Big sweep: migrate codebase to Jakarta EE 10 and use Payara 6 now (third iteration)

conf/docker-aio/0prep_deps.sh

@@ -4,9 +4,9 @@ if [ ! -d dv/deps ]; then
 fi
 wdir=`pwd`
 
-if [ ! -e dv/deps/payara-5.2022.3.zip ]; then
+if [ ! -e dv/deps/payara-6.2023.7.zip ]; then
 	echo "payara dependency prep"
-	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
+	wget https://nexus.payara.fish/repository/payara-community/fish/payara/distributions/payara/6.2023.7/payara-6.2023.7.zip  -O dv/deps/payara-6.2023.7.zip
 fi
 
 if [ ! -e dv/deps/solr-8.11.1dv.tgz ]; then

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-5.2022.3.zip ; ln -s /opt/payara5 /opt/glassfish4
+RUN cd /opt ; unzip /tmp/dv/deps/payara-6.2023.7.zip ; ln -s /opt/payara6 /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?
-#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'
 
@@ -59,7 +59,7 @@ 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
+RUN ln -s /opt/payara6 /usr/local/glassfish4
 COPY dv/install/ /opt/dv/
 COPY install.bash /opt/dv/
 COPY entrypoint.bash /opt/dv/

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

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
 

conf/docker-aio/testscripts/install

@@ -1,7 +1,7 @@
 #!/bin/sh
 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

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

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>

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.

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)

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

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"

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

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
 

doc/sphinx-guides/source/admin/harvestclients.rst

@@ -35,15 +35,15 @@ For example:
 
 .. code-block:: bash
 
-  sudo touch /usr/local/payara5/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
-  sudo chown dataverse /usr/local/payara5/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
+  sudo touch /usr/local/payara6/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
+  sudo chown dataverse /usr/local/payara6/glassfish/domains/domain1/logs/stopharvest_bigarchive.70916
 
 Note: If the application server is stopped and restarted, any running harvesting jobs will be killed but may remain marked as in progress in the database. We thus recommend using the mechanism here to stop ongoing harvests prior to a server restart.
 
 
 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.

doc/sphinx-guides/source/admin/make-data-count.rst

@@ -72,10 +72,9 @@ 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/payara6/glassfish/domains/domain1/logs/mdc``
 You can also decide to display MDC metrics along with Dataverse's traditional download counts from the time before MDC was enabled. To do this, set the :ref:`:MDCStartDate` to when you started MDC logging.
 
-The following discussion assumes ``:MDCLogPath`` has been set to ``/usr/local/payara5/glassfish/domains/domain1/logs/mdc``
-
 Configure Counter Processor
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -104,7 +103,7 @@ 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``
 

doc/sphinx-guides/source/admin/troubleshooting.rst

@@ -53,15 +53,13 @@ Long-Running Ingest Jobs Have Exhausted System Resources
 
 Ingest is both CPU- and memory-intensive, and depending on your system resources and the size and format of tabular data files uploaded, may render your Dataverse installation unresponsive or nearly inoperable. It is possible to cancel these jobs by purging the ingest queue.
 
-``/usr/local/payara5/mq/bin/imqcmd -u admin query dst -t q -n DataverseIngest`` will query the DataverseIngest destination. The password, unless you have changed it, matches the username.
+``/usr/local/payara6/mq/bin/imqcmd -u admin query dst -t q -n DataverseIngest`` will query the DataverseIngest destination. The password, unless you have changed it, matches the username.
 
-``/usr/local/payara5/mq/bin/imqcmd -u admin purge dst -t q -n DataverseIngest`` will purge the DataverseIngest queue, and prompt for your confirmation.
+``/usr/local/payara6/mq/bin/imqcmd -u admin purge dst -t q -n DataverseIngest`` will purge the DataverseIngest queue, and prompt for your confirmation.
 
 Finally, list destinations to verify that the purge was successful:
 
-``/usr/local/payara5/mq/bin/imqcmd -u admin list dst``
-
-If you are still running Glassfish, substitute glassfish4 for payara5 above. If you have installed your Dataverse installation in some other location, adjust the above paths accordingly.
+``/usr/local/payara6/mq/bin/imqcmd -u admin list dst``
 
 .. _troubleshooting-payara:
 
@@ -73,7 +71,7 @@ Payara
 Finding the Payara Log File
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-``/usr/local/payara5/glassfish/domains/domain1/logs/server.log`` is the main place to look when you encounter problems (assuming you installed Payara in the default directory). Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version or commit. Send more of the stack trace (the entire file if possible) to developers who can help (see "Getting Help", below) and be sure to say which version of the Dataverse Software you have installed.
+``/usr/local/payara6/glassfish/domains/domain1/logs/server.log`` is the main place to look when you encounter problems (assuming you installed Payara in the default directory). Hopefully an error message has been logged. If there's a stack trace, it may be of interest to developers, especially they can trace line numbers back to a tagged version or commit. Send more of the stack trace (the entire file if possible) to developers who can help (see "Getting Help", below) and be sure to say which version of the Dataverse Software you have installed.
 
 .. _increase-payara-logging: