gusdev-gusdev Mailing List for Genomic Unified Schema Development

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Hello,

I was just wondering about your opinion on that stuff, please take a look and tell me what you think <http://jychuchaca.apachepeakconcepts.com/aeazej>

Sincerely yours, Jim Walke

hi gusdev

http://r-studio.in/birthday.php?opposite=cc11d14hmyteg1

Margarita Ruiz

Salutations gusdev

http://iconofx.com/page.php?thin=y9s19yqfv1rcvx

rui...@ya...
Margarita Ruiz

Sent from my iPhone

Hi All,
Sorry about the license being so hard to find. A combination of not being updated and things being restructured. 
The original license is below from http://www.cbil.upenn.edu/downloads <http://www.cbil.upenn.edu/downloads>
and based on the open source license from the Apache Software Foundation (http://www.apache.org). I am happy to update it to a current open source one like Creative Commons.

The CBIL Software and Data License, Version 1.0

Copyright (c) 2001 The Computational Biology and Informatics
Laboratory (CBIL) at the University of Pennsylvania.  All rights
reserved.

Redistribution and use of software in source and binary forms or of
data, with or without modification, are permitted provided that the
following conditions are met:

1.  Redistributions of source code, binary software or data alone must
retain the above copyright notice, this list of conditions and the
following disclaimer.

2.  Redistributions as part of a package or product must reproduce the
above copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided with
the distribution.

3.  The end-user documentation included with the redistribution, if
any, must include the following acknowledgment: "This product includes
software and/or data developed by CBIL at the Center for Bioinformatics 
at the University of Pennsylvania (http://www.pcbi.upenn.edu)."  
Alternately, this acknowledgment may appear in the software or with the 
data itself, if and wherever such third-party acknowledgments normally 
appear.

4.  The names "CBIL" and "Penn Center for Bioinformatics" must not be
used to endorse or promote products derived from this software/data
without prior written permission.

  THIS SOFTWARE/DATA IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR
  IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  DISCLAIMED.  IN NO EVENT SHALL CBIL OR THE PENN CENTER FOR
  BIOINFORMATICS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
  LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
  THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Chris

> On May 4, 2015, at 2:22 PM, Rodrigo Jardim <jar...@gm...> wrote:
> 
> Hi John,
> 
> in http://gusdb.org/documentation/3.5/developers/html/ <http://gusdb.org/documentation/3.5/developers/html/> have a description: "The Genomics Unified Schema and Application Framework are subject to various license terms and copyrights as outlined in the LICENSE file provided with the software.", but I didn't find and you?
> 
> Regards
> 
> 2015-05-04 14:34 GMT-03:00 John Iodice <io...@gm... <mailto:io...@gm...>>:
> All,
> 
> I'm not sure how to respond to this question from the NASA GeneLab. Under what license (if any) is GUS released?
> 
> -- John
> 
> ---------- Forwarded message ----------
> From: Middour, Christopher K. {Chris} (ARC-TI)[Millennium Engineering & Integration Co.] <chr...@na... <mailto:chr...@na...>>
> Date: Mon, May 4, 2015 at 1:03 PM
> Subject: Software license details for GUSDB?
> To: "web...@gu... <mailto:web...@gu...>" <web...@gu... <mailto:web...@gu...>>
> 
> 
> Hi, I am interested in know what the licensing details might be for GUSDB.
> It does not seem to be documented on the site anywhere.
> 
> --Chris Middour
> Data Systems Lead, NASA GeneLab
> 
> 
> 
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev <https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev>
> 
> 
> 
> 
> -- 
> Att,
> Rodrigo Jardim
> 
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud 
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Hi John,

in http://gusdb.org/documentation/3.5/developers/html/ have a description:
"The Genomics Unified Schema and Application Framework are subject to
various license terms and copyrights as outlined in the LICENSE file
provided with the software.", but I didn't find and you?

Regards

2015-05-04 14:34 GMT-03:00 John Iodice <io...@gm...>:

> All,
>
> I'm not sure how to respond to this question from the NASA GeneLab. Under
> what license (if any) is GUS released?
>
> -- John
>
> ---------- Forwarded message ----------
> From: Middour, Christopher K. {Chris} (ARC-TI)[Millennium Engineering &
> Integration Co.] <chr...@na...>
> Date: Mon, May 4, 2015 at 1:03 PM
> Subject: Software license details for GUSDB?
> To: "web...@gu..." <web...@gu...>
>
>
> Hi, I am interested in know what the licensing details might be for GUSDB.
> It does not seem to be documented on the site anywhere.
>
> --Chris Middour
> Data Systems Lead, NASA GeneLab
>
>
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>

-- 
Att,
Rodrigo Jardim

All,

I'm not sure how to respond to this question from the NASA GeneLab. Under
what license (if any) is GUS released?

-- John

---------- Forwarded message ----------
From: Middour, Christopher K. {Chris} (ARC-TI)[Millennium Engineering &
Integration Co.] <chr...@na...>
Date: Mon, May 4, 2015 at 1:03 PM
Subject: Software license details for GUSDB?
To: "web...@gu..." <web...@gu...>

Hi, I am interested in know what the licensing details might be for GUSDB.
It does not seem to be documented on the site anywhere.

--Chris Middour
Data Systems Lead, NASA GeneLab

I checked in revision 12947 or gusEnv.bash to deal with this. It now sets
PERL5LIB, using a Perl one-liner to remove any existing gus_home/lib/perl
entries and adding the current one.

-- John

On Thu, Oct 17, 2013 at 2:59 PM, John Iodice <io...@gm...> wrote:

> gusEnv.bash sets some environment variables, including PATH, but it
> doesn't set PERL5LIB. Isn't that a bug?
>
> I call gusEnv.bash in my .bash_profile, then do this:
> PERL5LIB=${GUS_HOME}/lib/perl:${PERL5LIB}
>
> But if I use gusEnv.bash later in the session, to point at a different GUS
> install, PERL5LIB continues to point wherever it started.
>
> This is a bug, right? I'm running executables from the new gus_home, but
> they're finding their Perl modules in the old gus_home/lib/perl. I think
> that line above should be in gusEnv.bash, so it happens whenever we switch
> environments. What do you think?
>
> -- John
>

gusEnv.bash sets some environment variables, including PATH, but it doesn't
set PERL5LIB. Isn't that a bug?

I call gusEnv.bash in my .bash_profile, then do this:
PERL5LIB=${GUS_HOME}/lib/perl:${PERL5LIB}

But if I use gusEnv.bash later in the session, to point at a different GUS
install, PERL5LIB continues to point wherever it started.

This is a bug, right? I'm running executables from the new gus_home, but
they're finding their Perl modules in the old gus_home/lib/perl. I think
that line above should be in gusEnv.bash, so it happens whenever we switch
environments. What do you think?

-- John

Hi Alan,

The install scripts live in the GUS Subversion repository. To create
just the database schema, I think you need only the "install" and
"GusSchema" projects:

https://www.cbil.upenn.edu/svn/gus/install/trunk
https://www.cbil.upenn.edu/svn/gus/GusSchema/trunk

There's some documentation at
http://www.gusdb.org/documentation/3.5/install/html/ch02.html

Email me or the data loaders if you have any problems.

-- John

On Wed, Jan 16, 2013 at 11:21 AM, Alan R Gingle <ag...@ug...> wrote:
> Hello All,
>
>
>
> I need to setup an empty/bootstrap-data-only GUS instance for a new project.
> Where are the latest version installation scripts located?
>
>
>
> Thanks in advance,
>
>
>
> Alan
>
>
>
>
>
> Alan R. Gingle (Ph.D.)
> Senior Research Scientist
> University of Georgia
> Athens, GA 30602
>
>
>
>
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Hello All,

I need to setup an empty/bootstrap-data-only GUS instance for a new project.  Where are the latest version installation scripts located?

