From Sebastien.Carrere at toulouse.inra.fr  Thu Jun  5 03:41:44 2008
From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Thu, 05 Jun 2008 09:41:44 +0200
Subject: [MOBY-dev] Moby down ?
Message-ID: <484798B8.8080609@toulouse.inra.fr>

Hi all,

Is Moby main server down ?
Here, in France, we don't have access to http://moby.ucalgary.ca

Someone elese ?

Merci,

Sebastien
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From groscurt at mpiz-koeln.mpg.de  Thu Jun  5 03:47:56 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Thu, 05 Jun 2008 09:47:56 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>
	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>
Message-ID: <48479A2C.5060507@mpiz-koeln.mpg.de>

Hi all,

I like to announce that we are now offering the Dashboard as a Java 
Webstart project and therefore as a standalone version. Now one can 
explore the functionality of Dashboard without checking out the full 
moby cvs code :-)

You can find it at 
http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
test it if everything works normally. I created this by deleting more 
and more libraries which were stated in the classpath but apparently are 
not needed at all. The web start version of dashboard offers the 
possibilty of browsing the registries, registration and the simple 
clientn (of course the MoSeS Generator is skipped for this version). If 
you encounter any problems during testing let me know.

If possible i would suggest to add this to the clients overview of the 
biomoby.org page - so that people can use it :-)

Any comments / suggestions are welcome

Andreas

From M4o at gmx.de  Thu Jun  5 04:30:38 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Thu, 05 Jun 2008 10:30:38 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <484798B8.8080609@toulouse.inra.fr>
References: <484798B8.8080609@toulouse.inra.fr>
Message-ID: <20080605083038.161550@gmx.net>

Hi,

Yes from Germany the same thing:

2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException: (504)Gateway Time-out Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details:
[string: null]
[HttpErrorCode: null]
Fault string: (504)Gateway Time-out
Fault code:   {http://xml.apache.org/axis/}HTTP
Fault actor:  null
When calling:
	http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========

Thanks,

Moritz
-------- Original-Nachricht --------
> Datum: Thu, 05 Jun 2008 09:41:44 +0200
> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: [MOBY-dev] Moby down ?

> Hi all,
> 
> Is Moby main server down ?
> Here, in France, we don't have access to http://moby.ucalgary.ca
> 
> Someone elese ?
> 
> Merci,
> 
> Sebastien

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger

From MichaelGerlich at gmx.de  Thu Jun  5 04:41:29 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Thu, 5 Jun 2008 10:41:29 +0200
Subject: [MOBY-dev] invoking webservice from default registry and rdf
Message-ID: <000601c8c6e7$f35ccf30$da166d90$@de>

Hi all,

after testing my service several times, it's now ready to get into the
"real" registry. Doing so, I unregistered the service from testing registry
and registered again at default registry, passing by all required
information and an endpoint URL for the rdf.
After that, I copied the rdf to the right location so it can be found via
the RDF agent.

Now every time I try to invoke this service using dashboard's simple client
and using "Ask registry where service is, and call it" - nothing happens,
even after waiting some minutes.

If I invoke the service via "Use service's usual endpoint" or "Use this
endpoint:", everything is fine and a result is displayed within a couple of
seconds.

Same behavior for other services from other authorities I tested.

After calling RDF agent to check if everything is set up properly (yesterday
evening), the service is still there so I guess there's nothing wrong with
the rdf and the location I placed it.

Does anyone have an idea what I'am doing wrong?

The service is named "MassBank_Query_PeakList" at authority "ipb-halle.de".


EDIT:
Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
Could be reason right?


Regards,

Michael


From markw at illuminae.com  Thu Jun  5 11:41:45 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 08:41:45 -0700
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <20080605083038.161550@gmx.net>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
Message-ID: <op.ub98jvtunbznux@mark.ubic.ca>

Looks like it's back up now... can you confirm?

We were down yesterday for a while - somehow the machine got "pinned".   
Might have been a DOS attack??  We don't really know.

M



On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:

> Hi,
>
> Yes from Germany the same thing:
>
> 2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException:  
> (504)Gateway Time-out Exception in thread "main"  
> org.biomoby.shared.MobyException: ===ERROR=== Fault details:
> [string: null]
> [HttpErrorCode: null]
> Fault string: (504)Gateway Time-out
> Fault code:   {http://xml.apache.org/axis/}HTTP
> Fault actor:  null
> When calling:
> 	http://moby.ucalgary.ca/moby/MOBY-Central.pl
> ===========
>
> Thanks,
>
> Moritz
> -------- Original-Nachricht --------
>> Datum: Thu, 05 Jun 2008 09:41:44 +0200
>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: [MOBY-dev] Moby down ?
>
>> Hi all,
>>
>> Is Moby main server down ?
>> Here, in France, we don't have access to http://moby.ucalgary.ca
>>
>> Someone elese ?
>>
>> Merci,
>>
>> Sebastien
>



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From M4o at gmx.de  Thu Jun  5 11:45:19 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Thu, 05 Jun 2008 17:45:19 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <op.ub98jvtunbznux@mark.ubic.ca>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
	<op.ub98jvtunbznux@mark.ubic.ca>
Message-ID: <20080605154519.193610@gmx.net>

Hi,

yes from Germany, i could confirm that it's back up again. 


Thanks a lot :)

Moritz


-------- Original-Nachricht --------
> Datum: Thu, 05 Jun 2008 08:41:45 -0700
> Von: "Mark Wilkinson" <markw at illuminae.com>
> An: "Core developer announcements" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Moby down ?

> Looks like it's back up now... can you confirm?
> 
> We were down yesterday for a while - somehow the machine got "pinned".   
> Might have been a DOS attack??  We don't really know.
> 
> M
> 
> 
> 
> On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:
> 
> > Hi,
> >
> > Yes from Germany the same thing:
> >
> > 2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException:  
> > (504)Gateway Time-out Exception in thread "main"  
> > org.biomoby.shared.MobyException: ===ERROR=== Fault details:
> > [string: null]
> > [HttpErrorCode: null]
> > Fault string: (504)Gateway Time-out
> > Fault code:   {http://xml.apache.org/axis/}HTTP
> > Fault actor:  null
> > When calling:
> > 	http://moby.ucalgary.ca/moby/MOBY-Central.pl
> > ===========
> >
> > Thanks,
> >
> > Moritz
> > -------- Original-Nachricht --------
> >> Datum: Thu, 05 Jun 2008 09:41:44 +0200
> >> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: [MOBY-dev] Moby down ?
> >
> >> Hi all,
> >>
> >> Is Moby main server down ?
> >> Here, in France, we don't have access to http://moby.ucalgary.ca
> >>
> >> Someone elese ?
> >>
> >> Merci,
> >>
> >> Sebastien
> >
> 
> 
> 
> -- 
> Mark Wilkinson
> Assistant Professor
> Dept. of Medical Genetics, UBC
> PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
> iCAPTURE Centre
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! 
Ideal f?r Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

From edward.kawas at gmail.com  Thu Jun  5 12:08:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 5 Jun 2008 09:08:01 -0700
Subject: [MOBY-dev] invoking webservice from default registry and rdf
In-Reply-To: <000601c8c6e7$f35ccf30$da166d90$@de>
References: <000601c8c6e7$f35ccf30$da166d90$@de>
Message-ID: <48480f6e.17bb720a.5658.23d0@mx.google.com>

Hi Michael,

Can you confirm that this is still a problem? I cannot replicate the issue,
so I believe that it was a temporary issue.

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 Michael Gerlich
Sent: June-05-08 1:41 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] invoking webservice from default registry and rdf

Hi all,

after testing my service several times, it's now ready to get into the
"real" registry. Doing so, I unregistered the service from testing registry
and registered again at default registry, passing by all required
information and an endpoint URL for the rdf.
After that, I copied the rdf to the right location so it can be found via
the RDF agent.

Now every time I try to invoke this service using dashboard's simple client
and using "Ask registry where service is, and call it" - nothing happens,
even after waiting some minutes.

If I invoke the service via "Use service's usual endpoint" or "Use this
endpoint:", everything is fine and a result is displayed within a couple of
seconds.

Same behavior for other services from other authorities I tested.

After calling RDF agent to check if everything is set up properly (yesterday
evening), the service is still there so I guess there's nothing wrong with
the rdf and the location I placed it.

Does anyone have an idea what I'am doing wrong?

The service is named "MassBank_Query_PeakList" at authority "ipb-halle.de".


EDIT:
Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
Could be reason right?


Regards,

Michael

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Thu Jun  5 12:14:04 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 09:14:04 -0700
Subject: [MOBY-dev] invoking webservice from default registry and rdf
In-Reply-To: <000601c8c6e7$f35ccf30$da166d90$@de>
References: <000601c8c6e7$f35ccf30$da166d90$@de>
Message-ID: <op.ub991qcfnbznux@mark.ubic.ca>

Hi Michael,

MOBY Central has had a couple of problems in the past 24 hours - both with  
being offline as well as with a corrupted RDF cache.  Either or both of  
these might have caused the problems you encountered. Eddie and I have  
been working on fixing these and we *think* it's all back to normal now.   
Perhaps you could try again and tell us if you are still unsuccessful?

Thanks!

Mark




On Thu, 05 Jun 2008 01:41:29 -0700, Michael Gerlich  
<MichaelGerlich at gmx.de> wrote:

> Hi all,
>
> after testing my service several times, it's now ready to get into the
> "real" registry. Doing so, I unregistered the service from testing  
> registry
> and registered again at default registry, passing by all required
> information and an endpoint URL for the rdf.
> After that, I copied the rdf to the right location so it can be found via
> the RDF agent.
>
> Now every time I try to invoke this service using dashboard's simple  
> client
> and using "Ask registry where service is, and call it" - nothing happens,
> even after waiting some minutes.
>
> If I invoke the service via "Use service's usual endpoint" or "Use this
> endpoint:", everything is fine and a result is displayed within a couple  
> of
> seconds.
>
> Same behavior for other services from other authorities I tested.
>
> After calling RDF agent to check if everything is set up properly  
> (yesterday
> evening), the service is still there so I guess there's nothing wrong  
> with
> the rdf and the location I placed it.
>
> Does anyone have an idea what I'am doing wrong?
>
> The service is named "MassBank_Query_PeakList" at authority  
> "ipb-halle.de".
>
>
> EDIT:
> Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
> Could be reason right?
>
>
> Regards,
>
> Michael
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From MichaelGerlich at gmx.de  Thu Jun  5 13:53:01 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Thu, 5 Jun 2008 19:53:01 +0200
Subject: [MOBY-dev] invoking webservice from default registry and rdf
	[solved]
Message-ID: <000301c8c734$ff771440$fe653cc0$@de>

Hi all,

yes you were right. It was all about the non-reachable registry.
Now everything is working properly again.  

Thanks again,

Michael


From sebastien.carrere at toulouse.inra.fr  Thu Jun  5 16:05:14 2008
From: sebastien.carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Thu, 05 Jun 2008 22:05:14 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <op.ub98jvtunbznux@mark.ubic.ca>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
	<op.ub98jvtunbznux@mark.ubic.ca>
Message-ID: <484846FA.6060406@toulouse.inra.fr>

Yes it's okay in France !

Merci
Sebastien


Mark Wilkinson a ?crit :
> Looks like it's back up now... can you confirm?
>
> We were down yesterday for a while - somehow the machine got 
> "pinned".  Might have been a DOS attack??  We don't really know.
>
> M
>
>
>
> On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:
>
>> Hi,
>>
>> Yes from Germany the same thing:
>>
>> 2008-06-05 10:23:20,990 ERROR [main] 
>> org.biomoby.shared.MobyException: (504)Gateway Time-out Exception in 
>> thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault 
>> details:
>> [string: null]
>> [HttpErrorCode: null]
>> Fault string: (504)Gateway Time-out
>> Fault code:   {http://xml.apache.org/axis/}HTTP
>> Fault actor:  null
>> When calling:
>>     http://moby.ucalgary.ca/moby/MOBY-Central.pl
>> ===========
>>
>> Thanks,
>>
>> Moritz
>> -------- Original-Nachricht --------
>>> Datum: Thu, 05 Jun 2008 09:41:44 +0200
>>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>>> Betreff: [MOBY-dev] Moby down ?
>>
>>> Hi all,
>>>
>>> Is Moby main server down ?
>>> Here, in France, we don't have access to http://moby.ucalgary.ca
>>>
>>> Someone elese ?
>>>
>>> Merci,
>>>
>>> Sebastien
>>
>
>
>


From markw at illuminae.com  Thu Jun  5 19:58:36 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 16:58:36 -0700
Subject: [MOBY-dev] JDK requirement of dashboard...
Message-ID: <op.ucavjynqnbznux@mark.ubic.ca>

Isn't it a bit... odd... that we expect end-users of Dashboard to download  
the JDK rather than the JRE?

M


-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From martin.senger at gmail.com  Thu Jun  5 20:30:33 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 6 Jun 2008 08:30:33 +0800
Subject: [MOBY-dev] JDK requirement of dashboard...
In-Reply-To: <op.ucavjynqnbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>
Message-ID: <4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>

> Isn't it a bit... odd... that we expect end-users of Dashboard to download
> the JDK rather than the JRE?


No, because Dashboard includes Moses and Moses compiles generated Java
classes - so it needs JDK. An option would be to have it configured: and
disabled some panels when onlt JRE is present. Not sure, however, if it
worth to do it.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From groscurt at mpiz-koeln.mpg.de  Tue Jun 10 04:54:53 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 10 Jun 2008 10:54:53 +0200
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
Message-ID: <484E415D.9080600@mpiz-koeln.mpg.de>


   Hi,
   hope someone has an advice or encountered that problem before and knows a
   solution.
     * I try to install a moby central. The first machine i tried is running
       Solaris 10 and it failes because of the SOAP::Lite library. All web
       service clients which uses soap are failing with

     HTTP::Message content not bytes at
     /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361

     we tested it with Moby and with the EBI web service clients. Has anyone
     installed a working SOAP::Lite on Solaris 10 ?

     * After failing on a solaris machine we thought, a what the heck, lets do
       it on a linux machine. So i tried to install it on a 64bit machine. This
       time XML::CanonalizeXML is the problem. It aborts the make process with
       lots of lots of errors. Installing the same library on a 32bit machine
       works smoothly.

     Has anyone installed a working XML::CanonalizeXML on a 64bit machine ?

   So basically,  has anyone installed a moby central on a Solaris 10 machine
   or a linux 64bit and can give advices for our problems here ?
   Thanks
   andreas

From markw at illuminae.com  Tue Jun 10 09:37:17 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:37:17 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E415D.9080600@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
Message-ID: <op.ucjb4ff6nbznux@mark.ubic.ca>

The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...

M




On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

>
>    Hi,
>    hope someone has an advice or encountered that problem before and  
> knows a
>    solution.
>      * I try to install a moby central. The first machine i tried is  
> running
>        Solaris 10 and it failes because of the SOAP::Lite library. All  
> web
>        service clients which uses soap are failing with
>
>      HTTP::Message content not bytes at
>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>
>      we tested it with Moby and with the EBI web service clients. Has  
> anyone
>      installed a working SOAP::Lite on Solaris 10 ?
>
>      * After failing on a solaris machine we thought, a what the heck,  
> lets do
>        it on a linux machine. So i tried to install it on a 64bit  
> machine. This
>        time XML::CanonalizeXML is the problem. It aborts the make  
> process with
>        lots of lots of errors. Installing the same library on a 32bit  
> machine
>        works smoothly.
>
>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
> machine ?
>
>    So basically,  has anyone installed a moby central on a Solaris 10  
> machine
>    or a linux 64bit and can give advices for our problems here ?
>    Thanks
>    andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From groscurt at mpiz-koeln.mpg.de  Tue Jun 10 09:39:43 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 10 Jun 2008 15:39:43 +0200
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <op.ucjb4ff6nbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
Message-ID: <484E841F.4070008@mpiz-koeln.mpg.de>

Mark Wilkinson wrote:
> The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...
>
> M
>
so which soap lite version do you have installed ? have you ever 
encountered such problem as i mentioned ?

Andreas

>
>
>
> On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth 
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>>
>>    Hi,
>>    hope someone has an advice or encountered that problem before and 
>> knows a
>>    solution.
>>      * I try to install a moby central. The first machine i tried is 
>> running
>>        Solaris 10 and it failes because of the SOAP::Lite library. 
>> All web
>>        service clients which uses soap are failing with
>>
>>      HTTP::Message content not bytes at
>>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>>
>>      we tested it with Moby and with the EBI web service clients. Has 
>> anyone
>>      installed a working SOAP::Lite on Solaris 10 ?
>>
>>      * After failing on a solaris machine we thought, a what the 
>> heck, lets do
>>        it on a linux machine. So i tried to install it on a 64bit 
>> machine. This
>>        time XML::CanonalizeXML is the problem. It aborts the make 
>> process with
>>        lots of lots of errors. Installing the same library on a 32bit 
>> machine
>>        works smoothly.
>>
>>      Has anyone installed a working XML::CanonalizeXML on a 64bit 
>> machine ?
>>
>>    So basically,  has anyone installed a moby central on a Solaris 10 
>> machine
>>    or a linux 64bit and can give advices for our problems here ?
>>    Thanks
>>    andreas
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>


From markw at illuminae.com  Tue Jun 10 09:45:14 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:45:14 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E415D.9080600@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
Message-ID: <op.ucjchoqjnbznux@mark.ubic.ca>

One of the key things to getting it working on the Solaris machine was to  
use the Perl that came with CoolStack...  I know there were other problems  
too, but that one was key!





