From gllambi at fing.edu.uy  Sat May  1 17:12:23 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Sat, 01 May 2010 18:12:23 -0300
Subject: [MOBY-dev] Format Example
In-Reply-To: <003f01cae891$aa594700$ff0bd500$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
	<003f01cae891$aa594700$ff0bd500$@gmail.com>
Message-ID: <20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>

Hi Eddie!

Thanks a lot for both tutorials! I looked at them and if I have some  
trouble, take for sure I'll write here again. With this quick help,  
who won't ;)

Best regards
Guzman

Edward Kawas <edward.kawas at gmail.com> escribi?:

> Hi Guzman,
>
> There are a few tutorials for using moby with Taverna. There is this one
> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
> ndex.html), and while it refers to an older version of taverna, it should be
> relevant.
>
> Also, there is a power point presentation hosted @
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
> Taverna_Tutorial.ppt
>
> If these resources don't help, or if you have more questions, please do not
> hesitate to ask them here!
>
> Eddie
>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
>> Sent: Friday, April 30, 2010 8:28 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] Format Example
>>
>> Hi!
>>
>> First of all, sorry in advance if this is a very stupid question, but I'm
> new with
>> BioMoby.
>>
>> I've been searching in myexperiment website for a format example
>> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
>> example where you have things in Fasta, GFF, Genbank or any other format
>> and take advantage of the bioMoby friendly format features to make format
>> unaware.
>>
>> Does anybody knows a workflow example of this? or maybe I understood
>> wrong the objetives of BioMoby
>>
>> Best Regards
>> Guzman
>>
>> ----------------------------------------
>> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
>> URUGUAY
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY


From gllambi at fing.edu.uy  Sat May  1 17:13:46 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Sat, 01 May 2010 18:13:46 -0300
Subject: [MOBY-dev] Format Example
In-Reply-To: <op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>
References: <E1O7wea-0002hB-00@phoebus>
	<op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <20100501181346.16481gy1bipvqdgk@www.fing.edu.uy>

Hi Mark, Alan,

which tutorial you are talking about? Do you have some extra material  
I can use besides the one Eddie sent to me?

Thanks
Guzman

Mark Wilkinson <markw at illuminae.com> escribi?:

> Confirmed!  Thank you!
>
> Mark
>
>
>
> On Fri, 30 Apr 2010 13:17:40 -0700, Alan R Williams  
> <alanrw at cs.man.ac.uk> wrote:
>
>> Mark,
>>
>> The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
>> plugin.  It should show up under the standard plugins menu.
>>
>> Alan
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC, Canada
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY


From edward.kawas at gmail.com  Mon May  3 13:52:37 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 3 May 2010 10:52:37 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>
	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
Message-ID: <003a01caeae9$6e776b40$4b6641c0$@gmail.com>

Hello Again!

I updated the 'End user BioMOBY Applications' page on biomoby.org to reflect our most recent update to the taverna tutorial [1].

I am not sure if you (Guzman) have seen this already, but if you haven?t, I hope it helps!

Thanks,

Eddie

[1] http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna


> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> Sent: Saturday, May 01, 2010 2:12 PM
> To: moby-dev at lists.open-bio.org
> Subject: Re: [MOBY-dev] Format Example
> 
> Hi Eddie!
> 
> Thanks a lot for both tutorials! I looked at them and if I have some trouble,
> take for sure I'll write here again. With this quick help, who won't ;)
> 
> Best regards
> Guzman
> 
> Edward Kawas <edward.kawas at gmail.com> escribi?:
> 
> > Hi Guzman,
> >
> > There are a few tutorials for using moby with Taverna. There is this
> > one
> > (http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/taverna/g
> > uide/i ndex.html), and while it refers to an older version of taverna,
> > it should be relevant.
> >
> > Also, there is a power point presentation hosted @
> >
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMo
> b
> > y_and_
> > Taverna_Tutorial.ppt
> >
> > If these resources don't help, or if you have more questions, please
> > do not hesitate to ask them here!
> >
> > Eddie
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> >> Sent: Friday, April 30, 2010 8:28 AM
> >> To: moby-dev at lists.open-bio.org
> >> Subject: [MOBY-dev] Format Example
> >>
> >> Hi!
> >>
> >> First of all, sorry in advance if this is a very stupid question, but
> >> I'm
> > new with
> >> BioMoby.
> >>
> >> I've been searching in myexperiment website for a format example
> >> workflow using bioMoby, but I couldn't find anyone. I'm looking for
> >> an example where you have things in Fasta, GFF, Genbank or any other
> >> format and take advantage of the bioMoby friendly format features to
> >> make format unaware.
> >>
> >> Does anybody knows a workflow example of this? or maybe I understood
> >> wrong the objetives of BioMoby
> >>
> >> Best Regards
> >> Guzman
> >>
> >> ----------------------------------------
> >> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR
> >> - URUGUAY
> >>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> 
> 
> ----------------------------------------
> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
> URUGUAY
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From alanrw at cs.man.ac.uk  Tue May  4 04:31:11 2010
From: alanrw at cs.man.ac.uk (Alan Williams)
Date: Tue, 04 May 2010 09:31:11 +0100
Subject: [MOBY-dev] Format Example
In-Reply-To: <003a01caeae9$6e776b40$4b6641c0$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
	<003a01caeae9$6e776b40$4b6641c0$@gmail.com>
Message-ID: <4BDFDB4F.9040805@cs.man.ac.uk>

Edward Kawas wrote:
> Hello Again!

Hello

> I updated the 'End user BioMOBY Applications' page on biomoby.org to
> reflect our most recent update to the taverna tutorial [1].

The links for the User Applications don't work for me.

> I am not sure if you (Guzman) have seen this already, but if you
> haven?t, I hope it helps!
> 
> Thanks,
> 
> Eddie

Alan

> [1]
> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna

From gllambi at fing.edu.uy  Tue May  4 08:36:03 2010
From: gllambi at fing.edu.uy (=?utf-8?Q?Guzm=C3=A1n_Llamb=C3=ADas_-_INCO?=)
Date: Tue, 4 May 2010 09:36:03 -0300
Subject: [MOBY-dev] Format Example
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy><003a01caeae9$6e776b40$4b6641c0$@gmail.com>
	<4BDFDB4F.9040805@cs.man.ac.uk>
Message-ID: <CB082CD4D5C045D1AECD71C795A7AC8E@fing.edu.uy>

Hello Eddie,

I'm having the same problem Alan had. Is the link correct?

Regards
Guzm?n

----- Original Message ----- 
From: "Alan Williams" <alanrw at cs.man.ac.uk>
To: "Core developer announcements" <moby-dev at lists.open-bio.org>
Sent: Tuesday, May 04, 2010 5:31 AM
Subject: Re: [MOBY-dev] Format Example


> Edward Kawas wrote:
>> Hello Again!
>
> Hello
>
>> I updated the 'End user BioMOBY Applications' page on biomoby.org to
>> reflect our most recent update to the taverna tutorial [1].
>
> The links for the User Applications don't work for me.
>
>> I am not sure if you (Guzman) have seen this already, but if you
>> haven?t, I hope it helps!
>>
>> Thanks,
>>
>> Eddie
>
> Alan
>
>> [1]
>> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 


From gllambi at fing.edu.uy  Tue May  4 08:46:36 2010
From: gllambi at fing.edu.uy (=?utf-8?Q?Guzm=C3=A1n_Llamb=C3=ADas_-_INCO?=)
Date: Tue, 4 May 2010 09:46:36 -0300
Subject: [MOBY-dev] Format Example
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy><003a01caeae9$6e776b40$4b6641c0$@gmail.com><4BDFDB4F.9040805@cs.man.ac.uk>
	<CB082CD4D5C045D1AECD71C795A7AC8E@fing.edu.uy>
Message-ID: <F6F5657CA4BA4A478C7FD18302B29BE7@fing.edu.uy>

Now is working, sorry for the noise

Regards
Guzman
----- Original Message ----- 
From: "Guzm?n Llamb?as - INCO" <gllambi at fing.edu.uy>
To: "Core developer announcements" <moby-dev at lists.open-bio.org>
Sent: Tuesday, May 04, 2010 9:36 AM
Subject: Re: [MOBY-dev] Format Example


> Hello Eddie,
>
> I'm having the same problem Alan had. Is the link correct?
>
> Regards
> Guzm?n
>
> ----- Original Message ----- 
> From: "Alan Williams" <alanrw at cs.man.ac.uk>
> To: "Core developer announcements" <moby-dev at lists.open-bio.org>
> Sent: Tuesday, May 04, 2010 5:31 AM
> Subject: Re: [MOBY-dev] Format Example
>
>
>> Edward Kawas wrote:
>>> Hello Again!
>>
>> Hello
>>
>>> I updated the 'End user BioMOBY Applications' page on biomoby.org to
>>> reflect our most recent update to the taverna tutorial [1].
>>
>> The links for the User Applications don't work for me.
>>
>>> I am not sure if you (Guzman) have seen this already, but if you
>>> haven?t, I hope it helps!
>>>
>>> Thanks,
>>>
>>> Eddie
>>
>> Alan
>>
>>> [1]
>>> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 


From py at pingoured.fr  Mon May 10 04:13:42 2010
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Mon, 10 May 2010 10:13:42 +0200
Subject: [MOBY-dev] cvs down?
Message-ID: <1273479222.2580.48.camel@cyan.pingoured.fr>

Hi,

I am trying to retrieve the sources of jMoby from the cvs but it seems
to not be reachable (either by [1] or via eclipse).

Is it me ?

Regards,

Pierre

[1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby


From sneumann at ipb-halle.de  Mon May 10 04:37:13 2010
From: sneumann at ipb-halle.de (Steffen Neumann)
Date: Mon, 10 May 2010 10:37:13 +0200
Subject: [MOBY-dev] cvs down?
In-Reply-To: <1273479222.2580.48.camel@cyan.pingoured.fr>
References: <1273479222.2580.48.camel@cyan.pingoured.fr>
Message-ID: <assp.5746a99b8d.1273480633.3175.30.camel@paddy>

On Mon, 2010-05-10 at 10:13 +0200, Pierre-Yves Chibon wrote:
> Hi,
> 
> I am trying to retrieve the sources of jMoby from the cvs but it seems
> to not be reachable (either by [1] or via eclipse).

I also get an (61) Connection refused. 

> Is it me ?
For these cases, you could also try services like
http://downforeveryoneorjustme.com/

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409


From Richard.Finkers at wur.nl  Mon May 10 05:03:33 2010
From: Richard.Finkers at wur.nl (Richard Finkers)
Date: Mon, 10 May 2010 11:03:33 +0200
Subject: [MOBY-dev] cvs down?
In-Reply-To: <1273479222.2580.48.camel@cyan.pingoured.fr>
References: <1273479222.2580.48.camel@cyan.pingoured.fr>
Message-ID: <4BE7CBE5.2060200@wur.nl>

no problem from Wageningen.

Pierre-Yves Chibon wrote:
> Hi,
>
> I am trying to retrieve the sources of jMoby from the cvs but it seems
> to not be reachable (either by [1] or via eclipse).
>
> Is it me ?
>
> Regards,
>
> Pierre
>
> [1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>   


-- 
Dr. Richard Finkers
Researcher Plant Breeding
Wageningen UR Plant Breeding
P.O. Box 16, 6700 AA, Wageningen, The Netherlands
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB
Wageningen, The Netherlands
Tel. +31-317-484165 Fax +31-317-418094
http://www.plantbreeding.wur.nl/ <http://www.plantbreeding.wur.nl>
https://www.eu-sol.wur.nl/ <https://www.eu-sol.wur.nl>
https://cbsgdbase.wur.nl/ <https://cbsgdbase.wur.nl>
http://solgenomics.wur.nl/ <http://solgenomics.wur.nl>
http://www.disclaimer-uk.wur.nl/


From Dominique.Jeannin at avignon.inra.fr  Mon May 17 11:18:19 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Mon, 17 May 2010 17:18:19 +0200
Subject: [MOBY-dev] Error in CVS source
Message-ID: <4BF15E3B.8080301@avignon.inra.fr>

Hi,

We've just downloaded source code of jMoby by CVS but when I launch "ant 
install" (from ant view in eclipse), I get this log :

compile:
   [javac] Compiling 392 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
package foxtrot does not exist
   [javac] import foxtrot.Task; // for fancy synchronous GUI handling on 
data paste to external apps
   [javac]               ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
package foxtrot does not exist
   [javac] import foxtrot.Worker;
   [javac]               ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
cannot find symbol
   [javac] symbol  : class Task
   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
   [javac]                 targetTextType = (String) Worker.post(new 
Task(){
   [javac]                                                           ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
cannot find symbol
   [javac] symbol  : variable Worker
   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
   [javac]                 targetTextType = (String) Worker.post(new 
Task(){
   [javac]                                           ^
   [javac] Note: 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
uses or overrides a deprecated API.
   [javac] Note: Recompile with -Xlint:deprecation for details.
   [javac] Note: Some input files use unchecked or unsafe operations.
   [javac] Note: Recompile with -Xlint:unchecked for details.
   [javac] 4 errors

BUILD FAILED

What's wrong ?
Thanks for your help,

-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)


From gordonp at ucalgary.ca  Mon May 17 11:45:38 2010
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 17 May 2010 09:45:38 -0600
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF15E3B.8080301@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr>
Message-ID: <4BF164A2.6090502@ucalgary.ca>

Sorry, my bad.  I forgot to commit the project POM file update.  Fixing 
that now.

