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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 23, Issue 2
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From: Nicolas J. <nic...@gm...> - 2012-04-11 08:04:12
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Hi Steve,
Thanks, that worked!
I'm starting to get a hang of how these plugins work, so hopefully I won't
bug you guys too much in the future.
(Although I'm guessing I might when I start writing plugins myself... ;)
Best regards,
Nicolas
On Tue, Apr 10, 2012 at 22:08, Steve Fischer <sfi...@pc...>wrote:
> nicolas-
>
> you can hack around this.
>
> in $GUS_HOME/lib/perl/GUS/Supported/Plugins you should find a copy of this
> plugin file. in the file you will find this line:
>
> cvsRevision => '$Revision: 10163 $', # cvs fills this in
>
> (the number value will be different in your file)
>
> change the number to something larger, like 999999.
>
> steve
>
>
> On 4/9/2012 11:46 PM, Nicolas Joannin wrote:
>
> Hi Steve,
>
> I made the modification and ran it. It ran without producing any error
> message, so I ran it again, this time with the commit flag.
> As I should have expected this resulted in a md5 error: the plugin doesn't
> correspond to the original anymore and therefore will not proceed.
>
> The message suggests to either revert back to the original (from the
> svn), which brings me back to my initial problem; or to svn commit the
> modified plugin file.
> Is there any other alternative to this problem?
>
> Best regards,
> Nicolas
>
>
> On Mon, Apr 9, 2012 at 20:01, Nicolas Joannin <nic...@gm...>wrote:
>
>> Hi Steve,
>>
>> Thanks: I'll do that then.
>>
>> Best regards,
>> Nicolas
>>
>>
>>
>> On Mon, Apr 9, 2012 at 19:57, Steve Fischer <sfi...@pc...>wrote:
>>
>>> yes, nicolas, that will work.
>>>
>>> steve
>>>
>>>
>>> On 4/9/2012 3:20 AM, Nicolas Joannin wrote:
>>>
>>> Hi again,
>>>
>>> Disclaimer: I am not a Perl programmer, so please forgive me if I
>>> suggest something totally ridiculous etc.
>>>
>>> Going through the ExternalDatabaseRls plugin, I see at line 226 (and
>>> in subsequent GusRow and DbiRow modules) that it checks to see if the
>>> attribute "id_is_alias" exists in the table ExternalDatabaseRelease, which,
>>> in the GUS I retrieved from the svn, is absent.
>>> Would a quick and dirty fix be to comment out that line (as shown below)?
>>>
>>> Best regards,
>>> Nicolas
>>>
>>>
>>> The resulting sub in the ExternalDatabaseRls plugin would be as
>>> follows:
>>>
>>> sub makeNewReleaseId{
>>> my ($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
>>>>> gus...@li...
>>>>>
>>>>> To subscribe or unsubscribe via the World Wide Web, visit
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>> or, via email, send a message with subject or body 'help' to
>>>>> gus...@li...
>>>>>
>>>>> You can reach the person managing the list at
>>>>> gus...@li...
>>>>>
>>>>> 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
>>>>> >
>>>>> >
>>>>> > _______________________________________________
>>>>> > Gusdev-gusdev mailing list
>>>>> > Gus...@li...
>>>>> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>> -------------- next part --------------
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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
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>> 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...://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>
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