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

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

ok, we can look into this.   it might be that we ask for a volunteer.   
i don't yet know what is involved.

steve

MICHAEL LUCHTAN wrote:

>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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>
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