[GUSDEV] InsertSequenceFeatures.pm

[<mro...@cs...>]

Hi everybody,


In InsertSequenceFeatures.pm at line 308 I changed

   cvsRevision =3D> '$Revision$',
to cvsRevision =3D> '$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

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D
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     =20
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 =20
/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=20
/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/Ins=
ertSequenceFeatures.pm
line 319.

STACK TRACE:
 at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin/Ins=
ertSequenceFeatures.pm
line 319
        GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Support=
ed::Plugin::InsertSequenceFeatures=3DHASH(0x854891c)',
'HASH(0x8ea8aa8)') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 469
        eval {...} called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 461
        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Plu=
ginMgr::GusApplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 380
        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::=
GusApplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 288
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusA=
pplication=3DHASH(0x80f1174)',
'GUS::Supported::Plugin::InsertSequenceFeatures') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplica=
tion.pm
line 197
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusA=
pplication=3DHASH(0x80f1174)',
'ARRAY(0x80f8ee4)') called at
/home/acrl-storage-1/gusdb/GUS/gus_home/bin/ga line 11
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


I went to line 319 in InsertSequenceFeatures.pm and I get:


  $self->{mapperSet} =3D
    GUS::Supported::BioperlFeatMapperSet->new($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