As of Chado version 1.2, the Chado software distribution comes with a tool to upgrade the Chado schema from an old version (1.0 or newer) to a new one. This tool, gmod_update_chado.pl, will get installed with other scripts when you execute “make install” and depends on another tool, gmod_chado_properties.pl, which determines the version of the current Chado database and is also installed when you install Chado.
NOTE: Since this is a new tool, I strongly suggest you back up your database before trying to upgrade via this method! You have been warned! :-)
To use the updater, you can start the installation like you normally would:
perl Makefile.PL
make
sudo make install
and then, rather than doing the next step (make load_schema) which would wipe out the current database, do
make update
which will (hopefully) do the updating for you. Note that if you modified the schema after you installed Chado the last time, this update may fail. Please watch the output from the PostgreSQL server to look for “ERROR” statements.
You can also run this updater on the command line to update any Chado database by providing it’s name, like this:
gmod_update_chado.pl --dbprofile chado_db_name
which will make use of the database connection parameters stored in that database’s configuration file in $GMOD_ROOT/conf.
If you experience problems with this updating protocol, please send comments, questions and issue reports to gmod-schema@lists.sourceforge.net.