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

[Deborah F. P. <pi...@pc...>]

Hi Madhura,

The error you're seeing is due to there not being an external_database_id
and external_database_release_id for medline in your database's
sres.externaladatabase and sres.externaladatabaserelease tables.

You will have to insert those rows with the appropriate information. I 
generally use UpdateGusFromXML to enter rows into the db but I think you 
can use SubmitRow also. 

sres.externaladatabase is pretty minimal with only the name (MEDLINE) and 
lowercasename (medline) 

Entries in sres.externaladatabaserelease only require an 
external_database_id and version but the other fields are useful to track 
your data source properly.


                                                      Debbie  




On Thu, 6 May 2004, 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
>