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Re: [GUSDEV] InsertSequenceFeatures.pm
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From: <sfi...@pc...> - 2006-09-29 16:09:45
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michael-
i suspect the problem is that you have downloaded and installed
InsertSequenceFeature.pm into your previously existing gus installation.
but, it needs other support files.
you might be ok if you get all of GUS/Supported. save your old GUS/Supported
as a backup.
let's see how that goes. you might need more.
steve
Quoting mro...@cs...:
> Hi everybody,
>
>
> In InsertSequenceFeatures.pm at line 308 I changed
>
> cvsRevision => '$Revision$',
> to cvsRevision => '$Revision: 1000 $',
>
> and the revision error in no longer with me
>
>
> Then I run
>
> ga GUS::Supported::Plugin::InsertSequenceFeatures
> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
> --fileFormat genbank
> --extDbName "Pseudomonas_aeruginosa"
> --extDbRlsVer "unknown"
> --commit
>
> and got
>
> ================================
> Thu Sep 28 18:24:00 2006 ARGS algoinvo 1
> Thu Sep 28 18:24:00 2006 ARGS comment
> Thu Sep 28 18:24:00 2006 ARGS commit 1
> Thu Sep 28 18:24:00 2006 ARGS debug 0
> Thu Sep 28 18:24:00 2006 ARGS defaultOrganism
> Thu Sep 28 18:24:00 2006 ARGS extDbName
> Pseudomonas_aeruginosa
> Thu Sep 28 18:24:00 2006 ARGS extDbRlsVer unknown
> Thu Sep 28 18:24:00 2006 ARGS fileFormat genbank
> Thu Sep 28 18:24:00 2006 ARGS gff2GroupTag
> Thu Sep 28 18:24:00 2006 ARGS group
> Thu Sep 28 18:24:00 2006 ARGS gusconfigfile
> /home/acrl-storage-1/gusdb/GUS/gus.properties
> Thu Sep 28 18:24:00 2006 ARGS handlerExternalDbs
> Thu Sep 28 18:24:00 2006 ARGS help
> Thu Sep 28 18:24:00 2006 ARGS helpHTML
> Thu Sep 28 18:24:00 2006 ARGS inputFileExtension
> Thu Sep 28 18:24:00 2006 ARGS inputFileOrDir
> /home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/NC_002516.gbk
> Thu Sep 28 18:24:00 2006 ARGS makeSourceids
> Thu Sep 28 18:24:00 2006 ARGS mapFile
> /home/biorg-srv-2/mrobi002/pseudomonas aeruginosa/pa01/genbank2gus.xml
> Thu Sep 28 18:24:00 2006 ARGS naSequenceSubclass
> Thu Sep 28 18:24:00 2006 ARGS organism
> Thu Sep 28 18:24:00 2006 ARGS project
> Thu Sep 28 18:24:00 2006 ARGS seqExtDbName
> Thu Sep 28 18:24:00 2006 ARGS seqExtDbRlsVer
> Thu Sep 28 18:24:00 2006 ARGS seqIdColumn source_id
> Thu Sep 28 18:24:00 2006 ARGS seqSoTerm
> Thu Sep 28 18:24:00 2006 ARGS seqType
> Thu Sep 28 18:24:00 2006 ARGS soCvsVersion
> Thu Sep 28 18:24:00 2006 ARGS sqlVerbose 0
> Thu Sep 28 18:24:00 2006 ARGS testNumber
> Thu Sep 28 18:24:00 2006 ARGS user
> Thu Sep 28 18:24:00 2006 ARGS verbose 0
> Thu Sep 28 18:24:00 2006 ARGS veryVerbose 0
> Thu Sep 28 18:24:00 2006 COMMIT commit on
> Thu Sep 28 18:24:00 2006 ALGINVID 12
>
> ERROR:
> Can't locate object method "new" via package
> "GUS::Supported::BioperlFeatMapperSet" (perhaps you forgot to load
> "GUS::Supported::BioperlFeatMapperSet"?) at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 319.
>
> STACK TRACE:
> at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
> line 319
>
> GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x854891c)',
> 'HASH(0x8ea8aa8)') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 469
> eval {...} called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 461
>
> GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 380
>
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 288
>
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 197
>
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80f1174)',
> 'ARRAY(0x80f8ee4)') called at
> /home/acrl-storage-1/gusdb/GUS/gus_home/bin/ga line 11
> ==========================================
>
>
> I went to line 319 in InsertSequenceFeatures.pm and I get:
>
>
> $self->{mapperSet} =
> GUS::Supported::BioperlFeatMapperSet->new($self->getArg('mapFile'),
> $self)
>
>
> So should I assume that there is a problem with mapFile genbank2gus.xml?
>
> I have not modified any other Plugins, do I need to?
>
> In the Gus-dev I found that the other similar times with this problem it
> was caused by Source Repository being temporary unavailable.
>
>
> Thank you
>
>
> Michael
>
>
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