Dominique Jeannin wrote:
> Hi,
>
> We've just downloaded source code of jMoby by CVS but when I launch 
> "ant install" (from ant view in eclipse), I get this log :
>
> compile:
>   [javac] Compiling 392 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
> package foxtrot does not exist
>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
> on data paste to external apps
>   [javac]               ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
> package foxtrot does not exist
>   [javac] import foxtrot.Worker;
>   [javac]               ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
> cannot find symbol
>   [javac] symbol  : class Task
>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>   [javac]                 targetTextType = (String) Worker.post(new 
> Task(){
>   [javac]                                                           ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
> cannot find symbol
>   [javac] symbol  : variable Worker
>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>   [javac]                 targetTextType = (String) Worker.post(new 
> Task(){
>   [javac]                                           ^
>   [javac] Note: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
> uses or overrides a deprecated API.
>   [javac] Note: Recompile with -Xlint:deprecation for details.
>   [javac] Note: Some input files use unchecked or unsafe operations.
>   [javac] Note: Recompile with -Xlint:unchecked for details.
>   [javac] 4 errors
>
> BUILD FAILED
>
> What's wrong ?
> Thanks for your help,
>

From Dominique.Jeannin at avignon.inra.fr  Tue May 18 03:30:40 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Tue, 18 May 2010 09:30:40 +0200
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF164A2.6090502@ucalgary.ca>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
Message-ID: <4BF24220.6050600@avignon.inra.fr>

Paul Gordon a ?crit :
> Sorry, my bad.  I forgot to commit the project POM file update.  
> Fixing that now.
>
> Dominique Jeannin wrote:
>> Hi,
>>
>> We've just downloaded source code of jMoby by CVS but when I launch 
>> "ant install" (from ant view in eclipse), I get this log :
>>
>> compile:
>>   [javac] Compiling 392 source files to 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>> package foxtrot does not exist
>>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
>> on data paste to external apps
>>   [javac]               ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>> package foxtrot does not exist
>>   [javac] import foxtrot.Worker;
>>   [javac]               ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>> cannot find symbol
>>   [javac] symbol  : class Task
>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>   [javac]                 targetTextType = (String) Worker.post(new 
>> Task(){
>>   [javac]                                                           ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>> cannot find symbol
>>   [javac] symbol  : variable Worker
>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>   [javac]                 targetTextType = (String) Worker.post(new 
>> Task(){
>>   [javac]                                           ^
>>   [javac] Note: 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>> uses or overrides a deprecated API.
>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>   [javac] 4 errors
>>
>> BUILD FAILED
>>
>> What's wrong ?
>> Thanks for your help,
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
Thanks for the update, but we don't get this update because the server 
(cvs.open-bio.org) does not response (since yesterday about 7:00 pm in 
France).

-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)


From gordonp at ucalgary.ca  Tue May 18 09:53:17 2010
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 18 May 2010 07:53:17 -0600
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF24220.6050600@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
	<4BF24220.6050600@avignon.inra.fr>
Message-ID: <4BF29BCD.2060903@ucalgary.ca>

Hi Dominique,

In the interim, the following lines need to be added to the 
xmls/project.pom file:

   <dependency>
      <groupId>foxtrot</groupId>
      <artifactId>foxtrot</artifactId>
      <version>2.0</version>
    </dependency>

Cheers,

Paul

Dominique Jeannin wrote:
> Paul Gordon a ?crit :
>> Sorry, my bad.  I forgot to commit the project POM file update.  
>> Fixing that now.
>>
>> Dominique Jeannin wrote:
>>> Hi,
>>>
>>> We've just downloaded source code of jMoby by CVS but when I launch 
>>> "ant install" (from ant view in eclipse), I get this log :
>>>
>>> compile:
>>>   [javac] Compiling 392 source files to 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>>> package foxtrot does not exist
>>>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
>>> on data paste to external apps
>>>   [javac]               ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>>> package foxtrot does not exist
>>>   [javac] import foxtrot.Worker;
>>>   [javac]               ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>> cannot find symbol
>>>   [javac] symbol  : class Task
>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>> Task(){
>>>   [javac]                                                           ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>> cannot find symbol
>>>   [javac] symbol  : variable Worker
>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>> Task(){
>>>   [javac]                                           ^
>>>   [javac] Note: 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>>> uses or overrides a deprecated API.
>>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>>   [javac] 4 errors
>>>
>>> BUILD FAILED
>>>
>>> What's wrong ?
>>> Thanks for your help,
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
> Thanks for the update, but we don't get this update because the server 
> (cvs.open-bio.org) does not response (since yesterday about 7:00 pm in 
> France).
>

From edward.kawas at gmail.com  Tue May 18 10:04:47 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 18 May 2010 07:04:47 -0700
Subject: [MOBY-dev] publications
Message-ID: <003901caf693$1553a870$3ffaf950$@gmail.com>

Hello All,

 

I am updating the Publication & Press[1] page of the Biomoby.org page and I
was wondering if there were any relevant articles that I may have missed? If
so, please send them my way so that I can add them to the page.

 

Thanks,

 

Eddie

 

[1] http://biomoby.open-bio.org/index.php/what-is-moby/publications

 


From markw at illuminae.com  Tue May 18 10:00:24 2010
From: markw at illuminae.com (Mark)
Date: Tue, 18 May 2010 07:00:24 -0700
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF24220.6050600@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
	<4BF24220.6050600@avignon.inra.fr>
Message-ID: <op.vcwmiydmdeqt07@bighome>


> Thanks for the update, but we don't get this update because the server
> (cvs.open-bio.org) does not response (since yesterday about 7:00 pm in
> France).



I've submitted a ticket to the open-bio roots.  Hopefully it will be back  
soon!

M

From markw at illuminae.com  Tue May 18 10:56:04 2010
From: markw at illuminae.com (Mark)
Date: Tue, 18 May 2010 07:56:04 -0700
Subject: [MOBY-dev] publications
In-Reply-To: <003901caf693$1553a870$3ffaf950$@gmail.com>
References: <003901caf693$1553a870$3ffaf950$@gmail.com>
Message-ID: <op.vcwo3qczdeqt07@bighome>

LOL!  Hey Eddie, perhaps be a LITTLE bit more modest on the main link :-)

how about "To cite the BioMoby project, please cite THIS paper", and give  
the full reference so that people can copy/paste it into their  
bibliographies.

cheers!

M


On Tue, 18 May 2010 07:04:47 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:

> Hello All,
>
>
> I am updating the Publication & Press[1] page of the Biomoby.org page  
> and I
> was wondering if there were any relevant articles that I may have  
> missed? If
> so, please send them my way so that I can add them to the page.
>
>
> Thanks,
>
>
> Eddie
>
>
> [1] http://biomoby.open-bio.org/index.php/what-is-moby/publications
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Using Opera's revolutionary e-mail client: http://www.opera.com/mail/

From Dominique.Jeannin at avignon.inra.fr  Tue May 18 10:59:46 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Tue, 18 May 2010 16:59:46 +0200
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF29BCD.2060903@ucalgary.ca>
References: <4BF15E3B.8080301@avignon.inra.fr>
	<4BF164A2.6090502@ucalgary.ca>	<4BF24220.6050600@avignon.inra.fr>
	<4BF29BCD.2060903@ucalgary.ca>
Message-ID: <4BF2AB62.10408@avignon.inra.fr>

Paul,

The problem is solved :)
Thank you !

Dominique

Paul Gordon a ?crit :
> Hi Dominique,
>
> In the interim, the following lines need to be added to the 
> xmls/project.pom file:
>
>   <dependency>
>      <groupId>foxtrot</groupId>
>      <artifactId>foxtrot</artifactId>
>      <version>2.0</version>
>    </dependency>
>
> Cheers,
>
> Paul
>
> Dominique Jeannin wrote:
>> Paul Gordon a ?crit :
>>> Sorry, my bad.  I forgot to commit the project POM file update.  
>>> Fixing that now.
>>>
>>> Dominique Jeannin wrote:
>>>> Hi,
>>>>
>>>> We've just downloaded source code of jMoby by CVS but when I launch 
>>>> "ant install" (from ant view in eclipse), I get this log :
>>>>
>>>> compile:
>>>>   [javac] Compiling 392 source files to 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>>>> package foxtrot does not exist
>>>>   [javac] import foxtrot.Task; // for fancy synchronous GUI 
>>>> handling on data paste to external apps
>>>>   [javac]               ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>>>> package foxtrot does not exist
>>>>   [javac] import foxtrot.Worker;
>>>>   [javac]               ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>>> cannot find symbol
>>>>   [javac] symbol  : class Task
>>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>>> Task(){
>>>>   [javac]                                                           ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>>> cannot find symbol
>>>>   [javac] symbol  : variable Worker
>>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>>> Task(){
>>>>   [javac]                                           ^
>>>>   [javac] Note: 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>>>> uses or overrides a deprecated API.
>>>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>>>   [javac] 4 errors
>>>>
>>>> BUILD FAILED
>>>>
>>>> What's wrong ?
>>>> Thanks for your help,
>>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>> Thanks for the update, but we don't get this update because the 
>> server (cvs.open-bio.org) does not response (since yesterday about 
>> 7:00 pm in France).
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)


From Elise.Larsonneur at avignon.inra.fr  Wed May 26 05:03:10 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 11:03:10 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFCE3CE.4060504@avignon.inra.fr>

Hi !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France


From Elise.Larsonneur at avignon.inra.fr  Wed May 26 07:21:50 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 13:21:50 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFD044E.8040305@avignon.inra.fr>

Hello !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France

From edward.kawas at gmail.com  Wed May 26 09:29:30 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 26 May 2010 06:29:30 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFCE3CE.4060504@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>
Message-ID: <002401cafcd7$79cb3850$6d61a8f0$@gmail.com>

Hi Elise,

Did you make sure to generate the skeletons and their implementations first?
Hard to say what the problem is without knowing what you did to get here.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Wednesday, May 26, 2010 2:03 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] moby services deployment
> 
> Hi !
> 
> When I want to deploy moby services by ant dashboard on remote machine,
> I meet this problem :
> 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> What can I do for resolving this problem ?
> 
> Thanks,
> 
> Elise Larsonneur
> Bioinformatics trainee.
> UR GAFL
> INRA Avignon
> France
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From Elise.Larsonneur at avignon.inra.fr  Wed May 26 10:35:52 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 16:35:52 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
References: <4BFCE3CE.4060504@avignon.inra.fr>
	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
Message-ID: <4BFD31C8.1070008@avignon.inra.fr>

Before deploying webservices , I generated datatypes and skeletons in 
jMoby with the dashboard. Then, I wrote the implementations of skeletons 
in another project associated to jMoby.
So, after ant all, ant dashboard, when I launchs the deployment (after 
ant all) of these webservices (on remote or local machine) , only the 
wsdd files are created and the previous error displays.
I used a pattern for implementation class names in the Moses Generator 
Panel.

eclipse console : ant all :
Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
cleanapi:
clean:
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build
checkmaven:
initmaven:
init:
    [mkdir] Created dir: /home/av07/gafl/elarsonneur/workspace/jMoby/build
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/run
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/test
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
config:
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
     [copy] Copying 27 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/run
     [copy] Copying 10 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
     [copy] Copying 24 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
     [copy] Copying 163 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
compile:
    [javac] Compiling 392 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
    [javac] Note: 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] Compiling 26 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
docs:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: 
warning - @return tag has no arguments.
  [javadoc] 1 warning
jars:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-dashboard-1.1.1.jar
rdfagent-init:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
jar-rdfagent:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
     [copy] Copying 95 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
war:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cache
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
      [war] Building war: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jmoby.war
wardist:
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
bindist-rdfagent:
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 96 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/lib
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 6 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
      [tar] Building tar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.tar.gz
      [zip] Building zip: 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.zip
all:
BUILD SUCCESSFUL



ant dashboard :
Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
checkmaven:
initmaven:
init:
config:
compile:
moses-init:
samples-init:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/resources
dashboard-init:
dashboard-config:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-config.jar
dashboard:
[Dashboard] 144276 [Thread-49] ERROR SimpleAnt - 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
The following error occurred while executing this line:
[Dashboard] 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
[Dashboard] 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.



Dashboard console :
Selected authorities:
    avilin05.avignon.inra.fr

-find-services:
[Services names] 
Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_getExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperimentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis_getExperimentType,Solstis_getDatasetFromExp

compile-datatypes:
    [javac] Compiling 1796 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes

compile-services:
    [javac] Compiling 21 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons

jar-datatypes:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar

jar-services:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-skeletons.jar

deploy-remote:
    [mkdir] Created dir: 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26

create-wsdd:
[Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getTrait.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getAuthor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExperiment.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExpFromDataset.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getProject.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExperimentDesc.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getFactor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

BUILD FAILED
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.


Thanks,

Elise.






Edward Kawas wrote:
> Hi Elise,
>
> Did you make sure to generate the skeletons and their implementations first?
> Hard to say what the problem is without knowing what you did to get here.
>
> Eddie
>
>   
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>> Sent: Wednesday, May 26, 2010 2:03 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] moby services deployment
>>
>> Hi !
>>
>> When I want to deploy moby services by ant dashboard on remote machine,
>> I meet this problem :
>>
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>> What can I do for resolving this problem ?
>>
>> Thanks,
>>
>> Elise Larsonneur
>> Bioinformatics trainee.
>> UR GAFL
>> INRA Avignon
>> France
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>   


From Elise.Larsonneur at avignon.inra.fr  Wed May 26 10:51:36 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 16:51:36 +0200
Subject: [MOBY-dev] cvs repository of Biomoby
Message-ID: <4BFD3578.7040706@avignon.inra.fr>

Hi !

I used eclipse and since two weeks , I can't access to cvs repository of 
jMoby in France for updating : "cvs.open-bio.org:/home/repository/moby ".
Is there a new repository ?

