gusdev-gusdev

Re: [GUSDEV] Mailman privacy alert

[João D. L. <lir...@gm...>]

Hello,

I tried tu use GUS with postGreSQL, but i having some problems.
With some help i installed GUS, but i cant do the boostrap data from
tutorial in:

http://www.gusdb.org/wiki/index.php/Bootstrap%20data

I using GUS form svn and i receive the error


$ ga +create GUS::Common::Plugin::UpdateGusFromXML --commit

FATAL: Can't locate GUS/Common/Plugin/UpdateGusFromXML.pm in @INC (@INC
contains: /home/nugen/GUS/gus_home/lib/perl /etc/perl
/usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
/usr/local/lib/site_perl .) at (eval 16) line 1.


I tried to find this plugin in the GUS files, but i cant.

So i tried with Loadfrom XML

$  ga +create GUS::Supported::Plugin::LoadGusXml --commit

and worked, but after i tried:

$ ga GUS::Supported::Plugin::LoadGusXml --filename
/home/nugen/ExternalDatabase.xml --commit

and i receiver:

[...]
DBD::Pg::st execute failed: ERRO:  value is too long for type character
varying(255) at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 147.

 SQL ERROR!! involving

    UPDATE  Core.AlgorithmInvocation
    SET
    modification_date = ?,
    end_time = ?,
    row_alg_invocation_id = ?,
    result = ?
    WHERE   algorithm_invocation_id = ?
 Values: now(), now(), 12,
ERROR:
ERROR: attempting to access attribute 'lowercase_name' of table
ExternalDatabase, but that table does not have such an attribute

 at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 742
[...]

and anothers erros.

I doing something worng ?
I using postGreSQL. Can somebody help me ?

Are there any tutorial for bootstrap data ? And where can i find plugins
documentation ?

Thanks a lot,

-- 
João David de Lira
Universidade Estadual do Ceará - UECE

Re: [GUSDEV] Mailman privacy alert

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

João,

You're right that the plugin formerly known as "UpdateGusFromXML" is now
called "LoadGusXml".  I have updated the bootstrap-data wiki page.

Looking in my own instance, I also see that there's no "lowercase_name" in
sres.ExternalDatabase.  I suspect that the bootstrap XML dates from a time
when there was such a table.  I updated that on the wiki, too.

John

On Mon, Jun 15, 2009 at 10:12 AM, João David Lira <lir...@gm...>wrote:

> Hello,
>
> I tried tu use GUS with postGreSQL, but i having some problems.
> With some help i installed GUS, but i cant do the boostrap data from
> tutorial in:
>
> http://www.gusdb.org/wiki/index.php/Bootstrap%20data
>
> I using GUS form svn and i receive the error
>
>
> $ ga +create GUS::Common::Plugin::UpdateGusFromXML --commit
>
> FATAL: Can't locate GUS/Common/Plugin/UpdateGusFromXML.pm in @INC (@INC
> contains: /home/nugen/GUS/gus_home/lib/perl /etc/perl
> /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5
> /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
> /usr/local/lib/site_perl .) at (eval 16) line 1.
>
>
> I tried to find this plugin in the GUS files, but i cant.
>
> So i tried with Loadfrom XML
>
> $  ga +create GUS::Supported::Plugin::LoadGusXml --commit
>
> and worked, but after i tried:
>
> $ ga GUS::Supported::Plugin::LoadGusXml --filename
> /home/nugen/ExternalDatabase.xml --commit
>
> and i receiver:
>
> [...]
> DBD::Pg::st execute failed: ERRO:  value is too long for type character
> varying(255) at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 147.
>
>  SQL ERROR!! involving
>
>     UPDATE  Core.AlgorithmInvocation
>     SET
>     modification_date = ?,
>     end_time = ?,
>     row_alg_invocation_id = ?,
>     result = ?
>     WHERE   algorithm_invocation_id = ?
>  Values: now(), now(), 12,
> ERROR:
> ERROR: attempting to access attribute 'lowercase_name' of table
> ExternalDatabase, but that table does not have such an attribute
>
>  at /home/nugen/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 742
> [...]
>
> and anothers erros.
>
> I doing something worng ?
> I using postGreSQL. Can somebody help me ?
>
> Are there any tutorial for bootstrap data ? And where can i find plugins
> documentation ?
>
> Thanks a lot,
>
> --
> João David de Lira
> Universidade Estadual do Ceará - UECE
>
>
> ------------------------------------------------------------------------------
> Crystal Reports - New Free Runtime and 30 Day Trial
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>
>

Re: [GUSDEV] Mailman privacy alert

[João D. L. <lir...@gm...>]

Hello,

I saw the updated bootstrap data page and I think is still wrong.

In page I see:

ga +create GUS::Common::Plugin::LoadGusXml --commit

But, for me, didn't work. For me, only works:

ga +create GUS::*Supported*::Plugin::LoadGusXml --commit


And another mistake. The command line:

ga +create GUS::Common::Plugin::LoadTaxon --commit

must be:

ga +create GUS:*:Supported*::Plugin::LoadTaxon --commit


And, finally, in the command line:

ga +create GUS::Common::Plugin::LoadPfam --commit

Didnt work for me. I cant find the correct one. Changing the Common for
Supported didnt work for this one.

In the session Load Taxonomy, it is missing a argument in command line. (
--merge )
The compete command line is:

ga GUS::Supported::Plugin::LoadTaxon --gencode=/$YOUR_PATH/gencode.dmp
--names=/$YOUR_PATH/names.dmp --nodes=/$YOUR_PATH/nodes.dmp
--merged=/$YOUR_PATH/merged.dmp --commit


And another doubt.
In the final os session  Dots::SequenceType in bootstrap page, there is a
warning about the loadrow, and above the command line. This command line is
necessary ? I need to do it ? I didnt undestand this part. Its only a
comentary about this command line or its the right command line ?

ga GUS::Common::Plugin::SubmitRow --tablename DoTS::SequenceType
   --attrlist sequence_type_id,nucleotide_type,sub_type,strand,hierarchy,parent_sequence_type_id,name,description
   --valuelist "1^^^DNA^^^null^^^null^^^1^^^1^^^DNA^^^unkown strandedness"
   --commit



I  dont understand ver well the plugins. Where can I find the documentaion
of each plugin?
I dont understand well how can I choose  the data to populate GUS. I would
like to specify waht kind of  sequence i want to insert, but from ncbi, for
example. ( example: i only want sequences from leshimania ).

Thanks a lot.


Att,

-- 
João David de Lira
Universidade Estadual do Ceará - UECE

Re: [GUSDEV] Mailman privacy alert

[João D. L. <lir...@gm...>]

Hello,

With the changes in .xml files in bootstrap data page, it worked for me, but
now I'm having troubles with  Go Ontology Tables.
I think that has a deadlock in the process. I'm using the

SRes.GORelationshipType.xml

present in the page.

Can anyone help me ?

Thanks

-- 
João David de Lira
Universidade Estadual do Ceará - UECE


---------------

João,

You're right that the plugin formerly known as "UpdateGusFromXML" is now
called "LoadGusXml".  I have updated the bootstrap-data wiki page.

Looking in my own instance, I also see that there's no "lowercase_name" in
sres.ExternalDatabase.  I suspect that the bootstrap XML dates from a time
when there was such a table.  I updated that on the wiki, too.

John