Re: [GUSDEV] Generic GUS data loader for tab delimited files

[Terry C. <tc...@it...>]

Dear Eric,
We have a such an effort underway using XML formatted input data. 
Here's a pointer to the project 
  http://flora.ittc.ku.edu/xmlgus/
This method requires
  some_format -> GUS' XML -> GUS object layer

The system, running as a plugin, reads input in a GUS XML format that
is formatted to correspond with relational tables and GUS objects. 
The mapping is instantiated in the XMLGUS framework as a YACC grammar 
chosen for structure and the declarative approach for the plugin.
We're adding automation to some of the intermediate steps presently.
I'd be happy to help you try this out if you are interested.

all the best,

Terry

On  0, "Eric E. Snyder" <es...@vb...> wrote:
> Dear GUSdev,
> 
> We have been having some trouble loading DNA annotation data via the 
> gbparser plugin. We have been able to get around the problem in this 
> instance by using addrow, which is quite general but impossibly slow. I 
> cannot help but think there must be a generic tool for loading 
> tab-delimited data files into GUS.
> 
> Assuming there isn't, I think it would be time well spent if someone 
> wrote a plugin for GUS that would *efficiently* load data in 
> tab-delimited format based on instructions described in a 
> general-purpose data description file.  This file would identify the 
> tables and fields corresponding to each column in the input file.  It 
> would also need to define the rules for associating data from records 
> stored in multiple tables and probably do other things as well.
> 
> Any takers?  I would be happy to spend whatever time is necessary to 
> define the requirements for such a system.  If it doesn't already exist 
> somewhere in the GUS community, I certainly think it would be useful.
> 
> I apologize in advance if this is a recent or frequent topic for this 
> list.  I just subscribed and wasn't able to access sourceforge to check 
> the archives.
> 
> Thanks!
> eesnyder
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Washington Street Phase 1 (0447)
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061
> USA
> 
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