Thanks,

Elise Larsonneur
Bioinformatics trainee
UR GAFL
INRA Avignon
France

From markw at illuminae.com  Wed May 26 17:09:34 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 26 May 2010 14:09:34 -0700
Subject: [MOBY-dev] cvs repository of Biomoby
In-Reply-To: <4BFD3578.7040706@avignon.inra.fr>
References: <4BFD3578.7040706@avignon.inra.fr>
Message-ID: <op.vdbzp8uhnbznux@dd0710001l.icapture.ubc.ca>

I've submitted another ticket to the open-bio root list.  The CVS has been  
unstable for many months, and it's getting a bit frustrating!!

Mark



On Wed, 26 May 2010 07:51:36 -0700, Elise Larsonneur  
<Elise.Larsonneur at avignon.inra.fr> wrote:

> Hi !
>
> I used eclipse and since two weeks , I can't access to cvs repository of  
> jMoby in France for updating : "cvs.open-bio.org:/home/repository/moby ".
> Is there a new repository ?
>
> Thanks,
>
> Elise Larsonneur
> Bioinformatics trainee
> UR GAFL
> INRA Avignon
> France
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From Elise.Larsonneur at avignon.inra.fr  Thu May 27 04:18:33 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Thu, 27 May 2010 10:18:33 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFD31C8.1070008@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
	<4BFD31C8.1070008@avignon.inra.fr>
Message-ID: <4BFE2AD9.80300@avignon.inra.fr>

Hello !

I forgot to specify that I use a Tomcat 5.5.1 server.

Thanks

Elise.




Elise Larsonneur wrote:
> Before deploying webservices , I generated datatypes and skeletons in 
> jMoby with the dashboard. Then, I wrote the implementations of 
> skeletons in another project associated to jMoby.
> So, after ant all, ant dashboard, when I launchs the deployment of 
> these webservices (on remote or local machine) , only the wsdd files 
> are created and the previous error displays.
> I used a pattern for implementation class names in the Moses Generator 
> Panel.
>
> eclipse console : ant all :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> cleanapi:
> clean:
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> checkmaven:
> initmaven:
> init:
>    [mkdir] Created dir: /home/av07/gafl/elarsonneur/workspace/jMoby/build
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> config:
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [copy] Copying 27 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>     [copy] Copying 10 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>     [copy] Copying 24 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>     [copy] Copying 163 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> compile:
>    [javac] Compiling 392 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>    [javac] Note: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
> uses or overrides a deprecated API.
>    [javac] Note: Recompile with -Xlint:deprecation for details.
>    [javac] Note: Some input files use unchecked or unsafe operations.
>    [javac] Note: Recompile with -Xlint:unchecked for details.
>    [javac] Compiling 26 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> docs:
>  [javadoc] Generating Javadoc
>  [javadoc] Javadoc execution
>  [javadoc] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: 
> warning - @return tag has no arguments.
>  [javadoc] 1 warning
> jars:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-dashboard-1.1.1.jar 
>
> rdfagent-init:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> jar-rdfagent:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>     [copy] Copying 95 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> war:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cache
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>      [war] Building war: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jmoby.war
> wardist:
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> bindist-rdfagent:
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 96 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/lib
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 6 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [tar] Building tar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.tar.gz 
>
>      [zip] Building zip: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.zip 
>
> all:
> BUILD SUCCESSFUL
>
>
>
> ant dashboard :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> checkmaven:
> initmaven:
> init:
> config:
> compile:
> moses-init:
> samples-init:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/resources 
>
> dashboard-init:
> dashboard-config:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-config.jar 
>
> dashboard:
> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt - 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
> The following error occurred while executing this line:
> [Dashboard] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
> The following error occurred while executing this line:
> [Dashboard] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
> Property 'service.jar' is not defined.
>
>
>
> Dashboard console :
> Selected authorities:
>    avilin05.avignon.inra.fr
>
> -find-services:
> [Services names] 
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_getExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperimentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis_getExperimentType,Solstis_getDatasetFromExp 
>
>
> compile-datatypes:
>    [javac] Compiling 1796 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
>
> compile-services:
>    [javac] Compiling 21 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
>
> jar-datatypes:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar 
>
>
> jar-services:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-skeletons.jar 
>
>
> deploy-remote:
>    [mkdir] Created dir: 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26 
>
>
> create-wsdd:
> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getTrait.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getAuthor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExperiment.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getProject.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getFactor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> BUILD FAILED
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
> Property 'service.jar' is not defined.
>
>
> Thanks,
>
> Elise.
>
>
>
>
>
>
> Edward Kawas wrote:
>> Hi Elise,
>>
>> Did you make sure to generate the skeletons and their implementations 
>> first?
>> Hard to say what the problem is without knowing what you did to get 
>> here.
>>
>> Eddie
>>
>>  
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>>> Sent: Wednesday, May 26, 2010 2:03 AM
>>> To: moby-dev at lists.open-bio.org
>>> Subject: [MOBY-dev] moby services deployment
>>>
>>> Hi !
>>>
>>> When I want to deploy moby services by ant dashboard on remote machine,
>>> I meet this problem :
>>>
>>> The following error occurred while executing this line:
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>>> The following error occurred while executing this line:
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>>> Property 'service.jar' is not defined.
>>>
>>> What can I do for resolving this problem ?
>>>
>>> Thanks,
>>>
>>> Elise Larsonneur
>>> Bioinformatics trainee.
>>> UR GAFL
>>> INRA Avignon
>>> France
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>     
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>   
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Thu May 27 08:48:42 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 27 May 2010 05:48:42 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFD31C8.1070008@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
	<4BFD31C8.1070008@avignon.inra.fr>
Message-ID: <004101cafd9a$f1273570$d375a050$@gmail.com>

Hi Elise,

I cannot replicate your problem, so maybe I can help point you in the right
direction. 

[1]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopme
nt.html
[2]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators
.html 
[3]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-deploy.htm
l

I think that you may have seen some of these resources, judging by how far
you have gotten, but I think it would be a good idea to read over them. The
one thing that caught my eye is that when you did 'ant all', lots of
unrelated service tasks were executed. If you look at resource [1] and read
'Step 1: What is needed' 'ant all' is done from within your service project
and not from the root moby-live/Java folder.

Let me know if this was a good enough push!

Thanks,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Wednesday, May 26, 2010 7:36 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] moby services deployment
> 
> Before deploying webservices , I generated datatypes and skeletons in
> jMoby with the dashboard. Then, I wrote the implementations of skeletons
> in another project associated to jMoby.
> So, after ant all, ant dashboard, when I launchs the deployment (after ant
all)
> of these webservices (on remote or local machine) , only the wsdd files
are
> created and the previous error displays.
> I used a pattern for implementation class names in the Moses Generator
> Panel.
> 
> eclipse console : ant all :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> cleanapi:
> clean:
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> checkmaven:
> initmaven:
> init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> config:
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>      [copy] Copying 27 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>      [copy] Copying 10 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>      [copy] Copying 24 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>      [copy] Copying 163 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> compile:
>     [javac] Compiling 392 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [javac] Note:
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
> ices/util/PBERecorder.java
> uses or overrides a deprecated API.
>     [javac] Note: Recompile with -Xlint:deprecation for details.
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] Compiling 26 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> docs:
>   [javadoc] Generating Javadoc
>   [javadoc] Javadoc execution
>   [javadoc]
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
> warning - @return tag has no arguments.
>   [javadoc] 1 warning
> jars:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> dashboard-1.1.1.jar
> rdfagent-init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> jar-rdfagent:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>      [copy] Copying 95 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> war:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
> he
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>       [war] Building war:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
> oby.war
> wardist:
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> bindist-rdfagent:
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 96 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
> b
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 6 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>       [tar] Building tar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
> 05-26.tar.gz
>       [zip] Building zip:
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
> 05-26.zip
> all:
> BUILD SUCCESSFUL
> 
> 
> 
> ant dashboard :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> checkmaven:
> initmaven:
> init:
> config:
> compile:
> moses-init:
> samples-init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
> ources
> dashboard-init:
> dashboard-config:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
> config.jar
> dashboard:
> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> The following error occurred while executing this line:
> [Dashboard]
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> [Dashboard]
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> 
> 
> Dashboard console :
> Selected authorities:
>     avilin05.avignon.inra.fr
> 
> -find-services:
> [Services names]
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
> _getExperimentType,Solstis_getDatasetFromExp
> 
> compile-datatypes:
>     [javac] Compiling 1796 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
> 
> compile-services:
>     [javac] Compiling 21 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
> 
> jar-datatypes:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> datatypes.jar
> 
> jar-services:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> skeletons.jar
> 
> deploy-remote:
>     [mkdir] Created dir:
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26
> 
> create-wsdd:
> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getTrait.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getExperiment.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getProject.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getFactor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> BUILD FAILED
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> 
> Thanks,
> 
> Elise.
> 
> 
> 
> 
> 
> 
> Edward Kawas wrote:
> > Hi Elise,
> >
> > Did you make sure to generate the skeletons and their implementations
> first?
> > Hard to say what the problem is without knowing what you did to get
here.
> >
> > Eddie
> >
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >> Sent: Wednesday, May 26, 2010 2:03 AM
> >> To: moby-dev at lists.open-bio.org
> >> Subject: [MOBY-dev] moby services deployment
> >>
> >> Hi !
> >>
> >> When I want to deploy moby services by ant dashboard on remote
> >> machine, I meet this problem :
> >>
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >> What can I do for resolving this problem ?
> >>
> >> Thanks,
> >>
> >> Elise Larsonneur
> >> Bioinformatics trainee.
> >> UR GAFL
> >> INRA Avignon
> >> France
> >>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From Elise.Larsonneur at avignon.inra.fr  Thu May 27 11:35:36 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Thu, 27 May 2010 17:35:36 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <004101cafd9a$f1273570$d375a050$@gmail.com>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>	<4BFD31C8.1070008@avignon.inra.fr>
	<004101cafd9a$f1273570$d375a050$@gmail.com>
Message-ID: <4BFE9148.4020800@avignon.inra.fr>

Hi !

About the initial error : "Property 'service.jar' is not defined" which 
refers to the next lines in jMoby/xmls/deployBuild.xml file :



<!-- ================================================================== -->
<!-- Create a wsdd descriptor for given service in 'build/wsdd'         -->
<!--    parameter: ${service.name}  ... for which service               -->
<!--    parameter: ${wsdd.file}     ... what file to create             -->
<!-- ================================================================== -->
<target name="create-wsdd" depends="init">
  <property name="wsdd.template" 
value="${src.webapps}/standard.wsdd.template"/>
  <propertycopy property="impl.class" from="service.${service.name}" 
override="true"/>        ----------------------> line "224"
  <copy file="${wsdd.template}" tofile="${wsdd.file}" overwrite="true"
    taskname="Create ${service.name}.wsdd">
    <filterset>
      <filter token="SERVICE_NAME" value="${service.name}"/>
      <filter token="IMPL_CLASS" value="${impl.class}"/>
    </filterset>
  </copy>
</target>



I would to know how "${service.name}" on line "224" can be assigned to 
"jar".

Thanks a lot,

Elise



Edward Kawas wrote:
> Hi Elise,
>
> I cannot replicate your problem, so maybe I can help point you in the right
> direction. 
>
> [1]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopme
> nt.html
> [2]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators
> .html 
> [3]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-deploy.htm
> l
>
> I think that you may have seen some of these resources, judging by how far
> you have gotten, but I think it would be a good idea to read over them. The
> one thing that caught my eye is that when you did 'ant all', lots of
> unrelated service tasks were executed. If you look at resource [1] and read
> 'Step 1: What is needed' 'ant all' is done from within your service project
> and not from the root moby-live/Java folder.
>
> Let me know if this was a good enough push!
>
> Thanks,
>
> Eddie
>
>   
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>> Sent: Wednesday, May 26, 2010 7:36 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] moby services deployment
>>
>> Before deploying webservices , I generated datatypes and skeletons in
>> jMoby with the dashboard. Then, I wrote the implementations of skeletons
>> in another project associated to jMoby.
>> So, after ant all, ant dashboard, when I launchs the deployment (after ant
>>     
> all)
>   
>> of these webservices (on remote or local machine) , only the wsdd files
>>     
> are
>   
>> created and the previous error displays.
>> I used a pattern for implementation class names in the Moses Generator
>> Panel.
>>
>> eclipse console : ant all :
>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
>> cleanapi:
>> clean:
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>> checkmaven:
>> initmaven:
>> init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
>> config:
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>      [copy] Copying 27 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>>      [copy] Copying 10 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>>      [copy] Copying 24 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>>      [copy] Copying 163 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>> compile:
>>     [javac] Compiling 392 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>     [javac] Note:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
>> ices/util/PBERecorder.java
>> uses or overrides a deprecated API.
>>     [javac] Note: Recompile with -Xlint:deprecation for details.
>>     [javac] Note: Some input files use unchecked or unsafe operations.
>>     [javac] Note: Recompile with -Xlint:unchecked for details.
>>     [javac] Compiling 26 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>> docs:
>>   [javadoc] Generating Javadoc
>>   [javadoc] Javadoc execution
>>   [javadoc]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
>> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
>> warning - @return tag has no arguments.
>>   [javadoc] 1 warning
>> jars:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
>> dashboard-1.1.1.jar
>> rdfagent-init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>> jar-rdfagent:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>      [copy] Copying 95 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
>> war:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
>> he
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>>       [war] Building war:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
>> oby.war
>> wardist:
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
>> bindist-rdfagent:
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 96 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
>> b
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 6 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>       [tar] Building tar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
>> 05-26.tar.gz
>>       [zip] Building zip:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
>> 05-26.zip
>> all:
>> BUILD SUCCESSFUL
>>
>>
>>
>> ant dashboard :
>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
>> checkmaven:
>> initmaven:
>> init:
>> config:
>> compile:
>> moses-init:
>> samples-init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
>> ources
>> dashboard-init:
>> dashboard-config:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
>> config.jar
>> dashboard:
>> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
>> The following error occurred while executing this line:
>> [Dashboard]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> [Dashboard]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>>
>>
>> Dashboard console :
>> Selected authorities:
>>     avilin05.avignon.inra.fr
>>
>> -find-services:
>> [Services names]
>> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
>> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
>> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
>> _getExperimentType,Solstis_getDatasetFromExp
>>
>> compile-datatypes:
>>     [javac] Compiling 1796 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
>>
>> compile-services:
>>     [javac] Compiling 21 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
>>
>> jar-datatypes:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
>> datatypes.jar
>>
>> jar-services:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
>> skeletons.jar
>>
>> deploy-remote:
>>     [mkdir] Created dir:
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26
>>
>> create-wsdd:
>> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getTrait.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExperiment.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getProject.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getFactor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> BUILD FAILED
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>>
>> Thanks,
>>
>> Elise.
>>
>>
>>
>>
>>
>>
>> Edward Kawas wrote:
>>     
>>> Hi Elise,
>>>
>>> Did you make sure to generate the skeletons and their implementations
>>>       
>> first?
>>     
>>> Hard to say what the problem is without knowing what you did to get
>>>       
> here.
>   
>>> Eddie
>>>
>>>
>>>       
>>>> -----Original Message-----
>>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>>>> Sent: Wednesday, May 26, 2010 2:03 AM
>>>> To: moby-dev at lists.open-bio.org
>>>> Subject: [MOBY-dev] moby services deployment
>>>>
>>>> Hi !
>>>>
>>>> When I want to deploy moby services by ant dashboard on remote
>>>> machine, I meet this problem :
>>>>
>>>> The following error occurred while executing this line:
>>>>
>>>>         
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>>     
>>>> The following error occurred while executing this line:
>>>>
>>>>         
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>>     
>>>> Property 'service.jar' is not defined.
>>>>
>>>> What can I do for resolving this problem ?
>>>>
>>>> Thanks,
>>>>
>>>> Elise Larsonneur
>>>> Bioinformatics trainee.
>>>> UR GAFL
>>>> INRA Avignon
>>>> France
>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>>>         
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>       
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>   