On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

>
>    Hi,
>    hope someone has an advice or encountered that problem before and  
> knows a
>    solution.
>      * I try to install a moby central. The first machine i tried is  
> running
>        Solaris 10 and it failes because of the SOAP::Lite library. All  
> web
>        service clients which uses soap are failing with
>
>      HTTP::Message content not bytes at
>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>
>      we tested it with Moby and with the EBI web service clients. Has  
> anyone
>      installed a working SOAP::Lite on Solaris 10 ?
>
>      * After failing on a solaris machine we thought, a what the heck,  
> lets do
>        it on a linux machine. So i tried to install it on a 64bit  
> machine. This
>        time XML::CanonalizeXML is the problem. It aborts the make  
> process with
>        lots of lots of errors. Installing the same library on a 32bit  
> machine
>        works smoothly.
>
>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
> machine ?
>
>    So basically,  has anyone installed a moby central on a Solaris 10  
> machine
>    or a linux 64bit and can give advices for our problems here ?
>    Thanks
>    andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From markw at illuminae.com  Tue Jun 10 09:49:13 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:49:13 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E841F.4070008@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
Message-ID: <op.ucjcobhznbznux@mark.ubic.ca>

moby01:~# more /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm
# ======================================================================
#
# Copyright (C) 2000-2005 Paul Kulchenko (paulclinger at yahoo.com)
# SOAP::Lite is free software; you can redistribute it
# and/or modify it under the same terms as Perl itself.
#
# $Id: Lite.pm,v 1.43 2006/08/16 14:49:34 byrnereese Exp $
#
# ======================================================================

package SOAP::Lite;

use 5.004;
use strict;
use vars qw($VERSION);
#$VERSION = sprintf("%d.%s", map {s/_//g; $_} q$Name:  $ =~  
/-(\d+)_([\d_]+)/)
#  or warn "warning: unspecified/non-released version of ", __PACKAGE__,  
"\n";
$VERSION = '0.69';

# ======================================================================









On Tue, 10 Jun 2008 06:39:43 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> Mark Wilkinson wrote:
>> The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...
>>
>> M
>>
> so which soap lite version do you have installed ? have you ever  
> encountered such problem as i mentioned ?
>
> Andreas
>
>>
>>
>>
>> On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>>
>>>    Hi,
>>>    hope someone has an advice or encountered that problem before and  
>>> knows a
>>>    solution.
>>>      * I try to install a moby central. The first machine i tried is  
>>> running
>>>        Solaris 10 and it failes because of the SOAP::Lite library. All  
>>> web
>>>        service clients which uses soap are failing with
>>>
>>>      HTTP::Message content not bytes at
>>>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>>>
>>>      we tested it with Moby and with the EBI web service clients. Has  
>>> anyone
>>>      installed a working SOAP::Lite on Solaris 10 ?
>>>
>>>      * After failing on a solaris machine we thought, a what the heck,  
>>> lets do
>>>        it on a linux machine. So i tried to install it on a 64bit  
>>> machine. This
>>>        time XML::CanonalizeXML is the problem. It aborts the make  
>>> process with
>>>        lots of lots of errors. Installing the same library on a 32bit  
>>> machine
>>>        works smoothly.
>>>
>>>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
>>> machine ?
>>>
>>>    So basically,  has anyone installed a moby central on a Solaris 10  
>>> machine
>>>    or a linux 64bit and can give advices for our problems here ?
>>>    Thanks
>>>    andreas
>>> _______________________________________________
>>> 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



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From edward.kawas at gmail.com  Wed Jun 11 11:19:38 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 11 Jun 2008 08:19:38 -0700
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <48479A2C.5060507@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>
	<48479A2C.5060507@mpiz-koeln.mpg.de>
Message-ID: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>

Hi Andreas,

I recently created a new panel in dashboard for perl moses. How hard would
it be to get that running? The panel runs command line scripts in the
background, so I am not sure if the webstart sandbox allows that anyways...

Good work by the way!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-05-08 12:48 AM
To: Core developer announcements; moby-l at lists.open-bio.org
Subject: [MOBY-dev] Dashboard as Java WebStart

Hi all,

I like to announce that we are now offering the Dashboard as a Java 
Webstart project and therefore as a standalone version. Now one can 
explore the functionality of Dashboard without checking out the full 
moby cvs code :-)

You can find it at 
http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
test it if everything works normally. I created this by deleting more 
and more libraries which were stated in the classpath but apparently are 
not needed at all. The web start version of dashboard offers the 
possibilty of browsing the registries, registration and the simple 
clientn (of course the MoSeS Generator is skipped for this version). If 
you encounter any problems during testing let me know.

If possible i would suggest to add this to the clients overview of the 
biomoby.org page - so that people can use it :-)

Any comments / suggestions are welcome

Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From groscurt at mpiz-koeln.mpg.de  Wed Jun 11 11:33:07 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 17:33:07 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>
	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
Message-ID: <484FF033.30806@mpiz-koeln.mpg.de>

Hi Eddie,

is the panel already checked in the cvs ? whats it called ? ... 
apparently i missed that.

Mhm - the question is how these command line scripts are available - if 
they are some .pl scripts or .sh scripts or something it could be not 
working at all - but i will check that.

best
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de  Wed Jun 11 11:36:14 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 17:36:14 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>
	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
Message-ID: <484FF0EE.6010403@mpiz-koeln.mpg.de>

ah... i see the panel now ;-)

i will try to integrate it ...

cheers
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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  Wed Jun 11 11:41:07 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 11 Jun 2008 08:41:07 -0700
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484FF033.30806@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
	<484FF033.30806@mpiz-koeln.mpg.de>
Message-ID: <484ff215.16538c0a.6767.ffffdab9@mx.google.com>

Yeah, the panel is in the cvs. The documentation for it is in the cvs too
(both the dashboard internal help and an external one). I should link them
to other documents, so that google can find them.

The external one is at: http://tinyurl.com/63ucu3

The command line scripts are installed (by make) when users install the perl
module MOSES::MOBY from cpan (or the perl branch of the cvs).

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 Andreas Groscurth
Sent: June-11-08 8:33 AM
To: Core developer announcements
Cc: moby-l at lists.open-bio.org
Subject: Re: [MOBY-dev] Dashboard as Java WebStart

Hi Eddie,

is the panel already checked in the cvs ? whats it called ? ... 
apparently i missed that.

Mhm - the question is how these command line scripts are available - if 
they are some .pl scripts or .sh scripts or something it could be not 
working at all - but i will check that.

best
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that
anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas
Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de  Wed Jun 11 13:10:20 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 19:10:20 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <op.ucjcobhznbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
Message-ID: <485006FC.3060003@mpiz-koeln.mpg.de>

someone killed it again ;-(

connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl form 
Germany....

bring it back :p

PS: sorry mark - the first email was already supposed for the mailing list !

From markw at illuminae.com  Wed Jun 11 14:18:19 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 11 Jun 2008 11:18:19 -0700
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485006FC.3060003@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
Message-ID: <op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>

Looks like it was a temporary problem... it was down for me also, but is  
back up now.

M



On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> someone killed it again ;-(
>
> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl form  
> Germany....
>
> bring it back :p
>
> PS: sorry mark - the first email was already supposed for the mailing  
> list !
> _______________________________________________
> 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 gordonp at ucalgary.ca  Wed Jun 11 15:28:48 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 11 Jun 2008 13:28:48 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>
	<op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <48502770.6060905@ucalgary.ca>

The whole University of Calgary was cut off from the outside world for 
about an hour...for reasons still unexplained.


Mark Wilkinson wrote:
> Looks like it was a temporary problem... it was down for me also, but 
> is back up now.
>
> M
>
>
>
> On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth 
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>> someone killed it again ;-(
>>
>> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl 
>> form Germany....
>>
>> bring it back :p
>>
>> PS: sorry mark - the first email was already supposed for the mailing 
>> list !
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>

From gordonp at ucalgary.ca  Wed Jun 11 18:24:59 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 11 Jun 2008 16:24:59 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <48502770.6060905@ucalgary.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
	<48502770.6060905@ucalgary.ca>
Message-ID: <485050BB.4060001@ucalgary.ca>

FYI: It would appear that the university was subject to a multicast DOS 
attack, and the admins have rerouted around the troublesome Cybera 
connections.

Paul Gordon wrote:
> The whole University of Calgary was cut off from the outside world for 
> about an hour...for reasons still unexplained.
>
>
> Mark Wilkinson wrote:
>> Looks like it was a temporary problem... it was down for me also, but 
>> is back up now.
>>
>> M
>>
>>
>>
>> On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth 
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>> someone killed it again ;-(
>>>
>>> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl 
>>> form Germany....
>>>
>>> bring it back :p
>>>
>>> PS: sorry mark - the first email was already supposed for the 
>>> mailing list !
>>> _______________________________________________
>>> 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
>
> !DSPAM:60005,48502b5710950215499055!
>
>
>

From sneumann at ipb-halle.de  Thu Jun 12 03:41:06 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Thu, 12 Jun 2008 09:41:06 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485006FC.3060003@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de> <op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de> <op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
Message-ID: <1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>

On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
> someone killed it again ;-(

Hi,

wouldn't that be the time to call for redundancy for moby-central ?
Either some read-only secondary server which keeps 
at least the services running if the primary is unreachable,

or even a full-blown anycast a la Root-DNS servers 
with synchronized backend-something for the registry database ?

Or has that already been discussed and dismissed ?

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

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From schoof at mpiz-koeln.mpg.de  Thu Jun 12 06:00:07 2008
From: schoof at mpiz-koeln.mpg.de (Heiko Schoof)
Date: Thu, 12 Jun 2008 12:00:07 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>

Hi,
we have implemented synchronization of moby centrals. But it needs  
some testing under production conditions. Read-only should work fine.  
So if anyone is willing and able to host an alternative moby- 
central... we are in the process of setting one up, and could  
possibly act as European mirror. But I need to discuss this with  
Andreas first, and see in what time scale this is feasible.
Has anyone else been experimenting with the synchronization code from  
Andreas?

What would then be missing is the implementation for a fall-back in  
the client libraries, I think. In effect, the ability to give a  
second moby-central, which is used if connections to the primary fail.

Best, Heiko

On 12.06.2008, at 09:41, sneumann wrote:

> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>> someone killed it again ;-(
>
> Hi,
>
> wouldn't that be the time to call for redundancy for moby-central ?
> Either some read-only secondary server which keeps
> at least the services running if the primary is unreachable,
>
> or even a full-blown anycast a la Root-DNS servers
> with synchronized backend-something for the registry database ?
>
> Or has that already been discussed and dismissed ?
>
> 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
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From gordonp at ucalgary.ca  Thu Jun 12 13:11:22 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 12 Jun 2008 11:11:22 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
	<B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
Message-ID: <485158BA.2070802@ucalgary.ca>

It brings a tear (of joy) to my eye that Moby Central is becoming so 
essential, we need a backup. :-)

I think a European mirror is a great idea, because just having two 
servers here in Calgary would not have prevented the down-time 
experienced yesterday.  We'd need to change the dynamic Central lookup 
policy (which goes through biomoby.org) to change from returning one 
server to returning a list of servers.  Pretty simple, but still has a 
single point of failure, now at biomoby.org.  Dynamic Central lookup is 
disabled by default unless a connection to Central fails, so maybe it's 
not such a big deal (unless moby.ucalgary.ca AND biomoby.org in Boston 
(or wherever) fail at the same time).

The other (robust) option is to have an LSID that points to a document 
listing the servers.  The resolution protocol allows for redundant data 
serving in theory, but we'd need to set up moby as a "proper" authority 
that goes in the lsid.org DNSPTR records.

-Paul

Heiko Schoof wrote:
> Hi,
> we have implemented synchronization of moby centrals. But it needs 
> some testing under production conditions. Read-only should work fine. 
> So if anyone is willing and able to host an alternative 
> moby-central... we are in the process of setting one up, and could 
> possibly act as European mirror. But I need to discuss this with 
> Andreas first, and see in what time scale this is feasible.
> Has anyone else been experimenting with the synchronization code from 
> Andreas?
>
> What would then be missing is the implementation for a fall-back in 
> the client libraries, I think. In effect, the ability to give a second 
> moby-central, which is used if connections to the primary fail.
>
> Best, Heiko
>
> On 12.06.2008, at 09:41, sneumann wrote:
>
>> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>>> someone killed it again ;-(
>>
>> Hi,
>>
>> wouldn't that be the time to call for redundancy for moby-central ?
>> Either some read-only secondary server which keeps
>> at least the services running if the primary is unreachable,
>>
>> or even a full-blown anycast a la Root-DNS servers
>> with synchronized backend-something for the registry database ?
>>
>> Or has that already been discussed and dismissed ?
>>
>> 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
>>
>> _______________________________________________
>> 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
>
> !DSPAM:60005,4850f8cc10950795412468!
>
>
>

From gordonp at ucalgary.ca  Thu Jun 12 13:20:49 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 12 Jun 2008 11:20:49 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485158BA.2070802@ucalgary.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>	<B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
	<485158BA.2070802@ucalgary.ca>
Message-ID: <48515AF1.9050704@ucalgary.ca>

Actually, I lied. It's even easier.  If the LSID for the list of 
centrals is urn:lsid:biomoby.org:... we can just add lower priority LSID 
data servers to the biomoby.org SRV records for 
_lsid._tcp.biomoby.org...mirror LSID servers for Moby Central data. 

>
> The other (robust) option is to have an LSID that points to a document 
> listing the servers.  The resolution protocol allows for redundant 
> data serving in theory, but we'd need to set up moby as a "proper" 
> authority that goes in the lsid.org DNSPTR records.
>
> -Paul
>
> Heiko Schoof wrote:
>> Hi,
>> we have implemented synchronization of moby centrals. But it needs 
>> some testing under production conditions. Read-only should work fine. 
>> So if anyone is willing and able to host an alternative 
>> moby-central... we are in the process of setting one up, and could 
>> possibly act as European mirror. But I need to discuss this with 
>> Andreas first, and see in what time scale this is feasible.
>> Has anyone else been experimenting with the synchronization code from 
>> Andreas?
>>
>> What would then be missing is the implementation for a fall-back in 
>> the client libraries, I think. In effect, the ability to give a 
>> second moby-central, which is used if connections to the primary fail.
>>
>> Best, Heiko
>>
>> On 12.06.2008, at 09:41, sneumann wrote:
>>
>>> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>>>> someone killed it again ;-(
>>>
>>> Hi,
>>>
>>> wouldn't that be the time to call for redundancy for moby-central ?
>>> Either some read-only secondary server which keeps
>>> at least the services running if the primary is unreachable,
>>>
>>> or even a full-blown anycast a la Root-DNS servers
>>> with synchronized backend-something for the registry database ?
>>>
>>> Or has that already been discussed and dismissed ?
>>>
>>> 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
>>>
>>> _______________________________________________
>>> 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
>
> !DSPAM:60005,4851566410950685925024!
>
>
>

From markw at illuminae.com  Thu Jun 12 17:26:25 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 12 Jun 2008 14:26:25 -0700
Subject: [MOBY-dev] Apologies
Message-ID: <op.ucnm6by1nbznux@mark.ubic.ca>

Hi all,

It took most of the day today to fix the Dashboard WebStart from the  
biomoby.org homepage once I messed it up early this morning.  My apologies  
if you tried using it.  It's all fixed now!

Mark



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From groscurt at mpiz-koeln.mpg.de  Fri Jun 13 09:57:44 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 13 Jun 2008 15:57:44 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4851431d.1420720a.52bf.243d@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
Message-ID: <48527CD8.9060904@mpiz-koeln.mpg.de>

Hi,

just a short question about dead services.
I call some services with my aggregator, which are registered at the 
production central. Some of them always return and error and therefore 
arent useable at all.

E.g. getAREXGFPImageCollection from arexdb.org

if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
dead" - but on the "dead service" page it is not listed (and its dead 
for a longer time)

Also in the Java code in MobyService there are flags for the status of a 
service - but how to i find them out - after a findService call all 
service i retrieve have status 0 (unchecked).

So my questions/comment:

1. The dead service page does not show up all dead services.
2. How do I find out with JMoby if a service is dead ?

THX
Andreas

From edward.kawas at gmail.com  Fri Jun 13 10:04:52 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 13 Jun 2008 07:04:52 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48527CD8.9060904@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
Message-ID: <48527e8d.02578c0a.75ce.57f4@mx.google.com>

Hi Andreas,

The service seems to be up and running:
http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator (choose the service
provider from the drop down). I think that is why it isn't listed on the
dead services page.

I am not sure how to figure out if the service is dead in jMoby. Maybe the
easiest thing to do would be to add code into MobyService that actually
pings the service. But that should be better thought out. I know that the
RDF for services contains this information, but don't trust it. Ever since
we started caching, that information is no longer useful. Again, this value
should be removed or we should figure out how to ensure that this
information is valid.

Eddie




-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-13-08 6:58 AM
To: Core developer announcements
Subject: [MOBY-dev] Dead services and how to figure them out

Hi,

just a short question about dead services.
I call some services with my aggregator, which are registered at the 
production central. Some of them always return and error and therefore 
arent useable at all.

E.g. getAREXGFPImageCollection from arexdb.org

if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
dead" - but on the "dead service" page it is not listed (and its dead 
for a longer time)

Also in the Java code in MobyService there are flags for the status of a 
service - but how to i find them out - after a findService call all 
service i retrieve have status 0 (unchecked).