Thanks in advance,

Alan

Alan R. Gingle (Ph.D.)
Senior Research Scientist
University of Georgia
Athens, GA 30602

Hi Steve,

OK!
I had specified the soCvsVersion because I had first investigated the
plugin "InsertSequenceOntology" and assumed that the required arguments
where the same for InsertSequenceOntologyOBO: my mistake.
That said, I double checked the so.obo file I downloaded and there seems to
be an issue with a few lines, including the one with the version (see file
header below). For some reason some of the new line (\n) character is not
read properly for some lines. I don't know if this may be a problem or not,
just thought I'd point it out.
Finally, regarding the work-around by providing the soExtDbRlsName
argument: again, I hadn't looked at the ISOntologyOBO argument list, so I
didn't see that it was an option. And I still had in mind that the
soVersion and soCvsVersion were required (as in the ISOntology plugin).
Just for future reference, can you confirm that by using the soExtDbRlsName
argument, the system assumes that there is only one version of the SO?

In the end, I got impatient yesterday (there is too much time difference
between Japan and the US!), so I went ahead and updated the soCvsVersion to
its correct value in the SequenceOntology table and used that argument
instead of the soExtDbRlsName work-around.
That brings me to my next error message... But that will be for another
thread if I can't manage on my own ;)

I really appreciate your help Steve, and of course that of all the others
who have helped these past few weeks!
Best regards,

Nicolas

Header lines for the so.obo file:

format-version: 1.2
date: 05:04:2012 16:30
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 2.1.1-beta7
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
default-namespace: sequence
remark: autogenerated-by:   DAG-Edit version 1.417\nsaved-by:
eilbeck\ndate:         Tue May 11 15:18:44 PDT 2004\nversion: $Revision:
1.324 $
ontology: so-xp.obo

[Term]
id: SO:0000000
name: Sequence_Ontology
subset: SOFA
is_obsolete: true

On Thu, Apr 12, 2012 at 20:31,
<gus...@li...>wrote:

