[GUSDEV] (no subject)

[Isabelle P. <isa...@sb...>]

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