From edward.kawas at gmail.com  Thu May 27 12:03:48 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 27 May 2010 09:03:48 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFE9148.4020800@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>	<4BFD31C8.1070008@avignon.inra.fr>	<004101cafd9a$f1273570$d375a050$@gmail.com>
	<4BFE9148.4020800@avignon.inra.fr>
Message-ID: <005c01cafdb6$32c44840$984cd8c0$@gmail.com>

The ant file is meant to help you copy your class files from a specific
location (more about that in the links that I sent you) and creates the
services.jar file for you. If you have to edit the build file then you are
doing something wrong (in the sense that you aren't generating your services
in the manner that MoSeS wishes that you would).

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Thursday, May 27, 2010 8:36 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] moby services deployment
> 
> Hi !
> 
> About the initial error : "Property 'service.jar' is not defined" which
refers to
> the next lines in jMoby/xmls/deployBuild.xml file :
> 
> 
> 
> <!--
> ==========================================================
> ======== -->
> <!-- Create a wsdd descriptor for given service in 'build/wsdd'
-->
> <!--    parameter: ${service.name}  ... for which service
-->
> <!--    parameter: ${wsdd.file}     ... what file to create
-->
> <!--
> ==========================================================
> ======== -->
> <target name="create-wsdd" depends="init">
>   <property name="wsdd.template"
> value="${src.webapps}/standard.wsdd.template"/>
>   <propertycopy property="impl.class" from="service.${service.name}"
> override="true"/>        ----------------------> line "224"
>   <copy file="${wsdd.template}" tofile="${wsdd.file}" overwrite="true"
>     taskname="Create ${service.name}.wsdd">
>     <filterset>
>       <filter token="SERVICE_NAME" value="${service.name}"/>
>       <filter token="IMPL_CLASS" value="${impl.class}"/>
>     </filterset>
>   </copy>
> </target>
> 
> 
> 
> I would to know how "${service.name}" on line "224" can be assigned to
> "jar".
> 
> Thanks a lot,
> 
> Elise
> 
> 
> 
> Edward Kawas wrote:
> > Hi Elise,
> >
> > I cannot replicate your problem, so maybe I can help point you in the
right
> > direction.
> >
> > [1]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/ServiceDevelopme
> > nt.html
> > [2]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/Moses-generators
> > .html
> > [3]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/Moses-deploy.htm
> > l
> >
> > I think that you may have seen some of these resources, judging by how
> far
> > you have gotten, but I think it would be a good idea to read over them.
The
> > one thing that caught my eye is that when you did 'ant all', lots of
> > unrelated service tasks were executed. If you look at resource [1] and
read
> > 'Step 1: What is needed' 'ant all' is done from within your service
project
> > and not from the root moby-live/Java folder.
> >
> > Let me know if this was a good enough push!
> >
> > Thanks,
> >
> > Eddie
> >
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >> Sent: Wednesday, May 26, 2010 7:36 AM
> >> To: Core developer announcements
> >> Subject: Re: [MOBY-dev] moby services deployment
> >>
> >> Before deploying webservices , I generated datatypes and skeletons in
> >> jMoby with the dashboard. Then, I wrote the implementations of
> skeletons
> >> in another project associated to jMoby.
> >> So, after ant all, ant dashboard, when I launchs the deployment (after
ant
> >>
> > all)
> >
> >> of these webservices (on remote or local machine) , only the wsdd files
> >>
> > are
> >
> >> created and the previous error displays.
> >> I used a pattern for implementation class names in the Moses Generator
> >> Panel.
> >>
> >> eclipse console : ant all :
> >> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> >> cleanapi:
> >> clean:
> >>    [delete] Deleting directory
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> >> checkmaven:
> >> initmaven:
> >> init:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> >> config:
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>      [copy] Copying 27 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
> >>      [copy] Copying 10 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
> >>      [copy] Copying 24 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
> >>      [copy] Copying 163 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >> compile:
> >>     [javac] Compiling 392 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>     [javac] Note:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
> >> ices/util/PBERecorder.java
> >> uses or overrides a deprecated API.
> >>     [javac] Note: Recompile with -Xlint:deprecation for details.
> >>     [javac] Note: Some input files use unchecked or unsafe operations.
> >>     [javac] Note: Recompile with -Xlint:unchecked for details.
> >>     [javac] Compiling 26 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> >> docs:
> >>   [javadoc] Generating Javadoc
> >>   [javadoc] Javadoc execution
> >>   [javadoc]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
> >> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
> >> warning - @return tag has no arguments.
> >>   [javadoc] 1 warning
> >> jars:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> 1.1.1.jar
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> >> dashboard-1.1.1.jar
> >> rdfagent-init:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> >> jar-rdfagent:
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>      [copy] Copying 95 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>    [delete] Deleting directory
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> >> war:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
> >> he
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
> >>       [war] Building war:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
> >> oby.war
> >> wardist:
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> >> bindist-rdfagent:
> >>    [delete] Deleting directory
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 96 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
> >> b
> >>      [copy] Copying 1 file to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 1 file to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 6 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>       [tar] Building tar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-
> 2010-
> >> 05-26.tar.gz
> >>       [zip] Building zip:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-
> 2010-
> >> 05-26.zip
> >> all:
> >> BUILD SUCCESSFUL
> >>
> >>
> >>
> >> ant dashboard :
> >> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> >> checkmaven:
> >> initmaven:
> >> init:
> >> config:
> >> compile:
> >> moses-init:
> >> samples-init:
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
> >> ources
> >> dashboard-init:
> >> dashboard-config:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
> >> config.jar
> >> dashboard:
> >> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> >> The following error occurred while executing this line:
> >> [Dashboard]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >> [Dashboard]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >>
> >>
> >> Dashboard console :
> >> Selected authorities:
> >>     avilin05.avignon.inra.fr
> >>
> >> -find-services:
> >> [Services names]
> >>
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
> >>
> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
> >>
> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
> >> _getExperimentType,Solstis_getDatasetFromExp
> >>
> >> compile-datatypes:
> >>     [javac] Compiling 1796 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
> >>
> >> compile-services:
> >>     [javac] Compiling 21 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
> >>
> >> jar-datatypes:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> >> datatypes.jar
> >>
> >> jar-services:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> >> skeletons.jar
> >>
> >> deploy-remote:
> >>     [mkdir] Created dir:
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26
> >>
> >> create-wsdd:
> >> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getTrait.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getAuthor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExperiment.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getProject.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getFactor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> BUILD FAILED
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >>
> >> Thanks,
> >>
> >> Elise.
> >>
> >>
> >>
> >>
> >>
> >>
> >> Edward Kawas wrote:
> >>
> >>> Hi Elise,
> >>>
> >>> Did you make sure to generate the skeletons and their implementations
> >>>
> >> first?
> >>
> >>> Hard to say what the problem is without knowing what you did to get
> >>>
> > here.
> >
> >>> Eddie
> >>>
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >>>> Sent: Wednesday, May 26, 2010 2:03 AM
> >>>> To: moby-dev at lists.open-bio.org
> >>>> Subject: [MOBY-dev] moby services deployment
> >>>>
> >>>> Hi !
> >>>>
> >>>> When I want to deploy moby services by ant dashboard on remote
> >>>> machine, I meet this problem :
> >>>>
> >>>> The following error occurred while executing this line:
> >>>>
> >>>>
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >>
> >>>> The following error occurred while executing this line:
> >>>>
> >>>>
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >>
> >>>> Property 'service.jar' is not defined.
> >>>>
> >>>> What can I do for resolving this problem ?
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Elise Larsonneur
> >>>> Bioinformatics trainee.
> >>>> UR GAFL
> >>>> INRA Avignon
> >>>> France
> >>>>
> >>>> _______________________________________________
> >>>> MOBY-dev mailing list
> >>>> MOBY-dev at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>>
> >>>>
> >>> _______________________________________________
> >>> MOBY-dev mailing list
> >>> MOBY-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>
> >>>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From Elise.Larsonneur at avignon.inra.fr  Wed May 26 04:14:29 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 10:14:29 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFCD865.4050903@avignon.inra.fr>

Hi !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France



From gllambi at fing.edu.uy  Sat May  1 21:12:23 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Sat, 01 May 2010 18:12:23 -0300
Subject: [MOBY-dev] Format Example
In-Reply-To: <003f01cae891$aa594700$ff0bd500$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
	<003f01cae891$aa594700$ff0bd500$@gmail.com>
Message-ID: <20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>

Hi Eddie!

Thanks a lot for both tutorials! I looked at them and if I have some  
trouble, take for sure I'll write here again. With this quick help,  
who won't ;)

Best regards
Guzman

Edward Kawas <edward.kawas at gmail.com> escribi?:

> Hi Guzman,
>
> There are a few tutorials for using moby with Taverna. There is this one
> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
> ndex.html), and while it refers to an older version of taverna, it should be
> relevant.
>
> Also, there is a power point presentation hosted @
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
> Taverna_Tutorial.ppt
>
> If these resources don't help, or if you have more questions, please do not
> hesitate to ask them here!
>
> Eddie
>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
>> Sent: Friday, April 30, 2010 8:28 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] Format Example
>>
>> Hi!
>>
>> First of all, sorry in advance if this is a very stupid question, but I'm
> new with
>> BioMoby.
>>
>> I've been searching in myexperiment website for a format example
>> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
>> example where you have things in Fasta, GFF, Genbank or any other format
>> and take advantage of the bioMoby friendly format features to make format
>> unaware.
>>
>> Does anybody knows a workflow example of this? or maybe I understood
>> wrong the objetives of BioMoby
>>
>> Best Regards
>> Guzman
>>
>> ----------------------------------------
>> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
>> URUGUAY
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY



From gllambi at fing.edu.uy  Sat May  1 21:13:46 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Sat, 01 May 2010 18:13:46 -0300
Subject: [MOBY-dev] Format Example
In-Reply-To: <op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>
References: <E1O7wea-0002hB-00@phoebus>
	<op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <20100501181346.16481gy1bipvqdgk@www.fing.edu.uy>

Hi Mark, Alan,

which tutorial you are talking about? Do you have some extra material  
I can use besides the one Eddie sent to me?

Thanks
Guzman

Mark Wilkinson <markw at illuminae.com> escribi?:

> Confirmed!  Thank you!
>
> Mark
>
>
>
> On Fri, 30 Apr 2010 13:17:40 -0700, Alan R Williams  
> <alanrw at cs.man.ac.uk> wrote:
>
>> Mark,
>>
>> The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
>> plugin.  It should show up under the standard plugins menu.
>>
>> Alan
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC, Canada
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY



From edward.kawas at gmail.com  Mon May  3 17:52:37 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 3 May 2010 10:52:37 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>
	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
Message-ID: <003a01caeae9$6e776b40$4b6641c0$@gmail.com>

Hello Again!

I updated the 'End user BioMOBY Applications' page on biomoby.org to reflect our most recent update to the taverna tutorial [1].

I am not sure if you (Guzman) have seen this already, but if you haven?t, I hope it helps!