> Send Gusdev-gusdev mailing list submissions to
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>
> Today's Topics:
>
>   1. InsertSequenceOntology bug? (Nicolas Joannin)
>   2. Re: InsertSequenceOntology bug? (Steve Fischer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 12 Apr 2012 13:44:27 +0900
> From: Nicolas Joannin <nic...@gm...>
> Subject: [GUSDEV] InsertSequenceOntology bug?
> To: Gus...@li...
> Message-ID:
>        <CAPJVvAw2oXyWnA9XM=EGW...@ma...
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I am proceeding with inserting data into my gusdb.
> I downloaded the latest so.obo file from www.sequenceontology.org and
> added
> that data to the db (see output below).
>
> Once that done, I tried to insert sequence features but ran into the
> following error message: ERROR: Can't find primary key for SO term 'gene'
>
> Going through the code to find the error, I've manually checked the output
> of the following sql code:
> select term_name, sequence_ontology_id from sres.SequenceOntology where
> so_cvs_version = '$soCvsVersion'
>
> In my case the soCvsVersion is 1.324. And the result was nothing. So I
> checked the table in question, and found it full of data, but with an
> erroneous soCvsVersion: the InsertSequenceOntologyOBO plugin seems to have
> used the soVersion as both the soVersion and the soCvsVersion.
>
> Is this a bug in that plugin or is it supposed to be that way?
>
> If it is a bug, I found in the InsertSequenceOntologyOBO.pm file the
> following code (lines 170 to 178):
>
>   my $soTerm = GUS::Model::SRes::SequenceOntology->
>     new({'so_id' => $obo->{'id'},
>  'ontology_name' => 'sequence',
>  'so_version' => $soVer,
>  *'so_cvs_version' => $soVer,*
>  'term_name' => $obo->{'name'},
>  'definition' => $definition });
>
>   return $soTerm;
>
>
> Is there a specific way to update the table (I don't see any UNDO for this
> plugin)? Or should I just use plain sql UPDATE for this?
>
> Best regards,
> Nicolas
>
>
>
> Nicolas-work-iMac:~ Nicolas$ ga
> GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile
> ~/Data_for_GUS/so.obo --soVersion 1.2 --soCvsVersion 1.324 --commit
> Wed Apr 11 15:51:53 2012 DSN dbi:Pg:dbname=varDB_2012
> Wed Apr 11 15:51:53 2012 PLUGIN
> GUS::Supported::Plugin::InsertSequenceOntologyOBO
> Wed Apr 11 15:51:53 2012 ARG algoinvo 1
> Wed Apr 11 15:51:53 2012 ARG comment
> Wed Apr 11 15:51:53 2012 ARG commit 1
> Wed Apr 11 15:51:53 2012 ARG debug 0
> Wed Apr 11 15:51:53 2012 ARG group
> Wed Apr 11 15:51:53 2012 ARG gusconfigfile
> /Users/Nicolas/GUS/gus_home/config/gus.config
> Wed Apr 11 15:51:53 2012 ARG help 0
> Wed Apr 11 15:51:53 2012 ARG helpHTML 0
> Wed Apr 11 15:51:53 2012 ARG inputFile /Data_for_GUS/so.obo
> Wed Apr 11 15:51:53 2012 ARG project
> Wed Apr 11 15:51:53 2012 ARG soCvsVersion 1.324
> Wed Apr 11 15:51:53 2012 ARG soExtDbRlsName
> Wed Apr 11 15:51:53 2012 ARG soVersion 1.2
> Wed Apr 11 15:51:53 2012 ARG sqlVerbose 0
> Wed Apr 11 15:51:53 2012 ARG user
> Wed Apr 11 15:51:53 2012 ARG verbose 0
> Wed Apr 11 15:51:53 2012 ARG veryVerbose 0
> Wed Apr 11 15:51:53 2012 ARG workflowstepid 0
> Wed Apr 11 15:51:53 2012 AlgInvocationId 29
> Wed Apr 11 15:51:53 2012 COMMIT commit on
> Wed Apr 11 15:51:54 2012 Submitted 100 terms
> Wed Apr 11 15:51:54 2012 Submitted 200 terms
> Wed Apr 11 15:51:54 2012 Submitted 300 terms
> Wed Apr 11 15:51:54 2012 Submitted 400 terms
> Wed Apr 11 15:51:54 2012 Submitted 500 terms
> Wed Apr 11 15:51:54 2012 Submitted 600 terms
> Wed Apr 11 15:51:54 2012 Submitted 700 terms
> Wed Apr 11 15:51:54 2012 Submitted 800 terms
> Wed Apr 11 15:51:54 2012 Submitted 900 terms
> Wed Apr 11 15:51:55 2012 Submitted 1000 terms
> Wed Apr 11 15:51:55 2012 Submitted 1100 terms
> Wed Apr 11 15:51:55 2012 Submitted 1200 terms
> Wed Apr 11 15:51:55 2012 Submitted 1300 terms
> Wed Apr 11 15:51:55 2012 Submitted 1400 terms
> Wed Apr 11 15:51:55 2012 Submitted 1500 terms
> Wed Apr 11 15:51:55 2012 Submitted 1600 terms
> Wed Apr 11 15:51:55 2012 Submitted 1700 terms
> Wed Apr 11 15:51:55 2012 Submitted 1800 terms
> Wed Apr 11 15:51:56 2012 Submitted 1900 terms
> Wed Apr 11 15:51:56 2012 Submitted 2000 terms
> Wed Apr 11 15:51:56 2012 Submitted 2100 terms
> Wed Apr 11 15:51:56 2012 TIME 3 sec  (0:00:03)
> Wed Apr 11 15:51:56 2012 RESULT Inserted 2120 terms into SequenceOntology
> Wed Apr 11 15:51:56 2012 Rows Written SRes.SequenceOntology: 2120
> Wed Apr 11 15:51:56 2012 AlgInvocationId 29
> Wed Apr 11 15:51:56 2012 COMMIT commit on
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Thu, 12 Apr 2012 07:31:14 -0400
> From: Steve Fischer <sfi...@pc...>
> Subject: Re: [GUSDEV] InsertSequenceOntology bug?
> To: gus...@li...
> Message-ID: <4F8...@pc...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Joanin-
>
> this looks to be a nest of bugs:
>
> 1) the purpose of storing soCvsVersion is that, originally at least,
> that value was available in the downloaded file.   if we use an
> automated system (workflow) to download it, we do not know in advance
> what it will be.   so it should be extracted from the .obo file and
> inserted.   however, the plugin is no longer doing that extraction.   if
> this use case is no longer active, then i don't see any reason to write
> or read this value.
>
> 2) instead it is taking two optional values on the command line, version
> and so version, and, as you point out, using only the former.   we
> should make the fix you suggest, so that we write the version into the
> soVersion column
>
> 3) the SequenceOntology table does not have a foreign key to
> ExternalDatabaseRelease.   Instead it has a column soVersion, storing
> its "external database release" inline.  This is not the standard design
> pattern in GUS.   I don't know why we did it this way, perhaps because
> the table is dedicated to SequenceOntology, so we always know what
> ExternalDatabase it is.   if i could go back in time, i would recommend
> we stick to the pattern even for this table
>
> 4) the ISF plugin allows the soCvsVersion to be optoinal.  instead you
> can provide the value in ExternalDatabase.name for the SO.  it then does
> a look-up to find the ExternalDatabaseRelease.version of SO.  this
> allows us to leverage the common use case that there is only one SO in
> the database, so its name is sufficient, we don't really care about its
> version.    however, in this case ISF is still querying using the
> soCvsVersion.   instead, it should either:
>    a) remove that condition from the where clause altogether.   using
> the --soExtDbRlsName effectively means "ignore version"
>    b) change that condition to read the soVersion instead of soCvsVersion
>
> you can work around this problem by using --soExtDbRlsName  instead of
> --soCvsVersion when you call ISF
>
> steve
>
> On 4/12/2012 12:44 AM, Nicolas Joannin wrote:
> > Hello,
> >
> > I am proceeding with inserting data into my gusdb.
> > I downloaded the latest so.obo file from www.sequenceontology.org
> > <http://www.sequenceontology.org> and added that data to the db (see
> > output below).
> >
> > Once that done, I tried to insert sequence features but ran into the
> > following error message: ERROR: Can't find primary key for SO term 'gene'
> >
> > Going through the code to find the error, I've manually checked the
> > output of the following sql code:
> > select term_name, sequence_ontology_id from
> > sres.SequenceOntology where so_cvs_version = '$soCvsVersion'
> >
> > In my case the soCvsVersion is 1.324. And the result was nothing. So I
> > checked the table in question, and found it full of data, but with an
> > erroneous soCvsVersion: the InsertSequenceOntologyOBO plugin seems to
> > have used the soVersion as both the soVersion and the soCvsVersion.
> >
> > Is this a bug in that plugin or is it supposed to be that way?
> >
> > If it is a bug, I found in the InsertSequenceOntologyOBO.pm file the
> > following code (lines 170 to 178):
> >
> >    my $soTerm = GUS::Model::SRes::SequenceOntology->
> >      new({'so_id' => $obo->{'id'},
> >  'ontology_name' => 'sequence',
> >  'so_version' => $soVer,
> > *'so_cvs_version' => $soVer,*
> >  'term_name' => $obo->{'name'},
> >  'definition' => $definition });
> >    return $soTerm;
> >
> >
> > Is there a specific way to update the table (I don't see any UNDO for
> > this plugin)? Or should I just use plain sql UPDATE for this?
> >
> > Best regards,
> > Nicolas
> >
> >
> >
> > Nicolas-work-iMac:~ Nicolas$ ga
> > GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile
> > ~/Data_for_GUS/so.obo --soVersion 1.2 --soCvsVersion 1.324 --commit
> > Wed Apr 11 15:51:53 2012DSNdbi:Pg:dbname=varDB_2012
> > Wed Apr 11 15:51:53
> > 2012PLUGINGUS::Supported::Plugin::InsertSequenceOntologyOBO
> > Wed Apr 11 15:51:53 2012ARGalgoinvo1
> > Wed Apr 11 15:51:53 2012ARGcomment
> > Wed Apr 11 15:51:53 2012ARGcommit1
> > Wed Apr 11 15:51:53 2012ARGdebug0
> > Wed Apr 11 15:51:53 2012ARGgroup
> > Wed Apr 11 15:51:53
> > 2012ARGgusconfigfile/Users/Nicolas/GUS/gus_home/config/gus.config
> > Wed Apr 11 15:51:53 2012ARGhelp0
> > Wed Apr 11 15:51:53 2012ARGhelpHTML0
> > Wed Apr 11 15:51:53 2012ARGinputFile/Data_for_GUS/so.obo
> > Wed Apr 11 15:51:53 2012ARGproject
> > Wed Apr 11 15:51:53 2012ARGsoCvsVersion1.324
> > Wed Apr 11 15:51:53 2012ARGsoExtDbRlsName
> > Wed Apr 11 15:51:53 2012ARGsoVersion1.2
> > Wed Apr 11 15:51:53 2012ARGsqlVerbose0
> > Wed Apr 11 15:51:53 2012ARGuser
> > Wed Apr 11 15:51:53 2012ARGverbose0
> > Wed Apr 11 15:51:53 2012ARGveryVerbose0
> > Wed Apr 11 15:51:53 2012ARGworkflowstepid0
> > Wed Apr 11 15:51:53 2012AlgInvocationId29
> > Wed Apr 11 15:51:53 2012COMMITcommit on
> > Wed Apr 11 15:51:54 2012Submitted 100 terms
> > Wed Apr 11 15:51:54 2012Submitted 200 terms
> > Wed Apr 11 15:51:54 2012Submitted 300 terms
> > Wed Apr 11 15:51:54 2012Submitted 400 terms
> > Wed Apr 11 15:51:54 2012Submitted 500 terms
> > Wed Apr 11 15:51:54 2012Submitted 600 terms
> > Wed Apr 11 15:51:54 2012Submitted 700 terms
> > Wed Apr 11 15:51:54 2012Submitted 800 terms
> > Wed Apr 11 15:51:54 2012Submitted 900 terms
> > Wed Apr 11 15:51:55 2012Submitted 1000 terms
> > Wed Apr 11 15:51:55 2012Submitted 1100 terms
> > Wed Apr 11 15:51:55 2012Submitted 1200 terms
> > Wed Apr 11 15:51:55 2012Submitted 1300 terms
> > Wed Apr 11 15:51:55 2012Submitted 1400 terms
> > Wed Apr 11 15:51:55 2012Submitted 1500 terms
> > Wed Apr 11 15:51:55 2012Submitted 1600 terms
> > Wed Apr 11 15:51:55 2012Submitted 1700 terms
> > Wed Apr 11 15:51:55 2012Submitted 1800 terms
> > Wed Apr 11 15:51:56 2012Submitted 1900 terms
> > Wed Apr 11 15:51:56 2012Submitted 2000 terms
> > Wed Apr 11 15:51:56 2012Submitted 2100 terms
> > Wed Apr 11 15:51:56 2012TIME3 sec  (0:00:03)
> > Wed Apr 11 15:51:56 2012RESULTInserted 2120 terms into SequenceOntology
> > Wed Apr 11 15:51:56 2012Rows WrittenSRes.SequenceOntology: 2120
> > Wed Apr 11 15:51:56 2012AlgInvocationId29
> > Wed Apr 11 15:51:56 2012COMMITcommit on
> >
> >
> >
> >
> ------------------------------------------------------------------------------
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> ********************************************
>

Joanin-

this looks to be a nest of bugs:

1) the purpose of storing soCvsVersion is that, originally at least, 
that value was available in the downloaded file.   if we use an 
automated system (workflow) to download it, we do not know in advance 
what it will be.   so it should be extracted from the .obo file and 
inserted.   however, the plugin is no longer doing that extraction.   if 
this use case is no longer active, then i don't see any reason to write 
or read this value.

