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8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

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8ae137e
build!(deps): move dependencies to Jakarta EE 9.1 and Payara 6 #8305
poikilotherm Mar 23, 2022
3463aeb
refactor!(dataverse): move all usage of Java EE to Jakarta EE namespa…
poikilotherm Mar 23, 2022
177bd3d
build!(deps): switch to Primefaces 11 Jakarta Edition #8305
poikilotherm Mar 23, 2022
d8f1315
build(sword): switch to Jakarta-enabled SWORD2 preview release #8305
poikilotherm Mar 24, 2022
194607b
build(api): align Jersey deps with BOMs #8305
poikilotherm Mar 24, 2022
7943bdf
fix(sword): add exception signature in service doc servlet init() #8305
poikilotherm Mar 24, 2022
9b5aa41
build(deps): update to Jakartafied JSONLD library version #8305
poikilotherm Mar 24, 2022
8ef62d8
refactor(webapp): migrate web.xml to Jakarta Faces #8305
poikilotherm Mar 25, 2022
4b331ca
docs: fix Jakarta occurences in code comments #8305
poikilotherm Mar 25, 2022
aff1e25
fix(ingest): migrate JMS interface class string to Jakarta #8305
poikilotherm Mar 25, 2022
4f9f0c5
refactor(api): make Index API check on most specific exception type o…
poikilotherm Mar 25, 2022
35a5c34
style(webapp): switch URL path to Jakarta Faces #8305
poikilotherm Mar 25, 2022
099ad54
fix(webapp): remove deleted Primefaces PushServlet from web.xml #8305
poikilotherm Mar 25, 2022
10d85b4
chore(persistence): migrate persistence.xml to Jakarta EE 9 #8305
poikilotherm Mar 25, 2022
340f773
chore(jsf): migrate Faces config and web.xml to Jakarta EE 9 #8305
poikilotherm Mar 25, 2022
f7234c4
chore(cdi): migrate Bean config to Jakarta EE 9 #8305
poikilotherm Mar 25, 2022
b771d83
update docker-aio for Payara 6 #8305
pdurbin May 18, 2022
7e8c71e
Merge pull request #546 from IQSS/8305-payara6-docker-aio
poikilotherm May 19, 2022
d37af1d
get prettyfaces/rewrite working on EE9+
pdurbin May 24, 2022
ebcbb84
Merge branch 'develop' into payara6
pdurbin May 24, 2022
5083d63
#8305 Vagrantfile.payara6 deploys 8305-payara6 warfile on payara-6.20…
May 25, 2022
dfa2aa9
#8305 update Vagrantfile, don't provide second/testing copy
May 25, 2022
1c4595c
Merge pull request #8741 from OdumInstitute/origin/8305-payara6
pdurbin May 25, 2022
1fce7cd
update installer and dev guide for Payara 6 #8305
pdurbin May 25, 2022
6f54d1f
revert f7234c41fc (stick with bean-discovery-mode="all" for now) #8305
pdurbin May 27, 2022
d86e220
as of Payara 6, "attachment; " required to upload files to SWORD #8305
pdurbin May 27, 2022
8be36a3
stop using `@Context HttpServletRequest`, add sleep #8305
pdurbin Jun 3, 2022
54d465c
Merge branch 'develop' into 8305-payara6 #8305
pdurbin Jun 3, 2022
b1323e5
change Payara 5 to 6 in guides #8305
pdurbin Jun 3, 2022
ca7d3ab
change payara5 to 6 for jhove, other scripts #8305
pdurbin Jun 3, 2022
d1a19f3
Merge branch 'develop' into 8305-payara6
poikilotherm Jul 20, 2022
5cdfadf
refactor(mail): switch leftover import to Jakarta EE #8305
poikilotherm Jul 20, 2022
978f197
chore(deps): switch to Payara 6.2022.1-Alpha3 and Jakarta EE 10 #8305
poikilotherm Jul 20, 2022
0638e35
chore(deps): migrate to Jakarta EE 10 dependencies #8305
poikilotherm Jul 20, 2022
5a8a7a1
chore(deps): switch to Jakartified prettyfaces #8305
poikilotherm Jul 25, 2022
75fa11d
fix(deps): temporary remove PrettyFaces #8305
poikilotherm Jul 27, 2022
aeaba00
fix(deps): remove usages of PrettyFaces String utils
poikilotherm Jul 27, 2022
8d5e912
fix(deps): temporal remove of PrettyFaces Context #8305
poikilotherm Jul 27, 2022
ea0a346
Revert "fix(deps): temporary remove PrettyFaces #8305"
poikilotherm Oct 31, 2022
eb8f107
Revert "fix(deps): temporal remove of PrettyFaces Context #8305"
poikilotherm Oct 31, 2022
e1ced89
build(deps): upgrade to EE10 compatible release of Prettyfaces
poikilotherm Oct 31, 2022
a294f06
Merge branch 'develop' into 8305-payara6-ee10
poikilotherm Oct 31, 2022
643d8d2
build: update to Payara 6.2022.1.Alpha4 #8305
poikilotherm Oct 31, 2022
af6399b
build(deps): add second Maven Central snapshot repository
poikilotherm Nov 2, 2022
2e90978
build(deps): switch to Prettyfaces 6.0 snapshots
poikilotherm Nov 2, 2022
ed2941d
build(deps): remove Jakarta staging repository
poikilotherm Nov 2, 2022
c83e8b1
Merge branch 'develop' into 8305-payara6-ee10
poikilotherm Nov 2, 2022
8d633ef
fix(docker-aio): typo in Payara archive URL
poikilotherm Nov 2, 2022
2c97a9e
chore(deps): migrate new classes from develop to Jakarta EE namespace…
poikilotherm Nov 2, 2022
8e57027
fix path to asadmin #8305
pdurbin Nov 2, 2022
5a9ec90
build,doc: upgrade to Payara 6.2022.1 release
poikilotherm Nov 3, 2022
5155c70
"fixes" for the broken citation download links on the dataset and fil…
landreev Jan 10, 2023
a867538
Merge pull request #9271 from IQSS/8305-payara6-ee10-citationdownload…
poikilotherm Jan 10, 2023
c0fb759
Merge branch 'develop' into 8305-payara6-ee10
poikilotherm Jan 16, 2023
46d6c1f
chore(build): update to Payara 6.2022.2 release #8305
poikilotherm Jan 16, 2023
d58c507
tiny doc change to trigger CI (not sure which version) #8305
pdurbin Jan 26, 2023
53559a4
Merge branch 'develop' into 8305-payara6-ee10
poikilotherm Mar 16, 2023
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2 changes: 1 addition & 1 deletion Vagrantfile
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions conf/docker-aio/0prep_deps.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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-6.2022.1.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://s3.eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/6.2022.1/payara-6.2022.1.zip -O dv/deps/payara-6.2022.1.zip
fi

