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

[sucheta T. <su...@vb...>]

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