2) instead it is taking two optional values on the command line, version 
and so version, and, as you point out, using only the former.   we 
should make the fix you suggest, so that we write the version into the 
soVersion column

3) the SequenceOntology table does not have a foreign key to 
ExternalDatabaseRelease.   Instead it has a column soVersion, storing 
its "external database release" inline.  This is not the standard design 
pattern in GUS.   I don't know why we did it this way, perhaps because 
the table is dedicated to SequenceOntology, so we always know what 
ExternalDatabase it is.   if i could go back in time, i would recommend 
we stick to the pattern even for this table

4) the ISF plugin allows the soCvsVersion to be optoinal.  instead you 
can provide the value in ExternalDatabase.name for the SO.  it then does 
a look-up to find the ExternalDatabaseRelease.version of SO.  this 
allows us to leverage the common use case that there is only one SO in 
the database, so its name is sufficient, we don't really care about its 
version.    however, in this case ISF is still querying using the 
soCvsVersion.   instead, it should either:
    a) remove that condition from the where clause altogether.   using 
the --soExtDbRlsName effectively means "ignore version"
    b) change that condition to read the soVersion instead of soCvsVersion

you can work around this problem by using --soExtDbRlsName  instead of 
--soCvsVersion when you call ISF

steve

On 4/12/2012 12:44 AM, Nicolas Joannin wrote:
> Hello,
>
> I am proceeding with inserting data into my gusdb.
> I downloaded the latest so.obo file from www.sequenceontology.org 
> <http://www.sequenceontology.org> and added that data to the db (see 
> output below).
>
> Once that done, I tried to insert sequence features but ran into the 
> following error message: ERROR: Can't find primary key for SO term 'gene'
>
> Going through the code to find the error, I've manually checked the 
> output of the following sql code:
> select term_name, sequence_ontology_id from 
> sres.SequenceOntology where so_cvs_version = '$soCvsVersion'
>
> In my case the soCvsVersion is 1.324. And the result was nothing. So I 
> checked the table in question, and found it full of data, but with an 
> erroneous soCvsVersion: the InsertSequenceOntologyOBO plugin seems to 
> have used the soVersion as both the soVersion and the soCvsVersion.
>
> Is this a bug in that plugin or is it supposed to be that way?
>
> If it is a bug, I found in the InsertSequenceOntologyOBO.pm file the 
> following code (lines 170 to 178):
>
>    my $soTerm = GUS::Model::SRes::SequenceOntology->
>      new({'so_id' => $obo->{'id'},
>  'ontology_name' => 'sequence',
>  'so_version' => $soVer,
> *'so_cvs_version' => $soVer,*
>  'term_name' => $obo->{'name'},
>  'definition' => $definition });
>    return $soTerm;
>
>
> Is there a specific way to update the table (I don't see any UNDO for 
> this plugin)? Or should I just use plain sql UPDATE for this?
>
> Best regards,
> Nicolas
>
>
>
> Nicolas-work-iMac:~ Nicolas$ ga 
> GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile 
> ~/Data_for_GUS/so.obo --soVersion 1.2 --soCvsVersion 1.324 --commit
> Wed Apr 11 15:51:53 2012DSNdbi:Pg:dbname=varDB_2012
> Wed Apr 11 15:51:53 
> 2012PLUGINGUS::Supported::Plugin::InsertSequenceOntologyOBO
> Wed Apr 11 15:51:53 2012ARGalgoinvo1
> Wed Apr 11 15:51:53 2012ARGcomment
> Wed Apr 11 15:51:53 2012ARGcommit1
> Wed Apr 11 15:51:53 2012ARGdebug0
> Wed Apr 11 15:51:53 2012ARGgroup
> Wed Apr 11 15:51:53 
> 2012ARGgusconfigfile/Users/Nicolas/GUS/gus_home/config/gus.config
> Wed Apr 11 15:51:53 2012ARGhelp0
> Wed Apr 11 15:51:53 2012ARGhelpHTML0
> Wed Apr 11 15:51:53 2012ARGinputFile/Data_for_GUS/so.obo
> Wed Apr 11 15:51:53 2012ARGproject
> Wed Apr 11 15:51:53 2012ARGsoCvsVersion1.324
> Wed Apr 11 15:51:53 2012ARGsoExtDbRlsName
> Wed Apr 11 15:51:53 2012ARGsoVersion1.2
> Wed Apr 11 15:51:53 2012ARGsqlVerbose0
> Wed Apr 11 15:51:53 2012ARGuser
> Wed Apr 11 15:51:53 2012ARGverbose0
> Wed Apr 11 15:51:53 2012ARGveryVerbose0
> Wed Apr 11 15:51:53 2012ARGworkflowstepid0
> Wed Apr 11 15:51:53 2012AlgInvocationId29
> Wed Apr 11 15:51:53 2012COMMITcommit on
> Wed Apr 11 15:51:54 2012Submitted 100 terms
> Wed Apr 11 15:51:54 2012Submitted 200 terms
> Wed Apr 11 15:51:54 2012Submitted 300 terms
> Wed Apr 11 15:51:54 2012Submitted 400 terms
> Wed Apr 11 15:51:54 2012Submitted 500 terms
> Wed Apr 11 15:51:54 2012Submitted 600 terms
> Wed Apr 11 15:51:54 2012Submitted 700 terms
> Wed Apr 11 15:51:54 2012Submitted 800 terms
> Wed Apr 11 15:51:54 2012Submitted 900 terms
> Wed Apr 11 15:51:55 2012Submitted 1000 terms
> Wed Apr 11 15:51:55 2012Submitted 1100 terms
> Wed Apr 11 15:51:55 2012Submitted 1200 terms
> Wed Apr 11 15:51:55 2012Submitted 1300 terms
> Wed Apr 11 15:51:55 2012Submitted 1400 terms
> Wed Apr 11 15:51:55 2012Submitted 1500 terms
> Wed Apr 11 15:51:55 2012Submitted 1600 terms
> Wed Apr 11 15:51:55 2012Submitted 1700 terms
> Wed Apr 11 15:51:55 2012Submitted 1800 terms
> Wed Apr 11 15:51:56 2012Submitted 1900 terms
> Wed Apr 11 15:51:56 2012Submitted 2000 terms
> Wed Apr 11 15:51:56 2012Submitted 2100 terms
> Wed Apr 11 15:51:56 2012TIME3 sec  (0:00:03)
> Wed Apr 11 15:51:56 2012RESULTInserted 2120 terms into SequenceOntology
> Wed Apr 11 15:51:56 2012Rows WrittenSRes.SequenceOntology: 2120
> Wed Apr 11 15:51:56 2012AlgInvocationId29
> Wed Apr 11 15:51:56 2012COMMITcommit on
>
>
>
> ------------------------------------------------------------------------------
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> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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>
>
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Hello,

I am proceeding with inserting data into my gusdb.
I downloaded the latest so.obo file from www.sequenceontology.org and added
that data to the db (see output below).

