IQSS · pdurbin · Mar 23, 2022 · Mar 23, 2022 · Mar 23, 2022 · Mar 24, 2022
diff --git a/Vagrantfile b/Vagrantfile
@@ -4,7 +4,7 @@
 VAGRANTFILE_API_VERSION = "2"
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
-  config.vm.box = "bento/rockylinux-8.4"
+  config.vm.box = "bento/rockylinux-8.5"
 
   config.vm.provider "virtualbox" do |vbox|
     vbox.cpus = 4

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-6.2022.1.Alpha2.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/6.2022.1.Alpha2/payara-6.2022.1.Alpha2.zip -O dv/deps/payara-6.2022.1.Alpha2.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
@@ -24,11 +24,11 @@ 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-6.2022.1.Alpha2.zip
 
 # 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?
-#COPY domain-restmonitor.xml /opt/payara5/glassfish/domains/domain1/config/domain.xml
+#COPY domain-restmonitor.xml /opt/payara6/glassfish/domains/domain1/config/domain.xml
 
 RUN sudo -u postgres /usr/pgsql-13/bin/initdb -D /var/lib/pgsql/13/data -E 'UTF-8'
 
@@ -58,8 +58,6 @@ EXPOSE 9009
 
 RUN mkdir /opt/dv
 
-# keeping the symlink on the off chance that something else is still assuming /usr/local/glassfish4
-RUN ln -s /opt/payara5 /usr/local/glassfish4
 COPY dv/install/ /opt/dv/
 COPY install.bash /opt/dv/
 COPY entrypoint.bash /opt/dv/

diff --git a/conf/docker-aio/configure_doi.bash b/conf/docker-aio/configure_doi.bash
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-cd /opt/payara5
+cd /opt/payara6
 
 # if appropriate; reconfigure PID provider on the basis of environmental variables.
 if [ ! -z "${DoiProvider}" ]; then

diff --git a/conf/docker-aio/entrypoint.bash b/conf/docker-aio/entrypoint.bash
@@ -10,7 +10,7 @@ bin/solr create_core -c collection1 -d server/solr/collection1/conf -force
 apachectl -DFOREGROUND &
 
 # TODO: Run Payara as non-root.
-cd /opt/payara5
+cd /opt/payara6
 bin/asadmin start-domain --debug
 sleep infinity
 
diff --git a/conf/docker-aio/setupIT.bash b/conf/docker-aio/setupIT.bash
@@ -7,7 +7,9 @@ unzip dvinstall.zip
 cd /opt/dv/testdata
 ./scripts/deploy/phoenix.dataverse.org/prep
 ./db.sh
+echo "Calling install (bash script) from setupIT.bash..."
 ./install # modified from phoenix
-/usr/local/glassfish4/glassfish/bin/asadmin deploy /opt/dv/dvinstall/dataverse.war
+/opt/payara6/glassfish/bin/asadmin deploy /opt/dv/dvinstall/dataverse.war
+echo "Calling post (bash script) from setupIT.bash..."
 ./post # modified from phoenix
 
diff --git a/conf/docker-aio/seturl.bash b/conf/docker-aio/seturl.bash
@@ -1,3 +1,3 @@
 #!/usr/bin/env bash
 
-docker exec dv /usr/local/glassfish4/bin/asadmin create-jvm-options "\"-Ddataverse.siteUrl=http\://localhost\:8084\""
+docker exec dv /opt/payara6/bin/asadmin create-jvm-options "\"-Ddataverse.siteUrl=http\://localhost\:8084\""
diff --git a/conf/docker-aio/testscripts/install b/conf/docker-aio/testscripts/install
@@ -1,7 +1,8 @@
 #!/bin/sh
+echo "Calling testscripts/install..."
 export HOST_ADDRESS=localhost
-export GLASSFISH_ROOT=/opt/payara5
-export FILES_DIR=/opt/payara5/glassfish/domains/domain1/files
+export GLASSFISH_ROOT=/opt/payara6
+export FILES_DIR=/opt/payara6/glassfish/domains/domain1/files
 export DB_NAME=dvndb
 export DB_PORT=5432
 export DB_HOST=localhost

