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

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

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_ID") (DBD ERROR:
> OCIStmtExecute) at
> /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm
> line 270, <NRDB> line 156693.
> 
> Let me know what is null?
> 
> Thanks
> Chetna
> 
> --- "Deborah F. Pinney" <pi...@pc...> wrote:
> > Hi Chetna,
> > 
> > The plugin was written so that it could be run in
> > three parts: 1) making
> > the temp table, 2) inserting into the NRDBEntry and
> > ExternalAASequences
> > tables, 3) deleting obsolete rows in those tables. I
> > looked back at your 
> > previous e-mail and it looks as if you have not
> > included the option to 
> > create and fill the temp table, --maketemp. The
> > plugin should create the 
> > table if that is included on the command line. You
> > can see the table 
> > schema by looking into the code, sub makeTempTable.
> > I'm hoping to rewrite 
> > this plugin as it is complicated and could be put in
> > a better form.  
> > 
> > 
> >                                                    
> > Debbie
> > 
> 
> 
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