+   ```shell
+   sudo chown -R root:root /usr/local/payara7
+   ```
+
+1. Replace the brand new `payara7/glassfish/domains/domain1` with your old, preserved domain1.
+
+   ```shell
+   sudo mv /usr/local/payara7/glassfish/domains/domain1 /usr/local/payara7/glassfish/domains/domain1_DIST
+
+   sudo mv /usr/local/payara7-2026.8/glassfish/domains/domain1 /usr/local/payara7/glassfish/domains/
+   ```
+
+1. Set ownership of the domain for the service account ("dataverse" by default). Ownership should have been preserved during the move above, but this step assures that the domain is writable by the service account.
+
+   ```shell
+   sudo chown -R dataverse:dataverse /usr/local/payara7/glassfish/domains/domain1
+   ```
+
+1. Remove the cache directories.
+
+   ```shell
+   sudo rm -rf /usr/local/payara7/glassfish/domains/domain1/generated/
+
+   sudo rm -rf /usr/local/payara7/glassfish/domains/domain1/osgi-cache/
+   ```
+
+1. Start Payara.
+
+   ```shell
+   sudo systemctl start payara
+   ```
+
+1. Deploy the Dataverse 6.12.1 war file.
+
+   ```shell
+   wget https://github.com/IQSS/dataverse/releases/download/v6.12/dataverse-6.12.1.war
+
+   sudo -u dataverse /usr/local/payara7/bin/asadmin deploy dataverse-6.12.1.war
+   ```
+

doc/release-notes/6.12-release-notes.md

@@ -41,7 +41,7 @@ These are features that weren't already mentioned under "highlights" above.
 
 ## Other Changes
 
-- Payara 7.2026.8 is now the supported and recommended version. See upgrade instructions below and #12498. We are aware that Payara 7.2026.9 is out but it didn't "just work" so we don't recommend it yet. See #12715.
+- Payara 7.2026.9 is now the supported and recommended version. See upgrade instructions below, #12498 and #12715.
 - Database indexes were added to the guestbookresponse table to speed up queries. See #12616.
 - The QA Guide was added as an experiment in #10103 but has been removed because it has proved less useful than imagined. It can still be [viewed](https://guides.dataverse.org/en/6.11/qa/index.html) as it existed as of Dataverse 6.11. See #12582.
 
@@ -164,7 +164,7 @@ If you are running Payara as a non-root user (and you should be!), **remember no
 
 Also, we assume that Payara is installed in `/usr/local/payara7`. If not, adjust as needed.
 
-The instructions below describe the upgrade procedure based on moving your existing Payara 7.2026.2 domain directory into the new Payara 7.2026.8 distribution. We recommend this method because it is the easiest way to recreate your current configuration and preserve your data.
+The instructions below describe the upgrade procedure based on moving your existing Payara 7.2026.2 domain directory into the new Payara 7.2026.9 distribution. We recommend this method because it is the easiest way to recreate your current configuration and preserve your data.
 
 1. Undeploy Dataverse, if deployed, using the unprivileged service account ("dataverse", by default).
 
@@ -188,12 +188,12 @@ The instructions below describe the upgrade procedure based on moving your exist
    sudo mv /usr/local/payara7 /usr/local/payara7-2026.2
    ```
 
-1. Download the new Payara version 7.2026.8, and unzip it.
+1. Download the new Payara version 7.2026.9, and unzip it.
 
    ```shell
-   curl -L -O https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.8/payara-7.2026.8.zip
+   curl -L -O https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.9/payara-7.2026.9.zip
 
-   sudo unzip payara-7.2026.8.zip -d /usr/local/
+   sudo unzip payara-7.2026.9.zip -d /usr/local/
    ```
 1. Set permission for the service account ("dataverse" by default).
 
