Re: [GUSDEV] Problem with InsertExternalDatabaseRls plugin

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Nicolas-

The problem is a mismatch between the plugin and the schema.   The 
plugin has been upgraded to conform with an in-house schema 
enhancement.  Your schema does not have the enhancement.

We'll need to discuss this here, to figure out how to best resolve it.

Sorry for the inconvenience.

Steve

On 4/6/2012 3:10 AM, Nicolas Joannin wrote:
> 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 2012INFOPlugin 
> GUS::Supported::Plugin::InsertExternalDatabaseRls registered with cvs 
> revision '10163'
> Fri Apr  6 15:54:24 2012DSNdbi:Pg:dbname=varDB_2012
> Fri Apr  6 15:54:24 
> 2012PLUGINGUS::Supported::Plugin::InsertExternalDatabaseRls
> Fri Apr  6 15:54:24 2012ARGalgoinvo1
> Fri Apr  6 15:54:24 2012ARGcomment
> Fri Apr  6 15:54:24 2012ARGcommit0
> Fri Apr  6 15:54:24 2012ARGdatabaseNameGenbank
> Fri Apr  6 15:54:24 2012ARGdatabaseVersion188.0
> Fri Apr  6 15:54:24 2012ARGdebug0
> Fri Apr  6 15:54:24 2012ARGdescription
> Fri Apr  6 15:54:24 2012ARGdownloadUrlftp://ftp.ncbi.nih.gov/genbank/
> Fri Apr  6 15:54:24 2012ARGfileMd5
> Fri Apr  6 15:54:24 2012ARGfileName
> Fri Apr  6 15:54:24 2012ARGgroup
> Fri Apr  6 15:54:24 
> 2012ARGgusconfigfile/Users/Nicolas/GUS/gus_home/config/gus.config
> Fri Apr  6 15:54:24 2012ARGhelp0
> Fri Apr  6 15:54:24 2012ARGhelpHTML0
> Fri Apr  6 15:54:24 2012ARGidIsAlias0
> Fri Apr  6 15:54:24 2012ARGidType
> Fri Apr  6 15:54:24 2012ARGidUrl
> Fri Apr  6 15:54:24 2012ARGproject
> Fri Apr  6 15:54:24 2012ARGreleaseDate15 Feb 2012
> Fri Apr  6 15:54:24 2012ARGsecondaryIdType
> Fri Apr  6 15:54:24 2012ARGsecondaryIdUrl
> Fri Apr  6 15:54:24 2012ARGsqlVerbose0
> Fri Apr  6 15:54:24 2012ARGuser
> Fri Apr  6 15:54:24 2012ARGverbose0
> Fri Apr  6 15:54:24 2012ARGveryVerbose0
> Fri Apr  6 15:54:24 2012ARGworkflowstepid0
> Fri Apr  6 15:54:24 2012AlgInvocationId12
> Fri Apr  6 15:54:24 2012COMMITcommit 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
>
>
>
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