Re: [GUSDEV] Using LoadFastaSequences plugin

[Mark S. H. <mh...@ug...>]

Does anyone have any advice on this?

On Jan 18, 2007, at 8:50 AM, Dhivya Aras wrote:

> Hi,
>
> I'm trying to use the LoadFastaSequences plugin to load GUS tables  
> with the fasta sequences or certain nrdb proteins.
>
> But, when I run the plugin I get an error about a primary key  
> constraint violation. When I tested by removing the primary key  
> constraint, the plugin loaded duplicates (for primary key column,  
> algorithm_param_key_id) into algorithmparamkey table.
>
> I'm using GUS3.5 with postgres.
>
>
> On running the registration for the plugin
>
> ga +create GUS::Supported::Plugin::LoadFastaSequences --commit
>
>
> The stack trace contains the following:
>
> DBD::Pg::st execute failed: ERROR:  duplicate key violates unique  
> constraint "al
> gorithmparamkey_pkey" at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> ObjRelP/DbiDbHandle
> .pm line 147.
>
>  SQL ERROR!! involving
>
>     INSERT INTO Core.AlgorithmParamKey (  group_read,  
> algorithm_param_key_id, us
> er_read, algorithm_implementation_id, other_write,  
> modification_date, algorithm_
> param_key_type_id, row_group_id, algorithm_param_key, user_write,  
> group_write, o
> ther_read, description, row_user_id, row_alg_invocation_id,  
> row_project_id, is_l
> ist_valued )
>     VALUES   (  ?, ?, ?, ?, ?, now 
> (), ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ? )
>  Values: 1, 65, 1, 21, 0, 1, 1, regexSourceId, 1, 1, 1, The regular  
> expression t
> o pick the source_id of the sequence from the defline, 1, 1, 1, 0  
> at /home/gus/G
> US/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
>         GUS::ObjRelP::DbiDbHandle::death 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89bb1
> 8c)', '\x{a} SQL ERROR!! involving\x{a} \x{a}    INSERT INTO  
> Core.AlgorithmParam
> ...') called at /home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/ 
> DbiDbHandle.pm line
> 150
>         GUS::ObjRelP::DbiDbHandle::sqlExec 
> ('GUS::ObjRelP::DbiDbHandle=HASH(0x89b
> b18c)', 'GUS::ObjRelP::DbiDbHandle::st=HASH(0x8fbce10)', 'ARRAY 
> (0x8fbceac)', '\x
> {a}    INSERT INTO Core.AlgorithmParamKey (  group_read,  
> algori...') called at /
> home/gus/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 666
>         GUS::ObjRelP::DbiRow::quote_and_insert 
> ('GUS::Model::Core::AlgorithmParam
> Key=HASH(0x8fad2f8)', 'HASH(0x8fb8874)') called at /home/gus/GUS/ 
> gus_home/lib/pe
> rl/GUS/ObjRelP/DbiRow.pm line 613
>         GUS::ObjRelP::DbiRow::insert 
> ('GUS::Model::Core::AlgorithmParamKey=HASH(0
> x8fad2f8)') called at /home/gus/GUS/gus_home/lib/perl/GUS/Model/ 
> GusRow.pm line 1
> 692
>         GUS::Model::GusRow::submit 
> ('GUS::Model::Core::AlgorithmParamKey=HASH(0x8
> fad2f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> Model/GusRow
> .pm line 1779
>         GUS::Model::GusRow::submitChildrenInClass 
> ('GUS::Model::Core::AlgorithmIm
> plementation=HASH(0x8f5f7f8)',  
> 'GUS::Model::Core::AlgorithmParamKey') called at
> /home/gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>         GUS::Model::GusRow::submitAllChildren 
> ('GUS::Model::Core::AlgorithmImplem
> entation=HASH(0x8f5f7f8)') called at /home/gus/GUS/gus_home/lib/ 
> perl/GUS/Model/G
> usRow.pm line 1699
>         GUS::Model::GusRow::submit 
> ('GUS::Model::Core::AlgorithmImplementation=HA
> SH(0x8f5f7f8)', 'undef', 1) called at /home/gus/GUS/gus_home/lib/ 
> perl/GUS/Model/
> GusRow.pm line 1779
>         GUS::Model::GusRow::submitChildrenInClass 
> ('GUS::Model::Core::Algorithm=H                                      
> ASH(0x8f5d500)', 'GUS::Model::Core::AlgorithmImplementation')  
> called at /home/gu                                     s/GUS/ 
> gus_home/lib/perl/GUS/Model/GusRow.pm line 1760
>         GUS::Model::GusRow::submitAllChildren 
> ('GUS::Model::Core::Algorithm=HASH 
> (                                     0x8f5d500)') called at /home/ 
> gus/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm  
> line                                      1699
>         GUS::Model::GusRow::submit('GUS::Model::Core::Algorithm=HASH 
> (0x8f5d500)'                                     ) called at /home/ 
> gus/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm  
> line                                      900
>          
> GUS::PluginMgr::GusApplication::create_or_update_implementation 
> ('GUS::Pl                                      
> uginMgr::GusApplication=HASH(0x877dc20)', 0,  
> 'GUS::Supported::Plugin::LoadFastaS                                    
>   equences') called at /home/gus/GUS/gus_home/lib/perl/GUS/ 
> PluginMgr/GusApplicatio                                     n.pm  
> line 546
>         GUS::PluginMgr::GusApplication::doMajorMode_Create 
> ('GUS::PluginMgr::GusA                                      
> pplication=HASH(0x877dc20)',  
> 'GUS::Supported::Plugin::LoadFastaSequences')  
> calle                                     d at /home/gus/GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 337
>         GUS::PluginMgr::GusApplication::doMajorMode 
> ('GUS::PluginMgr::GusApplicat                                      
> ion=HASH(0x877dc20)', 'GUS::Supported::Plugin::LoadFastaSequences')  
> called at /h                                     ome/gus/GUS/ 
> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 246
>         GUS::PluginMgr::GusApplication::parseAndRun 
> ('GUS::PluginMgr::GusApplicat                                      
> ion HASH(0x877dc20)', 'ARRAY(0x87916d0)') called at /home/gus/GUS/ 
> gus_home/bin/ga line 11
>
>
>
> Any ideas about why this could be happening and how to fix it?
>
> Thanks
> dhivya arasappan
>
>
>
>
>
>
>
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