Thanks,

Eddie

[1] http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna


> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> Sent: Saturday, May 01, 2010 2:12 PM
> To: moby-dev at lists.open-bio.org
> Subject: Re: [MOBY-dev] Format Example
> 
> Hi Eddie!
> 
> Thanks a lot for both tutorials! I looked at them and if I have some trouble,
> take for sure I'll write here again. With this quick help, who won't ;)
> 
> Best regards
> Guzman
> 
> Edward Kawas <edward.kawas at gmail.com> escribi?:
> 
> > Hi Guzman,
> >
> > There are a few tutorials for using moby with Taverna. There is this
> > one
> > (http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/taverna/g
> > uide/i ndex.html), and while it refers to an older version of taverna,
> > it should be relevant.
> >
> > Also, there is a power point presentation hosted @
> >
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMo
> b
> > y_and_
> > Taverna_Tutorial.ppt
> >
> > If these resources don't help, or if you have more questions, please
> > do not hesitate to ask them here!
> >
> > Eddie
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> >> Sent: Friday, April 30, 2010 8:28 AM
> >> To: moby-dev at lists.open-bio.org
> >> Subject: [MOBY-dev] Format Example
> >>
> >> Hi!
> >>
> >> First of all, sorry in advance if this is a very stupid question, but
> >> I'm
> > new with
> >> BioMoby.
> >>
> >> I've been searching in myexperiment website for a format example
> >> workflow using bioMoby, but I couldn't find anyone. I'm looking for
> >> an example where you have things in Fasta, GFF, Genbank or any other
> >> format and take advantage of the bioMoby friendly format features to
> >> make format unaware.
> >>
> >> Does anybody knows a workflow example of this? or maybe I understood
> >> wrong the objetives of BioMoby
> >>
> >> Best Regards
> >> Guzman
> >>
> >> ----------------------------------------
> >> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR
> >> - URUGUAY
> >>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> 
> 
> ----------------------------------------
> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
> URUGUAY
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From alanrw at cs.man.ac.uk  Tue May  4 08:31:11 2010
From: alanrw at cs.man.ac.uk (Alan Williams)
Date: Tue, 04 May 2010 09:31:11 +0100
Subject: [MOBY-dev] Format Example
In-Reply-To: <003a01caeae9$6e776b40$4b6641c0$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy>
	<003a01caeae9$6e776b40$4b6641c0$@gmail.com>
Message-ID: <4BDFDB4F.9040805@cs.man.ac.uk>

Edward Kawas wrote:
> Hello Again!

Hello

> I updated the 'End user BioMOBY Applications' page on biomoby.org to
> reflect our most recent update to the taverna tutorial [1].

The links for the User Applications don't work for me.

> I am not sure if you (Guzman) have seen this already, but if you
> haven?t, I hope it helps!
> 
> Thanks,
> 
> Eddie

Alan

> [1]
> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna


From gllambi at fing.edu.uy  Tue May  4 12:36:03 2010
From: gllambi at fing.edu.uy (=?utf-8?Q?Guzm=C3=A1n_Llamb=C3=ADas_-_INCO?=)
Date: Tue, 4 May 2010 09:36:03 -0300
Subject: [MOBY-dev] Format Example
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy><003a01caeae9$6e776b40$4b6641c0$@gmail.com>
	<4BDFDB4F.9040805@cs.man.ac.uk>
Message-ID: <CB082CD4D5C045D1AECD71C795A7AC8E@fing.edu.uy>

Hello Eddie,

I'm having the same problem Alan had. Is the link correct?

Regards
Guzm?n

----- Original Message ----- 
From: "Alan Williams" <alanrw at cs.man.ac.uk>
To: "Core developer announcements" <moby-dev at lists.open-bio.org>
Sent: Tuesday, May 04, 2010 5:31 AM
Subject: Re: [MOBY-dev] Format Example


> Edward Kawas wrote:
>> Hello Again!
>
> Hello
>
>> I updated the 'End user BioMOBY Applications' page on biomoby.org to
>> reflect our most recent update to the taverna tutorial [1].
>
> The links for the User Applications don't work for me.
>
>> I am not sure if you (Guzman) have seen this already, but if you
>> haven?t, I hope it helps!
>>
>> Thanks,
>>
>> Eddie
>
> Alan
>
>> [1]
>> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 



From gllambi at fing.edu.uy  Tue May  4 12:46:36 2010
From: gllambi at fing.edu.uy (=?utf-8?Q?Guzm=C3=A1n_Llamb=C3=ADas_-_INCO?=)
Date: Tue, 4 May 2010 09:46:36 -0300
Subject: [MOBY-dev] Format Example
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>	<003f01cae891$aa594700$ff0bd500$@gmail.com>	<20100501181223.11842ka95jxxd0mc@www.fing.edu.uy><003a01caeae9$6e776b40$4b6641c0$@gmail.com><4BDFDB4F.9040805@cs.man.ac.uk>
	<CB082CD4D5C045D1AECD71C795A7AC8E@fing.edu.uy>
Message-ID: <F6F5657CA4BA4A478C7FD18302B29BE7@fing.edu.uy>

Now is working, sorry for the noise

Regards
Guzman
----- Original Message ----- 
From: "Guzm?n Llamb?as - INCO" <gllambi at fing.edu.uy>
To: "Core developer announcements" <moby-dev at lists.open-bio.org>
Sent: Tuesday, May 04, 2010 9:36 AM
Subject: Re: [MOBY-dev] Format Example


> Hello Eddie,
>
> I'm having the same problem Alan had. Is the link correct?
>
> Regards
> Guzm?n
>
> ----- Original Message ----- 
> From: "Alan Williams" <alanrw at cs.man.ac.uk>
> To: "Core developer announcements" <moby-dev at lists.open-bio.org>
> Sent: Tuesday, May 04, 2010 5:31 AM
> Subject: Re: [MOBY-dev] Format Example
>
>
>> Edward Kawas wrote:
>>> Hello Again!
>>
>> Hello
>>
>>> I updated the 'End user BioMOBY Applications' page on biomoby.org to
>>> reflect our most recent update to the taverna tutorial [1].
>>
>> The links for the User Applications don't work for me.
>>
>>> I am not sure if you (Guzman) have seen this already, but if you
>>> haven?t, I hope it helps!
>>>
>>> Thanks,
>>>
>>> Eddie
>>
>> Alan
>>
>>> [1]
>>> http://biomoby.open-bio.org/index.php/browser_clients/end-user-biomoby-applications/#taverna
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 



From py at pingoured.fr  Mon May 10 08:13:42 2010
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Mon, 10 May 2010 10:13:42 +0200
Subject: [MOBY-dev] cvs down?
Message-ID: <1273479222.2580.48.camel@cyan.pingoured.fr>

Hi,

I am trying to retrieve the sources of jMoby from the cvs but it seems
to not be reachable (either by [1] or via eclipse).

Is it me ?

Regards,

Pierre

[1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby



From sneumann at ipb-halle.de  Mon May 10 08:37:13 2010
From: sneumann at ipb-halle.de (Steffen Neumann)
Date: Mon, 10 May 2010 10:37:13 +0200
Subject: [MOBY-dev] cvs down?
In-Reply-To: <1273479222.2580.48.camel@cyan.pingoured.fr>
References: <1273479222.2580.48.camel@cyan.pingoured.fr>
Message-ID: <assp.5746a99b8d.1273480633.3175.30.camel@paddy>

On Mon, 2010-05-10 at 10:13 +0200, Pierre-Yves Chibon wrote:
> Hi,
> 
> I am trying to retrieve the sources of jMoby from the cvs but it seems
> to not be reachable (either by [1] or via eclipse).

I also get an (61) Connection refused. 

> Is it me ?
For these cases, you could also try services like
http://downforeveryoneorjustme.com/

Yours,
Steffen

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409



From Richard.Finkers at wur.nl  Mon May 10 09:03:33 2010
From: Richard.Finkers at wur.nl (Richard Finkers)
Date: Mon, 10 May 2010 11:03:33 +0200
Subject: [MOBY-dev] cvs down?
In-Reply-To: <1273479222.2580.48.camel@cyan.pingoured.fr>
References: <1273479222.2580.48.camel@cyan.pingoured.fr>
Message-ID: <4BE7CBE5.2060200@wur.nl>

no problem from Wageningen.

Pierre-Yves Chibon wrote:
> Hi,
>
> I am trying to retrieve the sources of jMoby from the cvs but it seems
> to not be reachable (either by [1] or via eclipse).
>
> Is it me ?
>
> Regards,
>
> Pierre
>
> [1] http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>   


-- 
Dr. Richard Finkers
Researcher Plant Breeding
Wageningen UR Plant Breeding
P.O. Box 16, 6700 AA, Wageningen, The Netherlands
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB
Wageningen, The Netherlands
Tel. +31-317-484165 Fax +31-317-418094
http://www.plantbreeding.wur.nl/ <http://www.plantbreeding.wur.nl>
https://www.eu-sol.wur.nl/ <https://www.eu-sol.wur.nl>
https://cbsgdbase.wur.nl/ <https://cbsgdbase.wur.nl>
http://solgenomics.wur.nl/ <http://solgenomics.wur.nl>
http://www.disclaimer-uk.wur.nl/



From Dominique.Jeannin at avignon.inra.fr  Mon May 17 15:18:19 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Mon, 17 May 2010 17:18:19 +0200
Subject: [MOBY-dev] Error in CVS source
Message-ID: <4BF15E3B.8080301@avignon.inra.fr>

Hi,

We've just downloaded source code of jMoby by CVS but when I launch "ant 
install" (from ant view in eclipse), I get this log :

compile:
   [javac] Compiling 392 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
package foxtrot does not exist
   [javac] import foxtrot.Task; // for fancy synchronous GUI handling on 
data paste to external apps
   [javac]               ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
package foxtrot does not exist
   [javac] import foxtrot.Worker;
   [javac]               ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
cannot find symbol
   [javac] symbol  : class Task
   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
   [javac]                 targetTextType = (String) Worker.post(new 
Task(){
   [javac]                                                           ^
   [javac] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
cannot find symbol
   [javac] symbol  : variable Worker
   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
   [javac]                 targetTextType = (String) Worker.post(new 
Task(){
   [javac]                                           ^
   [javac] Note: 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
uses or overrides a deprecated API.
   [javac] Note: Recompile with -Xlint:deprecation for details.
   [javac] Note: Some input files use unchecked or unsafe operations.
   [javac] Note: Recompile with -Xlint:unchecked for details.
   [javac] 4 errors

BUILD FAILED

What's wrong ?
Thanks for your help,

-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)



From gordonp at ucalgary.ca  Mon May 17 15:45:38 2010
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 17 May 2010 09:45:38 -0600
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF15E3B.8080301@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr>
Message-ID: <4BF164A2.6090502@ucalgary.ca>

Sorry, my bad.  I forgot to commit the project POM file update.  Fixing 
that now.

Dominique Jeannin wrote:
> Hi,
>
> We've just downloaded source code of jMoby by CVS but when I launch 
> "ant install" (from ant view in eclipse), I get this log :
>
> compile:
>   [javac] Compiling 392 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
> package foxtrot does not exist
>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
> on data paste to external apps
>   [javac]               ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
> package foxtrot does not exist
>   [javac] import foxtrot.Worker;
>   [javac]               ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
> cannot find symbol
>   [javac] symbol  : class Task
>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>   [javac]                 targetTextType = (String) Worker.post(new 
> Task(){
>   [javac]                                                           ^
>   [javac] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
> cannot find symbol
>   [javac] symbol  : variable Worker
>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>   [javac]                 targetTextType = (String) Worker.post(new 
> Task(){
>   [javac]                                           ^
>   [javac] Note: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
> uses or overrides a deprecated API.
>   [javac] Note: Recompile with -Xlint:deprecation for details.
>   [javac] Note: Some input files use unchecked or unsafe operations.
>   [javac] Note: Recompile with -Xlint:unchecked for details.
>   [javac] 4 errors
>
> BUILD FAILED
>
> What's wrong ?
> Thanks for your help,
>


From Dominique.Jeannin at avignon.inra.fr  Tue May 18 07:30:40 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Tue, 18 May 2010 09:30:40 +0200
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF164A2.6090502@ucalgary.ca>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
Message-ID: <4BF24220.6050600@avignon.inra.fr>

Paul Gordon a ?crit :
> Sorry, my bad.  I forgot to commit the project POM file update.  
> Fixing that now.
>
> Dominique Jeannin wrote:
>> Hi,
>>
>> We've just downloaded source code of jMoby by CVS but when I launch 
>> "ant install" (from ant view in eclipse), I get this log :
>>
>> compile:
>>   [javac] Compiling 392 source files to 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>> package foxtrot does not exist
>>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
>> on data paste to external apps
>>   [javac]               ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>> package foxtrot does not exist
>>   [javac] import foxtrot.Worker;
>>   [javac]               ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>> cannot find symbol
>>   [javac] symbol  : class Task
>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>   [javac]                 targetTextType = (String) Worker.post(new 
>> Task(){
>>   [javac]                                                           ^
>>   [javac] 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>> cannot find symbol
>>   [javac] symbol  : variable Worker
>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>   [javac]                 targetTextType = (String) Worker.post(new 
>> Task(){
>>   [javac]                                           ^
>>   [javac] Note: 
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>> uses or overrides a deprecated API.
>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>   [javac] 4 errors
>>
>> BUILD FAILED
>>
>> What's wrong ?
>> Thanks for your help,
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
Thanks for the update, but we don't get this update because the server 
(cvs.open-bio.org) does not response (since yesterday about 7:00 pm in 
France).

