Re: [Gusdev-gusdev] Problem loading Pfam data into GUS

[Steve F. <sfi...@pc...>]

madhura-  i am real busy right now, so, quickly, i think the problem is 
that the data has links to medline entries.   the plugin wants to insert 
that link, and do it in a formal way.    we represent external links in 
two tables (the ones mentioned in the error message).    you need to add 
a row in ExternalDatabase for medline, and one in 
ExternalDatabaseRelease.  I'll write shortly with what we have in our db 
for this.

steve

Madhura Sharangpani wrote:

> Hi
>  
> I am trying again to load Pfam data into GUS using LoadPfam plugin, 
> but after registering the LoadPfam plugin successfully, when I try 
> loading data into database, I get the following error:
>
> ***************************************************
> elaine15:~/RA/pfam> ga
> GUS::Common::Plugin::LoadPfam --parse_only --flat_file=Pfam-A.full.gz 
> --rele
> ase=13.0
> Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
> ImportPfam: COMMIT OFF
> ImportPfam: reading Pfam release 13.0 from Pfam-A.full.gz
> 0: PF00244.7
> Unable to find most recent ExternalDatabaseRelease for ExternalDatabase
> medline at
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 417, <PFAM> line 590.
>
> gunzip: stdout: Broken pipe
> ***************************************************
>
> I have downloaded latest release 13.0 from website
>
> Do I need to also specify external_database_release_id or something in the
> command? 
>
> Thanks!
>
> Madhura