Re: [Gusdev-gusdev] LoadNRDB: table not found

[Deborah F. P. <pi...@pc...>]

Hi Sucheta,

I was referring to LoadNRDB.pm

                              Debbie  




On Sun, 7 Dec 2003, sucheta Tripathy wrote:

> Hi Debbie,
> 
> I also got the same error as Chetna.
> 
> Which file do I need to update from the CVS?
> 
> Sucheta
> 
> 
> > Hi Chetna,
> >
> > The external_db_rel_id attribute holds the sres.externaldatabaserelease id
> > for each of the source databases that are found in the defline of nr
> > protein db records.
> >
> > I have modified the plugin and submitted it to cvs because we are now
> > maintaining two versions of the ncbi nr protein database. If you update
> > the new command line should be similar to the following:
> >
> >
> >
> > --temp_login $temp_login --sourceDB $sourceDB --temp_password
> > $temp_password --dbi_str $dbi_str --gitax $gitax --nrdb
> > $nrdb --extDbRelId $nrdbReleaseId --maketemp --plugin --delete
> >
> > $temp_login  = pinney
> > $temp_password = xxxxxx
> > $sourceDB =
> > 7475:gb,7476:emb,7477:dbj,7478:pir,7479:prf,7480:sp,7481:pdb,7514:pat,
> > 7515:bbs,7516:gnl,7474:ref,7517:lcl,7482:genpept,7483:tpe
> > $dbi_str = dbi:Oracle:host=cbilbld.pcbi.upenn.edu;sid=cbilbld
> > $nrdbReleaseId = 7484
> > etc.
> >
> > The previous version took the name of the source database and retrieved
> > the external_database_release_id while this version is given the id. I
> > think this is better because you don't have to run the risk of mistyping
> > the name and allows you to maintain more than one version of nrdb. It
> > still requires that you enter a row into sres.externaldatabase and
> > sres.externaldatabaserelease for each of the source db in the NCBI files
> > (see the README file at NCBI). (We have a couple extra here - if you can
> > query our db, you can get their descriptions). The ids can be permanent so
> > you don't have to come up with the command line and new ids every time.
> >
> > You also need to have a separate NRDB external_database_release_id for
> > NRDB on the whole and this will be put into dots.externalaasequence. We
> > also don't change this id, rather we update information in the
> > sres.externaldatabaserelease table row.
> >
> >                                                         Debbie
> >
> > On Fri, 5 Dec 2003, Chetna Warade wrote:
> >
> >> Hello,
> >>
> >> I tried with --maketemp and I am getting:
> >>
> >> DBD::Oracle::st execute failed: ORA-01400: cannot
> >> insert NULL into
> >> ("CHETNA"."NRDBTEMP"."EXTERNAL_DB_REL_I
> 
> 
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