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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 23, Issue 2
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From: Steve F. <sfi...@pc...> - 2012-04-09 10:57:44
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yes, nicolas, that will work.
steve
On 4/9/2012 3:20 AM, Nicolas Joannin wrote:
> Hi again,
>
> Disclaimer: I am not a Perl programmer, so please forgive me if I
> suggest something totally ridiculous etc.
>
> Going through the ExternalDatabaseRls plugin, I see at line 226 (and
> in subsequent GusRow and DbiRow modules) that it checks to see if the
> attribute "id_is_alias" exists in the table ExternalDatabaseRelease,
> which, in the GUS I retrieved from the svn, is absent.
> Would a quick and dirty fix be to comment out that line (as shown below)?
>
> Best regards,
> Nicolas
>
>
> The resulting sub in the ExternalDatabaseRls plugin would be as follows:
>
> sub makeNewReleaseId{
> my ($self, $id) = @_;
> my $dbVer = $self->getArg('databaseVersion');
>
> my $newRelease = GUS::Model::SRes::ExternalDatabaseRelease->new({
> external_database_id => $id,
> version => $dbVer,
> download_url => $self->getArg('downloadUrl'),
> id_type => $self->getArg('idType'),
> id_url => $self->getArg('idUrl'),
> #id_is_alias => $self->getArg('idIsAlias'),
> secondary_id_type => $self->getArg('secondaryIdType'),
> secondary_id_url => $self->getArg('secondaryIdUrl'),
> description => $self->getArg('description'),
> file_name => $self->getArg('fileName'),
> file_md5 => $self->getArg('fileMd5'),
> });
>
> $newRelease->submit();
> my $newReleasePk = $newRelease->getId();
>
> return $newReleasePk;
>
> }
>
>
> On Mon, Apr 9, 2012 at 15:25, Nicolas Joannin
> <nic...@gm... <mailto:nic...@gm...>> wrote:
>
> Hi Steve,
>
> Thanks for the quick response.
> Please let me know the conclusions to your discussions.
> In the mean time, I will go through the different modules to try
> and better understand what's going on.
>
> Best regards,
> Nicolas
>
> On Fri, Apr 6, 2012 at 22:55,
> <gus...@li...
> <mailto:gus...@li...>> wrote:
>
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> Today's Topics:
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> 1. Re: Problem with InsertExternalDatabaseRls plugin (Steve
> Fischer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 06 Apr 2012 09:55:29 -0400
> From: Steve Fischer <sfi...@pc...
> <mailto:sfi...@pc...>>
> Subject: Re: [GUSDEV] Problem with InsertExternalDatabaseRls
> plugin
> To: gus...@li...
> <mailto:gus...@li...>
> Message-ID: <4F7...@pc...
> <mailto:4F7...@pc...>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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/
> <http://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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> End of Gusdev-gusdev Digest, Vol 23, Issue 2
> ********************************************
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>
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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