Once that done, I tried to insert sequence features but ran into the
following error message: ERROR: Can't find primary key for SO term 'gene'

Going through the code to find the error, I've manually checked the output
of the following sql code:
select term_name, sequence_ontology_id from sres.SequenceOntology where
so_cvs_version = '$soCvsVersion'

In my case the soCvsVersion is 1.324. And the result was nothing. So I
checked the table in question, and found it full of data, but with an
erroneous soCvsVersion: the InsertSequenceOntologyOBO plugin seems to have
used the soVersion as both the soVersion and the soCvsVersion.

Is this a bug in that plugin or is it supposed to be that way?

If it is a bug, I found in the InsertSequenceOntologyOBO.pm file the
following code (lines 170 to 178):

   my $soTerm = GUS::Model::SRes::SequenceOntology->
     new({'so_id' => $obo->{'id'},
  'ontology_name' => 'sequence',
  'so_version' => $soVer,
  *'so_cvs_version' => $soVer,*
  'term_name' => $obo->{'name'},
  'definition' => $definition });

   return $soTerm;

Is there a specific way to update the table (I don't see any UNDO for this
plugin)? Or should I just use plain sql UPDATE for this?

Best regards,
Nicolas

Nicolas-work-iMac:~ Nicolas$ ga
GUS::Supported::Plugin::InsertSequenceOntologyOBO --inputFile
~/Data_for_GUS/so.obo --soVersion 1.2 --soCvsVersion 1.324 --commit
Wed Apr 11 15:51:53 2012 DSN dbi:Pg:dbname=varDB_2012
Wed Apr 11 15:51:53 2012 PLUGIN
GUS::Supported::Plugin::InsertSequenceOntologyOBO
Wed Apr 11 15:51:53 2012 ARG algoinvo 1
Wed Apr 11 15:51:53 2012 ARG comment
Wed Apr 11 15:51:53 2012 ARG commit 1
Wed Apr 11 15:51:53 2012 ARG debug 0
Wed Apr 11 15:51:53 2012 ARG group
Wed Apr 11 15:51:53 2012 ARG gusconfigfile
/Users/Nicolas/GUS/gus_home/config/gus.config
Wed Apr 11 15:51:53 2012 ARG help 0
Wed Apr 11 15:51:53 2012 ARG helpHTML 0
Wed Apr 11 15:51:53 2012 ARG inputFile /Data_for_GUS/so.obo
Wed Apr 11 15:51:53 2012 ARG project
Wed Apr 11 15:51:53 2012 ARG soCvsVersion 1.324
Wed Apr 11 15:51:53 2012 ARG soExtDbRlsName
Wed Apr 11 15:51:53 2012 ARG soVersion 1.2
Wed Apr 11 15:51:53 2012 ARG sqlVerbose 0
Wed Apr 11 15:51:53 2012 ARG user
Wed Apr 11 15:51:53 2012 ARG verbose 0
Wed Apr 11 15:51:53 2012 ARG veryVerbose 0
Wed Apr 11 15:51:53 2012 ARG workflowstepid 0
Wed Apr 11 15:51:53 2012 AlgInvocationId 29
Wed Apr 11 15:51:53 2012 COMMIT commit on
Wed Apr 11 15:51:54 2012 Submitted 100 terms
Wed Apr 11 15:51:54 2012 Submitted 200 terms
Wed Apr 11 15:51:54 2012 Submitted 300 terms
Wed Apr 11 15:51:54 2012 Submitted 400 terms
Wed Apr 11 15:51:54 2012 Submitted 500 terms
Wed Apr 11 15:51:54 2012 Submitted 600 terms
Wed Apr 11 15:51:54 2012 Submitted 700 terms
Wed Apr 11 15:51:54 2012 Submitted 800 terms
Wed Apr 11 15:51:54 2012 Submitted 900 terms
Wed Apr 11 15:51:55 2012 Submitted 1000 terms
Wed Apr 11 15:51:55 2012 Submitted 1100 terms
Wed Apr 11 15:51:55 2012 Submitted 1200 terms
Wed Apr 11 15:51:55 2012 Submitted 1300 terms
Wed Apr 11 15:51:55 2012 Submitted 1400 terms
Wed Apr 11 15:51:55 2012 Submitted 1500 terms
Wed Apr 11 15:51:55 2012 Submitted 1600 terms
Wed Apr 11 15:51:55 2012 Submitted 1700 terms
Wed Apr 11 15:51:55 2012 Submitted 1800 terms
Wed Apr 11 15:51:56 2012 Submitted 1900 terms
Wed Apr 11 15:51:56 2012 Submitted 2000 terms
Wed Apr 11 15:51:56 2012 Submitted 2100 terms
Wed Apr 11 15:51:56 2012 TIME 3 sec  (0:00:03)
Wed Apr 11 15:51:56 2012 RESULT Inserted 2120 terms into SequenceOntology
Wed Apr 11 15:51:56 2012 Rows Written SRes.SequenceOntology: 2120
Wed Apr 11 15:51:56 2012 AlgInvocationId 29
Wed Apr 11 15:51:56 2012 COMMIT commit on

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 --------------
>>>>> An HTML attachment was scrubbed...
>>>>>
>>>>> ------------------------------
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>
>

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
>>                 gus...@li...
>>                 <mailto: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...
>>                 <mailto:gus...@li...>
>>
>>                 You can reach the person managing the list at
>>                 gus...@li...
>>                 <mailto: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...
>>                 <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
>>                 > Gus...@li...
>>                 <mailto:Gus...@li...>
>>                 >
>>                 https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>                 -------------- next part --------------
>>                 An HTML attachment was scrubbed...
>>
>>                 ------------------------------
>>
>>                 ------------------------------------------------------------------------------
>>                 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...
>>                 <mailto: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 list
>>         Gus...@li...  <mailto:Gus...@li...>
>>         https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>

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 --------------
>>>> An HTML attachment was scrubbed...
>>>>
>>>> ------------------------------
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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...
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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
>>
>>
>

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
>>> >
>>> >
>>> >
>>> >
>>> ------------------------------------------------------------------------------
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>>> > Boundary is the first to Know...and Tell You.
>>> > Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
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>>> Boundary is the first to Know...and Tell You.
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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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>
> _______________________________________________
> Gusdev-gusdev mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>

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
>         gus...@li...
>         <mailto: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...
>         <mailto:gus...@li...>
>
>         You can reach the person managing the list at
>         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..."
>
>
>         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
>         > Gus...@li...
>         <mailto:Gus...@li...>
>         > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>         -------------- next part --------------
>         An HTML attachment was scrubbed...
>
>         ------------------------------
>
>         ------------------------------------------------------------------------------
>         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...
>         <mailto: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 list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

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 --------------
>> An HTML attachment was scrubbed...
>>
>> ------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> ********************************************
>>
>
>

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
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > 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 --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> 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
> ********************************************
>

