[GeneX-dev] Re: uploading data

[<ja...@op...>]

"Ron Ophir" <ls...@wi...> writes:

> I am one step further: I have a JAR file at the server side which
> includes the XML file and the rest. 

Good, glad to hear it. What was the problem? User Error, or a problem
in the GeneX system?

> I have stopped where the documentation stops, but no other script
> extracts the data and inserts them into GeneX. In other words what
> is next after save-expset.pl?  Harry already mentioned that it
> relate to xml2db.pl but what is the proper way to runit. Is it
> manually or save-expset.pl sould cal it.  

Right. xml2db.pl is the script you want to use. We didn't want to
automate this for every user, so we left it manual. The idea being the
DB curator get's an email, and it is up to the curator to run xml2db
and handle insertion into the DB. This concept was OK, as long as you
were running a National Resource DB (like ArrayExpress, or GEO), but
since most people want to run a lab DB, they want automated insertion
of data. Then new data loader will do that for you, the old Curation
Tool => xml2db combination is not set up that way. It should be
trivial to add it to save-experiment, though.

I'm running some test files with xml2db right now, and would be happy
to provide some pointers if you need them.

HTH,
jas.

PS. Please do reply to the list and not directly to me, this is very
useful information to all GeneX users, Thanks!