Re: [GUSDEV] Using LoadFastaSequences plugin

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Dhivya,

It's not clear what exactly is going wrong.  The uniqueness of  
algorithm_param_key_id values should be maintained using a database  
sequence.   One could picture a bug that results in a failure to get  
the sequence nextval, but it's hard to picture the sequence returning  
65 twice.

One could imagine that the primary-key incrementing is failing across  
the board, but that core.AlgorithmParamKey is the first table into  
which a second record gets written (after one record each are put  
into AlgorithmImplementation and AlgorithmInvocation).

Some questions:

Have other plugins run successfully?

Are there any rows in core.AlgorithmParamKey before you run the  
plugin?  (and, if so, what are their primary-key values?)

What happens when you give the following SQL statement to psql?
select nextval('core.algorithmparamkey_sq');

What happens when you run that statement a second time?

What version of PostgreSQL are you using?  (we're using 7.4.16)

John

On Feb 12, 2007, at 10:50 AM, Mark S. Heiges wrote:

> 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
>>
>>
>>
>>
>>
>>
>>
>> Bored stiff? Loosen up...
>> Download and play hundreds of games for free on Yahoo! Games.
>
>
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