Re: [Gusdev-gusdev] GBParser Failures...:(

[Steve F. <st...@pc...>]

michael-

look in the log that captures stdout for sql errors on or near line 144 
of DbDbiHandle.pm

that was the main clue last time.

steve

MICHAEL LUCHTAN wrote:

>Hello-
>We have advanced a little further in our effort to get the gbparser plugin
>running on a new GUS installation.  Thank you for the help so far, and we
>have resolved the dependency regarding the Dots.sequencetype table, but
>unfortunately we have new dependency errors.  Here a snapshot from the
>generated error log:
>
>
>
> ------------------ entry number 1 -----------------
>
> SQL ERROR!! involving
>
>    INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user_write,
>group_write, created_rel_ver, na_sequence_id, row_project_id, group_read,
>row_group_id, other_read, na_entry_id, source_id, modification_date,
>user_read, row_alg_invocation_id, other_write, version, division )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ?
>)
> Values: 2003-5-03 00:00:00, 6, 1, 1, 135, 1809, 2, 1, 3, 1, 205,
>AY140947, 1, 138, 0, 1, INV at
>/home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 184
>
>GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbd68)',
>'^J SQL ERROR!! involving^J ^J    INSERT INTO DoTS.NAEntry (  create...')
>called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 147
>
>GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8afbd68)',
>'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8f3e0ec)', 'ARRAY(0x8f3c990)', '^J
>INSERT INTO DoTS.NAEntry (  created_date, row_user_id, user...') called at
>/home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 674
>
>GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)',
>'HASH(0x8f3c810)') called at /home/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
>line 621
>
>GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)')
>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1677
>
>GUS::Model::GusRow::submit('GUS::Model::DoTS::NAEntry=HASH(0x8d72bf0)',
>undef, 1) called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1765
>
>GUS::Model::GusRow::submitChildrenInClass('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)',
>'GUS::Model::DoTS::NAEntry') called at
>/home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1746
>
>GUS::Model::GusRow::submitAllChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)')
>called at /home/gus_home/lib/perl/GUS/Model/GusRow.pm line 1684
>
>GUS::Model::GusRow::submit('GUS::Model::DoTS::ExternalNASequence=HASH(0x8d6b500)')
>called at /home/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 284
>
>GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x84be838)',
>'CBIL::Bio::GenBank::ArrayStream=HASH(0x8ccac48)') 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(0x84be838)',
>'HASH(0x8c60dc8)') called at
>/home/gus_home/lib/perl/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') called 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
>
>
>Thank you...
>
>Michael Luchtan
>http://www.cs.uga.edu/~luchtan
>
>
>
>
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