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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 07:20:49
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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:
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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...>
>> 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.
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>> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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