diff --git a/conf/docker-aio/testscripts/post b/conf/docker-aio/testscripts/post
@@ -6,6 +6,8 @@ psql -U dvnapp dvndb -f doc/sphinx-guides/source/_static/util/createsequence.sql
 scripts/search/tests/publish-dataverse-root
 #git checkout scripts/api/data/dv-root.json
 scripts/search/tests/grant-authusers-add-on-root
+echo "exiting post script early (not creating test users, etc.)"
+exit
 scripts/search/populate-users
 scripts/search/create-users
 scripts/search/tests/create-all-and-test

diff --git a/conf/jhove/jhove.conf b/conf/jhove/jhove.conf
@@ -3,7 +3,7 @@
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xmlns="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig"
  xsi:schemaLocation="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig
-                     file:///usr/local/payara5/glassfish/domains/domain1/config/jhoveConfig.xsd">
+                     file:///usr/local/payara6/glassfish/domains/domain1/config/jhoveConfig.xsd">
  <jhoveHome>/usr/local/src/jhove</jhoveHome>
  <defaultEncoding>utf-8</defaultEncoding>
  <tempDirectory>/tmp</tempDirectory>

diff --git a/doc/release-notes/8305-payara6.md b/doc/release-notes/8305-payara6.md
@@ -0,0 +1,3 @@
+## Backward Incompatible Changes
+
+- To upload files, the SWORD API now requires "Content-Disposition: attachment; filename=example.zip" rather than "Content-Disposition: filename=example.zip".
diff --git a/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml b/doc/sphinx-guides/source/_static/admin/counter-processor-config.yaml
@@ -1,8 +1,8 @@
 # currently no other option but to have daily logs and have year-month-day format in the name with
 # 4-digit year and 2-digit month and day
-# /usr/local/payara5/glassfish/domains/domain1/logs/counter_2019-01-11.log
+# /usr/local/payara6/glassfish/domains/domain1/logs/counter_2019-01-11.log
 #log_name_pattern: sample_logs/counter_(yyyy-mm-dd).log
-log_name_pattern: /usr/local/payara5/glassfish/domains/domain1/logs/mdc/counter_(yyyy-mm-dd).log
+log_name_pattern: /usr/local/payara6/glassfish/domains/domain1/logs/mdc/counter_(yyyy-mm-dd).log
 
 # path_types regular expressions allow matching to classify page urls as either an investigation or request
 # based on specific URL structure for your system.

diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.root
@@ -4,7 +4,7 @@
 
 set -e
 
-ASADMIN=/usr/local/payara5/bin/asadmin
+ASADMIN=/usr/local/payara6/bin/asadmin
 
 case "$1" in
   start)

diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service b/doc/sphinx-guides/source/_static/installation/files/etc/init.d/payara.init.service
@@ -3,7 +3,7 @@
 # description: Payara App Server
 set -e
 
-ASADMIN=/usr/local/payara5/bin/asadmin
+ASADMIN=/usr/local/payara6/bin/asadmin
 APP_SERVER_USER=dataverse
 
 case "$1" in

diff --git a/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service b/doc/sphinx-guides/source/_static/installation/files/etc/systemd/payara.service
@@ -4,9 +4,9 @@ After = syslog.target network.target
 
 [Service]
 Type = forking
-ExecStart = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar start-domain
-ExecStop = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar stop-domain
-ExecReload = /usr/bin/java -jar /usr/local/payara5/glassfish/lib/client/appserver-cli.jar restart-domain
+ExecStart = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar start-domain
+ExecStop = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar stop-domain
+ExecReload = /usr/bin/java -jar /usr/local/payara6/glassfish/lib/client/appserver-cli.jar restart-domain
 User=dataverse
 LimitNOFILE=32768
 Environment="LANG=en_US.UTF-8"

diff --git a/.../installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties b/.../installation/files/usr/local/payara5/glassfish/domains/domain1/config/logging.properties
diff --git a/doc/sphinx-guides/source/_static/util/clear_timer.sh b/doc/sphinx-guides/source/_static/util/clear_timer.sh
@@ -8,7 +8,7 @@
 # if you'd like to avoid that.
 
