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Armadillo minor release update

Minor Version Upgrade Manual: Procedures for y.z Releases

Note

This manual is intended for minor version updates within the latest major release. For example, you can use it to update from version 4.1 to 4.7.1. For upgrading to a new major version, please refer to the specific manuals dedicated to major version upgrades.

Check latest version

For the latest 4.y.z release check https://github.com/molgenis/molgenis-service-armadillo/releases/latest. This will redirect to a v4.y.z page.

Updating Armadillo

1. Stop docker containers

First, log in to the Armadillo UI and navigate to the Profiles tab. Now, click 'Stop' for each profile listed.

Next, stop any unnecessary containers.

The commands provided are indicative, so adjust them as needed.

# should return empty list (i.e. default, xenon, rock)
docker container list

# remove containers not needed
docker container stop <id>

2. Download required files

Make a note of the version number ie. v4.7.1 as you need to download some files from the terminal using the update script.

2.1 Update script

You need to be root user.

cd /root

# Make sure to change the versions number v4.y.z
mkdir v4.y.z
cd v4.y.z

# Check directory location
pwd

# Change the version number v4.y.z then run command
wget https://raw.githubusercontent.com/molgenis/molgenis-service-armadillo/v4.y.z/scripts/install/armadillo-check-update.sh

Make the script executable:

chmod u+x armadillo-check-update.sh

2.2 Run update script

You can run the following script to download the new Armadillo version.

Tip

The output could help us to help you fix problems.

# Change the version number v4.y.z
./armadillo-check-update.sh 4.y.z

Once the script has completed, you can verify that the Armadillo JAR file has been downloaded by checking the directory:

# See all jar files on your system
ls -ltr /usr/share/armadillo/application/

3. Make backup of system config

# Still in the correct directory? (`/root/v4.y.z`)
pwd

We make a backup into the same v4.y.z directory but that is not strictly needed.

cp -r /usr/share/armadillo/data/system ./

should result in:

ls system/
# access.json  profiles.json

4. Restart application using new version

Armadillo has not yet been updated, follow the following steps to do so:

4.1 Stop Armadillo

systemctl stop armadillo

# List application files
ls -l /usr/share/armadillo/application/

# Remove the linked file
rm /usr/share/armadillo/application/armadillo.jar

# Attach new linked file and dont forget to change the version number v4.y.z
ln -s /usr/share/armadillo/application/armadillo-4.y.z.jar /usr/share/armadillo/application/armadillo.jar

# Check result
ls -l /usr/share/armadillo/application/

4.3 Restart Armadillo

systemctl start armadillo
systemctl status armadillo

5. Log on to the UI

Go to your armadillo website. Is the version in the left top corner updated? This means the update was successful.

6. Start profiles

Login into the website and go to the profiles tab. Now you can start all the profiles again.

Everything should now be working correctly. You can try and login to your server via the central analysis server, using the DSMolgenisArmadillo (2.0.5 or up) package to test.