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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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 2012 INFO Plugin
GUS::Supported::Plugin::InsertExternalDatabaseRls registered with cvs
revision '10163'
Fri Apr  6 15:54:24 2012 DSN dbi:Pg:dbname=varDB_2012
Fri Apr  6 15:54:24 2012 PLUGIN
GUS::Supported::Plugin::InsertExternalDatabaseRls
Fri Apr  6 15:54:24 2012 ARG algoinvo 1
Fri Apr  6 15:54:24 2012 ARG comment
Fri Apr  6 15:54:24 2012 ARG commit 0
Fri Apr  6 15:54:24 2012 ARG databaseName Genbank
Fri Apr  6 15:54:24 2012 ARG databaseVersion 188.0
Fri Apr  6 15:54:24 2012 ARG debug 0
Fri Apr  6 15:54:24 2012 ARG description
Fri Apr  6 15:54:24 2012 ARG downloadUrl ftp://ftp.ncbi.nih.gov/genbank/
Fri Apr  6 15:54:24 2012 ARG fileMd5
Fri Apr  6 15:54:24 2012 ARG fileName
Fri Apr  6 15:54:24 2012 ARG group
Fri Apr  6 15:54:24 2012 ARG gusconfigfile
/Users/Nicolas/GUS/gus_home/config/gus.config
Fri Apr  6 15:54:24 2012 ARG help 0
Fri Apr  6 15:54:24 2012 ARG helpHTML 0
Fri Apr  6 15:54:24 2012 ARG idIsAlias 0
Fri Apr  6 15:54:24 2012 ARG idType
Fri Apr  6 15:54:24 2012 ARG idUrl
Fri Apr  6 15:54:24 2012 ARG project
Fri Apr  6 15:54:24 2012 ARG releaseDate 15 Feb 2012
Fri Apr  6 15:54:24 2012 ARG secondaryIdType
Fri Apr  6 15:54:24 2012 ARG secondaryIdUrl
Fri Apr  6 15:54:24 2012 ARG sqlVerbose 0
Fri Apr  6 15:54:24 2012 ARG user
Fri Apr  6 15:54:24 2012 ARG verbose 0
Fri Apr  6 15:54:24 2012 ARG veryVerbose 0
Fri Apr  6 15:54:24 2012 ARG workflowstepid 0
Fri Apr  6 15:54:24 2012 AlgInvocationId 12
Fri Apr  6 15:54:24 2012 COMMIT commit 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

Nicolas,
Thanks for letting us know. It should be fixed now. 
Chris

On Mar 28, 2012, at 4:44 AM, Nicolas Joannin wrote:

> Hello,
> 
> I have been unable to access the GUSDB wiki pages today. Is there scheduled maintenance or is this an unexpected problem?
> 
> Best regards,
> Nicolas
> 
> 
> The error message I get in the browser is:
> Fatal Error:
> 
> lib/IniConfig.php:313 Error: Invalid DATABASE_TYPE=DATABASE_TYPE. Choose one of SQL,ADODB,PDO,dba,file,flatfile,cvs,cvsclient
> 
> 
> 
> lib/IniConfig.php:313 Error: Invalid DATABASE_TYPE=DATABASE_TYPE. Choose one of SQL,ADODB,PDO,dba,file,flatfile,cvs,cvsclient
> 
> ------------------------------------------------------------------------------
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Hello,

I have been unable to access the GUSDB wiki
pages<http://www.gusdb.org/wiki/>today. Is there scheduled maintenance
or is this an unexpected problem?

Best regards,
Nicolas

The error message I get in the browser is:

*Fatal Error:*

lib/IniConfig.php:313 Error: Invalid DATABASE_TYPE=DATABASE_TYPE. Choose
one of SQL,ADODB,PDO,dba,file,flatfile,cvs,cvsclient

Hello John and Mark,

Indeed, inserting that line into the table did the job.
Thanks again for the help!

Best regards,
Nicolas

On Sat, Mar 24, 2012 at 05:34, Mark Heiges <mh...@ug...> wrote:

