[GUSDEV] Problem with InsertExternalDatabaseRls plugin

[Nicolas J. <nic...@gm...>]

Hello everyone,

I have successfully installed GUS and am now struggling a bit to get data
into it.
I am facing several problems, but will decline them in different email
threads as I get blocked on my way...

The current blocking point I'm at is with InsertExternalDatabaseRls.
In order to use InsertSequenceFeature, I need to have a database+version in
my DB. The data I'm trying to insert was downloaded strait from Genbank,
just to test the whole process.
I managed to insert a row with InsertExternalDatabase, but I am failing
with this one. You'll find below the output I get from the terminal.

I really can't figure out what I'm doing wrong. I hope you can help me!
Best regards,

Nicolas


Terminal output:

ga GUS::Supported::Plugin::InsertExternalDatabaseRls --databaseName Genbank
--releaseDate '15 Feb 2012' --databaseVersion 188.0 --downloadUrl
ftp://ftp.ncbi.nih.gov/genbank/
Fri Apr  6 15:54:24 2012 INFO Plugin
GUS::Supported::Plugin::InsertExternalDatabaseRls registered with cvs
revision '10163'
Fri Apr  6 15:54:24 2012 DSN dbi:Pg:dbname=varDB_2012
Fri Apr  6 15:54:24 2012 PLUGIN
GUS::Supported::Plugin::InsertExternalDatabaseRls
Fri Apr  6 15:54:24 2012 ARG algoinvo 1
Fri Apr  6 15:54:24 2012 ARG comment
Fri Apr  6 15:54:24 2012 ARG commit 0
Fri Apr  6 15:54:24 2012 ARG databaseName Genbank
Fri Apr  6 15:54:24 2012 ARG databaseVersion 188.0
Fri Apr  6 15:54:24 2012 ARG debug 0
Fri Apr  6 15:54:24 2012 ARG description
Fri Apr  6 15:54:24 2012 ARG downloadUrl ftp://ftp.ncbi.nih.gov/genbank/
Fri Apr  6 15:54:24 2012 ARG fileMd5
Fri Apr  6 15:54:24 2012 ARG fileName
Fri Apr  6 15:54:24 2012 ARG group
Fri Apr  6 15:54:24 2012 ARG gusconfigfile
/Users/Nicolas/GUS/gus_home/config/gus.config
Fri Apr  6 15:54:24 2012 ARG help 0
Fri Apr  6 15:54:24 2012 ARG helpHTML 0
Fri Apr  6 15:54:24 2012 ARG idIsAlias 0
Fri Apr  6 15:54:24 2012 ARG idType
Fri Apr  6 15:54:24 2012 ARG idUrl
Fri Apr  6 15:54:24 2012 ARG project
Fri Apr  6 15:54:24 2012 ARG releaseDate 15 Feb 2012
Fri Apr  6 15:54:24 2012 ARG secondaryIdType
Fri Apr  6 15:54:24 2012 ARG secondaryIdUrl
Fri Apr  6 15:54:24 2012 ARG sqlVerbose 0
Fri Apr  6 15:54:24 2012 ARG user
Fri Apr  6 15:54:24 2012 ARG verbose 0
Fri Apr  6 15:54:24 2012 ARG veryVerbose 0
Fri Apr  6 15:54:24 2012 ARG workflowstepid 0
Fri Apr  6 15:54:24 2012 AlgInvocationId 12
Fri Apr  6 15:54:24 2012 COMMIT commit off

ERROR:
ERROR: attempting to access attribute 'id_is_alias' of table
ExternalDatabaseRelease, but that table does not have such an attribute

 at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 746
 GUS::ObjRelP::DbiRow::checkAttribute('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'id_is_alias') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 753
 GUS::ObjRelP::DbiRow::checkAttributeHash('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'HASH(0x100c89568)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 179
 GUS::ObjRelP::DbiRow::setAttributes('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'HASH(0x100c30df0)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 42
 GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow',
'GUS::Model::SRes::ExternalDatabaseRelease', 'HASH(0x100c30df0)', undef,
undef) called at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm
line 25
 GUS::Model::GusRow::new('GUS::Model::SRes::ExternalDatabaseRelease',
'HASH(0x100c30df0)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDatabaseRls.pm
line 220
 GUS::Supported::Plugin::InsertExternalDatabaseRls::makeNewReleaseId('GUS::Supported::Plugin::InsertExternalDatabaseRls=HASH(0x100a...',
1) called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDatabaseRls.pm
line 180
 GUS::Supported::Plugin::InsertExternalDatabaseRls::run('GUS::Supported::Plugin::InsertExternalDatabaseRls=HASH(0x100a...',
'HASH(0x100c29838)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
602
 eval {...} called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
591
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls', 1) called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
508
 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
394
 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
303
 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'ARRAY(0x100829b60)') called at /Users/Nicolas/GUS/gus_home/bin/ga line 11

STACK TRACE:
 at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 746
GUS::ObjRelP::DbiRow::checkAttribute('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'id_is_alias') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 753
 GUS::ObjRelP::DbiRow::checkAttributeHash('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'HASH(0x100c89568)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 179
 GUS::ObjRelP::DbiRow::setAttributes('GUS::ObjRelP::DbiRow=HASH(0x100c30e50)',
'HASH(0x100c30df0)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 42
 GUS::ObjRelP::DbiRow::new('GUS::ObjRelP::DbiRow',
'GUS::Model::SRes::ExternalDatabaseRelease', 'HASH(0x100c30df0)', undef,
undef) called at /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/GusRow.pm
line 25
 GUS::Model::GusRow::new('GUS::Model::SRes::ExternalDatabaseRelease',
'HASH(0x100c30df0)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDatabaseRls.pm
line 220
 GUS::Supported::Plugin::InsertExternalDatabaseRls::makeNewReleaseId('GUS::Supported::Plugin::InsertExternalDatabaseRls=HASH(0x100a...',
1) called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertExternalDatabaseRls.pm
line 180
 GUS::Supported::Plugin::InsertExternalDatabaseRls::run('GUS::Supported::Plugin::InsertExternalDatabaseRls=HASH(0x100a...',
'HASH(0x100c29838)') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
602
 eval {...} called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
591
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls', 1) called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
508
 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
394
 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'GUS::Supported::Plugin::InsertExternalDatabaseRls') called at
/Users/Nicolas/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
303
 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x100803ae8)',
'ARRAY(0x100829b60)') called at /Users/Nicolas/GUS/gus_home/bin/ga line 11