 # directory where Payara is installed
-PAYARA_DIR=/usr/local/payara5
+PAYARA_DIR=/usr/local/payara6
 
 # directory within Payara (defaults)
 DV_DIR=${PAYARA_DIR}/glassfish/domains/domain1

diff --git a/doc/sphinx-guides/source/_static/util/counter_daily.sh b/doc/sphinx-guides/source/_static/util/counter_daily.sh
@@ -1,7 +1,7 @@
 #! /bin/bash
 
 COUNTER_PROCESSOR_DIRECTORY="/usr/local/counter-processor-0.1.04"
-MDC_LOG_DIRECTORY="/usr/local/payara5/glassfish/domains/domain1/logs/mdc"
+MDC_LOG_DIRECTORY="/usr/local/payara6/glassfish/domains/domain1/logs/mdc"
 
 # counter_daily.sh
 

diff --git a/doc/sphinx-guides/source/admin/harvestclients.rst b/doc/sphinx-guides/source/admin/harvestclients.rst
@@ -24,6 +24,6 @@ The process of creating a new, or editing an existing client, is largely self-ex
 What if a Run Fails?
 ~~~~~~~~~~~~~~~~~~~~
 
-Each harvesting client run logs a separate file per run to the app server's default logging directory (``/usr/local/payara5/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format  ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
+Each harvesting client run logs a separate file per run to the app server's default logging directory (``/usr/local/payara6/glassfish/domains/domain1/logs/`` unless you've changed it). Look for filenames in the format  ``harvest_TARGET_YYYY_MM_DD_timestamp.log`` to get a better idea of what's going wrong.
 
 Note that you'll want to run a minimum of Dataverse Software 4.6, optimally 4.18 or beyond, for the best OAI-PMH interoperability.
diff --git a/doc/sphinx-guides/source/admin/make-data-count.rst b/doc/sphinx-guides/source/admin/make-data-count.rst
@@ -72,7 +72,7 @@ Enable or Disable Display of Make Data Count Metrics
 
 By default, when MDC logging is enabled (when ``:MDCLogPath`` is set), your Dataverse installation will display MDC metrics instead of it's internal (legacy) metrics. You can avoid this (e.g. to collect MDC metrics for some period of time before starting to display them) by setting ``:DisplayMDCMetrics`` to false.
 
-The following discussion assumes ``:MDCLogPath`` has been set to ``/usr/local/payara5/glassfish/domains/domain1/logs/mdc``
+The following discussion assumes ``:MDCLogPath`` has been set to ``/usr/local/payara6/glassfish/domains/domain1/logs/mdc``
 
 Configure Counter Processor
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -102,7 +102,7 @@ Soon we will be setting up a cron job to run nightly but we start with a single
 
 * If you are running Counter Processor for the first time in the middle of a month, you will need create blank log files for the previous days. e.g.:
 
-  * ``cd /usr/local/payara5/glassfish/domains/domain1/logs/mdc``
+  * ``cd /usr/local/payara6/glassfish/domains/domain1/logs/mdc``
 
   * ``touch counter_2019-02-01.log``
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		## Backward Incompatible Changes

		- To upload files, the SWORD API now requires "Content-Disposition: attachment; filename=example.zip" rather than "Content-Disposition: filename=example.zip".
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,7 @@ @@
     set -e
-    ASADMIN=/usr/local/payara5/bin/asadmin
+    ASADMIN=/usr/local/payara6/bin/asadmin
     case "$1" in
       start)
@@ Expand Down @@