[Gusdev-gusdev] GBParser Failure

[MICHAEL L. <lu...@cs...>]

Hello-
We are still trying to get the gbparser pluging to work correctly.
Entries have been added in the Sres.ExternalDatabase and
Sres.ExternalDatabaseReference tables.  We are still getting some strange
errors at the terminal.  Here is the first few lines (I tried to send all
of the input but there was a problem with the sourceforge mailer as far as
the size of the file):
[luchtan@mango luchtan]$ ga GUS::Common::Plugin::GBParser --gbRel=135
--db_rel_id=135 --debug --file=/home/gusdev/gus3.0-checkouts/GenBank/TcN
CBIgenomic.gb --commit
Reading properties from /home/gus_home/config/GUS-PluginMgr.prop
Reading properties from /home/luchtan/gus.properties
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at /home/gus_home/
lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at /home/gus_home/
lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at /home/gus_home/
lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.
DBD::Oracle::db do failed: ORA-30019: Illegal rollback Segment operation
in Automatic Undo mode (DBD ERROR: OCIStmtExecute) at /home/gus_home/
lib/perl/GUS/ObjRelP/DbiDatabase.pm line 149.

The first part of the error file generated looks like this(Again the file
was too big to send as an attachment):
 ------------------ entry number 1 -----------------

 SQL ERROR!! involving

    INSERT INTO DoTS.ExternalNASequence (  c_count, description,
sequence_type_id, row_user_id, user_write, group_write,
secondary_identifier,
 na_sequence_id, row_project_id, name, taxon_id,
external_database_release_id, subclass_view, group_read, sequence,
sequence_version, row_grou
p_id, other_read, a_count, length, source_id, modification_date, t_count,
user_read, row_alg_invocation_id, g_count, other_write )
    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, SYSDATE, ?, ?, ?, ?, ? )
 Values: 268, Trypanosoma cruzi proline racemase copy B (PA45-B) gene,
PA45-B-1 allele, complete cds., 11, 6, 1, 1, GI:30349128, 810, 2, AY140
947, 184573, 1, ExternalNASequence, 1,
atgcgatttaagaaatcattgacatgcatcgacatgcatacggaaggtgaagcagcacggattgtgacgagtggtttgccacacattccaggttcgaatatgg
cggagaagaaagcatacctgcaggaaaacatggattatttgaggcgtggcataatgctggagccacgtggtcatgatgatatgtttggagcctttttatttgaccctattgaagaaggcgctgacttgggcatcgtattcat
ggataccggtggctatttaaatatgtgtggacataactcaattgcagcggttacggcggcagtggaaacgggaattttgagcgtgccggcgaaggcaacaaatgttccggttgtcctggacacacctgcggggttggtgcgc
ggtacggcacaccttcagagtggtactgagagtgaggtgtcaaatgcgagtattatcaatgtgccctcatttttgtatcagcaggatgtggtgattgttttgccaaagccctatggtgaggtacgggttgatattgcatttg
gaggcaattttttcgccattgttcccgcggagcacttgggaattgatatctccgttcaaaacctctccaggctgcaggaggcaggagaacttctgcgtactgaaatcaatcgcagtgtgaaggttcagcaccctcagctgcc
ccatattaacactgtggactgtgttgagatatacggtaacgcaacgaacccggaggcaaaatacaagaacgttgtgatatttggcaatcgccaggcggatcgctctccatgtgggacaggcaccagcgccaagatggcaaca
ctttatgccaaaggccagcttcgcatcggagagacttttgtgtacgagagcatactcggctcactcttccagggcagggtacttggggaggagcgaataccgggggtgaaggtgccggtgaccaaagatgccgaggaaggga
tgctcgttgtaacgacagaaattactggaaaggcttttatcatgggtttcaacaccatgctgtttgacccaacggatccgttcttaaacggattcacactaaagcggtagatctggtagagcacagaaactattggggaaca
cgtgcgaacaggtgctgctacgtaaagggtattgaatgaatcgtttttttttttttttttttattagtgcattatttttttttttttttgttttggggtttcaacggtaccacgttgggagcagggaaacgatagcggccgg
acaattttttacttttattttcattttcaccttcctacccaacccccttggttccaccggtcgcggcgggg,
1, 2, 1, 324, 1310, AY140947, 355, 1, 122, 363, 0 at /home/gus_home/l
ib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184

GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbb48)',
'^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.Exter
nalNASequenc...') called at
/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147

GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbb48)',
'GUS::ObjRelP::DbiDbHandle::st=HASH(0x9000b98)', 'ARRA
Y(0x90013e8)', '^J    INSERT INTO DoTS.ExternalNASequence (  c_count,
description...') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
 line 674

GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d880a0)',
'HASH(0x8fd9fa4)') called at /home/gus_
home/lib/perl/GUS/ObjRelP/DbiRow.pm line 621

GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d880a0)')
called at /home/gus_home/lib/perl/GUS/Model/GusRo
w.pm line 1677

GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d880a0)')
called at /home/gus_home/lib/perl/GUS/Common/Plugin
/GBParser.pm line 284

GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x84be7b8)',
'CBIL::Bio::GenBank::ArrayStream=HASH(0x8
ccaa28)') called at /home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm
line 185
        eval {...} called at
/home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184

GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x84be7b8)',
'HASH(0x8c60c10)') called at /home/gus_home/lib/pe
rl/GUS/PluginMgr/GusApplication.pm line 389
        eval {...} called at
/home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 385

GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::GBParser') cal
led at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 284

GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'GUS::Common::Plugin::GBParser') called
at /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 193

GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
'ARRAY(0x8105130)') called at /home/gus_
home/bin/ga line 11






If anyone can look at this and
see a quick oversight on our part, your advice would be much appreciated.
In the meantime we will be working on it.   Thanks,

Michael Luchtan
http://www.cs.uga.edu/~luchtan