Activation scripts and module files for users#

The core deployment will create activation scripts for various shell flavours. The following activation scripts are located in the <root_dir>/freva folder:

  • activate_sh: To be sourced by shell flavours like shell, bash, zsh etc.

  • activate_csh: To be sourced by c-shell flavours like csh, tcsh

  • activate_fish: To be source by fish

  • loadfreva.module: Modules file The source scripts can either be copied where they are automatically sourced or users can be instructed to use the source command for their shell. If modules is available on the host system you can copy the loadfreva.modules file into the MODULEPATH location.

Databrowser, database and web services:#

If the target machine where the services (databrowser, mariadb, web) were deployed are Linux machines you will have access to a systemd unit of the created service. In general the services can be accessed by <project_name>-<service_name>.service If for example the project_name key was set to clex-ces then the following services are created:

  • database: clex-ces-db.service, clex-ces-vault.serice

  • databrowser: clex-ces-databrowser.service

  • web ui: clex-ces-web.service

Note: If you have set up the services as an unprivileged user you need to access the services with help of the --user flag for example:

systemclt --user restart clex-ces-web.service

Access of service data on the host machine#

The data of the services, like the database or databrowser cores are stored “outside” the docker containers on the host machine. The default location for all the service data is /opt/freva or whatever folder was set as data_path variable. The following logic applies:

  • <data_path>/services/<project_name>/<service_name>_service/

for example:

  • /opt/freva/services/clex-ces/db_service

The compose files are also located in the <data_path> location, for example:

  • /opt/freva/services/compose_services

Simple backup scripts:#

The db and databrowser services offer a very simple backup script that can be run from outside the container. To issue a backup command simply call the following command docker/podman exec -it <project_name>-solr/db /usr/local/bin/daily_backup. For example:

podman exec -it clex-ces-solr /usr/local/bin/daily_backup

If you have anacron set up on your host machine then a cron script to automatically backup databases and solr cores is applied nightly. By default the script keeps the last 7 backups. Backup data can be found in:

  • db:/opt/freva/<project_name>/db_service>/backup

  • solr: /opt/freva/<project_name>/solr_service/<core_name>/data/snapshot.YYYYMMDDHHMMSSMS

This is only a rudimentary backup solution, ideally you should transfer those backups regularly to a different location. You can also disable this rudimentary backup strategy by deleting the backup scripts in /etc/cron.daily and replace it by a more sophisticated backup mechanism.

Note: If you have set up the services as an unprivileged user you can access the backup scripts using the crontab command.

The web UI admin Panel#

The web user interface is manged by django which offers a powerful admin panel to manage users, user history and add additional links as so called flat pages. More information on the django admin panel can be found online. To access the admin panel you will first have to login as user freva-admin using the master password you’ve created during deployment. Once logged in as freva-admin you should navigate to /admin of your homepage. For example https://www.clex.nci.org.au/admin assuming the web page url is https://www.clex.nci.org.au. Here you can transfer admin rights to other users, like your user name. Or create new flat-pages. Flat-pages are useful to create additional project specific information that can be displayed on the website. This information can be links to plugin documentation or legal notes (see below).

Adding privacy notes and terms of conditions to the Web UI#

For some incitations it might be necessary to add legal statements on privacy and terms of usage. Those statements can be added as flat-pages in the django admin panel. All flat-pages starting with the url /legal for example /legal/privacy/ will be added as a link to the footer of home page. Examples of the content of such flat-pages can be found in the Appendix.

On this page