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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 23, Issue 2
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From: Nicolas J. <nic...@gm...> - 2012-04-09 11:02:26
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Hi Steve,
Thanks: I'll do that then.
Best regards,
Nicolas
On Mon, Apr 9, 2012 at 19:57, Steve Fischer <sfi...@pc...> wrote:
> 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...>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...> wrote:
>>
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>>> Today's Topics:
>>>
>>> 1. Re: Problem with InsertExternalDatabaseRls plugin (Steve Fischer)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Fri, 06 Apr 2012 09:55:29 -0400
>>> From: Steve Fischer <sfi...@pc...>
>>> Subject: Re: [GUSDEV] Problem with InsertExternalDatabaseRls plugin
>>> To: gus...@li...
>>> Message-ID: <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/
>>> > 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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>>> ********************************************
>>>
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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!http://p.sf.net/sfu/Boundary-d2dvs2
>
>
>
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