Re: [GUSDEV] GUS 3.5 plugin registration error

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Indeed, the plan is to replace with something based on BioPerl  
parsers and as we heard at the GUS workshop, Ed and Steve have been  
working on this. Any update from you guys?

Chris

On Jul 19, 2005, at 5:08 PM, an...@ma... wrote:

> Yeah, that was me, but frankly I do not have the time to work on  
> this. I gave
> ownership of this to Debbie Pinney a few years back, and she had  
> put in fixes
> over time, but it is a known issues that we MUST replace this  
> plugin with
> something based on BioPerl parsers.
>
> -angel
> Quoting Jian Lu <jl...@vb...>:
>
>
>> Mike,
>>
>> Thank you for response and suggestion. Since GBParser has been  
>> heavily
>> used by community to load NCBI data, I think a high priority  
>> should be
>> considered to support GBParser. Who is the original author?
>>
>> Jian
>>
>> Michael Saffitz wrote:
>>
>>
>>> Hi Jian,
>>>
>>> Community plugins are provided as a point of reference, but are not
>>> generally compatible with the current schema and app framework.   
>>> They are
>>> not expected to work without (sometimes significant) modification.
>>>
>>> Be cautious for community plugins that do register-- they may  
>>> have runtime
>>> errors or worse, run without error but improperly load data.
>>>
>>> If there is a specific community plugin you'd like to use, I suggest
>>>
>> working
>>
>>> with the original plugin author or other interested parties in the
>>>
>> community
>>
>>> to review, update, and fix the plugin to the Plugin standard, and  
>>> then it
>>> can become a supported plugin!
>>>
>>> Thanks,
>>>
>>> Mike
>>>
>>>
>>>
>>>
>>> On 7/19/05 4:08 PM, "Jian Lu" <jl...@vb...> wrote:
>>>
>>>
>>>
>>>
>>>> I am trying to register GUS 3.5 plugins. The 'Supported' plugins  
>>>> are
>>>> successful, but 'Community' plugins all failed to register at  
>>>> the first
>>>> time run because most plugins have empty database versions like  
>>>> this
>>>> requiredDbVersion => {}. After adding database version 3.5, some  
>>>> got
>>>> registered, but  majorities still failed  (see below error log). I
>>>> corrected some like GBParser and registered them.
>>>>
>>>> ###################### ERROR LOG ##############################
>>>> GUS::Community::Plugin::AnnotatorsInterfaceSubmitter is already
>>>>
>> registered.
>>
>>>> Use '+update' if you need to register a new version.
>>>> Tue Jul 19 08:48:29 2005    INFO    Plugin
>>>> GUS::Community::Plugin::AssembliesWithflCD registered with cvs  
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate GUS/RAD/FileTranslator.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> BatchArrayResultLoad
>>>
>>>> er.pm
>>>> line 20.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> BatchArrayResultLoad
>>>
>>>> er.pm
>>>> line 20.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:31 2005    INFO    Plugin
>>>> GUS::Community::Plugin::DeleteFromTable registered with cvs  
>>>> revision
>>>>
>> '2924'
>>
>>>> Tue Jul 19 08:48:32 2005    INFO    Plugin
>>>> GUS::Community::Plugin::DeleteSimilarities registered with cvs  
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:35 2005    INFO    Plugin
>>>> GUS::Community::Plugin::DupNRDBRows registered with cvs revision  
>>>> '2924'
>>>>
>>>> Can't locate GUS/Model/SRes/ExternalDatabaseKeyword.pm in @INC  
>>>> (@INC
>>>> contains: /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>>> GBParser.pm
>>>> line 43.
>>>> BEGIN failed--compilation aborted at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>>> GBParser.pm
>>>> line 43.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> GenePixStudyModuleIL
>>>
>>>> oader.pm
>>>> line 13.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> GenePixStudyModuleIL
>>>
>>>> oader.pm
>>>> line 13.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> GUSLOGS ENV:
>>>> Tue Jul 19 08:48:38 2005    INFO    Plugin
>>>> GUS::Community::Plugin::GenericParser2Gus registered with cvs  
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:39 2005    INFO    Plugin
>>>> GUS::Community::Plugin::IdentifyAndLoadSnpsFromAssemblies  
>>>> registered
>>>> with cvs revision '2924'
>>>> String found where operator expected at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 615, near "'prediction_algorithm_id'"
>>>>    (Missing semicolon on previous line?)
>>>>
>>>> syntax error at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 615, near "'prediction_algorithm_id'"
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 616.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 618.
>>>> Global symbol "%hash" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$start" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$stop" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 621.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 635.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 636.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 637.
>>>> Global symbol "$pf" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 638.
>>>> Global symbol "$info" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 642.
>>>> Global symbol "$score" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$start" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$stop" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$motif_id" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 644.
>>>> Global symbol "$pf" requires explicit package name at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 648.
>>>> syntax error at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> line 656, near "}"
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> ImportPlasmoDBAAFeat
>>>
>>>> ures.pm
