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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 23, Issue 2
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From: Nicolas J. <nic...@gm...> - 2012-04-10 03:47:29
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Hi Steve,
I made the modification and ran it. It ran without producing any error
message, so I ran it again, this time with the commit flag.
As I should have expected this resulted in a md5 error: the plugin doesn't
correspond to the original anymore and therefore will not proceed.
The message suggests to either revert back to the original (from the svn),
which brings me back to my initial problem; or to svn commit the modified
plugin file.
Is there any other alternative to this problem?
Best regards,
Nicolas
On Mon, Apr 9, 2012 at 20:01, Nicolas Joannin <nic...@gm...>wrote:
> 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:
>>>
>>>> Send Gusdev-gusdev mailing list submissions to
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>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of Gusdev-gusdev digest..."
>>>>
>>>>
>>>> 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
>>>> >
>>>> >
>>>> >
>>>> >
>>>> ------------------------------------------------------------------------------
>>>> > 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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>>>> ------------------------------------------------------------------------------
>>>> 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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>>>>
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>>>>
>>>> End of Gusdev-gusdev Digest, Vol 23, Issue 2
>>>> ********************************************
>>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>>
>>
>>
>> _______________________________________________
>> Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
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