So my questions/comment:

1. The dead service page does not show up all dead services.
2. How do I find out with JMoby if a service is dead ?

THX
Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From Sebastien.Carrere at toulouse.inra.fr  Fri Jun 13 10:29:27 2008
From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Fri, 13 Jun 2008 16:29:27 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48527CD8.9060904@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
Message-ID: <48528447.7040807@toulouse.inra.fr>

Bonjour ,


Thanks Andreas to restart the discussion about DeadServices and cleaning 
the registry.
I encounter the same problem in Remora.
The DeadServices list provided  is not exhaustive as you say.

I launch every night a cleaner which do this thing:
- get all services registered in Mobycentral
- try to execute them with the perl command: eval 
{$service_instance->execute(XMLinputlist =>[[]])};

Here is my list of Dead services (Ihave got also list for the 3 past 
days for testRegistry and Inab registry) :
http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral

(Format is "service_name    auth_uri    registry_name    error_message")

Most of them are 404 or 500 errors.

If my test is correct, that means that around 10% of services are dead.
And here I cannot test if the returned message is well-formed (many 
changes happened since the birth of BioMOBY and maybe some services have 
not been updated), so it's at least 10%...

 From my point of view, this problem of dead/non-functionnal  services 
is really a critical one.
We develop tools based on web-services and we advice our users to use 
tools such as Taverna, Remora etc...
So if the basis (web-services) is not robust, we lost all our credibility.

We deploy here (Toulouse, France) procedures to test our services every 
night to ensure their availablity and stability.
I think it's time to currate the main registry.

What do you think about this ?

Sebastien




Andreas Groscurth wrote:
> Hi,
>
> just a short question about dead services.
> I call some services with my aggregator, which are registered at the 
> production central. Some of them always return and error and therefore 
> arent useable at all.
>
> E.g. getAREXGFPImageCollection from arexdb.org
>
> if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
> dead" - but on the "dead service" page it is not listed (and its dead 
> for a longer time)
>
> Also in the Java code in MobyService there are flags for the status of 
> a service - but how to i find them out - after a findService call all 
> service i retrieve have status 0 (unchecked).
>
> So my questions/comment:
>
> 1. The dead service page does not show up all dead services.
> 2. How do I find out with JMoby if a service is dead ?
>
> THX
> Andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

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From M4o at gmx.de  Fri Jun 13 11:32:08 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Fri, 13 Jun 2008 17:32:08 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48528447.7040807@toulouse.inra.fr>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
	<48528447.7040807@toulouse.inra.fr>
Message-ID: <20080613153208.307160@gmx.net>

Hi,

In my opinion there are about three or more questions we should think of:

1. Who should test the Services?
2. Who should host the Deadservices list?
3. How the should the Services be test. Only with the Empty Moby "Ping" or should there be some real example Data. In the Last months i worked with the Moby Services often Services respond to an Moby "Ping" but doesn?t Work correctly due to DB Connection, or Configuration Errors. (Like a lot of the mips.gsf.de) .
3a. Maybe a central system or Mailing list where User could comment the Function of the Services or "complain" about the misuse of Datatypes would be useful (for the Users ;-) ) Sure every user could email the problem to the Authority but I think it would be helpful to centralize the comments.
4. How could the Perl and Java API access the Dead list and use the Informations.

My small suggestions:
1 and 2. The best and less traffic way would it be if the MOBY Central test the Services keeps the list.

3. If it is to complicated to test the Services with real example Data then there should be a system to complain about the service and add it to the dead list if it is not working correctly (like db connections errors for about a week).

4. There are already Methods in the jMoby Api which could be extended if there is a reliabil Dead Servcies List.

In my Opinion, the reliability and Quality of the MOBY Services in the NON Testing MOBY Central should be more important then the quantity. 
Because if a user doesn?t find a Service that does what he wants he maybe set up one by himself. But if there are a few services that should does what he wants but are non working that?s frustrating.

But these are just my 2 cents. 

Thanks for all the (fish) work you have done.

Moritz



-------- Original-Nachricht --------
> Datum: Fri, 13 Jun 2008 16:29:27 +0200
> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Bonjour ,
> 
> 
> Thanks Andreas to restart the discussion about DeadServices and cleaning 
> the registry.
> I encounter the same problem in Remora.
> The DeadServices list provided  is not exhaustive as you say.
> 
> I launch every night a cleaner which do this thing:
> - get all services registered in Mobycentral
> - try to execute them with the perl command: eval 
> {$service_instance->execute(XMLinputlist =>[[]])};
> 
> Here is my list of Dead services (Ihave got also list for the 3 past 
> days for testRegistry and Inab registry) :
> http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral
> 
> (Format is "service_name    auth_uri    registry_name    error_message")
> 
> Most of them are 404 or 500 errors.
> 
> If my test is correct, that means that around 10% of services are dead.
> And here I cannot test if the returned message is well-formed (many 
> changes happened since the birth of BioMOBY and maybe some services have 
> not been updated), so it's at least 10%...
> 
>  From my point of view, this problem of dead/non-functionnal  services 
> is really a critical one.
> We develop tools based on web-services and we advice our users to use 
> tools such as Taverna, Remora etc...
> So if the basis (web-services) is not robust, we lost all our credibility.
> 
> We deploy here (Toulouse, France) procedures to test our services every 
> night to ensure their availablity and stability.
> I think it's time to currate the main registry.
> 
> What do you think about this ?
> 
> Sebastien
> 
> 
> 
> 
> Andreas Groscurth wrote:
> > Hi,
> >
> > just a short question about dead services.
> > I call some services with my aggregator, which are registered at the 
> > production central. Some of them always return and error and therefore 
> > arent useable at all.
> >
> > E.g. getAREXGFPImageCollection from arexdb.org
> >
> > if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
> > dead" - but on the "dead service" page it is not listed (and its dead 
> > for a longer time)
> >
> > Also in the Java code in MobyService there are flags for the status of 
> > a service - but how to i find them out - after a findService call all 
> > service i retrieve have status 0 (unchecked).
> >
> > So my questions/comment:
> >
> > 1. The dead service page does not show up all dead services.
> > 2. How do I find out with JMoby if a service is dead ?
> >
> > THX
> > Andreas
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger

From gordonp at ucalgary.ca  Fri Jun 13 11:48:15 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 13 Jun 2008 09:48:15 -0600
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080613153208.307160@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>
Message-ID: <485296BF.8010303@ucalgary.ca>

Hi all,

I'll respond to several posts at once:

1. There is a list of dead services at Moby Central, but it is not used 
by default in the jMoby API, and it's not part of the formal API. 
http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
2. There is a mechanism to flag services in MobyService, but it does not 
do the checking itself.  For an example of ping checking and flagging 
based on the aforementioned URL, see 
ca.ucalgary.seahawk.services.MobyClient and search for "MobyService.ALIVE".
3. We decided at the Hackathon in February to introduce service test 
cases in the service metadata (retrievable by LSID resolution), but I'm 
not sure if that made it into the documentation.  Mark?  I'll add 
support for this jMoby if someone points me to the docs.

Cheers,

Paul

M4o at gmx.de wrote:
> Hi,
>
> In my opinion there are about three or more questions we should think of:
>
> 1. Who should test the Services?
> 2. Who should host the Deadservices list?
> 3. How the should the Services be test. Only with the Empty Moby "Ping" or should there be some real example Data. In the Last months i worked with the Moby Services often Services respond to an Moby "Ping" but doesn?t Work correctly due to DB Connection, or Configuration Errors. (Like a lot of the mips.gsf.de) .
> 3a. Maybe a central system or Mailing list where User could comment the Function of the Services or "complain" about the misuse of Datatypes would be useful (for the Users ;-) ) Sure every user could email the problem to the Authority but I think it would be helpful to centralize the comments.
> 4. How could the Perl and Java API access the Dead list and use the Informations.
>
> My small suggestions:
> 1 and 2. The best and less traffic way would it be if the MOBY Central test the Services keeps the list.
>
> 3. If it is to complicated to test the Services with real example Data then there should be a system to complain about the service and add it to the dead list if it is not working correctly (like db connections errors for about a week).
>
> 4. There are already Methods in the jMoby Api which could be extended if there is a reliabil Dead Servcies List.
>
> In my Opinion, the reliability and Quality of the MOBY Services in the NON Testing MOBY Central should be more important then the quantity. 
> Because if a user doesn?t find a Service that does what he wants he maybe set up one by himself. But if there are a few services that should does what he wants but are non working that?s frustrating.
>
> But these are just my 2 cents. 
>
> Thanks for all the (fish) work you have done.
>
> Moritz
>
>
>
> -------- Original-Nachricht --------
>   
>> Datum: Fri, 13 Jun 2008 16:29:27 +0200
>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Bonjour ,
>>
>>
>> Thanks Andreas to restart the discussion about DeadServices and cleaning 
>> the registry.
>> I encounter the same problem in Remora.
>> The DeadServices list provided  is not exhaustive as you say.
>>
>> I launch every night a cleaner which do this thing:
>> - get all services registered in Mobycentral
>> - try to execute them with the perl command: eval 
>> {$service_instance->execute(XMLinputlist =>[[]])};
>>
>> Here is my list of Dead services (Ihave got also list for the 3 past 
>> days for testRegistry and Inab registry) :
>> http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral
>>
>> (Format is "service_name    auth_uri    registry_name    error_message")
>>
>> Most of them are 404 or 500 errors.
>>
>> If my test is correct, that means that around 10% of services are dead.
>> And here I cannot test if the returned message is well-formed (many 
>> changes happened since the birth of BioMOBY and maybe some services have 
>> not been updated), so it's at least 10%...
>>
>>  From my point of view, this problem of dead/non-functionnal  services 
>> is really a critical one.
>> We develop tools based on web-services and we advice our users to use 
>> tools such as Taverna, Remora etc...
>> So if the basis (web-services) is not robust, we lost all our credibility.
>>
>> We deploy here (Toulouse, France) procedures to test our services every 
>> night to ensure their availablity and stability.
>> I think it's time to currate the main registry.
>>
>> What do you think about this ?
>>
>> Sebastien
>>
>>
>>
>>
>> Andreas Groscurth wrote:
>>     
>>> Hi,
>>>
>>> just a short question about dead services.
>>> I call some services with my aggregator, which are registered at the 
>>> production central. Some of them always return and error and therefore 
>>> arent useable at all.
>>>
>>> E.g. getAREXGFPImageCollection from arexdb.org
>>>
>>> if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
>>> dead" - but on the "dead service" page it is not listed (and its dead 
>>> for a longer time)
>>>
>>> Also in the Java code in MobyService there are flags for the status of 
>>> a service - but how to i find them out - after a findService call all 
>>> service i retrieve have status 0 (unchecked).
>>>
>>> So my questions/comment:
>>>
>>> 1. The dead service page does not show up all dead services.
>>> 2. How do I find out with JMoby if a service is dead ?
>>>
>>> THX
>>> Andreas
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>       
>
>   

From markw at illuminae.com  Fri Jun 13 12:18:09 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 13 Jun 2008 09:18:09 -0700
Subject: [MOBY-dev] Fwd:  Unit testing of BioMoby Services
In-Reply-To: <op.t700xervnbznux@dd0710001l.icapture.ubc.ca>
References: <op.t700xervnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <op.uco2dkjmnbznux@dd0710001l.icapture.ubc.ca>

In response to the current discussion on automated testing of Moby  
services, I'm re-posting this email.

YES!  It needs to go into the formal API documentation.  My bad!  In the  
end, it became quite difficult to do the unit testing in perl because of  
the lack of support for OWL-RDF in Perl, so hopefully someone from the  
Java world will pick-up this ball and create the application that does it?

M



------- Forwarded message -------
From: "Mark Wilkinson" <markw at illuminae.com>
To: "moby Core developer announcements" <moby-dev at lists.open-bio.org>
Cc:
Subject: [MOBY-dev] Unit testing of BioMoby Services
Date: Fri, 14 Mar 2008 15:04:16 -0700

Hi all,

During the hackathon I was working on the OWL classes and predicates we
need for the ability to create unit tests in the Service metadata coming
  from the Service provider.  I just finished working things out with the
myGrid team, and here are the predicates and classes we have agreed on:

Namespace:  http://www.mygrid.org.uk/mygrid-moby-service#

Class:  #unitTest
usage:  can have one or more unitTests per service #operation


ObjectProperty:	#hasUnitTest
	domain:	#operation
	range:	#unitTest

DatatypeProperty:	#exampleInput
	domain:		#unitTest
	range:		xsd#string
	content:	the full SOAP payload XML of an invocation message
	
DatatypeProperty:	#validOutputXML
	domain:		#unitTest
	range:		xsd#string
	content:	the full SOAP payload of the associated output message

DatatypeProperty:	#validREGEX
	domain:		#unitTest
	range:		xsd#string
	content:	a regular expression that should match against the output SOAP
Payload of this unitTest

DatatypeProperty:	#validXPath
	domain:		#unitTest
	range:		xsd#string
	content:	an XPath expression that should match against the output SOAP
Payload of this unitTest


An example can be seen in the antirrhinum.net,getDragonAlleleLocus
service, whose signature RDF is available here:
http://moby.ucalgary.ca/signatures/antirrhinum.rdf

I'm almost finished writing a little Perl script that will go through and
test the services based on the Unit Test data - I'll put it in the CVS as
soon as it's done.

Cheers all!

Mark



-- 
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 edward.kawas at gmail.com  Mon Jun 16 13:36:50 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 16 Jun 2008 10:36:50 -0700
Subject: [MOBY-dev] sending data by reference
Message-ID: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>

Greetings all!

I remember that some time ago (Feb), we had a discussion on sending data by
reference and in fact agreed to some sort of mechanism, but I don't recall
the details. Does anyone else remember the specifics?

Thanks!

Eddie


From jmfernandez at cnio.es  Mon Jun 16 14:02:56 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Mon, 16 Jun 2008 20:02:56 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
Message-ID: <4856AAD0.50800@cnio.es>

Hi Eddie and everybody,
	AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were going to use 
XInclude for sending data by reference. We also talked about the need to 
create a "moby" URI protocol to specify the way to get referenced information 
reachable calling a MOBY service, and the need to negotiate between client and 
service the kind of reference protocols they share (i.e. they understand).

	If I have forgotten some detail, you are welcome to complement/correct my answer!

	Best Regards,
		Jos? Mar?a

Edward Kawas wrote:
> Greetings all!
> 
> I remember that some time ago (Feb), we had a discussion on sending data by
> reference and in fact agreed to some sort of mechanism, but I don't recall
> the details. Does anyone else remember the specifics?
> 
> Thanks!
> 
> Eddie
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

Jos? Mar?a Fern?ndez Gonz?lez
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinform?tica
Biolog?a Estructural y Biocomputaci?n	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncol?gicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)

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From serr at ac.uma.es  Tue Jun 17 02:41:02 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Tue, 17 Jun 2008 08:41:02 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
	<4856AAD0.50800@cnio.es>
Message-ID: <48575C7E.5040402@ac.uma.es>

Hello everybody,

I'm very interested in this theme.
I will truly appreciate if someone can sent me some examples of how the 
xml message will look.

Thanks in advance.
Sergio

Jos? Mar?a Fern?ndez Gonz?lez wrote:
> Hi Eddie and everybody,
>     AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were 
> going to use XInclude for sending data by reference. We also talked 
> about the need to create a "moby" URI protocol to specify the way to 
> get referenced information reachable calling a MOBY service, and the 
> need to negotiate between client and service the kind of reference 
> protocols they share (i.e. they understand).
>
>     If I have forgotten some detail, you are welcome to 
> complement/correct my answer!
>
>     Best Regards,
>         Jos? Mar?a
>
> Edward Kawas wrote:
>> Greetings all!
>>
>> I remember that some time ago (Feb), we had a discussion on sending 
>> data by
>> reference and in fact agreed to some sort of mechanism, but I don't 
>> recall
>> the details. Does anyone else remember the specifics?
>>
>> Thanks!
>>
>> Eddie
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>

-- 
Sergio Ram?rez Ram?rez
Instituto Nacional de Bioinform?tica (INB)
Integrated Bioinformatics Node (GNV-5)
Dpto. de Arquitectura de Computadores
Campus Universitario de Teatinos, despacho 2.3.9a
29071 M?laga (Spain) +34 95 213 3387


"Short-term decisions tend to fail in the long-term."
            Frank Herbert, God Emperor of Dune 


From dmitry.repchevski at bsc.es  Tue Jun 17 06:43:47 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Tue, 17 Jun 2008 12:43:47 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856AAD0.50800@cnio.es>
Message-ID: <48579563.3090303@bsc.es>

Doesn't we already have WSRF references?

I mean that they uniquely reference the resource that not necessary must 
be accessed from the same service that called "asynchronous" service.

Actually this is what WSRF is about - persistence rather than asynchrony.
We can use WS Addressing (as we do now) in the same way as for 
asynchronous services...
We can look also into WS-Naming specification from Open Grid consorcium 
(GDF-109.pdf).
The latest becomes the standard to reference webservices in a 
distributed world...

I am not sure how to include it into current Moby message... IMHO we 
desperately need a doc/lit schema based services to move forward (by the 
way, any news about Perl?).

I am going to rise all these question in INB meeting in Valencia 13-15 
of July.

