Release Notes - Yoda v2.1

Version: 2.1

Released: TBA

What’s new

Changes affecting functionality for data stewards and researchers

Changes affecting technical administrators

Other changes

iRODS: upgrade to v5.0.2
Python-irodsclient: update to v3.2.0
GoCommands: update to v0.11.6
Flask and dependencies: update to v3.1.3
Mailpit: update to v1.29.3

Known issues

Deadlock in msiDataObjRepl & msiDataObjCopy when called from Python (irods_rule_engine_plugin_python#54)

Upgrading from previous release

Software version requirements

The playbook requires Ansible 2.16.x or higher.

Version constraints:

Requires Yoda external user service to be on version 2.0.x or higher.
Requires Yoda public server to be on version 2.0.x or higher.

Upgrade process

Backup/copy custom configurations made to Yoda version 2.0.4 To view what files were changed from the defaults, run git diff.
After ensuring the configurations are stored safely in another folder, reset the Yoda folder using git stash or when you want to delete all changes made: git reset --hard.
Check out the v2.1.0-alpha.0 tag of the Yoda Git repository:
```
git checkout v2.1.0-alpha.0
```
Set the Yoda version to v2.1.0-alpha.0 in the configuration:
```
yoda_version: v2.1.0-alpha.0
```
If the old configuration contained an iRODS authentication scheme setting, update it to use pam_password. Example:
```
irods_authentication_scheme: pam_password
```
It is recommended to explicitly set the Ansible interpreter path in the group_vars (if the Yoda environment servers all have the same Linux distribution) or in the host_vars (if they have different Linux distributions) in order to prevent problems with Ansible using a different interpreter than expected.

For EL 9 environments:

  ansible_python_interpreter: /usr/bin/python3.9

For Ubuntu 24.04 LTS environments:

  ansible_python_interpreter: /usr/bin/python3.12

Install all Ansible collections needed to deploy Yoda:

ansible-galaxy collection install -r requirements.yml

Run the Ansible playbook in check mode:

ansible-playbook -i <path-to-your-environment> playbook.yml --check
### EXAMPLE ###
ansible-playbook -i /environments/development/allinone playbook.yml --check

If the playbook has finished successfully in check mode, run the Ansible playbook normally:

ansible-playbook -i <path-to-your-environment> playbook.yml
### EXAMPLE ###
ansible-playbook -i /environments/development/allinone playbook.yml

Update publication endpoints if there are published packages (DataCite, landingpages and OAI-PMH):

irule -r irods_rule_engine_plugin-irods_rule_language-instance -F /etc/irods/yoda-ruleset/tools/update-publications.r

Manually restart Apache on all portal and WebDAV servers

On Ubuntu:

sudo systemctl restart apache2

On RHEL:

sudo systemctl restart httpd

Manually restart the portal application on all portal servers

sudo touch /var/www/yoda/yoda.wsgi /var/www/yoda/yoda_debug.wsgi