-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)



From gordonp at ucalgary.ca  Tue May 18 13:53:17 2010
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Tue, 18 May 2010 07:53:17 -0600
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF24220.6050600@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
	<4BF24220.6050600@avignon.inra.fr>
Message-ID: <4BF29BCD.2060903@ucalgary.ca>

Hi Dominique,

In the interim, the following lines need to be added to the 
xmls/project.pom file:

   <dependency>
      <groupId>foxtrot</groupId>
      <artifactId>foxtrot</artifactId>
      <version>2.0</version>
    </dependency>

Cheers,

Paul

Dominique Jeannin wrote:
> Paul Gordon a ?crit :
>> Sorry, my bad.  I forgot to commit the project POM file update.  
>> Fixing that now.
>>
>> Dominique Jeannin wrote:
>>> Hi,
>>>
>>> We've just downloaded source code of jMoby by CVS but when I launch 
>>> "ant install" (from ant view in eclipse), I get this log :
>>>
>>> compile:
>>>   [javac] Compiling 392 source files to 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>>> package foxtrot does not exist
>>>   [javac] import foxtrot.Task; // for fancy synchronous GUI handling 
>>> on data paste to external apps
>>>   [javac]               ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>>> package foxtrot does not exist
>>>   [javac] import foxtrot.Worker;
>>>   [javac]               ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>> cannot find symbol
>>>   [javac] symbol  : class Task
>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>> Task(){
>>>   [javac]                                                           ^
>>>   [javac] 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>> cannot find symbol
>>>   [javac] symbol  : variable Worker
>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>> Task(){
>>>   [javac]                                           ^
>>>   [javac] Note: 
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>>> uses or overrides a deprecated API.
>>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>>   [javac] 4 errors
>>>
>>> BUILD FAILED
>>>
>>> What's wrong ?
>>> Thanks for your help,
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
> Thanks for the update, but we don't get this update because the server 
> (cvs.open-bio.org) does not response (since yesterday about 7:00 pm in 
> France).
>


From edward.kawas at gmail.com  Tue May 18 14:04:47 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 18 May 2010 07:04:47 -0700
Subject: [MOBY-dev] publications
Message-ID: <003901caf693$1553a870$3ffaf950$@gmail.com>

Hello All,

 

I am updating the Publication & Press[1] page of the Biomoby.org page and I
was wondering if there were any relevant articles that I may have missed? If
so, please send them my way so that I can add them to the page.

 

Thanks,

 

Eddie

 

[1] http://biomoby.open-bio.org/index.php/what-is-moby/publications

 



From markw at illuminae.com  Tue May 18 14:00:24 2010
From: markw at illuminae.com (Mark)
Date: Tue, 18 May 2010 07:00:24 -0700
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF24220.6050600@avignon.inra.fr>
References: <4BF15E3B.8080301@avignon.inra.fr> <4BF164A2.6090502@ucalgary.ca>
	<4BF24220.6050600@avignon.inra.fr>
Message-ID: <op.vcwmiydmdeqt07@bighome>


> Thanks for the update, but we don't get this update because the server
> (cvs.open-bio.org) does not response (since yesterday about 7:00 pm in
> France).



I've submitted a ticket to the open-bio roots.  Hopefully it will be back  
soon!

M


From markw at illuminae.com  Tue May 18 14:56:04 2010
From: markw at illuminae.com (Mark)
Date: Tue, 18 May 2010 07:56:04 -0700
Subject: [MOBY-dev] publications
In-Reply-To: <003901caf693$1553a870$3ffaf950$@gmail.com>
References: <003901caf693$1553a870$3ffaf950$@gmail.com>
Message-ID: <op.vcwo3qczdeqt07@bighome>

LOL!  Hey Eddie, perhaps be a LITTLE bit more modest on the main link :-)

how about "To cite the BioMoby project, please cite THIS paper", and give  
the full reference so that people can copy/paste it into their  
bibliographies.

cheers!

M


On Tue, 18 May 2010 07:04:47 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:

> Hello All,
>
>
> I am updating the Publication & Press[1] page of the Biomoby.org page  
> and I
> was wondering if there were any relevant articles that I may have  
> missed? If
> so, please send them my way so that I can add them to the page.
>
>
> Thanks,
>
>
> Eddie
>
>
> [1] http://biomoby.open-bio.org/index.php/what-is-moby/publications
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Using Opera's revolutionary e-mail client: http://www.opera.com/mail/


From Dominique.Jeannin at avignon.inra.fr  Tue May 18 14:59:46 2010
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Tue, 18 May 2010 16:59:46 +0200
Subject: [MOBY-dev] Error in CVS source
In-Reply-To: <4BF29BCD.2060903@ucalgary.ca>
References: <4BF15E3B.8080301@avignon.inra.fr>
	<4BF164A2.6090502@ucalgary.ca>	<4BF24220.6050600@avignon.inra.fr>
	<4BF29BCD.2060903@ucalgary.ca>
Message-ID: <4BF2AB62.10408@avignon.inra.fr>

Paul,

The problem is solved :)
Thank you !

Dominique

Paul Gordon a ?crit :
> Hi Dominique,
>
> In the interim, the following lines need to be added to the 
> xmls/project.pom file:
>
>   <dependency>
>      <groupId>foxtrot</groupId>
>      <artifactId>foxtrot</artifactId>
>      <version>2.0</version>
>    </dependency>
>
> Cheers,
>
> Paul
>
> Dominique Jeannin wrote:
>> Paul Gordon a ?crit :
>>> Sorry, my bad.  I forgot to commit the project POM file update.  
>>> Fixing that now.
>>>
>>> Dominique Jeannin wrote:
>>>> Hi,
>>>>
>>>> We've just downloaded source code of jMoby by CVS but when I launch 
>>>> "ant install" (from ant view in eclipse), I get this log :
>>>>
>>>> compile:
>>>>   [javac] Compiling 392 source files to 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:9: 
>>>> package foxtrot does not exist
>>>>   [javac] import foxtrot.Task; // for fancy synchronous GUI 
>>>> handling on data paste to external apps
>>>>   [javac]               ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:10: 
>>>> package foxtrot does not exist
>>>>   [javac] import foxtrot.Worker;
>>>>   [javac]               ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>>> cannot find symbol
>>>>   [javac] symbol  : class Task
>>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>>> Task(){
>>>>   [javac]                                                           ^
>>>>   [javac] 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/seahawk/gui/SeahawkTransferable.java:104: 
>>>> cannot find symbol
>>>>   [javac] symbol  : variable Worker
>>>>   [javac] location: class ca.ucalgary.seahawk.gui.SeahawkTransferable
>>>>   [javac]                 targetTextType = (String) Worker.post(new 
>>>> Task(){
>>>>   [javac]                                           ^
>>>>   [javac] Note: 
>>>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
>>>> uses or overrides a deprecated API.
>>>>   [javac] Note: Recompile with -Xlint:deprecation for details.
>>>>   [javac] Note: Some input files use unchecked or unsafe operations.
>>>>   [javac] Note: Recompile with -Xlint:unchecked for details.
>>>>   [javac] 4 errors
>>>>
>>>> BUILD FAILED
>>>>
>>>> What's wrong ?
>>>> Thanks for your help,
>>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>> Thanks for the update, but we don't get this update because the 
>> server (cvs.open-bio.org) does not response (since yesterday about 
>> 7:00 pm in France).
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
-- 
Dominique Jeannin

Bioinformatique
INRA, Institut National de la Recherche Agronomique
Centre d'Avignon
UR 1052, GAFL - Unit? de G?n?tique et Am?lioration des Fruits et L?gumes
BP 94 - 84143 MONTFAVET CEDEX (France)



From Elise.Larsonneur at avignon.inra.fr  Wed May 26 09:03:10 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 11:03:10 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFCE3CE.4060504@avignon.inra.fr>

Hi !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France



From Elise.Larsonneur at avignon.inra.fr  Wed May 26 11:21:50 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 13:21:50 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFD044E.8040305@avignon.inra.fr>

Hello !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France


From edward.kawas at gmail.com  Wed May 26 13:29:30 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 26 May 2010 06:29:30 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFCE3CE.4060504@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>
Message-ID: <002401cafcd7$79cb3850$6d61a8f0$@gmail.com>

Hi Elise,

Did you make sure to generate the skeletons and their implementations first?
Hard to say what the problem is without knowing what you did to get here.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Wednesday, May 26, 2010 2:03 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] moby services deployment
> 
> Hi !
> 
> When I want to deploy moby services by ant dashboard on remote machine,
> I meet this problem :
> 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> What can I do for resolving this problem ?
> 
> Thanks,
> 
> Elise Larsonneur
> Bioinformatics trainee.
> UR GAFL
> INRA Avignon
> France
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From Elise.Larsonneur at avignon.inra.fr  Wed May 26 14:35:52 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 16:35:52 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
References: <4BFCE3CE.4060504@avignon.inra.fr>
	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
Message-ID: <4BFD31C8.1070008@avignon.inra.fr>

Before deploying webservices , I generated datatypes and skeletons in 
jMoby with the dashboard. Then, I wrote the implementations of skeletons 
in another project associated to jMoby.
So, after ant all, ant dashboard, when I launchs the deployment (after 
ant all) of these webservices (on remote or local machine) , only the 
wsdd files are created and the previous error displays.
I used a pattern for implementation class names in the Moses Generator 
Panel.

eclipse console : ant all :
Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
cleanapi:
clean:
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build
checkmaven:
initmaven:
init:
    [mkdir] Created dir: /home/av07/gafl/elarsonneur/workspace/jMoby/build
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/run
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/test
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
config:
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
     [copy] Copying 27 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/run
     [copy] Copying 10 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
     [copy] Copying 24 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
     [copy] Copying 163 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
compile:
    [javac] Compiling 392 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
    [javac] Note: 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
uses or overrides a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] Compiling 26 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
docs:
  [javadoc] Generating Javadoc
  [javadoc] Javadoc execution
  [javadoc] 
/home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: 
warning - @return tag has no arguments.
  [javadoc] 1 warning
jars:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-dashboard-1.1.1.jar
rdfagent-init:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
jar-rdfagent:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
     [copy] Copying 95 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
war:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cache
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
      [war] Building war: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jmoby.war
wardist:
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
bindist-rdfagent:
   [delete] Deleting directory 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 96 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/lib
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 1 file to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
     [copy] Copying 6 files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
      [tar] Building tar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.tar.gz
      [zip] Building zip: 
/home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.zip
all:
BUILD SUCCESSFUL



ant dashboard :
Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
checkmaven:
initmaven:
init:
config:
compile:
moses-init:
samples-init:
    [mkdir] Created dir: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/resources
dashboard-init:
dashboard-config:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-config.jar
dashboard:
[Dashboard] 144276 [Thread-49] ERROR SimpleAnt - 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
The following error occurred while executing this line:
[Dashboard] 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
[Dashboard] 
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.



Dashboard console :
Selected authorities:
    avilin05.avignon.inra.fr

-find-services:
[Services names] 
Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_getExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperimentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis_getExperimentType,Solstis_getDatasetFromExp

compile-datatypes:
    [javac] Compiling 1796 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes

compile-services:
    [javac] Compiling 21 source files to 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons

jar-datatypes:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar

jar-services:
      [jar] Building jar: 
/home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-skeletons.jar

deploy-remote:
    [mkdir] Created dir: 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26

create-wsdd:
[Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getTrait.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getAuthor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExperiment.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExpFromDataset.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getProject.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getExperimentDesc.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

create-wsdd:
[Create Solstis_getFactor.wsdd] Copying 1 file to 
/tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd

BUILD FAILED
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.


Thanks,

Elise.






Edward Kawas wrote:
> Hi Elise,
>
> Did you make sure to generate the skeletons and their implementations first?
> Hard to say what the problem is without knowing what you did to get here.
>
> Eddie
>
>   
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>> Sent: Wednesday, May 26, 2010 2:03 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] moby services deployment
>>
>> Hi !
>>
>> When I want to deploy moby services by ant dashboard on remote machine,
>> I meet this problem :
>>
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>> What can I do for resolving this problem ?
>>
>> Thanks,
>>
>> Elise Larsonneur
>> Bioinformatics trainee.
>> UR GAFL
>> INRA Avignon
>> France
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>   



From Elise.Larsonneur at avignon.inra.fr  Wed May 26 14:51:36 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 16:51:36 +0200
Subject: [MOBY-dev] cvs repository of Biomoby
Message-ID: <4BFD3578.7040706@avignon.inra.fr>

Hi !

I used eclipse and since two weeks , I can't access to cvs repository of 
jMoby in France for updating : "cvs.open-bio.org:/home/repository/moby ".
Is there a new repository ?

Thanks,

Elise Larsonneur
Bioinformatics trainee
UR GAFL
INRA Avignon
France


From markw at illuminae.com  Wed May 26 21:09:34 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 26 May 2010 14:09:34 -0700
Subject: [MOBY-dev] cvs repository of Biomoby
In-Reply-To: <4BFD3578.7040706@avignon.inra.fr>
References: <4BFD3578.7040706@avignon.inra.fr>
Message-ID: <op.vdbzp8uhnbznux@dd0710001l.icapture.ubc.ca>

I've submitted another ticket to the open-bio root list.  The CVS has been  
unstable for many months, and it's getting a bit frustrating!!

Mark



On Wed, 26 May 2010 07:51:36 -0700, Elise Larsonneur  
<Elise.Larsonneur at avignon.inra.fr> wrote:

> Hi !
>
> I used eclipse and since two weeks , I can't access to cvs repository of  
> jMoby in France for updating : "cvs.open-bio.org:/home/repository/moby ".
> Is there a new repository ?
>
> Thanks,
>
> Elise Larsonneur
> Bioinformatics trainee
> UR GAFL
> INRA Avignon
> France
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From Elise.Larsonneur at avignon.inra.fr  Thu May 27 08:18:33 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Thu, 27 May 2010 10:18:33 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFD31C8.1070008@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
	<4BFD31C8.1070008@avignon.inra.fr>
Message-ID: <4BFE2AD9.80300@avignon.inra.fr>

Hello !

I forgot to specify that I use a Tomcat 5.5.1 server.

Thanks

Elise.




