IQSS · kcondon · Mar 21, 2022 · Mar 18, 2022 · Mar 21, 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-5.2021.5.zip ]; then
+if [ ! -e dv/deps/payara-5.2021.6.zip ]; then
 	echo "payara dependency prep"
-	wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.5/payara-5.2021.5.zip  -O dv/deps/payara-5.2021.5.zip
+	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
 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-5.2021.5.zip ; ln -s /opt/payara5 /opt/glassfish4
+RUN cd /opt ; unzip /tmp/dv/deps/payara-5.2021.6.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/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 5.201 or higher is required.
+Payara 5.2021.6 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/5.2021.5/payara-5.2021.5.zip``
+``sudo curl -O -L https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.6/payara-5.2021.6.zip``
 
-``sudo unzip payara-5.2021.5.zip``
+``sudo unzip payara-5.2021.6.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
@@ -100,10 +100,6 @@ The Dataverse Software uses JHOVE_ to help identify the file format (CSV, PNG, e
 
 .. _JHOVE: http://jhove.openpreservation.org
 
-**A note about Payara-5.2021.5:** as of this writing there exists a logging configuration bug in Payara-5.2021.5. Any change to the logging configuration results in the contents of ``/usr/local/payara/glassfish/domains/domain1/config/logging.properties`` getting clobbered. In the absence of a proper logging configuration, Payara logs a number of WELD INFO entries on Payara launch, then proceeds to attempt to update its logging configuration approximately twice a second. This will result in unnecessarily junked-up system logs.
-
-This bug appears to be triggered in new Payara installations during the Dataverse installation routine. As the ``default-logging.properties`` file doesn't match the ``logging.proprties`` file distributed with Payara, we are offering :download:`a copy of it here<../_static/installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties>`. Simply stopping Payara, replacing the file, and starting Payara should correct the issue.
-
 Logging In
 ----------
 

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 5.2021.5 is recommended. Newer versions might work fine, regular updates are recommended.
+Payara 5.2021.6 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/payara5`` in the example commands below)::
 
-	# wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2021.5/payara-5.2021.5.zip
-	# unzip payara-5.2021.5.zip
+	# 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
 	# 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/5.2021.5/payara-5.2021.5.zip
+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://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>5.2021.5</payara.version>
+        <payara.version>5.2021.6</payara.version>
         <postgresql.version>42.3.3</postgresql.version>
         <solr.version>8.8.1</solr.version>
         <aws.version>1.11.762</aws.version>
@@ -315,4 +315,4 @@
         -->
     </repositories>
 
-</project>
+</project>
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-5.2021.5.zip"
+PAYARA_ZIP="$DOWNLOAD_DIR/payara-5.2021.6.zip"
 SOLR_TGZ="$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...."

diff --git a/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java b/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java
@@ -38,7 +38,7 @@
 //})
 //
 // ... but at this time we don't think we need any. The full list
-// of properties can be found at https://docs.payara.fish/community/docs/5.2021.5/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
+// of properties can be found at https://docs.payara.fish/community/docs/5.2021.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties
 //
 // All these properties cannot be configured via MPCONFIG as Payara doesn't support this (yet). To be enhanced.
 // See also https://github.com/payara/Payara/issues/5024