[GUSDEV] Using LoadFastaSequences plugin

[Dhivya A. <dhi...@ya...>]

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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