Elise Larsonneur wrote:
> Before deploying webservices , I generated datatypes and skeletons in 
> jMoby with the dashboard. Then, I wrote the implementations of 
> skeletons in another project associated to jMoby.
> So, after ant all, ant dashboard, when I launchs the deployment of 
> these webservices (on remote or local machine) , only the wsdd files 
> are created and the previous error displays.
> I used a pattern for implementation class names in the Moses Generator 
> Panel.
>
> eclipse console : ant all :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> cleanapi:
> clean:
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> checkmaven:
> initmaven:
> init:
>    [mkdir] Created dir: /home/av07/gafl/elarsonneur/workspace/jMoby/build
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> config:
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [copy] Copying 27 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>     [copy] Copying 10 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>     [copy] Copying 24 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>     [copy] Copying 163 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> compile:
>    [javac] Compiling 392 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>    [javac] Note: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/services/util/PBERecorder.java 
> uses or overrides a deprecated API.
>    [javac] Note: Recompile with -Xlint:deprecation for details.
>    [javac] Note: Some input files use unchecked or unsafe operations.
>    [javac] Note: Recompile with -Xlint:unchecked for details.
>    [javac] Compiling 26 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> docs:
>  [javadoc] Generating Javadoc
>  [javadoc] Javadoc execution
>  [javadoc] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomoby/central/gui/model/MobyObjectPropertiesTableModel.java:72: 
> warning - @return tag has no arguments.
>  [javadoc] 1 warning
> jars:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-dashboard-1.1.1.jar 
>
> rdfagent-init:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> jar-rdfagent:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>     [copy] Copying 95 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> war:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cache
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>      [war] Building war: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jmoby.war
> wardist:
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> bindist-rdfagent:
>   [delete] Deleting directory 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 96 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/lib
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 1 file to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>     [copy] Copying 6 files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [tar] Building tar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.tar.gz 
>
>      [zip] Building zip: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-05-26.zip 
>
> all:
> BUILD SUCCESSFUL
>
>
>
> ant dashboard :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> checkmaven:
> initmaven:
> init:
> config:
> compile:
> moses-init:
> samples-init:
>    [mkdir] Created dir: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/resources 
>
> dashboard-init:
> dashboard-config:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-config.jar 
>
> dashboard:
> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt - 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
> The following error occurred while executing this line:
> [Dashboard] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
> The following error occurred while executing this line:
> [Dashboard] 
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
> Property 'service.jar' is not defined.
>
>
>
> Dashboard console :
> Selected authorities:
>    avilin05.avignon.inra.fr
>
> -find-services:
> [Services names] 
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_getExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperimentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis_getExperimentType,Solstis_getDatasetFromExp 
>
>
> compile-datatypes:
>    [javac] Compiling 1796 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
>
> compile-services:
>    [javac] Compiling 21 source files to 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
>
> jar-datatypes:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-datatypes.jar 
>
>
> jar-services:
>      [jar] Building jar: 
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-skeletons.jar 
>
>
> deploy-remote:
>    [mkdir] Created dir: 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26 
>
>
> create-wsdd:
> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getTrait.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getAuthor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExperiment.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getProject.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> create-wsdd:
> [Create Solstis_getFactor.wsdd] Copying 1 file to 
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-wsdd 
>
>
> BUILD FAILED
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306: 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
> Property 'service.jar' is not defined.
>
>
> Thanks,
>
> Elise.
>
>
>
>
>
>
> Edward Kawas wrote:
>> Hi Elise,
>>
>> Did you make sure to generate the skeletons and their implementations 
>> first?
>> Hard to say what the problem is without knowing what you did to get 
>> here.
>>
>> Eddie
>>
>>  
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>>> Sent: Wednesday, May 26, 2010 2:03 AM
>>> To: moby-dev at lists.open-bio.org
>>> Subject: [MOBY-dev] moby services deployment
>>>
>>> Hi !
>>>
>>> When I want to deploy moby services by ant dashboard on remote machine,
>>> I meet this problem :
>>>
>>> The following error occurred while executing this line:
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>>> The following error occurred while executing this line:
>>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>>> Property 'service.jar' is not defined.
>>>
>>> What can I do for resolving this problem ?
>>>
>>> Thanks,
>>>
>>> Elise Larsonneur
>>> Bioinformatics trainee.
>>> UR GAFL
>>> INRA Avignon
>>> France
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>     
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>   
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Thu May 27 12:48:42 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 27 May 2010 05:48:42 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFD31C8.1070008@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>
	<4BFD31C8.1070008@avignon.inra.fr>
Message-ID: <004101cafd9a$f1273570$d375a050$@gmail.com>

Hi Elise,

I cannot replicate your problem, so maybe I can help point you in the right
direction. 

[1]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopme
nt.html
[2]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators
.html 
[3]
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-deploy.htm
l

I think that you may have seen some of these resources, judging by how far
you have gotten, but I think it would be a good idea to read over them. The
one thing that caught my eye is that when you did 'ant all', lots of
unrelated service tasks were executed. If you look at resource [1] and read
'Step 1: What is needed' 'ant all' is done from within your service project
and not from the root moby-live/Java folder.

Let me know if this was a good enough push!

Thanks,

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Wednesday, May 26, 2010 7:36 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] moby services deployment
> 
> Before deploying webservices , I generated datatypes and skeletons in
> jMoby with the dashboard. Then, I wrote the implementations of skeletons
> in another project associated to jMoby.
> So, after ant all, ant dashboard, when I launchs the deployment (after ant
all)
> of these webservices (on remote or local machine) , only the wsdd files
are
> created and the previous error displays.
> I used a pattern for implementation class names in the Moses Generator
> Panel.
> 
> eclipse console : ant all :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> cleanapi:
> clean:
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> checkmaven:
> initmaven:
> init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> config:
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>      [copy] Copying 27 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>      [copy] Copying 10 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>      [copy] Copying 24 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>      [copy] Copying 163 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> compile:
>     [javac] Compiling 392 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>     [javac] Note:
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
> ices/util/PBERecorder.java
> uses or overrides a deprecated API.
>     [javac] Note: Recompile with -Xlint:deprecation for details.
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] Compiling 26 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> docs:
>   [javadoc] Generating Javadoc
>   [javadoc] Javadoc execution
>   [javadoc]
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
> warning - @return tag has no arguments.
>   [javadoc] 1 warning
> jars:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> dashboard-1.1.1.jar
> rdfagent-init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> jar-rdfagent:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>      [copy] Copying 95 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> war:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
> he
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>       [war] Building war:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
> oby.war
> wardist:
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> bindist-rdfagent:
>    [delete] Deleting directory
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 96 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
> b
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 1 file to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>      [copy] Copying 6 files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>       [tar] Building tar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
> 05-26.tar.gz
>       [zip] Building zip:
> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
> 05-26.zip
> all:
> BUILD SUCCESSFUL
> 
> 
> 
> ant dashboard :
> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> checkmaven:
> initmaven:
> init:
> config:
> compile:
> moses-init:
> samples-init:
>     [mkdir] Created dir:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
> ources
> dashboard-init:
> dashboard-config:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
> config.jar
> dashboard:
> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> The following error occurred while executing this line:
> [Dashboard]
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> [Dashboard]
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> 
> 
> Dashboard console :
> Selected authorities:
>     avilin05.avignon.inra.fr
> 
> -find-services:
> [Services names]
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
> _getExperimentType,Solstis_getDatasetFromExp
> 
> compile-datatypes:
>     [javac] Compiling 1796 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
> 
> compile-services:
>     [javac] Compiling 21 source files to
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
> 
> jar-datatypes:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> datatypes.jar
> 
> jar-services:
>       [jar] Building jar:
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> skeletons.jar
> 
> deploy-remote:
>     [mkdir] Created dir:
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26
> 
> create-wsdd:
> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getTrait.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getExperiment.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getProject.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> create-wsdd:
> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
> deploy-2010-05-26/deploy-wsdd
> 
> create-wsdd:
> [Create Solstis_getFactor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
> wsdd
> 
> BUILD FAILED
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> The following error occurred while executing this line:
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> Property 'service.jar' is not defined.
> 
> 
> Thanks,
> 
> Elise.
> 
> 
> 
> 
> 
> 
> Edward Kawas wrote:
> > Hi Elise,
> >
> > Did you make sure to generate the skeletons and their implementations
> first?
> > Hard to say what the problem is without knowing what you did to get
here.
> >
> > Eddie
> >
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >> Sent: Wednesday, May 26, 2010 2:03 AM
> >> To: moby-dev at lists.open-bio.org
> >> Subject: [MOBY-dev] moby services deployment
> >>
> >> Hi !
> >>
> >> When I want to deploy moby services by ant dashboard on remote
> >> machine, I meet this problem :
> >>
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >> What can I do for resolving this problem ?
> >>
> >> Thanks,
> >>
> >> Elise Larsonneur
> >> Bioinformatics trainee.
> >> UR GAFL
> >> INRA Avignon
> >> France
> >>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From Elise.Larsonneur at avignon.inra.fr  Thu May 27 15:35:36 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Thu, 27 May 2010 17:35:36 +0200
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <004101cafd9a$f1273570$d375a050$@gmail.com>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>	<4BFD31C8.1070008@avignon.inra.fr>
	<004101cafd9a$f1273570$d375a050$@gmail.com>
Message-ID: <4BFE9148.4020800@avignon.inra.fr>

Hi !

About the initial error : "Property 'service.jar' is not defined" which 
refers to the next lines in jMoby/xmls/deployBuild.xml file :



<!-- ================================================================== -->
<!-- Create a wsdd descriptor for given service in 'build/wsdd'         -->
<!--    parameter: ${service.name}  ... for which service               -->
<!--    parameter: ${wsdd.file}     ... what file to create             -->
<!-- ================================================================== -->
<target name="create-wsdd" depends="init">
  <property name="wsdd.template" 
value="${src.webapps}/standard.wsdd.template"/>
  <propertycopy property="impl.class" from="service.${service.name}" 
override="true"/>        ----------------------> line "224"
  <copy file="${wsdd.template}" tofile="${wsdd.file}" overwrite="true"
    taskname="Create ${service.name}.wsdd">
    <filterset>
      <filter token="SERVICE_NAME" value="${service.name}"/>
      <filter token="IMPL_CLASS" value="${impl.class}"/>
    </filterset>
  </copy>
</target>



I would to know how "${service.name}" on line "224" can be assigned to 
"jar".

Thanks a lot,

Elise



Edward Kawas wrote:
> Hi Elise,
>
> I cannot replicate your problem, so maybe I can help point you in the right
> direction. 
>
> [1]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/ServiceDevelopme
> nt.html
> [2]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-generators
> .html 
> [3]
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Moses-deploy.htm
> l
>
> I think that you may have seen some of these resources, judging by how far
> you have gotten, but I think it would be a good idea to read over them. The
> one thing that caught my eye is that when you did 'ant all', lots of
> unrelated service tasks were executed. If you look at resource [1] and read
> 'Step 1: What is needed' 'ant all' is done from within your service project
> and not from the root moby-live/Java folder.
>
> Let me know if this was a good enough push!
>
> Thanks,
>
> Eddie
>
>   
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>> Sent: Wednesday, May 26, 2010 7:36 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] moby services deployment
>>
>> Before deploying webservices , I generated datatypes and skeletons in
>> jMoby with the dashboard. Then, I wrote the implementations of skeletons
>> in another project associated to jMoby.
>> So, after ant all, ant dashboard, when I launchs the deployment (after ant
>>     
> all)
>   
>> of these webservices (on remote or local machine) , only the wsdd files
>>     
> are
>   
>> created and the previous error displays.
>> I used a pattern for implementation class names in the Moses Generator
>> Panel.
>>
>> eclipse console : ant all :
>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
>> cleanapi:
>> clean:
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>> checkmaven:
>> initmaven:
>> init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
>> config:
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>      [copy] Copying 27 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
>>      [copy] Copying 10 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
>>      [copy] Copying 24 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
>>      [copy] Copying 163 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>> compile:
>>     [javac] Compiling 392 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
>>     [javac] Note:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
>> ices/util/PBERecorder.java
>> uses or overrides a deprecated API.
>>     [javac] Note: Recompile with -Xlint:deprecation for details.
>>     [javac] Note: Some input files use unchecked or unsafe operations.
>>     [javac] Note: Recompile with -Xlint:unchecked for details.
>>     [javac] Compiling 26 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
>> docs:
>>   [javadoc] Generating Javadoc
>>   [javadoc] Javadoc execution
>>   [javadoc]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
>> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
>> warning - @return tag has no arguments.
>>   [javadoc] 1 warning
>> jars:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-1.1.1.jar
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
>> dashboard-1.1.1.jar
>> rdfagent-init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>> jar-rdfagent:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>      [copy] Copying 95 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
>> war:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
>> he
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
>>       [war] Building war:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
>> oby.war
>> wardist:
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
>> bindist-rdfagent:
>>    [delete] Deleting directory
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 96 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
>> b
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 1 file to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>      [copy] Copying 6 files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
>>       [tar] Building tar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
>> 05-26.tar.gz
>>       [zip] Building zip:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-2010-
>> 05-26.zip
>> all:
>> BUILD SUCCESSFUL
>>
>>
>>
>> ant dashboard :
>> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
>> checkmaven:
>> initmaven:
>> init:
>> config:
>> compile:
>> moses-init:
>> samples-init:
>>     [mkdir] Created dir:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
>> ources
>> dashboard-init:
>> dashboard-config:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
>> config.jar
>> dashboard:
>> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
>> The following error occurred while executing this line:
>> [Dashboard]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> [Dashboard]
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>>
>>
>> Dashboard console :
>> Selected authorities:
>>     avilin05.avignon.inra.fr
>>
>> -find-services:
>> [Services names]
>> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
>> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
>> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
>> _getExperimentType,Solstis_getDatasetFromExp
>>
>> compile-datatypes:
>>     [javac] Compiling 1796 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
>>
>> compile-services:
>>     [javac] Compiling 21 source files to
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
>>
>> jar-datatypes:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
>> datatypes.jar
>>
>> jar-services:
>>       [jar] Building jar:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
>> skeletons.jar
>>
>> deploy-remote:
>>     [mkdir] Created dir:
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26
>>
>> create-wsdd:
>> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getTrait.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getAuthor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExperiment.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getProject.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> create-wsdd:
>> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
>> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-to-
>> deploy-2010-05-26/deploy-wsdd
>>
>> create-wsdd:
>> [Create Solstis_getFactor.wsdd] Copying 1 file to /tmp/mobyremotedeploy-
>> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-26/deploy-
>> wsdd
>>
>> BUILD FAILED
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>> The following error occurred while executing this line:
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>> Property 'service.jar' is not defined.
>>
>>
>> Thanks,
>>
>> Elise.
>>
>>
>>
>>
>>
>>
>> Edward Kawas wrote:
>>     
>>> Hi Elise,
>>>
>>> Did you make sure to generate the skeletons and their implementations
>>>       
>> first?
>>     
>>> Hard to say what the problem is without knowing what you did to get
>>>       
> here.
>   
>>> Eddie
>>>
>>>
>>>       
>>>> -----Original Message-----
>>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
>>>> Sent: Wednesday, May 26, 2010 2:03 AM
>>>> To: moby-dev at lists.open-bio.org
>>>> Subject: [MOBY-dev] moby services deployment
>>>>
>>>> Hi !
>>>>
>>>> When I want to deploy moby services by ant dashboard on remote
>>>> machine, I meet this problem :
>>>>
>>>> The following error occurred while executing this line:
>>>>
>>>>         
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
>>     
>>>> The following error occurred while executing this line:
>>>>
>>>>         
>> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
>>     
>>>> Property 'service.jar' is not defined.
>>>>
>>>> What can I do for resolving this problem ?
>>>>
>>>> Thanks,
>>>>
>>>> Elise Larsonneur
>>>> Bioinformatics trainee.
>>>> UR GAFL
>>>> INRA Avignon
>>>> France
>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>>>         
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>       
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>   



