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[Gusdev-gusdev] Problems GBParser
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From: Thomas O. <ot...@fi...> - 2004-07-30 18:24:04
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Hello,
since the last update of GUS, my GBParser doesn't work anymore properly.
Used it like before.
Who might help me?
Thanks,
Thomas
errors:
##############################
********GEtting loc below1188486
DBD::Oracle::st execute failed: ORA-00913: too many values (DBD ERROR:
OCIStmtExecute) at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145,
<GEN0> line 33579.
Fri Jul 30 14:51:50 2004 Genbank entries inserted= 0; updated=
0; total #(inserted::updated::deleted)=16::::59
Fri Jul 30 14:51:50 2004 FAILURES Unable to process 1
entries. See gbparserFailures/
errorlog:
------------------ entry number 1 -----------------
SQL ERROR!! involving
Values: 93444 at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33f5c)','\x{a}
SQL ERROR!! involving\x{a} \x{a} Values: 93444')
called at /home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33f5c)','GUS::ObjRelP::DbiDbHandle::st=HASH(0xbd9cd90)','ARRAY(
0xbd9ccf4)') called at
/home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm line 1798
GUS::Model::GusRow::version('GUS::Model::DoTS::Repeats=HASH(0xb9ae250)')
called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1628
GUS::Model::GusRow::submit('GUS::Model::DoTS::Repeats=HASH(0xb9ae250)')
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBP
arser.pm line 1113
GUS::Common::Plugin::GBParser::processChildren('GUS::Model::DoTS::ExternalNASequence=HASH(0xafaf33c)','ARRAY(0x8ba0d44)','ARRAY(0x8ba0
d5c)') called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 272
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8599870)','CBIL::Bio::GenBank::ArrayStream=HASH(0x90
4fec8)') called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
eval {...} called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8599870)','HASH(0x8e6c154)')
called at /home/oracle/gus_home/
lib/perl/GUS/PluginMgr/GusApplication.pm line 453
eval {...} called at
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParse
r',1) called at
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
call
ed at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 289
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
called a
t /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060684)')
called at /home/oracl
e/gus_home/bin/ga line 11
##############################3
DBD::Oracle::st execute failed: ORA-00001: unique constraint
(DOTS.PK_NAGENE) violated (DBD ERROR: OCIStmtExecute) at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145,
<GEN0> line 1039.
Fri Jul 30 14:46:27 2004 Genbank entries inserted= 0; updated=
0; total #(inserted::updated::deleted)=16::::
Fri Jul 30 14:46:27 2004 FAILURES Unable to process 2
entries. See gbparserFailures/
Fri Jul 30 14:46:27 2004 RESULT Genbank entries inserted= 0;
updated= 0; failed= 2
//the next sequence of na_gene is 43 or so...
SQL ERROR!! involving
INSERT INTO DoTS.NAGene ( group_write, other_read, group_read,
name, user_read, row_user_id, is_verified, other_write, modification_date,
row_alg_invocation_id, row_project_id, na_gene_id, row_group_id,
user_write )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
Values: 1, 1, 1, F49E11.11, 1, 1, 0, 0, 50250, 1, 21, 1, 1 at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 185
GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33e4c)','\x{a}
SQL ERROR!! involving\x{a} \x{a} INSERT INTO Do
TS.NAGene ( grou...') called at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 148
GUS::ObjRelP::DbiDbHandle::sqlExec('GUS::ObjRelP::DbiDbHandle=HASH(0x8c33e4c)','GUS::ObjRelP::DbiDbHandle::st=HASH(0x9121740)','ARRAY(
0x9121788)','\x{a} INSERT INTO DoTS.NAGene ( group_write,
other_read, grou...') called at
/home/oracle/gus_home/lib/perl/GUS/ObjRelP/DbiRo
w.pm line 681
GUS::ObjRelP::DbiRow::quote_and_insert('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)','HASH(0x9111424)')
called at /home/oracle/gus_home/l
ib/perl/GUS/ObjRelP/DbiRow.pm line 628
GUS::ObjRelP::DbiRow::insert('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)')
called at /home/oracle/gus_home/lib/perl/GUS/Model/GusRow.pm
line 1677
GUS::Model::GusRow::submit('GUS::Model::DoTS::NAGene=HASH(0x9104bcc)')
called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBPa
rser.pm line 727
GUS::Common::Plugin::GBParser::getNAGeneId('F49E11.11') called
at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 71
4
GUS::Common::Plugin::GBParser::buildGene('CBIL::Bio::GenBank::Qualifier=HASH(0x8f7de60)','CBIL::Bio::GenBank::Feature=HASH(0x8f7ad48)'
) called at /home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm
line 503
GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBParser=HASH(0x8599604)','CBIL::Bio::GenBank::Entry=HASH(0x8ef2790
)','GUS::Model::DoTS::ExternalNASequence=HASH(0x8ffa638)') called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParser=HASH(0x8599604)','CBIL::Bio::GenBank::ArrayStream=HASH(0x8e
ff678)') called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 185
eval {...} called at
/home/oracle/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=HASH(0x8599604)','HASH(0x8e6bdc4)')
called at /home/oracle/gus_home/
lib/perl/GUS/PluginMgr/GusApplication.pm line 453
eval {...} called at
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParse
r',1) called at
/home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 383
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
call
ed at /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 289
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','GUS::Common::Plugin::GBParser')
called a
t /home/oracle/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d00c)','ARRAY(0x8060684)')
called at /home/oracl
e/gus_home/bin/ga line 11
#############################################
VLD CBIL::Bio::GenBank::Origin 1
ERR LINE=33578 unparsed line
ERR LINE=33579 unparsed line
Fri Jul 30 14:45:13 2004 STATUS N=1 ACC=NC_005063
TOTAL_OBJECTS=16
Fri Jul 30 14:45:13 2004 Genbank entries inserted= 0; updated=
0; total #(inserted::updated::deleted)=16::::
Fri Jul 30 14:45:13 2004 RESULT Genbank entries inserted= 0;
updated= 0; failed= 0
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