Journal System Upgrade
To upgrade OJS this general process is used. I run all the backup processes as my osgeo1 user account in ~/backup/ojs.
Backup Database
Dump ojs database into a sql dump file. Takes about 5 seconds and produces a file that is only a couple megabytes.
sudo mysqldump ojs > ojs-2.2.0-pre-upgrade-2.3.mysql
Backup File System
Main files are in /var/www/ojs2. Two folders need to be backed up, the files and htdocs. Only the htdocs files will end up being updated, but they suggest backing up both.
The files folder will always be larger as all the uploaded abstracts, finals PDFs, etc. are in there - pretty important :) It's about 350MB at time of writing. Creating the tgz file takes about 5 minutes and is about 315MB in size.
sudo tar -czvf ojs-2.2.0-files.tgz /var/www/ojs2/files
Next back up the htdocs folder. Several past versions of OJS are also installed, with htdocs being symlinked to the current version.