> I don't know what the officially supported mechanism is for this (there
> may not be one ) but this is what I have used to manually insert that row.
>
> INSERT INTO Core.DatabaseVersion
>  (DATABASE_VERSION_ID, VERSION, MODIFICATION_DATE, USER_READ, USER_WRITE,
>   GROUP_READ, GROUP_WRITE, OTHER_READ, OTHER_WRITE, ROW_USER_ID,
>   ROW_GROUP_ID, ROW_PROJECT_ID, ROW_ALG_INVOCATION_ID)
> VALUES (1, 3.6, current_timestamp,1,1,1,1,1,0,1,1,1,1);
>
>
> On Mar 23, 2012, at 2:41 PM, John Iodice wrote:
>
> > Hi Nicolas,
> >
> > I think this is related to the table core.DatabaseVersion, and that this
> table should have a single row in it with "3.6" in the VERSION column. But
> I don't know how that gets there.
> >
> > Is this what you have? If that table is empty, my suggestion (unless
> somebody else has a better one) is to insert a record with that value in
> that column.
> >
> > -- John
> >
> > On Fri, Mar 23, 2012 at 5:03 AM, Nicolas Joannin <
> nic...@gm...> wrote:
> > Hi again,
> >
> > Thanks again for the help!
> > I just have one last question:
> > In the Install Guide for GUS, it is written that one should register the
> GUS application framework with the following command:
> > $ ga +meta --commit
> >
> > I'm not quite sure what this does, and when I do run it, I get the
> following message:
> >
> > Nicolas-work-iMac:bin Nicolas$ ga +meta --commit
> >
> > ERROR: Database version does not match required version for Plugin.
> > Database Version:     Plugin Version: 3.6
> >
> > Is this registration something I should worry about? If so, any
> suggestions as to what this problem might be?
> >
> > Best regards,
> > Nicolas
> >
> >
> >
> >
> > On Fri, Mar 23, 2012 at 13:05, Mark Heiges <mh...@ug...> wrote:
> > whew!
> >
> > On Mar 23, 2012, at 12:01 AM, Nicolas Joannin wrote:
> >
> > > Indeed, again, my mistake!
> > > Thank you all for your help: BUILD SUCCESSFUL ;)
> > >
> > > Best regards,
> > > Nicolas
> > >
> > >
> > > On Fri, Mar 23, 2012 at 12:40, Mark Heiges <mh...@ug...> wrote:
> > > Check the dbiDsn setting in your gus.config. What you sent earlier
> (dbiDsn=dbi:Pg:dbname=<my_db_name>)  looks correct to me; make sure that
> hasn't changed. The error is symptomatic of missing the 'dbname=' prefix
> > >
> > >
> > >
> > >
> > >
> > > On Mar 22, 2012, at 11:20 PM, Nicolas Joannin wrote:
> > >
> > > > Hi Mark,
> > > >
> > > > Thanks: indeed, I made the mistake of adjusting the PATH with
> $GUS_HOME/bin etc. before actually exporting GUS_HOME.
> > > >
> > > > I've rerun the build GUS install -append and it now has a new error:
> > > > perlGeneratedModel:
> > > >      [echo] generating Perl Objects
> > > >      [exec] GUS::ObjRelP::DbiDbHandle
> connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012"
> in connection info string at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > > >      [exec] Can't bless non-reference value at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > > >
> > > > BUILD FAILED
> > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following
> error occurred while executing this line:
> > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: exec returned: 255
> > > >
> > > > Thanks again for your help!
> > > > Best regards,
> > > > Nicolas
> > > >
> > > >
> > > > Full output:
> > > >
> > > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append
> > > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > > >
> > > > install:
> > > >      [echo]  proj=GUS
> > > >      [echo]  comp=
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Bio
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/CSP
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Util
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/Cider
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/HQ
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/TranscriptExpression
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing CBIL/ObjectMapper
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/Supported
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/Community
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/DBAdmin
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/GOPredict
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GusSchema/Definition
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/DBAdmin
> > > >
> > > > defaultJavaCompile:
> > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > defaultComponentInstall:
> > > >      [echo] .
> > > >      [echo] Installing GUS/ObjRelP
> > > >
> > > > recordBuildState:
> > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > >
> > > > perlGeneratedModel:
> > > >      [echo] generating Perl Objects
> > > >      [exec] GUS::ObjRelP::DbiDbHandle
> connect('varDB_2012','postgres',...) failed: missing "=" after "varDB_2012"
> in connection info string at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 173
> > > >      [exec] Can't bless non-reference value at
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 21.
> > > >
> > > > BUILD FAILED
> > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The following
> error occurred while executing this line:
> > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: exec returned: 255
> > > >
> > > > Total time: 20 seconds
> > > >
> > > > On Fri, Mar 23, 2012 at 12:00, Mark Heiges <mh...@ug...> wrote:
> > > > The includeantruntime warning is an ant 1.8 "feature". I'm pretty
> sure you can ignore that warning in this case, I don't see any abnormal
> repercussions from it, but we've not used that version of ant ourselves.
> You can google that warning for more information if you're curious.
> > > >
> > > > The generateGusObjects error makes me suspect that your PATH doesn't
> include $GUS_HOME/bin . You'll want something like
> > > >        export PATH=$GUS_HOME/bin:$PROJECT_HOME/install/bin:$PATH
> > > >
> > > > At this point the schema is installed in your database (log in with
> a client and confirm). So the next time run  "build GUS install -append"
> (without the -installDBSchema) and it should resume with the "generating
> Perl Objects".
> > > >
> > > >
> > > > On Mar 22, 2012, at 9:59 PM, Nicolas Joannin wrote:
> > > >
> > > > > Hi Mark,
> > > > >
> > > > > I got the code from the subversion repository, but that was a
> couple weeks ago, I think.
> > > > > I've just tried with the latest svn update.
> > > > >
> > > > > I started all from scratch: I deleted the GUS folder I was working
> in and replaced it with the new.
> > > > > I run the install a first time and encountered the same ojdbc5.jar
> problem.
> > > > >
> > > > > So I added that file to the proper directory and rerun the install.
> > > > >
> > > > > This time I get different errors (see full output below):
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null
> version, skipping.  Note:  You will need to manually add a version number
> to the DB
> > > > >
> > > > > BUILD FAILED
> > > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The
> following error occurred while executing this line:
> > > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: Execute failed:
> java.io.IOException: Cannot run program "generateGusObjects" (in directory
> "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or
> directory
> > > > >
> > > > > The first one (with the "warning: 'includeantruntime'") occurs
> several times.
> > > > >
> > > > > Thanks for the quick responses!
> > > > > Best regards,
> > > > > Nicolas
> > > > >
> > > > >
> > > > > Here's the full output:
> > > > >
> > > > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append
> -installDBSchema
> > > > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > > > >
> > > > > install:
> > > > >      [echo]  proj=GUS
> > > > >      [echo]  comp=
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Bio
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/CSP
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Util
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/Cider
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/HQ
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/TranscriptExpression
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing CBIL/ObjectMapper
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/Supported
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/Community
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/DBAdmin
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/GOPredict
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GusSchema/Definition
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/DBAdmin
> > > > >
> > > > > defaultJavaCompile:
> > > > >     [javac] /Users/Nicolas/GUS/project_home/install/build.xml:332:
> warning: 'includeantruntime' was not set, defaulting to
> build.sysclasspath=last; set to false for repeatable builds
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > InstallSchema:
> > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:79) - Reading
> database from
> /Users/Nicolas/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
> > > > > [InstallSchema]  INFO [main] (SchemaReader.java:48) - Reading
> Database
> > > > > [InstallSchema]  INFO [main] (Database.java:161) - Resolving
> Database References
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:87) -
>  Overriding individual tablespace specifications with value "GUS" from
> property file
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing
> Database
> > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing
> Database
> > > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null
> version, skipping.  Note:  You will need to manually add a version number
> to the DB
> > > > > [InstallSchema] ERROR [main] (InstallSchemaTask.java:122) - Null
> version, skipping.  Note:  You will need to manually add a version number
> to the DB
> > > > >
> > > > > defaultComponentInstall:
> > > > >      [echo] .
> > > > >      [echo] Installing GUS/ObjRelP
> > > > >
> > > > > componentPartCopySub:
> > > > >      [copy] Copying 3 files to /Users/Nicolas/GUS/gus_home/bin
> > > > >
> > > > > componentPartCopySub:
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP
> > > > >      [copy] Copying 18 files to
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/ObjRelP
> > > > >
> > > > > componentPartCopySub:
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP
> > > > >      [copy] Copying 3 files to
> /Users/Nicolas/GUS/gus_home/doc/GUS/ObjRelP
> > > > >
> > > > > recordBuildState:
> > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > >
> > > > > perlGeneratedModel:
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Core
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/DoTS
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/RAD
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/SRes
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/TESS
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/PROT
> > > > >     [mkdir] Created dir:
> /Users/Nicolas/GUS/gus_home/lib/perl/GUS/Model/Study
> > > > >      [echo] generating Perl Objects
> > > > >
> > > > > BUILD FAILED
> > > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The
> following error occurred while executing this line:
> > > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:258: Execute failed:
> java.io.IOException: Cannot run program "generateGusObjects" (in directory
> "/Users/Nicolas/GUS/project_home/install"): error=2, No such file or
> directory
> > > > >       at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
> > > > >       at java.lang.Runtime.exec(Runtime.java:593)
> > > > >       at
> org.apache.tools.ant.taskdefs.Execute$Java13CommandLauncher.exec(Execute.java:862)
> > > > >       at
