Upgrade to v4.x.y

[clemens-tolboom]

Are you ready for Rock only

• [ ] Check the new profiles datashield/rock-base:latest or datashield/rock-dolomite-xenon:latest are compatible with your needs.

Upgrade to v4 latest (pre) release

• [ ] Make sure enough space is available for the Rock only images ... use shell examples below
• [ ] If possible download them from shell docker pull beforehand
• [ ] Download latest (pre) release v4.x.y from https://github.com/molgenis/molgenis-service-armadillo/tags
• [ ] Compare/migrate to application.template.yml
• [ ] Make backup from data/system/profiles.json
• [ ] Make sure to start java with SPRING_CONFIG_ADDITIONAL_LOCATION ie in the service config ie /etc/systemd/system/armadillo.service
• [ ] Update profile images on /#/profiles are datashield/rock-base:latest or datashield/rock-dolomite-xenon:latest
• [ ] Test the profiles
• [ ] Check the version number

Clean up docker containers/images

# Check space on VM
df -H

# should contain only rock images
docker container list --all

# remove containers not needed
docker container stop <id>
docker container rm <id>

# remove unneeded images
docker image list
docker image rm <id>

[clemens-tolboom]

Steps are not correct when having the newer install scripts available on https://github.com/molgenis/molgenis-service-armadillo/tree/master/scripts/install

• [x] ~Should we use the --cleanup instead to have all reinstalled?~ ==> NO ... as data is deleted too
• [ ] Is the armadillo-check-update.sh script installed and added to cron ... which we still are not sure

[marikaris]

Steps are not correct when having the newer install scripts available on https://github.com/molgenis/molgenis-service-armadillo/tree/master/scripts/install

• [ ] Should we use the --cleanup instead to have all reinstalled?
• [ ] Is the armadillo-check-update.sh script installed and added to cron ... which we still are not sure we want

I don't think we want to use --cleanup, as I believe this throws away the data as well.

[clemens-tolboom]

Steps are missing the version intended

Download files from your version located in

• /scripts/install/armadillo-check-update.sh
• /application.template.yml

Example using v4.1.1

• https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/v4.1.1/application.template.yml
• https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/v4.1.1/scripts/install/armadillo-check-update.sh

[clemens-tolboom]

armadillo.application.yml on v4.1.1

diff --side-by-side /etc/armadillo/application.yml v4.1.1/application.template.yml 

[clemens-tolboom]

Auto upgrade

./v4.1.1/armadillo-check-update.sh 
Updater version: 0.1.0
Mode           : prd
Auto install   : n
Armadillo home : /usr/share/armadillo
Current version: 3.4.0

Current version is not upgradeable. It must be higher then 3.9999.0

What armadillo versions are available on your system

ls -l /usr/share/armadillo/application

[clemens-tolboom]

Manual change version

systemctl stop armadillo
systemctl status armadillo

cd /usr/share/armadillo/application/
ls -l
rm armadillo.jar 
ln -s /usr/share/armadillo/application/armadillo-4.1.1.jar armadillo.jar
ls -l

systemctl start armadillo
systemctl status armadillo

[clemens-tolboom]

Docker volumes

docker volume ls

# Where located
docker volume inspect ca0e9a34466a7543e42624421a332fc10266f23d0a809eb8f20933c8b15f0e9c

# Same list as above
ls -l /var/lib/docker/volumes/

# How much (seems only in kilobytes)
du -h -s /var/lib/docker/volumes/*
docker volume prune

[clemens-tolboom]

Log files

ls -l /var/log/armadillo/
ls -l /usr/share/armadillo/

less /var/log/armadillo/armadillo.log 

tail -f /var/log/armadillo/*

[clemens-tolboom]

This lead to PR #629 which got merged and released.