From edward.kawas at gmail.com  Thu May 27 16:03:48 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 27 May 2010 09:03:48 -0700
Subject: [MOBY-dev] moby services deployment
In-Reply-To: <4BFE9148.4020800@avignon.inra.fr>
References: <4BFCE3CE.4060504@avignon.inra.fr>	<002401cafcd7$79cb3850$6d61a8f0$@gmail.com>	<4BFD31C8.1070008@avignon.inra.fr>	<004101cafd9a$f1273570$d375a050$@gmail.com>
	<4BFE9148.4020800@avignon.inra.fr>
Message-ID: <005c01cafdb6$32c44840$984cd8c0$@gmail.com>

The ant file is meant to help you copy your class files from a specific
location (more about that in the links that I sent you) and creates the
services.jar file for you. If you have to edit the build file then you are
doing something wrong (in the sense that you aren't generating your services
in the manner that MoSeS wishes that you would).

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> Sent: Thursday, May 27, 2010 8:36 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] moby services deployment
> 
> Hi !
> 
> About the initial error : "Property 'service.jar' is not defined" which
refers to
> the next lines in jMoby/xmls/deployBuild.xml file :
> 
> 
> 
> <!--
> ==========================================================
> ======== -->
> <!-- Create a wsdd descriptor for given service in 'build/wsdd'
-->
> <!--    parameter: ${service.name}  ... for which service
-->
> <!--    parameter: ${wsdd.file}     ... what file to create
-->
> <!--
> ==========================================================
> ======== -->
> <target name="create-wsdd" depends="init">
>   <property name="wsdd.template"
> value="${src.webapps}/standard.wsdd.template"/>
>   <propertycopy property="impl.class" from="service.${service.name}"
> override="true"/>        ----------------------> line "224"
>   <copy file="${wsdd.template}" tofile="${wsdd.file}" overwrite="true"
>     taskname="Create ${service.name}.wsdd">
>     <filterset>
>       <filter token="SERVICE_NAME" value="${service.name}"/>
>       <filter token="IMPL_CLASS" value="${impl.class}"/>
>     </filterset>
>   </copy>
> </target>
> 
> 
> 
> I would to know how "${service.name}" on line "224" can be assigned to
> "jar".
> 
> Thanks a lot,
> 
> Elise
> 
> 
> 
> Edward Kawas wrote:
> > Hi Elise,
> >
> > I cannot replicate your problem, so maybe I can help point you in the
right
> > direction.
> >
> > [1]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/ServiceDevelopme
> > nt.html
> > [2]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/Moses-generators
> > .html
> > [3]
> > http://biomoby.open-bio.org/CVS_CONTENT/moby-
> live/Java/docs/Moses-deploy.htm
> > l
> >
> > I think that you may have seen some of these resources, judging by how
> far
> > you have gotten, but I think it would be a good idea to read over them.
The
> > one thing that caught my eye is that when you did 'ant all', lots of
> > unrelated service tasks were executed. If you look at resource [1] and
read
> > 'Step 1: What is needed' 'ant all' is done from within your service
project
> > and not from the root moby-live/Java folder.
> >
> > Let me know if this was a good enough push!
> >
> > Thanks,
> >
> > Eddie
> >
> >
> >> -----Original Message-----
> >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >> Sent: Wednesday, May 26, 2010 7:36 AM
> >> To: Core developer announcements
> >> Subject: Re: [MOBY-dev] moby services deployment
> >>
> >> Before deploying webservices , I generated datatypes and skeletons in
> >> jMoby with the dashboard. Then, I wrote the implementations of
> skeletons
> >> in another project associated to jMoby.
> >> So, after ant all, ant dashboard, when I launchs the deployment (after
ant
> >>
> > all)
> >
> >> of these webservices (on remote or local machine) , only the wsdd files
> >>
> > are
> >
> >> created and the previous error displays.
> >> I used a pattern for implementation class names in the Moses Generator
> >> Panel.
> >>
> >> eclipse console : ant all :
> >> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> >> cleanapi:
> >> clean:
> >>    [delete] Deleting directory
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> >> checkmaven:
> >> initmaven:
> >> init:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/registry_servlets
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/test
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/core
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/coreservice
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/central
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/model
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/modelgui
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/generator
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/ontology
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/inb/visualizers
> >> config:
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>      [copy] Copying 27 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/run
> >>      [copy] Copying 10 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients/help
> >>      [copy] Copying 24 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes/templates
> >>      [copy] Copying 163 files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >> compile:
> >>     [javac] Compiling 392 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/classes
> >>     [javac] Note:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/ca/ucalgary/serv
> >> ices/util/PBERecorder.java
> >> uses or overrides a deprecated API.
> >>     [javac] Note: Recompile with -Xlint:deprecation for details.
> >>     [javac] Note: Some input files use unchecked or unsafe operations.
> >>     [javac] Note: Recompile with -Xlint:unchecked for details.
> >>     [javac] Compiling 26 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/Clients
> >> docs:
> >>   [javadoc] Generating Javadoc
> >>   [javadoc] Javadoc execution
> >>   [javadoc]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/src/main/org/inb/biomob
> >> y/central/gui/model/MobyObjectPropertiesTableModel.java:72:
> >> warning - @return tag has no arguments.
> >>   [javadoc] 1 warning
> >> jars:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> 1.1.1.jar
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/jmoby-
> >> dashboard-1.1.1.jar
> >> rdfagent-init:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> >> jar-rdfagent:
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>      [copy] Copying 95 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>    [delete] Deleting directory
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/temp_lib
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/RDFagent.jar
> >> war:
> >>     [mkdir] Created dir:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/cac
> >> he
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby
> >>       [war] Building war:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/webapps/jmoby/jm
> >> oby.war
> >> wardist:
> >>      [copy] Copying 1 file to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist
> >> bindist-rdfagent:
> >>    [delete] Deleting directory
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 96 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent/li
> >> b
> >>      [copy] Copying 1 file to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 1 file to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>      [copy] Copying 6 files to
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/rdfagent/rdfagent
> >>       [tar] Building tar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-
> 2010-
> >> 05-26.tar.gz
> >>       [zip] Building zip:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/docs/dist/rdfagent-
> 2010-
> >> 05-26.zip
> >> all:
> >> BUILD SUCCESSFUL
> >>
> >>
> >>
> >> ant dashboard :
> >> Buildfile: /home/av07/gafl/elarsonneur/workspace/jMoby/build.xml
> >> checkmaven:
> >> initmaven:
> >> init:
> >> config:
> >> compile:
> >> moses-init:
> >> samples-init:
> >>     [mkdir] Created dir:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/samples/res
> >> ources
> >> dashboard-init:
> >> dashboard-config:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/dashboard-
> >> config.jar
> >> dashboard:
> >> [Dashboard] 144276 [Thread-49] ERROR SimpleAnt -
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> >> The following error occurred while executing this line:
> >> [Dashboard]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >> [Dashboard]
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >>
> >>
> >> Dashboard console :
> >> Selected authorities:
> >>     avilin05.avignon.inra.fr
> >>
> >> -find-services:
> >> [Services names]
> >>
> Solstis_getExpDescFromAuthor,Solstis_getTrait,Solstis_getAuthor,Solstis_ge
> >>
> tExperiment,Solstis_getExpFromDataset,Solstis_getProject,Solstis_getExperi
> >>
> mentDesc,Solstis_getDatasetDescFromKeyword,Solstis_getFactor,jar,Solstis
> >> _getExperimentType,Solstis_getDatasetFromExp
> >>
> >> compile-datatypes:
> >>     [javac] Compiling 1796 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/datatypes
> >>
> >> compile-services:
> >>     [javac] Compiling 21 source files to
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/others/skeletons
> >>
> >> jar-datatypes:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> >> datatypes.jar
> >>
> >> jar-services:
> >>       [jar] Building jar:
> >> /home/av07/gafl/elarsonneur/workspace/jMoby/build/lib/biomoby-
> >> skeletons.jar
> >>
> >> deploy-remote:
> >>     [mkdir] Created dir:
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26
> >>
> >> create-wsdd:
> >> [Create Solstis_getExpDescFromAuthor.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getTrait.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getAuthor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExperiment.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExpFromDataset.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getProject.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getExperimentDesc.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getDatasetDescFromKeyword.wsdd] Copying 1 file to
> >> /tmp/mobyremotedeploy-elarsonneur/null1398203687/moby-services-
> to-
> >> deploy-2010-05-26/deploy-wsdd
> >>
> >> create-wsdd:
> >> [Create Solstis_getFactor.wsdd] Copying 1 file to
> /tmp/mobyremotedeploy-
> >> elarsonneur/null1398203687/moby-services-to-deploy-2010-05-
> 26/deploy-
> >> wsdd
> >>
> >> BUILD FAILED
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:306:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >> The following error occurred while executing this line:
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >> Property 'service.jar' is not defined.
> >>
> >>
> >> Thanks,
> >>
> >> Elise.
> >>
> >>
> >>
> >>
> >>
> >>
> >> Edward Kawas wrote:
> >>
> >>> Hi Elise,
> >>>
> >>> Did you make sure to generate the skeletons and their implementations
> >>>
> >> first?
> >>
> >>> Hard to say what the problem is without knowing what you did to get
> >>>
> > here.
> >
> >>> Eddie
> >>>
> >>>
> >>>
> >>>> -----Original Message-----
> >>>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> >>>> bounces at lists.open-bio.org] On Behalf Of Elise Larsonneur
> >>>> Sent: Wednesday, May 26, 2010 2:03 AM
> >>>> To: moby-dev at lists.open-bio.org
> >>>> Subject: [MOBY-dev] moby services deployment
> >>>>
> >>>> Hi !
> >>>>
> >>>> When I want to deploy moby services by ant dashboard on remote
> >>>> machine, I meet this problem :
> >>>>
> >>>> The following error occurred while executing this line:
> >>>>
> >>>>
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371:
> >>
> >>>> The following error occurred while executing this line:
> >>>>
> >>>>
> >>
> /home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224:
> >>
> >>>> Property 'service.jar' is not defined.
> >>>>
> >>>> What can I do for resolving this problem ?
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Elise Larsonneur
> >>>> Bioinformatics trainee.
> >>>> UR GAFL
> >>>> INRA Avignon
> >>>> France
> >>>>
> >>>> _______________________________________________
> >>>> MOBY-dev mailing list
> >>>> MOBY-dev at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>>
> >>>>
> >>> _______________________________________________
> >>> MOBY-dev mailing list
> >>> MOBY-dev at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>>
> >>>
> >> _______________________________________________
> >> MOBY-dev mailing list
> >> MOBY-dev at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/moby-dev
> >>
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From Elise.Larsonneur at avignon.inra.fr  Wed May 26 08:14:29 2010
From: Elise.Larsonneur at avignon.inra.fr (Elise Larsonneur)
Date: Wed, 26 May 2010 10:14:29 +0200
Subject: [MOBY-dev] moby services deployment
Message-ID: <4BFCD865.4050903@avignon.inra.fr>

Hi !

When I want to deploy moby services by ant dashboard on remote machine, 
I meet this problem :

The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:371: 
The following error occurred while executing this line:
/home/av07/gafl/elarsonneur/workspace/jMoby/xmls/deployBuild.xml:224: 
Property 'service.jar' is not defined.

What can I do for resolving this problem ?

Thanks,

Elise Larsonneur
Bioinformatics trainee.
UR GAFL
INRA Avignon
France