[Gmod-help] bulkfiles errors

[Scott Cain]

Hi Barry,

I'm going to cc this to the schema mailing list as well as Don Gilbert
who is the author of GMODTools.  I poked around looking for the
problem query and didn't find it immediately either; I'll keep working
on it.

Scott


On Fri, May 15, 2009 at 10:36 AM, Barry Dancis <bdancis at digiconasp.com> wrote:
> Hi--
>
>  I am using the GMODTools to unload a genome for submission to genbank. I am getting the error:
>
>  DBD::Pg::st execute failed: ERROR:  column "chromosome" does not exist
> LINE 19:   featcv.name in ( chromosome )
>                            ^ at lib/Bio/GMOD/Bulkfiles.pm line 2464.
>
> I printed the query and got a similar error when executing it with psql. If I added quotes to give:
>
>   featcv.name in ( 'chromosome' )
>
> the query worked just fine. It seems to me the query generator should have added the quotes as opposed to requiring the quotes to be in an xml file. My question is which pm and what line is where the ${golden_path} in the sql query is replaced so that I can modify it to add quotes to the replacement if they are not already there?
>
> I am also getting the error:
>
> DBD::Pg::db do failed: ERROR:  syntax error at or near "0"
> LINE 22:     and (cv.name in ( ARRAY(0x8b39e9c) ))
>                                     ^ at lib/Bio/GMOD/Bulkfiles.pm line 2376.
>
> and when I look at the actual query text, there are 3 different subqueries which have that error.
> Seaching the xml's, I found 4 places in chadogenepagessql.xml, all with the form:
>
>    and (cv.name in ( ${featureprops} ))
>
> Obviously, the array is not being converted into a quoted, comma separated list as is required. Can someone point me to the place in the code where the substitution is occurring so that I can fix it.
>
> Thanks,
>
> Barry
>
> ps It's been almost a week since I changed my email address on Sourceforge to barry.dancis at digiconasp.com, but it is still going to my old address. It there somewhere else that I have to change it.
>
> B^)
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research