Hello, Thanks to the helpfull message of John, I am now able to backup and retrieve my users from a galaxy to another without using directly the database (by using the galaxy model and sql alchemy). I am trying to do the same thing for workflows, libraries, datasets and histories. The repository is here: https://github.com/remyd1/galaxy_backup Any interest/participation is welcome. Best Regards Remy 2014-11-21 17:50 GMT+01:00 John Chilton <jmchilton@gmail.com>:
This is a tough question - I suspect it will be difficult no matter how you proceed. The API objects don't map 100% directly to database objects and may not have complete coverage - but using the database directly will require one to learn a lot of Galaxy's data model I suspect.
A middle ground - would be to just use the Galaxy code and ORM layer without running a Galaxy server (see scripts/db_shell.py for instance).
My gut tells me it is probably be easiest (least difficult anyway) to target the database directly - but this could be wrong.
-John
Hi,
I would like to create a code to backup and migrate(*) galaxy datas,
On Wed, Nov 19, 2014 at 6:21 AM, Rémy Dernat <remy.d1@gmail.com> wrote: based
on the api and/or with the script I did here:
https://github.com/remyd1/galaxy_debug_params/blob/master/source/Templates/p...
To do that, I would use the galaxy model, to retrieve everything in the
one and recreate everything in the new one.
However, I would like to be able to do that without my web server running. That is to say, a "cold" migration to avoid any current task to write additionnal things into the database. Obviously, that is a problem for
old the
api because this one use the web server.
Could you give some advice to do that ? Should I recreate a code from 0 ? Could I use the code in the api ? Is there a way to create a code that could use the api differently (recreate a copy of the api without the web server) ?
Kind regards,
Remy
(*) this is important; that means you could import data from an old galaxy to a recent one (or the opposite); a simple backup of files and a dump of the db is not enough.
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