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

[MICHAEL L. <lu...@cs...>]

Hello-
Such a thing--an XML from CBIL with all of the ExternalDatabase table
entries and matching ExternalDatabaseRelease rows would probably be useful
to almost everyone running or with plans to run GUS.  So much of the perl
plugin codebase already has ties to this.  I think making it available as
an option in the install would help solve MANY issues that arise in
installing/populating/retrieving data from GUS using the perl object layer
and the WDK.  Are there any issues with having people standardized on an
ExternalDatabaseID?  Everyone is probably using some subset of a standard
set of external databases, and it is easy to add another one.

Michael Luchtan
http://www.cs.uga.edu/~luchtan


On Thu, 6 May 2004 pj...@sa... wrote:

>
> If I remember correctly I got an XML dump from CBIL with
> all of the ExternalDatabase table entries with the matching
> ExternalDatabaseRelease rows. I added a few entries that GeneDB needed.
>
> Is the ExternalReleaseTable populated with bootstrap data when a new GUS schema
> is created?
>
> I have a copy of those files that I can send to you but I can't access it right now.
>
>
> Quoting Madhura Sharangpani <sma...@st...>:
>
> > 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
> >
>
>
>
>
>
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