@@ -223,7 +223,7 @@ The instructions below describe the upgrade procedure based on moving your exist
 
 1. Update configuration files in the moved domain.
 
-   The file `glassfish-acc.xml` from Payara 7.2026.2 has been renamed to `payara-acc.xml` in Payara 7.2026.8. Also `default-logging.properties` has been updated in the Payara 7.2026.8. We recommend copying these new files from the Payara 7.2026.8 distribution domain into the domain you copied over from your Payara 7.2026.2 installation.
+   The file `glassfish-acc.xml` from Payara 7.2026.2 has been renamed to `payara-acc.xml` in Payara 7.2026.9. Also `default-logging.properties` has been updated in the Payara 7.2026.9. We recommend copying these new files from the Payara 7.2026.9 distribution domain into the domain you copied over from your Payara 7.2026.2 installation.
 
    ```shell
    sudo rm /usr/local/payara7/glassfish/domains/domain1/config/glassfish-acc.xml
@@ -257,8 +257,6 @@ The instructions below describe the upgrade procedure based on moving your exist
    sudo -u dataverse /usr/local/payara7/bin/asadmin deploy dataverse-6.12.war
    ```
 
-   Please note: when watching logs while waiting for the deployment to finish, you may encounter `SEVERE` level warnings like "Leaking injection manager found in the current thread. Very likely because it wasn't removed in a previous invocation and leaked into this invocation." We have not found severe issues during testing this release and advise to ignore but monitor for unusual resource usage. We plan to address the underlying issue with the next release. See #12715 for more details.
-
 1. Update metadata blocks.
 
    In #12346 we added the value "Translator" under "contributorType" field and we need to reload the citation.tsv file because of this.

doc/sphinx-guides/source/installation/prerequisites.rst

@@ -44,7 +44,7 @@ On RHEL/derivative you can make Java 21 the default with the ``alternatives`` co
 Payara
 ------
 
-Payara 7.2026.8 is recommended. Payara 7.2026.9 doesn't "just work". See https://github.com/IQSS/dataverse/issues/12715 for details.
+Payara 7.2026.9 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/payara7`` in the example commands below)::
 
-	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.8/payara-7.2026.8.zip
-	# unzip payara-7.2026.8.zip
+	# wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/7.2026.9/payara-7.2026.9.zip
+	# unzip payara-7.2026.9.zip
 	# mv payara7 /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/

modules/dataverse-parent/pom.xml

@@ -149,7 +149,7 @@
         <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>7.2026.8</payara.version>
+        <payara.version>7.2026.9</payara.version>
         <postgresql.version>42.7.12</postgresql.version>
         <solr.version>9.8.0</solr.version>
         <postgresql.server.version>16</postgresql.server.version>

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

@@ -20,17 +20,16 @@
 import java.util.logging.Logger;
 
 import jakarta.ejb.EJB;
+import jakarta.inject.Inject;
 import jakarta.json.JsonObject;
 import jakarta.servlet.http.HttpServletRequest;
 import jakarta.ws.rs.BadRequestException;
-import jakarta.ws.rs.ClientErrorException;
 import jakarta.ws.rs.ServiceUnavailableException;
 import jakarta.ws.rs.WebApplicationException;
 import jakarta.ws.rs.Consumes;
 import jakarta.ws.rs.ForbiddenException;
 import jakarta.ws.rs.POST;
 import jakarta.ws.rs.Path;
-import jakarta.ws.rs.core.Context;
 import jakarta.ws.rs.core.Response;
 import org.eclipse.microprofile.openapi.annotations.Operation;
 import org.eclipse.microprofile.openapi.annotations.parameters.RequestBody;
@@ -58,7 +57,7 @@ public class LDNInbox extends AbstractApiBean {
     @EJB
     RoleAssigneeServiceBean roleAssigneeService;
 
-    @Context
+    @Inject
     protected HttpServletRequest httpRequest;
 
     public static final JsonLDNamespace activityStreams = JsonLDNamespace.defineNamespace("as",