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Re: [GUSDEV] Gusdev-gusdev Digest, Vol 23, Issue 2
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From: Steve F. <sfi...@pc...> - 2012-04-10 13:08:48
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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 $', # cvs fills this in
(the number value will be different in your file)
change the number to something larger, like 999999.
steve
On 4/9/2012 11:46 PM, Nicolas Joannin wrote:
> Hi Steve,
>
> I made the modification and ran it. It ran without producing any error
> message, so I ran it again, this time with the commit flag.
> As I should have expected this resulted in a md5 error: the plugin
> doesn't correspond to the original anymore and therefore will not proceed.
>
> The message suggests to either revert back to the original (from the
> svn), which brings me back to my initial problem; or to svn commit the
> modified plugin file.
> Is there any other alternative to this problem?
>
> Best regards,
> Nicolas
>
>
> On Mon, Apr 9, 2012 at 20:01, Nicolas Joannin
> <nic...@gm... <mailto:nic...@gm...>> wrote:
>
> Hi Steve,
>
> Thanks: I'll do that then.
>
> Best regards,
> Nicolas
>
>
>
> On Mon, Apr 9, 2012 at 19:57, Steve Fischer
> <sfi...@pc... <mailto:sfi...@pc...>> wrote:
>
> yes, nicolas, that will work.
>
> steve
>
>
> On 4/9/2012 3:20 AM, Nicolas Joannin wrote:
>> Hi again,
>>
>> Disclaimer: I am not a Perl programmer, so please forgive me
>> if I suggest something totally ridiculous etc.
>>
>> Going through the ExternalDatabaseRls plugin, I see at line
>> 226 (and in subsequent GusRow and DbiRow modules) that it
>> checks to see if the attribute "id_is_alias" exists in the
>> table ExternalDatabaseRelease, which, in the GUS I retrieved
>> from the svn, is absent.
>> Would a quick and dirty fix be to comment out that line (as
>> shown below)?
>>
>> Best regards,
>> Nicolas
>>
>>
>> The resulting sub in the ExternalDatabaseRls plugin would be
>> as follows:
>>
>> sub makeNewReleaseId{
>> my ($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...
>> <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:
>>
>> Send Gusdev-gusdev mailing list submissions to
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>> <mailto:gus...@li...>
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>>
>> When replying, please edit your Subject line so it is
>> more specific
>> than "Re: Contents of Gusdev-gusdev digest..."
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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...
>> <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
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > 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
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>> <mailto:Gus...@li...>
>> >
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
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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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>>
>> 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 list
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