Best regards,

Dmitry

From groscurt at mpiz-koeln.mpg.de  Tue Jun 17 08:17:27 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 17 Jun 2008 14:17:27 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <485296BF.8010303@ucalgary.ca>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>
	<485296BF.8010303@ucalgary.ca>
Message-ID: <4857AB57.8010203@mpiz-koeln.mpg.de>

Paul Gordon wrote:
> Hi all,
>
> I'll respond to several posts at once:
>
> 1. There is a list of dead services at Moby Central, but it is not 
> used by default in the jMoby API, and it's not part of the formal API. 
> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
thanks for the link - but for me it stops at

moby.ucalgary.ca

what about the other authorities ?

Thanks
andreas

From serr at ac.uma.es  Tue Jun 17 08:21:28 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Tue, 17 Jun 2008 14:21:28 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
	<4856AAD0.50800@cnio.es>
Message-ID: <4857AC48.4070803@ac.uma.es>

Hello everybody,

I'm very interested in this theme.
I will truly appreciate if someone can sent me some examples of how the
xml message will look.

Thanks in advance.
Sergio

Jos? Mar?a Fern?ndez Gonz?lez wrote:
> Hi Eddie and everybody,
>     AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were 
> going to use XInclude for sending data by reference. We also talked 
> about the need to create a "moby" URI protocol to specify the way to 
> get referenced information reachable calling a MOBY service, and the 
> need to negotiate between client and service the kind of reference 
> protocols they share (i.e. they understand).
>
>     If I have forgotten some detail, you are welcome to 
> complement/correct my answer!
>
>     Best Regards,
>         Jos? Mar?a
>
> Edward Kawas wrote:
>> Greetings all!
>>
>> I remember that some time ago (Feb), we had a discussion on sending 
>> data by
>> reference and in fact agreed to some sort of mechanism, but I don't 
>> recall
>> the details. Does anyone else remember the specifics?
>>
>> Thanks!
>>
>> Eddie
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>

-- 
Sergio Ram?rez Ram?rez
Instituto Nacional de Bioinform?tica (INB)
Integrated Bioinformatics Node (GNV-5)
Dpto. de Arquitectura de Computadores
Campus Universitario de Teatinos, despacho 2.3.9a
29071 M?laga (Spain) +34 95 213 3387


"Short-term decisions tend to fail in the long-term."
            Frank Herbert, God Emperor of Dune



From M4o at gmx.de  Tue Jun 17 08:30:59 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Tue, 17 Jun 2008 14:30:59 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857AB57.8010203@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>
Message-ID: <20080617123059.152780@gmx.net>

Hi all,

Andreas maybe try a reload.
For me it works for all auths.

In my Tool I use the adress with param: http://moby.ucalgary.ca/moby/ValidateService?getDeadServices

Maybe it is possible to extend the testing of the VaildateService function.

Moritz

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Paul Gordon wrote:
> > Hi all,
> >
> > I'll respond to several posts at once:
> >
> > 1. There is a list of dead services at Moby Central, but it is not 
> > used by default in the jMoby API, and it's not part of the formal API. 
> > http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> thanks for the link - but for me it stops at
> 
> moby.ucalgary.ca
> 
> what about the other authorities ?
> 
> Thanks
> andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger

From groscurt at mpiz-koeln.mpg.de  Tue Jun 17 08:40:04 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 17 Jun 2008 14:40:04 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617123059.152780@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>
	<20080617123059.152780@gmx.net>
Message-ID: <4857B0A4.2000005@mpiz-koeln.mpg.de>

weird..

also with deleting the browser cache - i only get the list to

moby.ucalgary.ca


regardlessly with or without param :(

andreas

M4o at gmx.de wrote:
> Hi all,
>
> Andreas maybe try a reload.
> For me it works for all auths.
>
> In my Tool I use the adress with param: http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
>
> Maybe it is possible to extend the testing of the VaildateService function.
>
> Moritz
>
> -------- Original-Nachricht --------
>   
>> Datum: Tue, 17 Jun 2008 14:17:27 +0200
>> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Paul Gordon wrote:
>>     
>>> Hi all,
>>>
>>> I'll respond to several posts at once:
>>>
>>> 1. There is a list of dead services at Moby Central, but it is not 
>>> used by default in the jMoby API, and it's not part of the formal API. 
>>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
>>>       
>> thanks for the link - but for me it stops at
>>
>> moby.ucalgary.ca
>>
>> what about the other authorities ?
>>
>> Thanks
>> andreas
>> _______________________________________________
>> 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  Tue Jun 17 10:01:45 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 07:01:45 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857B0A4.2000005@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
Message-ID: <4857c3de.1cba720a.3b23.5d4f@mx.google.com>

I get the same behaviour ... I am looking into it!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-17-08 5:40 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

weird..

also with deleting the browser cache - i only get the list to

moby.ucalgary.ca


regardlessly with or without param :(

andreas

M4o at gmx.de wrote:
> Hi all,
>
> Andreas maybe try a reload.
> For me it works for all auths.
>
> In my Tool I use the adress with param:
http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
>
> Maybe it is possible to extend the testing of the VaildateService
function.
>
> Moritz
>
> -------- Original-Nachricht --------
>   
>> Datum: Tue, 17 Jun 2008 14:17:27 +0200
>> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Paul Gordon wrote:
>>     
>>> Hi all,
>>>
>>> I'll respond to several posts at once:
>>>
>>> 1. There is a list of dead services at Moby Central, but it is not 
>>> used by default in the jMoby API, and it's not part of the formal API. 
>>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
>>>       
>> thanks for the link - but for me it stops at
>>
>> moby.ucalgary.ca
>>
>> what about the other authorities ?
>>
>> Thanks
>> andreas
>> _______________________________________________
>> 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 M4o at gmx.de  Tue Jun 17 10:45:21 2008
From: M4o at gmx.de (Moritz W)
Date: Tue, 17 Jun 2008 16:45:21 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857c3de.1cba720a.3b23.5d4f@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
Message-ID: <20080617144521.97370@gmx.net>

That's strange... 
I tried under my windows maschine with ie and firefox.
And also under a linux box with lynx:
Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt

Wget doesn't work (maybe wrong my wrong/missing params):
linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
--16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
           => `ValidateService'
Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
Connecting to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
HTTP Anforderung gesendet, warte auf Antwort... 200 OK
L??nge: nicht spezifiziert [text/plain]
ValidateService: Keine Berechtigung

I attached my result.

Hope my tests make sense...

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:01:45 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> I get the same behaviour ... I am looking into it!
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas
> Groscurth
> Sent: June-17-08 5:40 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> weird..
> 
> also with deleting the browser cache - i only get the list to
> 
> moby.ucalgary.ca
> 
> 
> regardlessly with or without param :(
> 
> andreas
> 
> M4o at gmx.de wrote:
> > Hi all,
> >
> > Andreas maybe try a reload.
> > For me it works for all auths.
> >
> > In my Tool I use the adress with param:
> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> >
> > Maybe it is possible to extend the testing of the VaildateService
> function.
> >
> > Moritz
> >
> > -------- Original-Nachricht --------
> >   
> >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> >>     
> >
> >   
> >> Paul Gordon wrote:
> >>     
> >>> Hi all,
> >>>
> >>> I'll respond to several posts at once:
> >>>
> >>> 1. There is a list of dead services at Moby Central, but it is not 
> >>> used by default in the jMoby API, and it's not part of the formal API.
> >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> >>>       
> >> thanks for the link - but for me it stops at
> >>
> >> moby.ucalgary.ca
> >>
> >> what about the other authorities ?
> >>
> >> Thanks
> >> andreas
> >> _______________________________________________
> >> 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

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
-------------- next part --------------

    The following are services, sorted by Service Provider, have been identified as "dead" by the MOBY Service Testing agent.
      
      A "dead" service is one that does not respond correctly to a MOBY "ping"; where a correct "ping" request/response is:
      
      REQUEST
      
            <MOBY>
            	<mobyContent></mobyContent>
            </MOBY>
      
      RESPONSE
      
            <MOBY>
            	<mobyContent></mobyContent>
            </MOBY>
      
      The status of all services is tested hourly, and is recorded in the 
      LSID metadata for each service as a boolean value in the RDF tag
       "isAlive", which may be used by client software to filter-out
       non-functional services.



	CDK.SF.NET
		CalculateAccurateMass

	ab.wur.nl
		MetwareGetExperimentRaw
		random_number
		xcmsFindPeaks

	arabidopsis.info
		getArabidopsisImageByNASCinsertNumber
		getArabidopsisImageByNASCstockCode

	arexdb.org
		getGOCollection

	asrp.cgrb.oregonstate.edu
		ASRP_miRNA_target_in_AGI
		ASRP_smallRNA_hit_in_IGR_downstream_of_AGI
		ASRP_smallRNA_hit_in_IGR_upstream_of_AGI
		ASRP_smallRNA_sequence_from_chromosomal_AGI

	bibiserv.techfak.uni-bielefeld.de
		RNAShapes_ConsensusShapes
		RNAShapes_Sampling
		RNAShapes_ShapeFolding
		RNAShapes_ShapeProbabilities
		RNAShapes_SuboptimalShapeFolding

	bioassist.nl
		BioAssistSequenceSorter

	bioinfo.cipf.es
		displayDifferentialExpressionTest
		runDifferentialExpressionTest

	bioinfo.icapture.ubc.ca
		GeneticMap2GFF
		getGoTerm
		getGoTermAssociations
		RetrieveGOFromKeywords

	bioinfo.mpimp-golm.mpg.de
		getTrypticPeptideSequenceByAGI

	biomoby.renci.org
		AntiGenic
		BackTranAmbig
		BackTranSeq
		Banana
		Biosed
		Blast
		Btwisted
		Cai
		Chaos
		Charge
		Checktrans
		Chips
		Clustalw
		Codcmp
		CompSeq
		Cons
		Consense
		CPGPlot
		CPGReport
		Cusp
		DeGapSeq
		DescSeq
		DiffSeq
		DNAComp
		DNADist
		DNAPars
		DNAPenny
		DotMatcher
		DotPath
		Dottup
		Drawgram
		Drawtree
		DReg
		EInverted
		Emowse
		EQuickTandem
		Est2Genome
		ETandem
		ExtractBlastReportSequences
		ExtractFeat
		ExtractSeq
		Fitch
		Freak
		FuzzNuc
		FuzzPro
		FuzzTran
		Garnier
		Geecee
		GetOrf
		HelixTurnHelix
		Iep
		InfoAlign
		IsNucleotideSequence
		IsoChore
		Kitsch
		Listor
		LookupSequence
		MakeNucSeq
		MakeProtSeq
		MarScan
		MaskFeat
		Matcher
		MegaMerger
		Merger
		MSBAR
		Needle
		Neighbor
		NewCPGReport
		NewCPGSeek
		NotSeq
		Octanol
		OddComp
		Palindrome
		PatMatDB
		PatMatMotifs
		PepCoil
		PepInfo
		PepNet
		PepStats
		PepWheel
		PepWindow
		PepWindowAll
		PlotCon
		PlotOrf
		PolyDot
		PrettyPlot
		PrettySeq
		ProtDist
		ProtPars
		Recoder
		RegisterAminoAcidSequence
		RegisterNucleotideSequence
		RegisterSequence
		RevSeq
		SeqMatchAll
		SeqRetSplit
		ShowAlign
		ShowFeat
		ShowOrf
		ShowSeq
		SigCleave
		Splitter
		Stretcher
		SuperMatcher
		Syco
		TFScan
		TranSeq
		TrimEST
		TrimSeq
		Union
		Water
		Wobble
		WordCount
		WordMatch

	bioserv.rpbs.jussieu.fr
		ASA
		ASAfromPDBid
		Automat
		BasicBuilder
		Clustalw
		CysPred
		ExtractTurn
		HBonds
		HCA
		Jnet
		Mead_PKa
		Mead_Pot
		NetAsa
		PredAcc
		PSea
		psiBlast
		psiPred
		Stride
		Substitution

	bioweb.pasteur.fr
		Melting

	ccgb.umn.edu
		GI2ScientificName
		MtKeyword

	ccrc.uga.edu
		ccrctest

	cshl.edu
		getArabidoposisAMIRNA

	heaven.mshri.on.ca
		GridService

	imb.uq.edu.au
		IMB_Get_MaximallyRepresentativeCluster

	inblosam.com
		extractGeneProteinNames

	itdinges.mine.nu
		Echo
		helloWorld

	llama.med.harvard.edu
		CCSBHI1
		CorrelatedCoexpression
		GavinSpoke
		Giot
		Harbison
		Ito2001
		Johnson
		LCI
		LeeTF
		Phosphorylome
		Shyamsundar
		Stelzl
		Su
		Tong2004
		Uetz
		Zhang

	metnetdb.org
		getMetNetComments
		getMetNetPathways

	migale.jouy.inra.fr
		Water

	mips.gsf.de
		BlastFastaVsArabiProteincoding
		BlastRawSeqVsArabiContigs
		BlastRawSeqVsArabiProteincoding
		getCosBBHForGene
		MIPSBlast
		MIPSBlastBetterE13
		MIPSBlastXML
		MIPSBlastXMLClickableImage

	mncn.csic.es
		getCoordinatesOfTaxon

	moby.ucalgary.ca
		ABIChromatogramToDNASequence
		ReverseComplementSequence
		TrimSequenceEndsOfAmbiguities
		TrimSequencePolyATail
		TrimSequenceVector


From edward.kawas at gmail.com  Tue Jun 17 10:46:47 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 07:46:47 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617144521.97370@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
	<20080617144521.97370@gmx.net>
Message-ID: <4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>

Yeah, some results are there, but like andreas mentioned ealier, the list
stops at moby.ucalgary.ca.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 7:45 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

That's strange... 
I tried under my windows maschine with ie and firefox.
And also under a linux box with lynx:
Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt

Wget doesn't work (maybe wrong my wrong/missing params):
linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
--16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
           => `ValidateService'
Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80 Connecting
to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
HTTP Anforderung gesendet, warte auf Antwort... 200 OK
L??nge: nicht spezifiziert [text/plain]
ValidateService: Keine Berechtigung

I attached my result.

Hope my tests make sense...

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:01:45 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> I get the same behaviour ... I am looking into it!
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> Groscurth
> Sent: June-17-08 5:40 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> weird..
> 
> also with deleting the browser cache - i only get the list to
> 
> moby.ucalgary.ca
> 
> 
> regardlessly with or without param :(
> 
> andreas
> 
> M4o at gmx.de wrote:
> > Hi all,
> >
> > Andreas maybe try a reload.
> > For me it works for all auths.
> >
> > In my Tool I use the adress with param:
> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> >
> > Maybe it is possible to extend the testing of the VaildateService
> function.
> >
> > Moritz
> >
> > -------- Original-Nachricht --------
> >   
> >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> >>     
> >
> >   
> >> Paul Gordon wrote:
> >>     
> >>> Hi all,
> >>>
> >>> I'll respond to several posts at once:
> >>>
> >>> 1. There is a list of dead services at Moby Central, but it is not 
> >>> used by default in the jMoby API, and it's not part of the formal API.
> >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> >>>       
> >> thanks for the link - but for me it stops at
> >>
> >> moby.ucalgary.ca
> >>
> >> what about the other authorities ?
> >>
> >> Thanks
> >> andreas
> >> _______________________________________________
> >> 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

--
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
downloaden: http://www.gmx.net/de/go/browser



From M4o at gmx.de  Tue Jun 17 11:16:13 2008
From: M4o at gmx.de (Moritz W)
Date: Tue, 17 Jun 2008 17:16:13 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>
	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
Message-ID: <20080617151613.198390@gmx.net>

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser

From edward.kawas at gmail.com  Tue Jun 17 11:18:14 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 08:18:14 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617151613.198390@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
Message-ID: <4857d5cc.08b38c0a.6aec.265a@mx.google.com>

No problem, I actually misread it a few times too!

Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 8:16 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From duncan.hull at cs.man.ac.uk  Tue Jun 17 11:30:12 2008
From: duncan.hull at cs.man.ac.uk (Duncan Hull)
Date: Tue, 17 Jun 2008 16:30:12 +0100
Subject: [MOBY-dev] BioMOBY gets fishy
In-Reply-To: <4857d5cc.08b38c0a.6aec.265a@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>
	<4857d5cc.08b38c0a.6aec.265a@mx.google.com>
Message-ID: <4857D884.4090609@cs.man.ac.uk>

Hello

Just spotted this, might be of interest...

http://pubmed.gov/18554176

FishMap: A Community Resource for Zebrafish Genomics (uses BioMOBY)

via the biomoby feed
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0vWF7uqpQRiVaiVbzYGm2HeVCqdj2BZfCXLbzPc6TZj

-- 
Duncan Hull
http://duncan.hull.name
+44 (0) 161 306 5138


From markw at illuminae.com  Tue Jun 17 14:15:45 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 17 Jun 2008 11:15:45 -0700
Subject: [MOBY-dev] BioMOBY gets fishy
In-Reply-To: <4857D884.4090609@cs.man.ac.uk>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net> <485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>
	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
	<20080617144521.97370@gmx.net>
	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
	<4857d5cc.08b38c0a.6aec.265a@mx.google.com>
	<4857D884.4090609@cs.man.ac.uk>
Message-ID: <op.ucwnojdqnbznux@mark.ubic.ca>

Cool :-)

Thanks Dull Hunk!

