Re: [Gusdev-gusdev] error when loading nrdb

[John I. <io...@pc...>]

Marc,

In this case, when you're adding a new database release to your GUS
instance, it will be necessary to add a new record to the
SRes.ExternalDatabaseRelease table.  If this is the first time NRDB has
been loaded into your instance, you must also create a record for NRDB
in SRes.ExternalDatabase.  Both records can be created with the
UpdateGUSFromXML plugin.

First, check to see if there's already an NRDB record in
ExternalDatabase.  If there isn't you can create one by giving this XML
to UpdateGUSFromXML:

<SRes::ExternalDatabase>
  <name>NRDB</name>
  <lowercase_name>nrdb</lowercase_name>
</SRes::ExternalDatabase>

Once you have found or created the ExternalDatabase record for NRDB,
plug its external_database_release_id ("123" in this example) into this:

<SRes::ExternalDatabaseRelease>
  <external_database_id>123</external_database_id>
  <release_date>2005-01-18 00:00:00</release_date>
  <version>continuous</version>
  <id_type>accession</id_type>
  <description>Non-redundant composite of protein data</description>
</SRes::ExternalDatabaseRelease>

John



On Tue, 2005-01-18 at 12:28, marc jackson wrote:
> Hi John,
> 
> I've  been looking thru the documentation.  How does one discover the
> release_ID of a database?
> 
> Regards,
> 
> Marc
> 
> 
> 
> 
> >From: io...@pc... 
> >To: marc jackson <de...@ho...> 
> >CC: gus...@li... 
> >Subject: Re: [Gusdev-gusdev] error when loading nrdb 
> >Date: Sat, 15 Jan 2005 12:48:28 -0500 
> > 
> >Marc, 
> > 
> >I wasn't familiar with the details of that plugin, so I got the
> parameter list 
> >by typing: 
> > 
> >ga GUS::Common::Plugin::LoadNRDB --help 
> > 
> >The resulting list shows that the plugin takes the
> external_database_release_id 
> >for NRDB as a command-line argument in the format --extDbRelId=i
> (where "i" is 
> >the release ID).  The message you got seems to imply that this
> argument is 
> >required (which makes sense, since NRDB is an external database and
> its records 
> >must be distinguished by release). 
> > 
> >John 
> > 
> > 
> >Quoting marc jackson <de...@ho...>: 
> > 
> > > Hello, 
> > > 
> > > Does anyone know what the following error means? 
> > > 
> > > prompt>  ga GUS::Common::Plugin::LoadNRDB --nrdb=./nr.tar.gz
> --commit 
> > > 
> > > output: 
> > > 
> > > Fri Jan 14 15:06:20 2005        ***COMMIT ON*** 
> > > 
> > > external_database_release_id not supplied\n at 
> > > /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 112.
> > > 
> > > 
> > > 
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> > 
-- 
John Iodice
Programmer/Analyst
Computational Biology and Informatics Lab
University of Pennsylvania
http://cbil.upenn.edu