Re: [GUSDEV] GUS 3.5 plugin registration error

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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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