M


On Tue, 17 Jun 2008 08:30:12 -0700, Duncan Hull <duncan.hull at cs.man.ac.uk>  
wrote:

> Hello
>
> Just spotted this, might be of interest...
>
> http://pubmed.gov/18554176
>
> FishMap: A Community Resource for Zebrafish Genomics (uses BioMOBY)
>
> via the biomoby feed
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0vWF7uqpQRiVaiVbzYGm2HeVCqdj2BZfCXLbzPc6TZj
>



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From edward.kawas at gmail.com  Tue Jun 17 16:53:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 13:53:01 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617151613.198390@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
Message-ID: <48582444.22ba720a.14d5.ffffda5d@mx.google.com>

Okay, it works again.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 8:16 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From groscurt at mpiz-koeln.mpg.de  Wed Jun 18 09:10:21 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 18 Jun 2008 15:10:21 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48582444.22ba720a.14d5.ffffda5d@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>
	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>
Message-ID: <4859093D.4050800@mpiz-koeln.mpg.de>

Hi,

thanks for that it works....

one question i have about that - two of our services are marked as dead:

mpiz-koeln.mpg.de
	buildMultipleAlignmentWithMAFFT
	RPSBlast

and I'm wondering why ?

i tested them with the contract I know... giving an empty input should 
return an empty output.
They return an error message if no input is given - so this could be the 
reason, but all our other services do the same and they are not marked 
as dead ? so what is the base of this decision ?

now i'm also confused :D

Andreas

Edward Kawas wrote:
> Okay, it works again.
>
> Eddie
>


From edward.kawas at gmail.com  Wed Jun 18 09:14:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 18 Jun 2008 06:14:01 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4859093D.4050800@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>
	<4859093D.4050800@mpiz-koeln.mpg.de>
Message-ID: <48590a1a.1f588c0a.0b64.1fcf@mx.google.com>

Hi Andreas,

If you go to http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and
enter the service details, you will see what the service tester sees.

The first service in your list seems to return a page that starts with
'syntax error ...'

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-18-08 6:10 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Hi,

thanks for that it works....

one question i have about that - two of our services are marked as dead:

mpiz-koeln.mpg.de
	buildMultipleAlignmentWithMAFFT
	RPSBlast

and I'm wondering why ?

i tested them with the contract I know... giving an empty input should 
return an empty output.
They return an error message if no input is given - so this could be the 
reason, but all our other services do the same and they are not marked 
as dead ? so what is the base of this decision ?

now i'm also confused :D

Andreas

Edward Kawas wrote:
> Okay, it works again.
>
> Eddie
>

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From groscurt at mpiz-koeln.mpg.de  Wed Jun 18 09:26:39 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 18 Jun 2008 15:26:39 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48590a1a.1f588c0a.0b64.1fcf@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>	<4859093D.4050800@mpiz-koeln.mpg.de>
	<48590a1a.1f588c0a.0b64.1fcf@mx.google.com>
Message-ID: <48590D0F.6020404@mpiz-koeln.mpg.de>

Mistake on our side (they are registered on a host which is not visible 
to the outside....).... as usual - you did a good job ;-)

thanks
Andreas

Edward Kawas wrote:
> Hi Andreas,
>
> If you go to http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and
> enter the service details, you will see what the service tester sees.
>
> The first service in your list seems to return a page that starts with
> 'syntax error ...'
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-18-08 6:10 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
>
> Hi,
>
> thanks for that it works....
>
> one question i have about that - two of our services are marked as dead:
>
> mpiz-koeln.mpg.de
> 	buildMultipleAlignmentWithMAFFT
> 	RPSBlast
>
> and I'm wondering why ?
>
> i tested them with the contract I know... giving an empty input should 
> return an empty output.
> They return an error message if no input is given - so this could be the 
> reason, but all our other services do the same and they are not marked 
> as dead ? so what is the base of this decision ?
>
> now i'm also confused :D
>
> Andreas
>
> Edward Kawas wrote:
>   
>> Okay, it works again.
>>
>> Eddie
>>
>>     
>
> _______________________________________________
> 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 jflo at imim.es  Wed Jun 18 11:36:05 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 17:36:05 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
Message-ID: <48592B65.2030704@imim.es>

Hello everybody,

I have a "problem" with dashboard, when I "generate datatypes" I see a 
list of 630 datatypes, inside this list it appears text-xml, 
text-formatted, text_xml and text_formatted, but when I check the 
content of the jar, that is generated, it contains the text_ classes but 
not the text- ones.

In my jmoby project (eclipse) I can see that the datatypes that I create 
appear there, so I understand that I have the latest version of the list 
of datatypes, between them I cannot see the text- versions I just see 
the text_

Anyone has an idea about what can I do to have access to the text- 
objects? Am I missing something?

Thanks in advance,
j

From edward.kawas at gmail.com  Wed Jun 18 11:50:29 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 18 Jun 2008 08:50:29 -0700
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592B65.2030704@imim.es>
References: <48592B65.2030704@imim.es>
Message-ID: <48592ec7.1cbc720a.21de.1ac4@mx.google.com>

Hi Judith,

In java, '-' is a reserved token and so dashboard probably replaces it with
an '_'.

Martin can tell you for sure how it works.

Eddie



-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
Sent: June-18-08 8:36 AM
To: Core developer announcements
Subject: [MOBY-dev] dashboard problem generating datatypes

Hello everybody,

I have a "problem" with dashboard, when I "generate datatypes" I see a 
list of 630 datatypes, inside this list it appears text-xml, 
text-formatted, text_xml and text_formatted, but when I check the 
content of the jar, that is generated, it contains the text_ classes but 
not the text- ones.

In my jmoby project (eclipse) I can see that the datatypes that I create 
appear there, so I understand that I have the latest version of the list 
of datatypes, between them I cannot see the text- versions I just see 
the text_

Anyone has an idea about what can I do to have access to the text- 
objects? Am I missing something?

Thanks in advance,
j
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From jflo at imim.es  Wed Jun 18 12:02:55 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 18:02:55 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592ec7.1cbc720a.21de.1ac4@mx.google.com>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
Message-ID: <485931AF.5080300@imim.es>

Hi,
But the generated moby message contains also text_xml objects and not 
text-xml... :(
j

Edward Kawas wrote:
> Hi Judith,
>
> In java, '-' is a reserved token and so dashboard probably replaces it with
> an '_'.
>
> Martin can tell you for sure how it works.
>
> Eddie
>
>
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
> Sent: June-18-08 8:36 AM
> To: Core developer announcements
> Subject: [MOBY-dev] dashboard problem generating datatypes
>
> Hello everybody,
>
> I have a "problem" with dashboard, when I "generate datatypes" I see a 
> list of 630 datatypes, inside this list it appears text-xml, 
> text-formatted, text_xml and text_formatted, but when I check the 
> content of the jar, that is generated, it contains the text_ classes but 
> not the text- ones.
>
> In my jmoby project (eclipse) I can see that the datatypes that I create 
> appear there, so I understand that I have the latest version of the list 
> of datatypes, between them I cannot see the text- versions I just see 
> the text_
>
> Anyone has an idea about what can I do to have access to the text- 
> objects? Am I missing something?
>
> Thanks in advance,
> j
> _______________________________________________
> 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 martin.senger at gmail.com  Wed Jun 18 12:58:59 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 00:58:59 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592B65.2030704@imim.es>
References: <48592B65.2030704@imim.es>
Message-ID: <4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>

> I have a "problem" with dashboard, when I "generate datatypes" I see a list
> of 630 datatypes, inside this list it appears text-xml, text-formatted,
> text_xml and text_formatted, but when I check the content of the jar, that
> is generated, it contains the text_ classes but not the text- ones.


MoSeS generator changes dashes to underscore. Which means that both Moby
data types text-plain and text_plain are represented by only one class. You
cannot distinguish them. However, MoSeS and Dashboard know what moby data
type is expected by a service and send a correct type (text-plain, or
text_plain). I forgot already how it is done, but it seems to work fine (you
can try - in Dashboard - to generate XML input, for example for a service
TestService and you will se there text-plain object.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From markw at illuminae.com  Wed Jun 18 13:00:58 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 18 Jun 2008 10:00:58 -0700
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>
References: <48592B65.2030704@imim.es>
	<4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>
Message-ID: <op.ucyevwkrnbznux@dd0710001l.icapture.ubc.ca>

I think we should curate the ontology... are there still services that use  
both nodes?

M



On Wed, 18 Jun 2008 09:58:59 -0700, Martin Senger  
<martin.senger at gmail.com> wrote:

>> I have a "problem" with dashboard, when I "generate datatypes" I see a  
>> list
>> of 630 datatypes, inside this list it appears text-xml, text-formatted,
>> text_xml and text_formatted, but when I check the content of the jar,  
>> that
>> is generated, it contains the text_ classes but not the text- ones.
>
>
> MoSeS generator changes dashes to underscore. Which means that both Moby
> data types text-plain and text_plain are represented by only one class.  
> You
> cannot distinguish them. However, MoSeS and Dashboard know what moby data
> type is expected by a service and send a correct type (text-plain, or
> text_plain). I forgot already how it is done, but it seems to work fine  
> (you
> can try - in Dashboard - to generate XML input, for example for a service
> TestService and you will se there text-plain object.
>
> Martin
>



-- 
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 martin.senger at gmail.com  Wed Jun 18 13:10:13 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:10:13 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485931AF.5080300@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
Message-ID: <4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>

> But the generated moby message contains also text_xml objects and not
> text-xml...


Well, show me the message . Are you talking about a request or response?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From jflo at imim.es  Wed Jun 18 13:32:44 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 19:32:44 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
Message-ID: <485946BC.5090603@imim.es>

This is the message that I send to the service (it is a tcpmon capture 
with all the &lt; and &gt! changed to < and >):

<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope 
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" 
xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:runByoDyn 
soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" 
xmlns:ns1="http://biomoby.org/"><ns1:arg0 xsi:type="soapenc:string" 
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"><?xml 
version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?>
<moby:MOBY xmlns:moby=&quot;http://www.biomoby.org/moby>
  <moby:mobyContent>
    <moby:mobyData moby:queryID=&quot;job_0>
      <moby:Simple moby:articleName=&quot;input>
        <moby:*text_xml* moby:id=&quot;BIOMD0000000050.xml&quot; 
moby:namespace=&quot;text-xml>
          <moby:String moby:id=&quot;&quot; moby:namespace=&quot;&quot; 
moby:articleName=&quot;content>

BLA BLA LBA

    </moby:String>
        </moby:*text_xml*>
      </moby:Simple>
 
      <moby:Simple moby:articleName=&quot;parameters>
        <moby:*text_formatted* moby:id=&quot;runnerFile&quot; 
moby:namespace=&quot;text-formatted>
          <moby:String moby:id=&quot;&quot; moby:namespace=&quot;&quot; 
moby:articleName=&quot;content>


BLA BLA BLA

     </moby:String>
        </moby:*text_formatted*>
      </moby:Simple>
    </moby:mobyData>
  </moby:mobyContent>
</moby:MOBY>
S
 
</ns1:arg0></ns1:runByoDyn></soapenv:Body></soapenv:Envelope>

The service that i'm calling uses the text- objects...

Martin Senger wrote:
>> But the generated moby message contains also text_xml objects and not
>> text-xml...
>>     
>
>
> Well, show me the message . Are you talking about a request or response?
>
> Martin
>
>   

From martin.senger at gmail.com  Wed Jun 18 13:48:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:48:06 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485946BC.5090603@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
Message-ID: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>

> This is the message that I send to the service...


Which service it is? Do I have access to its description? Or perhaps even to
call it?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Wed Jun 18 13:48:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:48:06 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485946BC.5090603@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
Message-ID: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>

> This is the message that I send to the service...


Which service it is? Do I have access to its description? Or perhaps even to
call it?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From judit.flo at gmail.com  Wed Jun 18 16:58:47 2008
From: judit.flo at gmail.com (Judith Flo)
Date: Wed, 18 Jun 2008 22:58:47 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
Message-ID: <48597707.1030505@imim.es>

The service is registered under the moby-dev repository, it is called 
runByoDyn, created by the auth inb.bsc.es


Martin Senger escribi?:
>> This is the message that I send to the service...
>>     
>
>
> Which service it is? Do I have access to its description? Or perhaps even to
> call it?
>
> Martin
>
>   

From jflo at imim.es  Wed Jun 18 17:00:38 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 23:00:38 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
Message-ID: <48597776.1070804@imim.es>

The service is registered under the moby-dev repository, it is called
runByoDyn, created by the auth inb.bsc.es


Martin Senger escribi?:
>> This is the message that I send to the service...
>>     
>
>
> Which service it is? Do I have access to its description? Or perhaps even to
> call it?
>
> Martin
>
>   



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From martin.senger at gmail.com  Wed Jun 18 22:08:21 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 10:08:21 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48597776.1070804@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
Message-ID: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>

> The service is registered under the moby-dev repository, it is called
> runByoDyn, created by the auth inb.bsc.es
>


Okay, I see the service now. And *it is clear now what is the problem*. The
service runByoDyn is an asynchronous service. And neither Dashboard nor
MoSeS have support for asynchronous services. I should be working on it, but
it is not there yet (not a priority in my current funding, unfortunately).
Bad luck for you, sorry.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From jflo at imim.es  Thu Jun 19 05:33:23 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 19 Jun 2008 11:33:23 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
Message-ID: <485A27E3.8000007@imim.es>

But I run it and got results using dashboard!

It returns a Zip_encoded object (base64), the service is async because 
there are some executions that takes lot of time and consume the 
timeout... But for "simple" executions it should return this zip_encoded 
object (in fact as I said, I test it and it works)

Does the dashboard use different libraries than moses (to generate the 
datatypes), I'm asking this to understand why my message is different 
(in terms of text_ objects) from the one that the dashboard generates...

(Sorry Martin, you'll receive this message twice, I don't know if there 
is someone in the list that can put some light on this...)

Martin Senger wrote:
>
> Okay, I see the service now. And *it is clear now what is the problem*. The
> service runByoDyn is an asynchronous service. And neither Dashboard nor
> MoSeS have support for asynchronous services. I should be working on it, but
> it is not there yet (not a priority in my current funding, unfortunately).
> Bad luck for you, sorry.
>
> Martin

From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 04:52:08 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 25 Jun 2008 10:52:08 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <485A27E3.8000007@imim.es>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es>
Message-ID: <48620738.7050103@mpiz-koeln.mpg.de>

Hi,

i dont know if i missed that somehow or if this is still an issue - but 
it came up here as currently biomoby.org is unavailable.

Is there a possibilty to use the cached ontologies for the jMoby API ?

My problem is that each time i start an application which e.g. calles a 
BioMoby service the datatype ontology and namespace ontology are fetched 
from http://biomoby.org.
Is it possible somehow to tell the API not to download it from the net 
but to use a local cache?

I'm not sure whether this was already a discussion before and i remember 
something about the Registry - but please give me some hints if and how 
this is possible ?

Thanks
andreas

From martin.senger at gmail.com  Wed Jun 25 04:59:45 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 16:59:45 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <48620738.7050103@mpiz-koeln.mpg.de>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es> <48620738.7050103@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>

> My problem is that each time i start an application which e.g. calles a
> BioMoby service the datatype ontology and namespace ontology are fetched
> from http://biomoby.org.
> Is it possible somehow to tell the API not to download it from the net but
> to use a local cache?


For calling a service, you do not need any ontology at all - you just need
to know the service URL and what data type it expects.

Depending on the librray you are using, you can get even the information
that you do not need, from a local cache. Exactly the same way as Dashboard
does it. It uses
CentralDigestCachedImpl class (to access moby registry).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 05:41:56 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 25 Jun 2008 11:41:56 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>	<485A27E3.8000007@imim.es>
	<48620738.7050103@mpiz-koeln.mpg.de>
	<4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
Message-ID: <486212E4.2030304@mpiz-koeln.mpg.de>

thx martin,

but if i understand it correctly the CentralDigestCachedImpl does access 
a default moby registry and then caches it locally. What I'm interessted 
in is not to access any registry at all for getting the ontologies.
My sitatuation is that i query the moby central to find some services 
based on e.g. their input and output parameters. So I use 
MobyNames.getMobyNamespace("gi"); for example. This will download the 
ontgologies from biomoby.org.

So did i understand this wrong ? all classes will download the 
ontologies once and then some caches them ? this would mean that at 
start it will always download the ontologies ?

thx
andreas

Martin Senger wrote:
>> My problem is that each time i start an application which e.g. calles a
>> BioMoby service the datatype ontology and namespace ontology are fetched
>> from http://biomoby.org.
>> Is it possible somehow to tell the API not to download it from the net but
>> to use a local cache?
>>     
>
>
> For calling a service, you do not need any ontology at all - you just need
> to know the service URL and what data type it expects.
>
> Depending on the librray you are using, you can get even the information
> that you do not need, from a local cache. Exactly the same way as Dashboard
> does it. It uses
> CentralDigestCachedImpl class (to access moby registry).
>
> Martin
>
>   


From martin.senger at gmail.com  Wed Jun 25 06:54:43 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 18:54:43 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <486212E4.2030304@mpiz-koeln.mpg.de>
References: <48592B65.2030704@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es> <48620738.7050103@mpiz-koeln.mpg.de>
	<4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
	<486212E4.2030304@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>

> but if i understand it correctly the CentralDigestCachedImpl does access a
> default moby registry and then caches it locally.


Actually no. The class gets, in its constructor, a local directory where the
cached ontology are located, and uses it. Only if the cache is empty, it
tries to fill it.


> What I'm interessted in is not to access any registry at all for getting
> the ontologies.
> My sitatuation is that i query the moby central to find some services based
> on e.g. their input and output parameters.


