Re: [Gusdev-gusdev] GBParser Failure

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Michael-

i'll have a look at this.

in case you didn't know, the stuff starting with "death" and below is a 
perl "stack trace."  it shows you the succession of subroutine calls 
(and their args) that lead to the problem.  sometimes that provides a 
major clue; sometimes not.

steve

MICHAEL LUCHTAN wrote:

>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
>
>
>
>
>
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