Configure XNAT Post Install

Configure Host Cron Jobs:

Several optional scripts are available to run on the host, under scripts_host directory.

cronjobs.txt - this contains suggested cronjobs.

Nginx base image is alpine and does not have cron installed. Therefore to perform logrotate, it needs to be performed as a cron job on the host server. It is HIGHLY recommended to install this, else your nginx log files will increase to a very large size.

site_monitor.sh: This will restart the xnat containers if the server is not responding.

You may want to rsync backups from the server. A cronjob exists to do this.

Configure Container Service registry:

As of XNAT 1.9, the container service sets the Image Hosts registry as https..dockerhub. This will fail with Swarm mode enabled, and 'https://' must be removed. Edit the settings. If using a private registry, omit the https://.

Click on Plugin Settings under Administer.
Click on Edit for the registry: Compute Backend -> Image Hosts -> Edit
remove https:// - https:// hub.docker.com -> hub.docker.com

Set new admin password, Disable Default Admin and Guest users:

Log on as user: admin, pwd: admin.
Click on Users under Administer.
Click on the xnat_admin user defined in xnat.cfg. Make sure the user is Verified and Enabled. Click on Change Password to set a new password.
Click Save
Log off the default Admin user. Log on using the new admin account. Go back to the Users page.
Click on user Admin.
Deselect Enabled.
Repeat for Guest.

add_user

Adding LDAP server.

Under ./Linux/LDAP is a script and instructions to install LDAP connectivity. You need the LDAP xnat plugin installed (configure in xnat.cfg).

Please read the documentaion fully:

https://wiki.xnat.org/xnat-tools/xnat-ldap-authentication-plugin

In ./Linux/LDAP edit the *-provider.properties file(s) with your authenticator server(s).

Run:

docker build -f Dockerfile-add-ldap -t xnat:ldap .

Note, if you are not using the default xnat:latest docker image in your docker-compose.yml file, then edit Dockerfile-add-ldap before running the above, using your image as the base image.

Change the docker image used by xnat-web in docker-compose.yml to xnat-ldap and run ./restart.sh

In User Auth Settings add additional authenticator, for example:

localdb,ldapsandbox

The dockerfile-add-ldap file adds the authenticator properties file inside the container:

/data/xnat/home/config/auth/

Adding External Storage:

The archive, database and log files are localted int eh /xnat-data directory as explained the XNAT Setup Overview

To change the location, for example locating the archive data on external storage, read Maintenance and Scripts

Backup

You can backup all the containers and storage using the script:

cd Linux sudo ./save_and_restore.sh save

This will create a directory backup. Back this up.

All the storage is located by default under /xnat-data.

The archive is located in:

/xnat-data/xnat/archive

The postgresql database is located in:

/xnat-data/postgresql

A nightly dump of the database is made:

/xnat-data/xnat/scripts/pg_dump

These should be regularly backed up. For example, if you ahve network storage, you could sync this folder nightly and add as a nightly job. This example syncs pg_dump at 2am every night:

sudo crontab -l > mycronjobs
echo "00 02 * * * rsync -avu --delete /xnat-data/xnat/scripts/pg_dump  [path to network location]" >> mycronjobs
sudo crontab -u root mycronjobs