The cache does not have the "find" method - we did not want to replicate the
whole registry's API. But because all ontologies are locally available, it
is easy to get them all (that's why the class is also called "digest",
because it provides the cumulative methods that the registry's API does not
provide in all cases) and iterate over them and make your search as you
wish.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 07:28:55 2008
From: groscurt at mpiz-koeln.mpg.de (groscurt)
Date: Wed, 25 Jun 2008 13:28:55 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>
Message-ID: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>

this is an example code:

Central central = new CentralDigestCachedImpl(
"/home/pcb/groscurt/moby-live/Java/myCache" );
MobyService mobyService = new MobyService();
mobyService.setAuthority( "arabidopsis.org" );
mobyService.setName( "Locus2Publications" );
mobyService.setCategory( "" );
mobyService = central.findService( mobyService )[0];

MobyRequest mobyRequest = new MobyRequest( central );
mobyRequest.setService( mobyService );
mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );

running this starts to download the ontologies from biomoby.org. I guess the
handling of the MobyRequest stuff is the problem here - but how to solve
that ?

Best and thanks
andreas

----------------original message-----------------
From: "Martin Senger" martin.senger at gmail.com
To: "Core developer announcements" moby-dev at lists.open-bio.org
Date: Wed, 25 Jun 2008 18:54:43 +0800
-------------------------------------------------
>> but if i understand it correctly the CentralDigestCachedImpl does access
a
>> default moby registry and then caches it locally.
> 
> 
> Actually no. The class gets, in its constructor, a local directory where
the
> cached ontology are located, and uses it. Only if the cache is empty, it
> tries to fill it.
> 
> 
>> What I'm interessted in is not to access any registry at all for getting
>> the ontologies.
>> My sitatuation is that i query the moby central to find some services
based
>> on e.g. their input and output parameters.
> 
> 
> The cache does not have the "find" method - we did not want to replicate
the
> whole registry's API. But because all ontologies are locally available, it
> is easy to get them all (that's why the class is also called "digest",
> because it provides the cumulative methods that the registry's API does
not
> provide in all cases) and iterate over them and make your search as you
> wish.
> 
> Martin
> 
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 




From martin.senger at gmail.com  Wed Jun 25 08:42:08 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 20:42:08 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>
	<83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250542w1c9bbed3h44567239cd83a6d5@mail.gmail.com>

> running this starts to download the ontologies from biomoby.org. I guess
> the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?


No idea, I do not use MobyRequest. It's rhe Paul's branche of jMoby...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From gordonp at ucalgary.ca  Wed Jun 25 10:20:30 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 25 Jun 2008 08:20:30 -0600
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4862542E.7050009@ucalgary.ca>

Hi Andreas,

I still need to update some of the code to use the new caching that 
Eddie implemented in February while we were in Japan.  I've been out of 
the Moby loop for a while, but starting this week I'll be able to start 
working on it again, so it should cache by default Real Soon Now(TM).

Paul

groscurt wrote:
> this is an example code:
>
> Central central = new CentralDigestCachedImpl(
> "/home/pcb/groscurt/moby-live/Java/myCache" );
> MobyService mobyService = new MobyService();
> mobyService.setAuthority( "arabidopsis.org" );
> mobyService.setName( "Locus2Publications" );
> mobyService.setCategory( "" );
> mobyService = central.findService( mobyService )[0];
>
> MobyRequest mobyRequest = new MobyRequest( central );
> mobyRequest.setService( mobyService );
> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );
>
> running this starts to download the ontologies from biomoby.org. I guess the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?
>
> Best and thanks
> andreas
>
> ----------------original message-----------------
> From: "Martin Senger" martin.senger at gmail.com
> To: "Core developer announcements" moby-dev at lists.open-bio.org
> Date: Wed, 25 Jun 2008 18:54:43 +0800
> -------------------------------------------------
>   
>>> but if i understand it correctly the CentralDigestCachedImpl does access
>>>       
> a
>   
>>> default moby registry and then caches it locally.
>>>       
>> Actually no. The class gets, in its constructor, a local directory where
>>     
> the
>   
>> cached ontology are located, and uses it. Only if the cache is empty, it
>> tries to fill it.
>>
>>
>>     
>>> What I'm interessted in is not to access any registry at all for getting
>>> the ontologies.
>>> My sitatuation is that i query the moby central to find some services
>>>       
> based
>   
>>> on e.g. their input and output parameters.
>>>       
>> The cache does not have the "find" method - we did not want to replicate
>>     
> the
>   
>> whole registry's API. But because all ontologies are locally available, it
>> is easy to get them all (that's why the class is also called "digest",
>> because it provides the cumulative methods that the registry's API does
>>     
> not
>   
>> provide in all cases) and iterate over them and make your search as you
>> wish.
>>
>> Martin
>>
>> -- 
>> Martin Senger
>> email: martin.senger at gmail.com,m.senger at cgiar.org
>> skype: martinsenger
>> _______________________________________________
>> 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
>
> !DSPAM:60005,48622972109501804129376!
>
>
>
>   

From dmitry.repchevski at bsc.es  Thu Jun 26 06:49:31 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Thu, 26 Jun 2008 12:49:31 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
Message-ID: <4863743B.3040909@bsc.es>

Hello Martin,
> Okay, I see the service now. And *it is clear now what is the problem*. The
> service runByoDyn is an asynchronous service. And neither Dashboard nor
> MoSeS have support for asynchronous services. I should be working on it, but
> it is not there yet (not a priority in my current funding, unfortunately).
> Bad luck for you, sorry.
When you mention Dashboard/MoSeS or JMoby?
Should we understand it that there is no java asynchrony planned for JMoby?

 > Judith:

You can try my library that supports asynchrony (if you need to call an 
asynchronous service from Java).
You can download it at http://inb.bsc.es/documents/java/index.html

I am going to talk about it in Valencia, but don't hesitate to write me 
if you will face some problem with it.

Dmitry


From martin.senger at gmail.com  Thu Jun 26 07:45:14 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 26 Jun 2008 19:45:14 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4863743B.3040909@bsc.es>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<4863743B.3040909@bsc.es>
Message-ID: <4d93f07c0806260445wbadd4davb22080e279282434@mail.gmail.com>

> When you mention Dashboard/MoSeS or JMoby?
> Should we understand it that there is no java asynchrony planned for JMoby?


It is planned.
M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From jflo at imim.es  Thu Jun 26 11:25:20 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 26 Jun 2008 17:25:20 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4863743B.3040909@bsc.es>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<4863743B.3040909@bsc.es>
Message-ID: <4863B4E0.7040503@imim.es>

Hi everyone,

I suppose that I'm confused about my problem with the text_ objects 
because noone has answered...

Anyway, I really need this "asynchronous thing" working and I can't wait 
:( --nor switch to perl--

I checked this library from Dmitry and I have to say that his job is 
really good, I changed my code and everything is working now! No 
problems with sync netiher async services!

Thanks Dmitry!
j


Dmitry Repchevsky wrote:
> Hello Martin,
>> Okay, I see the service now. And *it is clear now what is the 
>> problem*. The
>> service runByoDyn is an asynchronous service. And neither Dashboard nor
>> MoSeS have support for asynchronous services. I should be working on 
>> it, but
>> it is not there yet (not a priority in my current funding, 
>> unfortunately).
>> Bad luck for you, sorry.
> When you mention Dashboard/MoSeS or JMoby?
> Should we understand it that there is no java asynchrony planned for 
> JMoby?
>
> > Judith:
>
> You can try my library that supports asynchrony (if you need to call 
> an asynchronous service from Java).
> You can download it at http://inb.bsc.es/documents/java/index.html
>
> I am going to talk about it in Valencia, but don't hesitate to write 
> me if you will face some problem with it.
>
> Dmitry

From gordonp at ucalgary.ca  Thu Jun 26 11:44:09 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 26 Jun 2008 09:44:09 -0600
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4863B949.9020204@ucalgary.ca>

Hi Andreas & Martin,

The issue is that you should really be calling

new MobyDataObject("AGI_LocusCode", "at4g30110", central)

on the last line of your example, but of course it's not your fault.  
The org.biomoby.shared.data package takes Registry as an optional 
argument for all of the constructors, and I had a mechanism that allowed 
you to associate a Registry object with a cache.  Because we are moving 
to a unified caching mechanism, the ideal solution from my perspective 
would be for Registry to become an interface, Central extends Registry, 
and all of the CentralImpls are children of the old Registry object 
(which becomes RegistryImpl).  Martin, would you have any objections if 
I did this?  I think the Registry -> Central hierarchy makes sense as 
you move from metadata to metadata+data.

Of course, if you wanted to use the default central endpoint and caching 
directory, the

new MobyDataObject("AGI_LocusCode", "at4g30110")

call would be all that is required under the new system.

Regards,

Paul

groscurt wrote:
> this is an example code:
>
> Central central = new CentralDigestCachedImpl(
> "/home/pcb/groscurt/moby-live/Java/myCache" );
> MobyService mobyService = new MobyService();
> mobyService.setAuthority( "arabidopsis.org" );
> mobyService.setName( "Locus2Publications" );
> mobyService.setCategory( "" );
> mobyService = central.findService( mobyService )[0];
>
> MobyRequest mobyRequest = new MobyRequest( central );
> mobyRequest.setService( mobyService );
> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );
>
> running this starts to download the ontologies from biomoby.org. I guess the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?
>
> Best and thanks
> andreas
>
> ----------------original message-----------------
> From: "Martin Senger" martin.senger at gmail.com
> To: "Core developer announcements" moby-dev at lists.open-bio.org
> Date: Wed, 25 Jun 2008 18:54:43 +0800
> -------------------------------------------------
>   
>>> but if i understand it correctly the CentralDigestCachedImpl does access
>>>       
> a
>   
>>> default moby registry and then caches it locally.
>>>       
>> Actually no. The class gets, in its constructor, a local directory where
>>     
> the
>   
>> cached ontology are located, and uses it. Only if the cache is empty, it
>> tries to fill it.
>>
>>
>>     
>>> What I'm interessted in is not to access any registry at all for getting
>>> the ontologies.
>>> My sitatuation is that i query the moby central to find some services
>>>       
> based
>   
>>> on e.g. their input and output parameters.
>>>       
>> The cache does not have the "find" method - we did not want to replicate
>>     
> the
>   
>> whole registry's API. But because all ontologies are locally available, it
>> is easy to get them all (that's why the class is also called "digest",
>> because it provides the cumulative methods that the registry's API does
>>     
> not
>   
>> provide in all cases) and iterate over them and make your search as you
>> wish.
>>
>> Martin
>>
>> -- 
>> Martin Senger
>> email: martin.senger at gmail.com,m.senger at cgiar.org
>> skype: martinsenger
>> _______________________________________________
>> 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
>
> !DSPAM:60005,48622972109501804129376!
>
>
>
>   

From groscurt at mpiz-koeln.mpg.de  Fri Jun 27 03:04:22 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 27 Jun 2008 09:04:22 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <486490F6.7060706@mpiz-koeln.mpg.de>

Hi Paul,

as far as i can oversee that, this sounds quite reasonable for me. I was 
always wondered what a Central is if not a registry... so it sounds ok 
to make a connection between them programmatically. As long as this wont 
destroy current usage of the code - but that does not seems to be the 
case as you described it.

Looking forward for this :)

Andreas

Paul Gordon wrote:
> Hi Andreas & Martin,
>
> The issue is that you should really be calling
>
> new MobyDataObject("AGI_LocusCode", "at4g30110", central)
>
> on the last line of your example, but of course it's not your fault.  
> The org.biomoby.shared.data package takes Registry as an optional 
> argument for all of the constructors, and I had a mechanism that 
> allowed you to associate a Registry object with a cache.  Because we 
> are moving to a unified caching mechanism, the ideal solution from my 
> perspective would be for Registry to become an interface, Central 
> extends Registry, and all of the CentralImpls are children of the old 
> Registry object (which becomes RegistryImpl).  Martin, would you have 
> any objections if I did this?  I think the Registry -> Central 
> hierarchy makes sense as you move from metadata to metadata+data.
>
> Of course, if you wanted to use the default central endpoint and 
> caching directory, the
>
> new MobyDataObject("AGI_LocusCode", "at4g30110")
>
> call would be all that is required under the new system.
>
> Regards,
>
> Paul
>
> groscurt wrote:
>> this is an example code:
>>
>> Central central = new CentralDigestCachedImpl(
>> "/home/pcb/groscurt/moby-live/Java/myCache" );
>> MobyService mobyService = new MobyService();
>> mobyService.setAuthority( "arabidopsis.org" );
>> mobyService.setName( "Locus2Publications" );
>> mobyService.setCategory( "" );
>> mobyService = central.findService( mobyService )[0];
>>
>> MobyRequest mobyRequest = new MobyRequest( central );
>> mobyRequest.setService( mobyService );
>> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", 
>> "at4g30110") );
>>
>> running this starts to download the ontologies from biomoby.org. I 
>> guess the
>> handling of the MobyRequest stuff is the problem here - but how to solve
>> that ?
>>
>> Best and thanks
>> andreas
>>
>> ----------------original message-----------------
>> From: "Martin Senger" martin.senger at gmail.com
>> To: "Core developer announcements" moby-dev at lists.open-bio.org
>> Date: Wed, 25 Jun 2008 18:54:43 +0800
>> -------------------------------------------------
>>  
>>>> but if i understand it correctly the CentralDigestCachedImpl does 
>>>> access
>>>>       
>> a
>>  
>>>> default moby registry and then caches it locally.
>>>>       
>>> Actually no. The class gets, in its constructor, a local directory 
>>> where
>>>     
>> the
>>  
>>> cached ontology are located, and uses it. Only if the cache is 
>>> empty, it
>>> tries to fill it.
>>>
>>>
>>>    
>>>> What I'm interessted in is not to access any registry at all for 
>>>> getting
>>>> the ontologies.
>>>> My sitatuation is that i query the moby central to find some services
>>>>       
>> based
>>  
>>>> on e.g. their input and output parameters.
>>>>       
>>> The cache does not have the "find" method - we did not want to 
>>> replicate
>>>     
>> the
>>  
>>> whole registry's API. But because all ontologies are locally 
>>> available, it
>>> is easy to get them all (that's why the class is also called "digest",
>>> because it provides the cumulative methods that the registry's API does
>>>     
>> not
>>  
>>> provide in all cases) and iterate over them and make your search as you
>>> wish.
>>>
>>> Martin
>>>
>>> -- 
>>> Martin Senger
>>> email: martin.senger at gmail.com,m.senger at cgiar.org
>>> skype: martinsenger
>>> _______________________________________________
>>> 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
>>
>> !DSPAM:60005,48622972109501804129376!
>>
>>
>>
>>   
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From martin.senger at gmail.com  Sun Jun 29 23:14:09 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Mon, 30 Jun 2008 11:14:09 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <4d93f07c0806292014m310611f8ieba71594b9968d6d@mail.gmail.com>

> Central extends Registry...


Central already has constructors taking the registry. No need to change
anything - I think. But I cannot check it now, not being on my computer. I
will reply once again later.

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Mon Jun 30 14:19:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 1 Jul 2008 02:19:06 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <4d93f07c0806301119s6bf0fc71geee901bf51c223c9@mail.gmail.com>

> Because we are moving to a unified caching mechanism, the ideal solution
> from my perspective would be for Registry to become an interface


Sorry, Paul, but from my perspective, I would keep it as it is. The
CentralImpl has an ability (in constructors) to specify which registry to
talk to, and always had. If you wish to use it (and you should, but it is
jut my personal perspective) you should comply with it.

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From andreas.groscurth at web.de  Mon Jun 30 10:53:54 2008
From: andreas.groscurth at web.de (Andreas Groscurthh)
Date: Mon, 30 Jun 2008 16:53:54 +0200
Subject: [MOBY-dev] question about mobycentral database
Message-ID: <4868F382.4000907@web.de>

Hi,

a short question about the database schema of mobycentral.

There are 2 databases (ofc among others) - mobyservice and mobycentral. 
mobyservice contains the table service and mobycentral service_instance.

If a service is registered - in which table is the information written ? 
in both ? and is then the service_instance_id from service_instance the 
same as service_id from service ? or is there another difference between 
these two tables ?

mhm ok - more than one question actually ;-)

Thanks
Andreas

From edward.kawas at gmail.com  Mon Jun 30 16:19:44 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 30 Jun 2008 13:19:44 -0700
Subject: [MOBY-dev] question about mobycentral database
In-Reply-To: <4868F382.4000907@web.de>
References: <4868F382.4000907@web.de>
Message-ID: <48693ff1.16538c0a.7690.1984@mx.google.com>

Hi Andreas,

The db mobycentral contains all the information for service instances, while
the db mobyservice contains information for service types.

When you register a new service instance, the information is kept in
mobycentral.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurthh
Sent: June-30-08 7:54 AM
To: Core developer announcements
Subject: [MOBY-dev] question about mobycentral database

Hi,

a short question about the database schema of mobycentral.

There are 2 databases (ofc among others) - mobyservice and mobycentral. 
mobyservice contains the table service and mobycentral service_instance.

If a service is registered - in which table is the information written ? 
in both ? and is then the service_instance_id from service_instance the 
same as service_id from service ? or is there another difference between 
these two tables ?

mhm ok - more than one question actually ;-)

Thanks
Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From martin.senger at gmail.com  Mon Jun 30 16:20:18 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 1 Jul 2008 04:20:18 +0800
Subject: [MOBY-dev] jMoby does not compile!
Message-ID: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>

Whoever committed it please rectify it.

