Re: [Gusdev-gusdev] Problem using LoadTaxon plugin

[Madhura S. <sma...@st...>]

Hi Debbie

I used the modified LoadTaxon.pm file and looks like it worked!  The output
is as follows:

(putting just the end of output)
------------
processed ncbi_tax_id : 143293
processed ncbi_tax_id : 192120
processed ncbi_tax_id : 192121
processed ncbi_tax_id : 248763
processed ncbi_tax_id : 102264
processed ncbi_tax_id : 40049
processed ncbi_tax_id : 192122
278364 taxon names processed
0 TaxonName entries deleted
Wed May 19 11:18:36 2004        RESULT  1


Is this correct output?
I currently ran it without commit, let me run it with commit now..

Thanks!

Madhura


----- Original Message ----- 
From: "Deborah F. Pinney" <pi...@pc...>
To: "Madhura Sharangpani" <sma...@st...>
Sent: Wednesday, May 19, 2004 9:14 AM
Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin


> Hi Madhura,
>
> I apologize for the problem. I have added, what I hope is the appropriate
> fix and checked it in. I wonder if you could test it again? I tested to
> the extent that I know it runs but I don't know if I have fixed the
> original problem, running all the way through without commit on.
>
> I appreciate your collaboration.
>
>                                                  Debbie
>
>
>
> On Tue, 18 May 2004, Madhura Sharangpani wrote:
>
> > Hi Debbie
> >
> > I got the updated version but I still get the exact same error, except
it is
> > for getDbHandle instead of getDBHandle this time
> >
> > Madhura
> >
> > ----- Original Message ----- 
> > From: "Deborah F. Pinney" <pi...@pc...>
> > To: "Madhura Sharangpani" <sma...@st...>
> > Cc: <gus...@li...>
> > Sent: Tuesday, May 18, 2004 1:51 PM
> > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin
> >
> >
> > > Hi,
> > >
> > >
> > > I fixed the error that led to this error. getDBHandle should be
> > > getDbHandle. I'm checking it in right now. Sorry, perhaps you could
check
> > > it again?
> > >
> > >
> > >
> > >                                              Debbie
> > >
> > >
> > > On Tue, 18 May 2004, Madhura
> > > Sharangpani wrote:
> > >
> > > > Hi Debbie
> > > >
> > > > I cvs updated LoadTaxon.pm, then did a build and a ga +update for
> > > > LoadTaxon.pm plugin, but after that while trying to run the plugin
again
> > > > without commit, I get the following error, did I miss some step?
> > > >
> > > > elaine43:~/RA/taxdump> ga
> > > >
> >
GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode
> > > > =gencode.dmp
> > > > 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
> > > >
> > > > ***COMMIT TURNED OFF***
> > > > processed ncbi_tax_id : 1
> > > > Can't locate object method "getDBHandle" via package
> > > > "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load
> > > > "GUS::Common::Plugin::LoadTaxon"?) at
> > > >
> >
/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> > > > line 239, <NODES> line 217936
> > > >
> > > > Madhura
> > > >
> > > >
> > > >
> > > > ----- Original Message ----- 
> > > > From: "Deborah F. Pinney" <pi...@pc...>
> > > > To: "Madhura Sharangpani" <sma...@st...>
> > > > Cc: <gus...@li...>
> > > > Sent: Tuesday, May 18, 2004 12:15 PM
> > > > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin
> > > >
> > > >
> > > > >
> > > > >
> > > > > I think I have fixed the bug in LoadTaxon.pm. I've checked it into
> > cvs.
> > > > > Could you give a test with commit off and let us know if it is OK?
> > > > >
> > > > >
> > > > >                                                        Debbie
> > > > >
> > > >
> > > >
> > > >
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