Re: [GUSDEV] (no subject)

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Hi Isabelle,
You might try some pointers here: http://gusdb.org/wiki/index.php/How%20we%20built%20TheileriaDB.org
which is for a post-gres  version.

John, can you help?
Thanks,
Chris

On Dec 9, 2008, at 10:04 PM, Isabelle Phan wrote:

> Hello
>
> I just installed GUS 3.5 from www.gusdb.org/download . I am using
> Postgres and trying to load ExternalDatabase.xml as described in
> http://wiki.biowebdb.org/index.php/ 
> Gus#GUS::Supported::Plugin::LoadGusXm
> l
>
> It does not work (see stack trace below), apparently because of a
> mismatch with the schema created during the installation.
>
> Where do I find a copy of ExternalDatabase.xml that is compatible with
> the GUS 3.5 schema?
>
> Thanks,
>
>
> Isabelle
>
> $> ga GUS::Supported::Plugin::LoadGusXml --filename
> ../data/ExternalDatabase.xml
> Tue Dec  9 18:30:22 2008        ARGS    algoinvo        1
> Tue Dec  9 18:30:22 2008        ARGS    comment
> Tue Dec  9 18:30:22 2008        ARGS    commit  0
> Tue Dec  9 18:30:22 2008        ARGS    debug   0
> Tue Dec  9 18:30:22 2008        ARGS    filename
> ../data/ExternalDatabase.xml
> Tue Dec  9 18:30:22 2008        ARGS    group
> Tue Dec  9 18:30:22 2008        ARGS    gusconfigfile
> /core/trypdb/gus-test/GUS/gus.properties
> Tue Dec  9 18:30:22 2008        ARGS    help
> Tue Dec  9 18:30:22 2008        ARGS    helpHTML
> Tue Dec  9 18:30:22 2008        ARGS    project
> Tue Dec  9 18:30:22 2008        ARGS    refresh
> Tue Dec  9 18:30:22 2008        ARGS    sqlVerbose      0
> Tue Dec  9 18:30:22 2008        ARGS    user
> Tue Dec  9 18:30:22 2008        ARGS    verbose 0
> Tue Dec  9 18:30:22 2008        ARGS    veryVerbose     0
> Tue Dec  9 18:30:22 2008        COMMIT  commit off
> Tue Dec  9 18:30:22 2008        ALGINVID        5
>
> ERROR:
> ERROR: attempting to access attribute 'lowercase_name' of table
> ExternalDatabase, but that table does not have such an attribute
>
> at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 729
>
> GUS 
> ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase
> =HASH(0xf3b4530)', 'lowercase_name') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line
> 88
>
> GUS 
> ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b
> 4530)', 'lowercase_name', 'assembly') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line
> 1902
>
> GUS 
> ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x
> f3b4530)', 'ARRAY(0xee1ce10)', 1) called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line
> 1952
>
> GUS 
> ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH
> (0xf0572b0)', 'ARRAY(0xee1ce10)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> LoadGus
> Xml.pm line 140
>
> GUS 
> ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa
> dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> LoadGus
> Xml.pm line 117
>
> GUS 
> ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus
> Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 469
>        eval {...} called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 461
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
> :GusApplication=HASH(0xe6512a0)',  
> 'GUS::Supported::Plugin::LoadGusXml',
> 1) called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 380
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
> ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called
> at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 288
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
> ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 197
>
> GUS 
> ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
> ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at
> /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11
>
> STACK TRACE:
> at /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm
> line 729
>
> GUS 
> ::ObjRelP::DbiRow::checkAttribute('GUS::Model::SRes::ExternalDatabase
> =HASH(0xf3b4530)', 'lowercase_name') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line
> 88
>
> GUS 
> ::ObjRelP::DbiRow::set('GUS::Model::SRes::ExternalDatabase=HASH(0xf3b
> 4530)', 'lowercase_name', 'assembly') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line
> 1902
>
> GUS 
> ::Model::GusRow::parseXML('GUS::Model::SRes::ExternalDatabase=HASH(0x
> f3b4530)', 'ARRAY(0xee1ce10)', 1) called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm line
> 1952
>
> GUS 
> ::Model::GusRow::parseXML('GUS::Model::Core::AlgorithmInvocation=HASH
> (0xf0572b0)', 'ARRAY(0xee1ce10)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> LoadGus
> Xml.pm line 140
>
> GUS 
> ::Supported::Plugin::LoadGusXml::process('GUS::Supported::Plugin::Loa
> dGusXml=HASH(0xe677420)', 'ARRAY(0xee1ce10)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ 
> LoadGus
> Xml.pm line 117
>
> GUS 
> ::Supported::Plugin::LoadGusXml::run('GUS::Supported::Plugin::LoadGus
> Xml=HASH(0xe677420)', 'HASH(0xf2e57b0)') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 469
>        eval {...} called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 461
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr:
> :GusApplication=HASH(0xe6512a0)',  
> 'GUS::Supported::Plugin::LoadGusXml',
> 1) called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 380
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl
> ication=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called
> at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 288
>
> GUS 
> ::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat
> ion=HASH(0xe6512a0)', 'GUS::Supported::Plugin::LoadGusXml') called at
> /core/trypdb/gus-test/GUS/gus_home/lib/perl/GUS/PluginMgr/ 
> GusApplication
> .pm line 197
>
> GUS 
> ::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat
> ion=HASH(0xe6512a0)', 'ARRAY(0xe651d70)') called at
> /core/trypdb/gus-test/GUS/gus_home/bin/ga line 11
> --
> Isabelle Phan, DPhil
> Seattle Biomedical Research Institute
> +1(206)256 7113
>
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