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

[Chetna W. <wa...@ya...>]

Hello Steve and Debbie,

Heres the snapshot. Do I need to create the temp table
NRDBTemp (whats the schmema?) for the user account.
Are there any other tables and what is  their schema?
It will be great if I could get the schema scripts.


There are 12 entries in the database hash
Fri Dec  5 11:27:00 2003        There are 3233042 gi
to taxon_id pairs

DBD::Oracle::db prepare failed: ORA-00942: table or
view does not exist (DBD ERROR:
OCIStmtExecute/Describe) at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 78.
Prepare FAILED: ORA-00942: table or view does not
exist (DBD ERROR: OCIStmtExecute/Describe)
 sql_cmd:
 select max(set_num) from chetna.NRDBTemp
Can't call method "execute" without a package or
object reference at
/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 79.

 
Thanks 
Chetna

--- Steve Fischer <st...@pc...> wrote:
> Chetna-
> 
> the latest version of
> $PROJECT_HOME/GUS/ObjRelP/lib/perl/DbiDbHandle.pm 
> has a fix for that error message.  it now shows the
> problematic sql.
> 
> can you please get it from the cvs site and then do
> a build.
> 
> (before you do, save your current DbiDbHandle.pm
> just in case)
> 
> steve
> 
> Chetna Warade wrote:
> 
> >Hello,
> >
> >I am getting following error while I am trying to
> load
> >NRDB into GUS. Which table is it complaining for, I
> >tried with --debug or --verbose but ga didnt show
> any
> >useful error message. I will appreciate any help.
> >
> >
> >ga GUS::Common::Plugin::LoadNRDB --temp_login
> chetna
> >--sourceDB 'GENBANK (NRDB):gb,EMBL DATA LIBRARY
> >(NRDB):emb,DDBJ (NRDB):dbj,NBRF PIR
> (NRDB):pir,PROTEIN
> >RESEARCH FOUNDATION (NRDB):prf,SWISS-PROT
> >(NRDB):sp,BROOKHAVEN PROTEIN DATA BANK
> >(NRDB):pdb,PATENTS (NRDB):pat,GENINFO BACKBONE ID
> >(NRDB):bbs,GENERAL DATABASE IDENTIFIER
> (NRDB):gnl,NCBI
> >REFERENCE SEQUENCE (NRDB):ref,LOCAL SEQUENCE
> >IDENTIFIER:lcl' --temp_password chetna123 --dbi_str
> >'dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD'
> --gitax
>
>/home/chetna/gus-app/ncbi-taxonomy/gi_taxid_prot.dmp
> >--nrdb
>
>/opt/app/oracle/db_storage/data/downloadNRDB/downloadNRDB/nr.Z
> >--extDbRelId 15 --plugin --delete
> >Wed Dec  3 17:09:57 2003        **COMMIT TURNED
> OFF**
> >
> >There are 12 entries in the database hash
> >Wed Dec  3 17:10:30 2003        There are 3233042
> gi
> >to taxon_id pairs
> >
> >DBD::Oracle::db prepare failed: ORA-00942: table or
> >view does not exist (DBD ERROR:
> >OCIStmtExecute/Describe) at
>
>/var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> >line 78.
> >prepareAndExecute FAILED:
> >GUS::ObjRelP::DbiDbHandle=HASH(0x86c9d48)->errstr
> >
> >Thanks,
> >Chetna
> >
> >
> >
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