Thanks,
Martin

compile:
    [javac] Compiling 348 source files to
/home/senger/moby-live/Java/build/classes
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/test/WSDLServiceTestCase.java:8:
cannot find symbol
    [javac] symbol  : class WSDLService
    [javac] location: package ca.ucalgary.services
    [javac] import ca.ucalgary.services.WSDLService;
    [javac]                             ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:406:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]     NodeList schemaElements =
wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:422:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]
if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI()))
&&
    [javac]                                       ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:436:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                     NodeList contentElements =
schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:440:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                             ((Element)
contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:443:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                             NodeList attributeElements =
((Element)
restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:465:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]
if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
    [javac]                                                               ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:472:
cannot find symbol
    [javac] symbol  : method isLSID(java.lang.String)
    [javac] location: class org.biomoby.shared.LSIDResolver
    [javac]
if(lsidResolver.isLSID(schemaMapping)){
    [javac]                                                                ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:494:
cannot find symbol
    [javac] symbol  : method isLSID(java.lang.String)
    [javac] location: class org.biomoby.shared.LSIDResolver
    [javac]                 if(lsidResolver.isLSID(schemaMapping)){
    [javac]                                    ^
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 9 errors



-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From gordonp at ucalgary.ca  Mon Jun 30 17:28:10 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 30 Jun 2008 15:28:10 -0600
Subject: [MOBY-dev] jMoby does not compile!
In-Reply-To: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>
References: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>
Message-ID: <48694FEA.3070107@ucalgary.ca>

Fixed now.  Sorry, I was in the middle of a string of commits and had to 
leave the office unexpectedly.  One argument for svn I suppose...

Martin Senger wrote:
> Whoever committed it please rectify it.
>
> Thanks,
> Martin
>
> compile:
>     [javac] Compiling 348 source files to
> /home/senger/moby-live/Java/build/classes
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/test/WSDLServiceTestCase.java:8:
> cannot find symbol
>     [javac] symbol  : class WSDLService
>     [javac] location: package ca.ucalgary.services
>     [javac] import ca.ucalgary.services.WSDLService;
>     [javac]                             ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:406:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]     NodeList schemaElements =
> wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:422:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]
> if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI()))
> &&
>     [javac]                                       ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:436:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                     NodeList contentElements =
> schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:440:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                             ((Element)
> contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:443:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                             NodeList attributeElements =
> ((Element)
> restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:465:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]
> if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
>     [javac]                                                               ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:472:
> cannot find symbol
>     [javac] symbol  : method isLSID(java.lang.String)
>     [javac] location: class org.biomoby.shared.LSIDResolver
>     [javac]
> if(lsidResolver.isLSID(schemaMapping)){
>     [javac]                                                                ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:494:
> cannot find symbol
>     [javac] symbol  : method isLSID(java.lang.String)
>     [javac] location: class org.biomoby.shared.LSIDResolver
>     [javac]                 if(lsidResolver.isLSID(schemaMapping)){
>     [javac]                                    ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 9 errors
>
>
>
>   

From Sebastien.Carrere at toulouse.inra.fr  Thu Jun  5 07:41:44 2008
From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Thu, 05 Jun 2008 09:41:44 +0200
Subject: [MOBY-dev] Moby down ?
Message-ID: <484798B8.8080609@toulouse.inra.fr>

Hi all,

Is Moby main server down ?
Here, in France, we don't have access to http://moby.ucalgary.ca

Someone elese ?

Merci,

Sebastien
-------------- next part --------------
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From groscurt at mpiz-koeln.mpg.de  Thu Jun  5 07:47:56 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Thu, 05 Jun 2008 09:47:56 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <200802071539.09914.groscurt@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>
	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>
Message-ID: <48479A2C.5060507@mpiz-koeln.mpg.de>

Hi all,

I like to announce that we are now offering the Dashboard as a Java 
Webstart project and therefore as a standalone version. Now one can 
explore the functionality of Dashboard without checking out the full 
moby cvs code :-)

You can find it at 
http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
test it if everything works normally. I created this by deleting more 
and more libraries which were stated in the classpath but apparently are 
not needed at all. The web start version of dashboard offers the 
possibilty of browsing the registries, registration and the simple 
clientn (of course the MoSeS Generator is skipped for this version). If 
you encounter any problems during testing let me know.

If possible i would suggest to add this to the clients overview of the 
biomoby.org page - so that people can use it :-)

Any comments / suggestions are welcome

Andreas


From M4o at gmx.de  Thu Jun  5 08:30:38 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Thu, 05 Jun 2008 10:30:38 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <484798B8.8080609@toulouse.inra.fr>
References: <484798B8.8080609@toulouse.inra.fr>
Message-ID: <20080605083038.161550@gmx.net>

Hi,

Yes from Germany the same thing:

2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException: (504)Gateway Time-out Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details:
[string: null]
[HttpErrorCode: null]
Fault string: (504)Gateway Time-out
Fault code:   {http://xml.apache.org/axis/}HTTP
Fault actor:  null
When calling:
	http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========

Thanks,

Moritz
-------- Original-Nachricht --------
> Datum: Thu, 05 Jun 2008 09:41:44 +0200
> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: [MOBY-dev] Moby down ?

> Hi all,
> 
> Is Moby main server down ?
> Here, in France, we don't have access to http://moby.ucalgary.ca
> 
> Someone elese ?
> 
> Merci,
> 
> Sebastien

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger


From MichaelGerlich at gmx.de  Thu Jun  5 08:41:29 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Thu, 5 Jun 2008 10:41:29 +0200
Subject: [MOBY-dev] invoking webservice from default registry and rdf
Message-ID: <000601c8c6e7$f35ccf30$da166d90$@de>

Hi all,

after testing my service several times, it's now ready to get into the
"real" registry. Doing so, I unregistered the service from testing registry
and registered again at default registry, passing by all required
information and an endpoint URL for the rdf.
After that, I copied the rdf to the right location so it can be found via
the RDF agent.

Now every time I try to invoke this service using dashboard's simple client
and using "Ask registry where service is, and call it" - nothing happens,
even after waiting some minutes.

If I invoke the service via "Use service's usual endpoint" or "Use this
endpoint:", everything is fine and a result is displayed within a couple of
seconds.

Same behavior for other services from other authorities I tested.

After calling RDF agent to check if everything is set up properly (yesterday
evening), the service is still there so I guess there's nothing wrong with
the rdf and the location I placed it.

Does anyone have an idea what I'am doing wrong?

The service is named "MassBank_Query_PeakList" at authority "ipb-halle.de".


EDIT:
Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
Could be reason right?


Regards,

Michael



From markw at illuminae.com  Thu Jun  5 15:41:45 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 08:41:45 -0700
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <20080605083038.161550@gmx.net>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
Message-ID: <op.ub98jvtunbznux@mark.ubic.ca>

Looks like it's back up now... can you confirm?

We were down yesterday for a while - somehow the machine got "pinned".   
Might have been a DOS attack??  We don't really know.

M



On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:

> Hi,
>
> Yes from Germany the same thing:
>
> 2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException:  
> (504)Gateway Time-out Exception in thread "main"  
> org.biomoby.shared.MobyException: ===ERROR=== Fault details:
> [string: null]
> [HttpErrorCode: null]
> Fault string: (504)Gateway Time-out
> Fault code:   {http://xml.apache.org/axis/}HTTP
> Fault actor:  null
> When calling:
> 	http://moby.ucalgary.ca/moby/MOBY-Central.pl
> ===========
>
> Thanks,
>
> Moritz
> -------- Original-Nachricht --------
>> Datum: Thu, 05 Jun 2008 09:41:44 +0200
>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: [MOBY-dev] Moby down ?
>
>> Hi all,
>>
>> Is Moby main server down ?
>> Here, in France, we don't have access to http://moby.ucalgary.ca
>>
>> Someone elese ?
>>
>> Merci,
>>
>> Sebastien
>



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre



From M4o at gmx.de  Thu Jun  5 15:45:19 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Thu, 05 Jun 2008 17:45:19 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <op.ub98jvtunbznux@mark.ubic.ca>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
	<op.ub98jvtunbznux@mark.ubic.ca>
Message-ID: <20080605154519.193610@gmx.net>

Hi,

yes from Germany, i could confirm that it's back up again. 


Thanks a lot :)

Moritz


-------- Original-Nachricht --------
> Datum: Thu, 05 Jun 2008 08:41:45 -0700
> Von: "Mark Wilkinson" <markw at illuminae.com>
> An: "Core developer announcements" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Moby down ?

> Looks like it's back up now... can you confirm?
> 
> We were down yesterday for a while - somehow the machine got "pinned".   
> Might have been a DOS attack??  We don't really know.
> 
> M
> 
> 
> 
> On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:
> 
> > Hi,
> >
> > Yes from Germany the same thing:
> >
> > 2008-06-05 10:23:20,990 ERROR [main] org.biomoby.shared.MobyException:  
> > (504)Gateway Time-out Exception in thread "main"  
> > org.biomoby.shared.MobyException: ===ERROR=== Fault details:
> > [string: null]
> > [HttpErrorCode: null]
> > Fault string: (504)Gateway Time-out
> > Fault code:   {http://xml.apache.org/axis/}HTTP
> > Fault actor:  null
> > When calling:
> > 	http://moby.ucalgary.ca/moby/MOBY-Central.pl
> > ===========
> >
> > Thanks,
> >
> > Moritz
> > -------- Original-Nachricht --------
> >> Datum: Thu, 05 Jun 2008 09:41:44 +0200
> >> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: [MOBY-dev] Moby down ?
> >
> >> Hi all,
> >>
> >> Is Moby main server down ?
> >> Here, in France, we don't have access to http://moby.ucalgary.ca
> >>
> >> Someone elese ?
> >>
> >> Merci,
> >>
> >> Sebastien
> >
> 
> 
> 
> -- 
> Mark Wilkinson
> Assistant Professor
> Dept. of Medical Genetics, UBC
> PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
> iCAPTURE Centre
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! 
Ideal f?r Modem und ISDN: http://www.gmx.net/de/go/smartsurfer


From edward.kawas at gmail.com  Thu Jun  5 16:08:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 5 Jun 2008 09:08:01 -0700
Subject: [MOBY-dev] invoking webservice from default registry and rdf
In-Reply-To: <000601c8c6e7$f35ccf30$da166d90$@de>
References: <000601c8c6e7$f35ccf30$da166d90$@de>
Message-ID: <48480f6e.17bb720a.5658.23d0@mx.google.com>

Hi Michael,

Can you confirm that this is still a problem? I cannot replicate the issue,
so I believe that it was a temporary issue.

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 Michael Gerlich
Sent: June-05-08 1:41 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] invoking webservice from default registry and rdf

Hi all,

after testing my service several times, it's now ready to get into the
"real" registry. Doing so, I unregistered the service from testing registry
and registered again at default registry, passing by all required
information and an endpoint URL for the rdf.
After that, I copied the rdf to the right location so it can be found via
the RDF agent.

Now every time I try to invoke this service using dashboard's simple client
and using "Ask registry where service is, and call it" - nothing happens,
even after waiting some minutes.

If I invoke the service via "Use service's usual endpoint" or "Use this
endpoint:", everything is fine and a result is displayed within a couple of
seconds.

Same behavior for other services from other authorities I tested.

After calling RDF agent to check if everything is set up properly (yesterday
evening), the service is still there so I guess there's nothing wrong with
the rdf and the location I placed it.

Does anyone have an idea what I'am doing wrong?

The service is named "MassBank_Query_PeakList" at authority "ipb-halle.de".


EDIT:
Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
Could be reason right?


Regards,

Michael

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Thu Jun  5 16:14:04 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 09:14:04 -0700
Subject: [MOBY-dev] invoking webservice from default registry and rdf
In-Reply-To: <000601c8c6e7$f35ccf30$da166d90$@de>
References: <000601c8c6e7$f35ccf30$da166d90$@de>
Message-ID: <op.ub991qcfnbznux@mark.ubic.ca>

Hi Michael,

MOBY Central has had a couple of problems in the past 24 hours - both with  
being offline as well as with a corrupted RDF cache.  Either or both of  
these might have caused the problems you encountered. Eddie and I have  
been working on fixing these and we *think* it's all back to normal now.   
Perhaps you could try again and tell us if you are still unsuccessful?

Thanks!

Mark




On Thu, 05 Jun 2008 01:41:29 -0700, Michael Gerlich  
<MichaelGerlich at gmx.de> wrote:

> Hi all,
>
> after testing my service several times, it's now ready to get into the
> "real" registry. Doing so, I unregistered the service from testing  
> registry
> and registered again at default registry, passing by all required
> information and an endpoint URL for the rdf.
> After that, I copied the rdf to the right location so it can be found via
> the RDF agent.
>
> Now every time I try to invoke this service using dashboard's simple  
> client
> and using "Ask registry where service is, and call it" - nothing happens,
> even after waiting some minutes.
>
> If I invoke the service via "Use service's usual endpoint" or "Use this
> endpoint:", everything is fine and a result is displayed within a couple  
> of
> seconds.
>
> Same behavior for other services from other authorities I tested.
>
> After calling RDF agent to check if everything is set up properly  
> (yesterday
> evening), the service is still there so I guess there's nothing wrong  
> with
> the rdf and the location I placed it.
>
> Does anyone have an idea what I'am doing wrong?
>
> The service is named "MassBank_Query_PeakList" at authority  
> "ipb-halle.de".
>
>
> EDIT:
> Hmm, seems like central registry at http://moby.ucalgary.ca/ is down.
> Could be reason right?
>
>
> Regards,
>
> Michael
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From MichaelGerlich at gmx.de  Thu Jun  5 17:53:01 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Thu, 5 Jun 2008 19:53:01 +0200
Subject: [MOBY-dev] invoking webservice from default registry and rdf
	[solved]
Message-ID: <000301c8c734$ff771440$fe653cc0$@de>

Hi all,

yes you were right. It was all about the non-reachable registry.
Now everything is working properly again.  

Thanks again,

Michael



From sebastien.carrere at toulouse.inra.fr  Thu Jun  5 20:05:14 2008
From: sebastien.carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Thu, 05 Jun 2008 22:05:14 +0200
Subject: [MOBY-dev] Moby down ?
In-Reply-To: <op.ub98jvtunbznux@mark.ubic.ca>
References: <484798B8.8080609@toulouse.inra.fr> <20080605083038.161550@gmx.net>
	<op.ub98jvtunbznux@mark.ubic.ca>
Message-ID: <484846FA.6060406@toulouse.inra.fr>

Yes it's okay in France !

Merci
Sebastien


Mark Wilkinson a ?crit :
> Looks like it's back up now... can you confirm?
>
> We were down yesterday for a while - somehow the machine got 
> "pinned".  Might have been a DOS attack??  We don't really know.
>
> M
>
>
>
> On Thu, 05 Jun 2008 01:30:38 -0700, <M4o at gmx.de> wrote:
>
>> Hi,
>>
>> Yes from Germany the same thing:
>>
>> 2008-06-05 10:23:20,990 ERROR [main] 
>> org.biomoby.shared.MobyException: (504)Gateway Time-out Exception in 
>> thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault 
>> details:
>> [string: null]
>> [HttpErrorCode: null]
>> Fault string: (504)Gateway Time-out
>> Fault code:   {http://xml.apache.org/axis/}HTTP
>> Fault actor:  null
>> When calling:
>>     http://moby.ucalgary.ca/moby/MOBY-Central.pl
>> ===========
>>
>> Thanks,
>>
>> Moritz
>> -------- Original-Nachricht --------
>>> Datum: Thu, 05 Jun 2008 09:41:44 +0200
>>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>>> Betreff: [MOBY-dev] Moby down ?
>>
>>> Hi all,
>>>
>>> Is Moby main server down ?
>>> Here, in France, we don't have access to http://moby.ucalgary.ca
>>>
>>> Someone elese ?
>>>
>>> Merci,
>>>
>>> Sebastien
>>
>
>
>



From markw at illuminae.com  Thu Jun  5 23:58:36 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 05 Jun 2008 16:58:36 -0700
Subject: [MOBY-dev] JDK requirement of dashboard...
Message-ID: <op.ucavjynqnbznux@mark.ubic.ca>

Isn't it a bit... odd... that we expect end-users of Dashboard to download  
the JDK rather than the JRE?

M


-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From martin.senger at gmail.com  Fri Jun  6 00:30:33 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 6 Jun 2008 08:30:33 +0800
Subject: [MOBY-dev] JDK requirement of dashboard...
In-Reply-To: <op.ucavjynqnbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>
Message-ID: <4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>

> Isn't it a bit... odd... that we expect end-users of Dashboard to download
> the JDK rather than the JRE?


No, because Dashboard includes Moses and Moses compiles generated Java
classes - so it needs JDK. An option would be to have it configured: and
disabled some panels when onlt JRE is present. Not sure, however, if it
worth to do it.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From groscurt at mpiz-koeln.mpg.de  Tue Jun 10 08:54:53 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 10 Jun 2008 10:54:53 +0200
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
Message-ID: <484E415D.9080600@mpiz-koeln.mpg.de>


   Hi,
   hope someone has an advice or encountered that problem before and knows a
   solution.
     * I try to install a moby central. The first machine i tried is running
       Solaris 10 and it failes because of the SOAP::Lite library. All web
       service clients which uses soap are failing with

     HTTP::Message content not bytes at
     /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361

     we tested it with Moby and with the EBI web service clients. Has anyone
     installed a working SOAP::Lite on Solaris 10 ?

