Re: [Gusdev-gusdev] source_id error with LoadNRDB - add

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

Hi,

It slipped my mind but the last time I ran this, when I had a problem with 
an entry, I added an eval statement that should print to a log rather than 
failing when it encounters an error. It is rather unorthodox but the 
sequence is also printed. The error I encountered in the nr record 
prevented the plugin from "knowing" the source_id and the gi so I had no 
identifiers to use. Entry into the GUS db occurs only when there is a 
sequence so that I was confident that would be known and a substring could 
be used to search for the record in the file.

Try to update your LoadNRDB.pm from cvs and try it again.

                                                           Debbie

On Thu, 5 Aug 2004, Pablo N. Mendes wrote:

> Hello all,
> I've been "playing" with the loadNRDB module in the previous weeks, but
> it is still crashing. I got this "cannot insert NULL into source_id
> (DoTS.NRDBEntry)" error when reading line 8298021 of my NR file.
>
> That line is:
>> gi|45549465|gb|AAS67649.1| spike glycoprotein S1 subunit precursor
> [Avian infectious bronchitis virus]
>
> I cannot see why this would crash. I'm looking into the code, but maybe
> someone who already knows the module can help me with guesses.
>
> Here part of the dump:
>
> [pablo@mkiwi loadNRDB]$ ga GUS::Common::Plugin::LoadNRDB
> --comment="loading NRDB data from July" --extDbRelId=48
> --gitax="/home/luchtan/GUS/loadNRDB/June232004/gi_taxid_prot.dmp"
> --nrdb="/scratch/pablo/nr"
> --SourceDB="84:tpe,76:pdb,77:dbj,78:prf,79:emb,81:sp,82:pir,80:gb,83:ref,80:tpg,151:genpept,153:tpd" --plugin --temp_login='pablo' --temp_password='pablo123' --dbi_str='dbi:Oracle:host=kiwi.rcr.uga.edu;sid=CTEGD' --commit | tee loadnrdb.log
> (...)
> Submitted set number:1462975
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("DOTS"."NRDBENTRY"."SOURCE_ID") (DBD ERROR: OCIStmtExecute) at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, <NRDB>
> line 8298021.
>
> SQL ERROR!! involving
>
>    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, user_write,
> group_write, nrdb_entry_id, is_preferred, row_project_id, taxon_id,
> external_database_release_id, group_read, aa_sequence_id, row_group_id,
> other_read, gid, source_id, modification_date, user_read,
> row_alg_invocation_id, other_write )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, '', SYSDATE,
> ?, ?, ? )
> Values: Luminal binding protein 3 (BiP 3) (78 kDa glucose-regulated
> protein homolog 3) (GRP 78-3), 8, 1, 1, 5063019, 1, 2, 169692, 81, 1,
> 2943307, 2, 1, 729619, 1, 30713, 0 at
> /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
>
> GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', '^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NRDBEntry (  desc...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
>
> GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x85d0184)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x450007d8)', 'ARRAY(0x40a8ffd0)', '^J    INSERT INTO DoTS.NRDBEntry (  description, row_user_id, use...') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 681
>
> GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', 'HASH(0x11e51efc)') called at /var/local/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 628
>
> GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::NRDBEntry=HASH(0x97d9f58)', undef, 1) called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1764
>
> GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)', 'GUS::Model::DoTS::NRDBEntry') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1745
>
> GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
> GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalAASequence=HASH(0x43ede594)') called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 335
>
> GUS::Common::Plugin::LoadNRDB::makeNRDBAndExternalAASequence('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x85a26cc)', 'HASH(0x85a23cc)', 48) called at /var/local/gus_home/lib/perl/GUS/Common/Plugin/LoadNRDB.pm line 127
>
> GUS::Common::Plugin::LoadNRDB::run('GUS::Common::Plugin::LoadNRDB=HASH(0x856d7c0)', 'HASH(0x8811950)') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 430
>        eval {...} called at
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 427
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS::Common::Plugin::LoadNRDB') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11
>
> Thanks,
> Pablo
>
>
> --
> -----------------------------
> Pablo Nascimento Mendes
> Research Scholar
> Kissinger Lab
> Department of Genetics
> University of Georgia
> C210 Life Sciences Bldg.
> Athens, Georgia 30602
> Phone:706 542-1447
> E-mail: pa...@ug...
>
>
>
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