if [ ! -e dv/deps/solr-8.11.1dv.tgz ]; then
Expand Down
6 changes: 2 additions & 4 deletions conf/docker-aio/c8.dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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-6.2022.1.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'

Expand Down Expand Up @@ -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/
Expand Down
2 changes: 1 addition & 1 deletion conf/docker-aio/configure_doi.bash
Original file line number Diff line number Diff line change
@@ -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
Expand Down
2 changes: 1 addition & 1 deletion conf/docker-aio/entrypoint.bash
Original file line number Diff line number Diff line change
Expand Up @@ -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

4 changes: 3 additions & 1 deletion conf/docker-aio/setupIT.bash
Original file line number Diff line number Diff line change
Expand Up @@ -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

2 changes: 1 addition & 1 deletion conf/docker-aio/seturl.bash
Original file line number Diff line number Diff line change
@@ -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/glassfish/bin/asadmin create-jvm-options "\"-Ddataverse.siteUrl=http\://localhost\:8084\""
5 changes: 3 additions & 2 deletions conf/docker-aio/testscripts/install
Original file line number Diff line number Diff line change
@@ -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
Expand Down
2 changes: 2 additions & 0 deletions conf/docker-aio/testscripts/post
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion conf/jhove/jhove.conf
Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand Down
3 changes: 3 additions & 0 deletions doc/release-notes/8305-payara6.md
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 number Diff line change
@@ -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.
Expand Down
Original file line number Diff 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
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down

This file was deleted.

2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/_static/util/clear_timer.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/_static/util/counter_daily.sh
Original file line number Diff line number Diff line change
@@ -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

Expand Down
2 changes: 1 addition & 1 deletion doc/sphinx-guides/source/admin/harvestclients.rst
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,6 @@ Note: If the application server is stopped and restarted, any running harvesting
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.
4 changes: 2 additions & 2 deletions doc/sphinx-guides/source/admin/make-data-count.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -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``

Expand Down
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