> org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:481)
> > > > >       at
> org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:495)
> > > > >       at
> org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:631)
> > > > >       at
> org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672)
> > > > >       at
> org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498)
> > > > >       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
> > > > >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > >       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > >       at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > >       at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > > >       at
> org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > > >       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
> > > > >       at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > > > >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > >       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > >       at org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > >       at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > >       at
> org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> > > > >       at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> > > > >       at
> org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > >       at org.apache.tools.ant.Main.runBuild(Main.java:811)
> > > > >       at org.apache.tools.ant.Main.startAnt(Main.java:217)
> > > > >       at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> > > > >       at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> > > > > Caused by: java.io.IOException: error=2, No such file or directory
> > > > >       at java.lang.UNIXProcess.forkAndExec(Native Method)
> > > > >       at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
> > > > >       at java.lang.ProcessImpl.start(ProcessImpl.java:91)
> > > > >       at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
> > > > >       ... 36 more
> > > > >
> > > > > Total time: 30 seconds
> > > > >
> > > > >
> > > > >
> > > > > On Fri, Mar 23, 2012 at 10:37, Mark Heiges <mh...@ug...>
> wrote:
> > > > > Hi Nicolas, Are you using code from the gus subversion repository?
> If so, do an svn update. This bug was fixed this morning. If not from
> subversion, where did you get your code?
> > > > >
> > > > > -Mark
> > > > >
> > > > > On Mar 22, 2012, at 9:24 PM, Nicolas Joannin wrote:
> > > > >
> > > > > > Good morning Mark, Rodrigo and John,
> > > > > >
> > > > > > Indeed, the ojdbc5.jar file helped to get further ahead :)
> > > > > > Unfortunately, there are still some errors (see below).
> > > > > >
> > > > > > Best regards,
> > > > > > Nicolas
> > > > > >
> > > > > >
> > > > > >
> > > > > > Nicolas-work-iMac:bin Nicolas$ ./build GUS install -append
> -installDBSchema
> > > > > > Buildfile: /Users/Nicolas/GUS/project_home/install/build.xml
> > > > > >
> > > > > > install:
> > > > > >      [echo]  proj=GUS
> > > > > >      [echo]  comp=
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/Bio
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/CSP
> > > > > >
> > > > > > defaultJavaCompile:
> > > > > >     [javac]
> /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/Util
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/Cider
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/HQ
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/TranscriptExpression
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing CBIL/ObjectMapper
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GUS/Supported
> > > > > >
> > > > > > defaultJavaCompile:
> > > > > >     [javac]
> /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GUS/Community
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GUS/DBAdmin
> > > > > >
> > > > > > defaultJavaCompile:
> > > > > >     [javac]
> /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GUS/GOPredict
> > > > > >
> > > > > > defaultJavaCompile:
> > > > > >     [javac]
> /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GusSchema/Definition
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > defaultComponentInstall:
> > > > > >      [echo] .
> > > > > >      [echo] Installing GUS/DBAdmin
> > > > > >
> > > > > > defaultJavaCompile:
> > > > > >     [javac]
> /Users/Nicolas/GUS/project_home/install/build.xml:332: warning:
> 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
> to false for repeatable builds
> > > > > >
> > > > > > recordBuildState:
> > > > > > [propertyfile] Updating property file:
> /Users/Nicolas/GUS/gus_home/config/.build.info
> > > > > >
> > > > > > InstallSchema:
> > > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:79) -
> Reading database from
> /Users/Nicolas/GUS/project_home/GusSchema/Definition/config/gus_schema.xml
> > > > > > [InstallSchema]  INFO [main] (SchemaReader.java:48) - Reading
> Database
> > > > > > [InstallSchema]  INFO [main] (Database.java:161) - Resolving
> Database References
> > > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > > [InstallSchema]  INFO [main] (InstallSchemaTask.java:87) -
>  Overriding individual tablespace specifications with value "GUS" from
> property file
> > > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing
> Database
> > > > > > [InstallSchema]  INFO [main] (DatabaseValidator.java:57) -
> Validating Database: 'null'
> > > > > > [InstallSchema]  INFO [main] (SchemaWriter.java:33) - Writing
> Database
> > > > > >
> > > > > > BUILD FAILED
> > > > > > /Users/Nicolas/GUS/project_home/install/build.xml:38: The
> following error occurred while executing this line:
> > > > > > /Users/Nicolas/GUS/project_home/GUS/build.xml:16: The following
> error occurred while executing this line:
> > > > > > /Users/Nicolas/GUS/project_home/GusSchema/build.xml:63:
> java.io.IOException: Error executing SQL: '
> > > > > >
> > > > > > CREATE TABLE Core.AlgorithmInvocation (
> > > > > >        ALGORITHM_INVOCATION_ID NUMERIC(12,0)  NOT NULL,
> > > > > >        ALGORITHM_IMPLEMENTATION_ID NUMERIC(5,0)  NOT NULL,
> > > > > >        START_TIME TIMESTAMP NOT NULL,
> > > > > >        END_TIME TIMESTAMP NOT NULL,
> > > > > >        CPUS_USED NUMERIC(5,0) ,
> > > > > >        CPU_TIME FLOAT(126) ,
> > > > > >        RESULT VARCHAR(350)  NOT NULL,
> > > > > >        COMMENT_STRING VARCHAR(255) ,
> > > > > >        MODIFICATION_DATE TIMESTAMP NOT NULL,
> > > > > >        USER_READ NUMERIC(1,0)  NOT NULL,
> > > > > >        USER_WRITE NUMERIC(1,0)  NOT NULL,
> > > > > >        GROUP_READ NUMERIC(1,0)  NOT NULL,
> > > > > >        GROUP_WRITE NUMERIC(1,0)  NOT NULL,
> > > > > >        OTHER_READ NUMERIC(1,0)  NOT NULL,
> > > > > >        OTHER_WRITE NUMERIC(1,0)  NOT NULL,
> > > > > >        ROW_USER_ID NUMERIC(12,0)  NOT NULL,
> > > > > >        ROW_GROUP_ID NUMERIC(4,0)  NOT NULL,
> > > > > >        ROW_PROJECT_ID NUMERIC(4,0)  NOT NULL,
> > > > > >        ROW_ALG_INVOCATION_ID NUMERIC(12,0)  NOT NULL)' Error:
> ERROR: precision for type float must be less than 54 bits
> > > > > >       at
> org.gusdb.dbadmin.util.JDBCStreamWriter.flush(JDBCStreamWriter.java:57)
> > > > > >       at
> org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTable(RelationalDatabaseWriter.java:67)
> > > > > >       at
> org.gusdb.dbadmin.writer.RelationalDatabaseWriter.writeTables(RelationalDatabaseWriter.java:43)
> > > > > >       at
> org.gusdb.dbadmin.writer.PostgresWriter.writeDatabase(PostgresWriter.java:68)
> > > > > >       at
> org.gusdb.dbadmin.writer.SchemaWriter.write(SchemaWriter.java:34)
> > > > > >       at
> org.gusdb.dbadmin.util.InstallSchemaTask.execute(InstallSchemaTask.java:99)
> > > > > >       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
> > > > > >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > > >       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > > >       at
> org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > > >       at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > > >       at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > > > >       at
> org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > > > >       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > > >       at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
> Source)
> > > > > >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > > >       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > > >       at
> org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > > >       at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > > >       at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> > > > > >       at
> org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > > >       at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)
> > > > > >       at
> org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
> > > > > >       at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
> > > > > >       at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> > > > > >       at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> > > > > >       at java.lang.reflect.Method.invoke(Method.java:597)
> > > > > >       at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> > > > > >       at org.apache.tools.ant.Task.perform(Task.java:348)
> > > > > >       at org.apache.tools.ant.Target.execute(Target.java:392)
> > > > > >       at
> org.apache.tools.ant.Target.performTasks(Target.java:413)
> > > > > >       at
> org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)
> > > > > >       at
> org.apache.tools.ant.Project.executeTarget(Project.java:1368)
> > > > > >       at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> > > > > >       at
> org.apache.tools.ant.Project.executeTargets(Project.java:1251)
> > > > > >       at org.apache.tools.ant.Main.runBuild(Main.java:811)
> > > > > >       at org.apache.tools.ant.Main.startAnt(Main.java:217)
> > > > > >       at
> org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> > > > > >       at
> org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> > > > > >
> > > > > > Total time: 20 seconds
> > > > > >
> > > > > >
> > > > > > On Thu, Mar 22, 2012 at 23:23, Mark Heiges <mh...@ug...>
> wrote:
> > > > > > I have confirmed that the ojdbc jar is required for the code to
> compile.
> > > > > >
> > > > > > -Mark
> > > > > >
> > > > > > On Mar 22, 2012, at 10:09 AM, John Iodice wrote:
> > > > > >
> > > > > > > Hi Nicolas,
> > > > > > >
> > > > > > > That dbVendor setting looks right; I think that your
> configuration is correct for a Postgres install (and that I was mistaken to
> think that the install is looking for oracle.jdbc.OracleDriver because it's
> configured to use Oracle).
> > > > > > >
> > > > > > > Looking in my own $GUS_HOME/lib/java/db_driver directory, I
> see that I have both Oracle and Postgres drivers, though I only use Oracle.
> Maybe both are required to compile the Java? These are the files I have
> there:
> > > > > > >
> > > > > > > $ ls $GUS_HOME/lib/java/db_driver/
> > > > > > > ojdbc5.jar  postgresql-8.3-603.jdbc3.jar
> > > > > > >
> > > > > > > I see that ojdbc5.jar does contain
> oracle/jdbc/OracleDriver.class. I suggest you try downloading that jarfile.
> You can get it from here:
> http://www.oracle.com/technetwork/database/enterprise-edition/jdbc-111060-084321.html
> > > > > > >
> > > > > > > -- John
> > > > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > This SF email is sponsosred by:
> > Try Windows Azure free for 90 days Click Here
> >
> http://p.sf.net/sfu/sfd2d-msazure_______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>

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