>>>> has too many errors.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:42 2005    INFO    Plugin
>>>> GUS::Community::Plugin::ImportPlasmoDBPrediction registered with  
>>>> cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:48:44 2005    INFO    Plugin
>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNASequence registered  
>>>> with
>>>> cvs revision '2924'
>>>> Tue Jul 19 08:48:46 2005    INFO    Plugin
>>>> GUS::Community::Plugin::InsertDbRefAndDbRefNaSequenceGeneral  
>>>> registered
>>>> with cvs revision '2924'
>>>> Tue Jul 19 08:48:47 2005    INFO    Plugin
>>>> GUS::Community::Plugin::InsertNAFeatureComment registered with cvs
>>>> revision '2924'
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyEntry" at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyRelationshipType" at  
>>>> (eval 8) line
>>>>
>> 1.
>>
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertOntologyTermType" at (eval 8)  
>>>> line 1.
>>>>
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::InsertPhylogeneticProfiles" at (eval 8)  
>>>> line 1.
>>>>
>>>>
>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> InsertSeqsAndFeature
>>>
>>>> s.pm
>>>> line 6.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> InsertSeqsAndFeature
>>>
>>>> s.pm
>>>> line 6.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:48:53 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadBLATAlignments registered with cvs  
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:54 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadBlastSimilaritiesPK registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:48:56 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadDocumentation registered with cvs  
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:48:57 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadEnzymeDatabase registered with cvs  
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate object method "new" via package
>>>> "GUS::Community::Plugin::LoadFromdbESTMirror" at (eval 8) line 1.
>>>>
>>>>
>>>> Can't locate XML/Simple.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> LoadGeneFeaturesFrom
>>>
>>>> XML.pm
>>>> line 16.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> LoadGeneFeaturesFrom
>>>
>>>> XML.pm
>>>> line 16.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:00 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadGenomeGaps registered with cvs  
>>>> revision '2924'
>>>>
>>>> Can't locate GUS/Model/RAD3/SAGETag.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> LoadGenomicSageData.
>>>
>>>> pm
>>>> line 11.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> LoadGenomicSageData.
>>>
>>>> pm
>>>> line 11.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:03 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadHspsOnly registered with cvs  
>>>> revision '2924'
>>>> Tue Jul 19 08:49:04 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadMutualInformationScores registered  
>>>> with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:05 2005    INFO    Plugin
>>>> GUS::Community::Plugin::LoadPfam registered with cvs revision  
>>>> '2924'
>>>> GUS::Community::Plugin::LoadSageResults is already registered.
>>>> Use '+update' if you need to register a new version.
>>>>
>>>> Can't locate GUS/Model/RAD3/Study.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> MAS5StudyModuleILoad
>>>
>>>> er.pm
>>>> line 12.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> MAS5StudyModuleILoad
>>>
>>>> er.pm
>>>> line 12.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:09 2005    INFO    Plugin
>>>> GUS::Community::Plugin::MakeBestSimilarityPair registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:10 2005    INFO    Plugin
>>>> GUS::Community::Plugin::MakeDtd registered with cvs revision '2924'
>>>> Tue Jul 19 08:49:11 2005    INFO    Plugin
>>>> GUS::Community::Plugin::MakeIndexWordLink registered with cvs  
>>>> revision
>>>> '2924'
>>>> Tue Jul 19 08:49:12 2005    INFO    Plugin
>>>> GUS::Community::Plugin::MakeIndexWordSimLink registered with cvs
>>>> revision '2924'
>>>> Tue Jul 19 08:49:13 2005    INFO    Plugin
>>>> GUS::Community::Plugin::OrthologGroupsMCL registered with cvs  
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate GUS/Model/RAD3/Quantification.pm in @INC (@INC  
>>>> contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> SimpleArrayResultLoa
>>>
>>>> der.pm
>>>> line 28.
>>>> BEGIN failed--compilation aborted at
>>>>
>>
>>
>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>> SimpleArrayResultLoa
>>>
>>>> der.pm
>>>> line 28.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>> Tue Jul 19 08:49:15 2005    INFO    Plugin
>>>> GUS::Community::Plugin::UpdateNASequences registered with cvs  
>>>> revision
>>>> '2924'
>>>>
>>>> Can't locate V.pm in @INC (@INC contains:
>>>> /home/brcgusts/GUS/gus_home/lib/perl
>>>> /usr/lib/perl5/site_perl/5.8.0/i486-linux /usr/lib/perl5/ 
>>>> site_perl/5.8.0
>>>> /home/gmod/bioperl/bioperl-1.4 /usr/lib/perl5/5.8.0/i486-linux
>>>> /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl .) at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>>> XdbLister.pm
>>>> line 10.
>>>> BEGIN failed--compilation aborted at
>>>> /home/brcgusts/GUS/gus_home/lib/perl/GUS/Community/Plugin/ 
>>>> XdbLister.pm
>>>> line 10.
>>>> Compilation failed in require at (eval 8) line 1.
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>> -------------------------------------------------------
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>> Strategies
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>>
>
>
> -- 
>
>
>
> -------------------------------------------------------
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