     * After failing on a solaris machine we thought, a what the heck, lets do
       it on a linux machine. So i tried to install it on a 64bit machine. This
       time XML::CanonalizeXML is the problem. It aborts the make process with
       lots of lots of errors. Installing the same library on a 32bit machine
       works smoothly.

     Has anyone installed a working XML::CanonalizeXML on a 64bit machine ?

   So basically,  has anyone installed a moby central on a Solaris 10 machine
   or a linux 64bit and can give advices for our problems here ?
   Thanks
   andreas


From markw at illuminae.com  Tue Jun 10 13:37:17 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:37:17 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E415D.9080600@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
Message-ID: <op.ucjb4ff6nbznux@mark.ubic.ca>

The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...

M




On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

>
>    Hi,
>    hope someone has an advice or encountered that problem before and  
> knows a
>    solution.
>      * I try to install a moby central. The first machine i tried is  
> running
>        Solaris 10 and it failes because of the SOAP::Lite library. All  
> web
>        service clients which uses soap are failing with
>
>      HTTP::Message content not bytes at
>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>
>      we tested it with Moby and with the EBI web service clients. Has  
> anyone
>      installed a working SOAP::Lite on Solaris 10 ?
>
>      * After failing on a solaris machine we thought, a what the heck,  
> lets do
>        it on a linux machine. So i tried to install it on a 64bit  
> machine. This
>        time XML::CanonalizeXML is the problem. It aborts the make  
> process with
>        lots of lots of errors. Installing the same library on a 32bit  
> machine
>        works smoothly.
>
>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
> machine ?
>
>    So basically,  has anyone installed a moby central on a Solaris 10  
> machine
>    or a linux 64bit and can give advices for our problems here ?
>    Thanks
>    andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From groscurt at mpiz-koeln.mpg.de  Tue Jun 10 13:39:43 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 10 Jun 2008 15:39:43 +0200
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <op.ucjb4ff6nbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
Message-ID: <484E841F.4070008@mpiz-koeln.mpg.de>

Mark Wilkinson wrote:
> The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...
>
> M
>
so which soap lite version do you have installed ? have you ever 
encountered such problem as i mentioned ?

Andreas

>
>
>
> On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth 
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>>
>>    Hi,
>>    hope someone has an advice or encountered that problem before and 
>> knows a
>>    solution.
>>      * I try to install a moby central. The first machine i tried is 
>> running
>>        Solaris 10 and it failes because of the SOAP::Lite library. 
>> All web
>>        service clients which uses soap are failing with
>>
>>      HTTP::Message content not bytes at
>>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>>
>>      we tested it with Moby and with the EBI web service clients. Has 
>> anyone
>>      installed a working SOAP::Lite on Solaris 10 ?
>>
>>      * After failing on a solaris machine we thought, a what the 
>> heck, lets do
>>        it on a linux machine. So i tried to install it on a 64bit 
>> machine. This
>>        time XML::CanonalizeXML is the problem. It aborts the make 
>> process with
>>        lots of lots of errors. Installing the same library on a 32bit 
>> machine
>>        works smoothly.
>>
>>      Has anyone installed a working XML::CanonalizeXML on a 64bit 
>> machine ?
>>
>>    So basically,  has anyone installed a moby central on a Solaris 10 
>> machine
>>    or a linux 64bit and can give advices for our problems here ?
>>    Thanks
>>    andreas
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>



From markw at illuminae.com  Tue Jun 10 13:45:14 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:45:14 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E415D.9080600@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
Message-ID: <op.ucjchoqjnbznux@mark.ubic.ca>

One of the key things to getting it working on the Solaris machine was to  
use the Perl that came with CoolStack...  I know there were other problems  
too, but that one was key!





On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

>
>    Hi,
>    hope someone has an advice or encountered that problem before and  
> knows a
>    solution.
>      * I try to install a moby central. The first machine i tried is  
> running
>        Solaris 10 and it failes because of the SOAP::Lite library. All  
> web
>        service clients which uses soap are failing with
>
>      HTTP::Message content not bytes at
>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>
>      we tested it with Moby and with the EBI web service clients. Has  
> anyone
>      installed a working SOAP::Lite on Solaris 10 ?
>
>      * After failing on a solaris machine we thought, a what the heck,  
> lets do
>        it on a linux machine. So i tried to install it on a 64bit  
> machine. This
>        time XML::CanonalizeXML is the problem. It aborts the make  
> process with
>        lots of lots of errors. Installing the same library on a 32bit  
> machine
>        works smoothly.
>
>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
> machine ?
>
>    So basically,  has anyone installed a moby central on a Solaris 10  
> machine
>    or a linux 64bit and can give advices for our problems here ?
>    Thanks
>    andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From markw at illuminae.com  Tue Jun 10 13:49:13 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 10 Jun 2008 06:49:13 -0700
Subject: [MOBY-dev] Perl problems while Moby central installation
In-Reply-To: <484E841F.4070008@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
Message-ID: <op.ucjcobhznbznux@mark.ubic.ca>

moby01:~# more /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm
# ======================================================================
#
# Copyright (C) 2000-2005 Paul Kulchenko (paulclinger at yahoo.com)
# SOAP::Lite is free software; you can redistribute it
# and/or modify it under the same terms as Perl itself.
#
# $Id: Lite.pm,v 1.43 2006/08/16 14:49:34 byrnereese Exp $
#
# ======================================================================

package SOAP::Lite;

use 5.004;
use strict;
use vars qw($VERSION);
#$VERSION = sprintf("%d.%s", map {s/_//g; $_} q$Name:  $ =~  
/-(\d+)_([\d_]+)/)
#  or warn "warning: unspecified/non-released version of ", __PACKAGE__,  
"\n";
$VERSION = '0.69';

# ======================================================================









On Tue, 10 Jun 2008 06:39:43 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> Mark Wilkinson wrote:
>> The MOBY Central at moby.ucalgary.ca is a Solaris 10 machine...
>>
>> M
>>
> so which soap lite version do you have installed ? have you ever  
> encountered such problem as i mentioned ?
>
> Andreas
>
>>
>>
>>
>> On Tue, 10 Jun 2008 01:54:53 -0700, Andreas Groscurth  
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>>
>>>    Hi,
>>>    hope someone has an advice or encountered that problem before and  
>>> knows a
>>>    solution.
>>>      * I try to install a moby central. The first machine i tried is  
>>> running
>>>        Solaris 10 and it failes because of the SOAP::Lite library. All  
>>> web
>>>        service clients which uses soap are failing with
>>>
>>>      HTTP::Message content not bytes at
>>>      /usr/local/perl/lib/site_perl/SOAP/Transport/HTTP.pm line 361
>>>
>>>      we tested it with Moby and with the EBI web service clients. Has  
>>> anyone
>>>      installed a working SOAP::Lite on Solaris 10 ?
>>>
>>>      * After failing on a solaris machine we thought, a what the heck,  
>>> lets do
>>>        it on a linux machine. So i tried to install it on a 64bit  
>>> machine. This
>>>        time XML::CanonalizeXML is the problem. It aborts the make  
>>> process with
>>>        lots of lots of errors. Installing the same library on a 32bit  
>>> machine
>>>        works smoothly.
>>>
>>>      Has anyone installed a working XML::CanonalizeXML on a 64bit  
>>> machine ?
>>>
>>>    So basically,  has anyone installed a moby central on a Solaris 10  
>>> machine
>>>    or a linux 64bit and can give advices for our problems here ?
>>>    Thanks
>>>    andreas
>>> _______________________________________________
>>> 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



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre



From edward.kawas at gmail.com  Wed Jun 11 15:19:38 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 11 Jun 2008 08:19:38 -0700
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <48479A2C.5060507@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>
	<48479A2C.5060507@mpiz-koeln.mpg.de>
Message-ID: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>

Hi Andreas,

I recently created a new panel in dashboard for perl moses. How hard would
it be to get that running? The panel runs command line scripts in the
background, so I am not sure if the webstart sandbox allows that anyways...

Good work by the way!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-05-08 12:48 AM
To: Core developer announcements; moby-l at lists.open-bio.org
Subject: [MOBY-dev] Dashboard as Java WebStart

Hi all,

I like to announce that we are now offering the Dashboard as a Java 
Webstart project and therefore as a standalone version. Now one can 
explore the functionality of Dashboard without checking out the full 
moby cvs code :-)

You can find it at 
http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
test it if everything works normally. I created this by deleting more 
and more libraries which were stated in the classpath but apparently are 
not needed at all. The web start version of dashboard offers the 
possibilty of browsing the registries, registration and the simple 
clientn (of course the MoSeS Generator is skipped for this version). If 
you encounter any problems during testing let me know.

If possible i would suggest to add this to the clients overview of the 
biomoby.org page - so that people can use it :-)

Any comments / suggestions are welcome

Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From groscurt at mpiz-koeln.mpg.de  Wed Jun 11 15:33:07 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 17:33:07 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>
	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
Message-ID: <484FF033.30806@mpiz-koeln.mpg.de>

Hi Eddie,

is the panel already checked in the cvs ? whats it called ? ... 
apparently i missed that.

Mhm - the question is how these command line scripts are available - if 
they are some .pl scripts or .sh scripts or something it could be not 
working at all - but i will check that.

best
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de  Wed Jun 11 15:36:14 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 17:36:14 +0200
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484fed0b.1f588c0a.5fe1.6929@mx.google.com>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>
	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
Message-ID: <484FF0EE.6010403@mpiz-koeln.mpg.de>

ah... i see the panel now ;-)

i will try to integrate it ...

cheers
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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  Wed Jun 11 15:41:07 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 11 Jun 2008 08:41:07 -0700
Subject: [MOBY-dev] Dashboard as Java WebStart
In-Reply-To: <484FF033.30806@mpiz-koeln.mpg.de>
References: <op.t54hj0tcnbznux@homecomp>	<200802071539.09914.groscurt@mpiz-koeln.mpg.de>	<48479A2C.5060507@mpiz-koeln.mpg.de>	<484fed0b.1f588c0a.5fe1.6929@mx.google.com>
	<484FF033.30806@mpiz-koeln.mpg.de>
Message-ID: <484ff215.16538c0a.6767.ffffdab9@mx.google.com>

Yeah, the panel is in the cvs. The documentation for it is in the cvs too
(both the dashboard internal help and an external one). I should link them
to other documents, so that google can find them.

The external one is at: http://tinyurl.com/63ucu3

The command line scripts are installed (by make) when users install the perl
module MOSES::MOBY from cpan (or the perl branch of the cvs).

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 Andreas Groscurth
Sent: June-11-08 8:33 AM
To: Core developer announcements
Cc: moby-l at lists.open-bio.org
Subject: Re: [MOBY-dev] Dashboard as Java WebStart

Hi Eddie,

is the panel already checked in the cvs ? whats it called ? ... 
apparently i missed that.

Mhm - the question is how these command line scripts are available - if 
they are some .pl scripts or .sh scripts or something it could be not 
working at all - but i will check that.

best
andreas

Edward Kawas wrote:
> Hi Andreas,
>
> I recently created a new panel in dashboard for perl moses. How hard would
> it be to get that running? The panel runs command line scripts in the
> background, so I am not sure if the webstart sandbox allows that
anyways...
>
> Good work by the way!
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas
Groscurth
> Sent: June-05-08 12:48 AM
> To: Core developer announcements; moby-l at lists.open-bio.org
> Subject: [MOBY-dev] Dashboard as Java WebStart
>
> Hi all,
>
> I like to announce that we are now offering the Dashboard as a Java 
> Webstart project and therefore as a standalone version. Now one can 
> explore the functionality of Dashboard without checking out the full 
> moby cvs code :-)
>
> You can find it at 
> http://bioinfo.mpiz-koeln.mpg.de/dashboard/dashboard.jnlp - feel free to 
> test it if everything works normally. I created this by deleting more 
> and more libraries which were stated in the classpath but apparently are 
> not needed at all. The web start version of dashboard offers the 
> possibilty of browsing the registries, registration and the simple 
> clientn (of course the MoSeS Generator is skipped for this version). If 
> you encounter any problems during testing let me know.
>
> If possible i would suggest to add this to the clients overview of the 
> biomoby.org page - so that people can use it :-)
>
> Any comments / suggestions are welcome
>
> Andreas
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de  Wed Jun 11 17:10:20 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 11 Jun 2008 19:10:20 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <op.ucjcobhznbznux@mark.ubic.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
Message-ID: <485006FC.3060003@mpiz-koeln.mpg.de>

someone killed it again ;-(

connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl form 
Germany....

bring it back :p

PS: sorry mark - the first email was already supposed for the mailing list !


From markw at illuminae.com  Wed Jun 11 18:18:19 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 11 Jun 2008 11:18:19 -0700
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485006FC.3060003@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
Message-ID: <op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>

Looks like it was a temporary problem... it was down for me also, but is  
back up now.

M



On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> someone killed it again ;-(
>
> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl form  
> Germany....
>
> bring it back :p
>
> PS: sorry mark - the first email was already supposed for the mailing  
> list !
> _______________________________________________
> 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 gordonp at ucalgary.ca  Wed Jun 11 19:28:48 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 11 Jun 2008 13:28:48 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>
	<op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <48502770.6060905@ucalgary.ca>

The whole University of Calgary was cut off from the outside world for 
about an hour...for reasons still unexplained.


Mark Wilkinson wrote:
> Looks like it was a temporary problem... it was down for me also, but 
> is back up now.
>
> M
>
>
>
> On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth 
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>> someone killed it again ;-(
>>
>> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl 
>> form Germany....
>>
>> bring it back :p
>>
>> PS: sorry mark - the first email was already supposed for the mailing 
>> list !
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>


From gordonp at ucalgary.ca  Wed Jun 11 22:24:59 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 11 Jun 2008 16:24:59 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <48502770.6060905@ucalgary.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<op.ucljstuxnbznux@dd0710001l.icapture.ubc.ca>
	<48502770.6060905@ucalgary.ca>
Message-ID: <485050BB.4060001@ucalgary.ca>

FYI: It would appear that the university was subject to a multicast DOS 
attack, and the admins have rerouted around the troublesome Cybera 
connections.

Paul Gordon wrote:
> The whole University of Calgary was cut off from the outside world for 
> about an hour...for reasons still unexplained.
>
>
> Mark Wilkinson wrote:
>> Looks like it was a temporary problem... it was down for me also, but 
>> is back up now.
>>
>> M
>>
>>
>>
>> On Wed, 11 Jun 2008 10:10:20 -0700, Andreas Groscurth 
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>> someone killed it again ;-(
>>>
>>> connection timeout for http://moby.ucalgary.ca/moby/MOBY-Central.pl 
>>> form Germany....
>>>
>>> bring it back :p
>>>
>>> PS: sorry mark - the first email was already supposed for the 
>>> mailing list !
>>> _______________________________________________
>>> 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
>
> !DSPAM:60005,48502b5710950215499055!
>
>
>


From sneumann at ipb-halle.de  Thu Jun 12 07:41:06 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Thu, 12 Jun 2008 09:41:06 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485006FC.3060003@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de> <op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de> <op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
Message-ID: <1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>

On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
> someone killed it again ;-(

Hi,

wouldn't that be the time to call for redundancy for moby-central ?
Either some read-only secondary server which keeps 
at least the services running if the primary is unreachable,

or even a full-blown anycast a la Root-DNS servers 
with synchronized backend-something for the registry database ?

Or has that already been discussed and dismissed ?

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

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From schoof at mpiz-koeln.mpg.de  Thu Jun 12 10:00:07 2008
From: schoof at mpiz-koeln.mpg.de (Heiko Schoof)
Date: Thu, 12 Jun 2008 12:00:07 +0200
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>
	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>
	<484E415D.9080600@mpiz-koeln.mpg.de>
	<op.ucjb4ff6nbznux@mark.ubic.ca>
	<484E841F.4070008@mpiz-koeln.mpg.de>
	<op.ucjcobhznbznux@mark.ubic.ca>
	<485006FC.3060003@mpiz-koeln.mpg.de>
	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>

Hi,
we have implemented synchronization of moby centrals. But it needs  
some testing under production conditions. Read-only should work fine.  
So if anyone is willing and able to host an alternative moby- 
central... we are in the process of setting one up, and could  
possibly act as European mirror. But I need to discuss this with  
Andreas first, and see in what time scale this is feasible.
Has anyone else been experimenting with the synchronization code from  
Andreas?

What would then be missing is the implementation for a fall-back in  
the client libraries, I think. In effect, the ability to give a  
second moby-central, which is used if connections to the primary fail.

Best, Heiko

On 12.06.2008, at 09:41, sneumann wrote:

> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>> someone killed it again ;-(
>
> Hi,
>
> wouldn't that be the time to call for redundancy for moby-central ?
> Either some read-only secondary server which keeps
> at least the services running if the primary is unreachable,
>
> or even a full-blown anycast a la Root-DNS servers
> with synchronized backend-something for the registry database ?
>
> Or has that already been discussed and dismissed ?
>
> 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
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From gordonp at ucalgary.ca  Thu Jun 12 17:11:22 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 12 Jun 2008 11:11:22 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>
	<B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
Message-ID: <485158BA.2070802@ucalgary.ca>

It brings a tear (of joy) to my eye that Moby Central is becoming so 
essential, we need a backup. :-)

I think a European mirror is a great idea, because just having two 
servers here in Calgary would not have prevented the down-time 
experienced yesterday.  We'd need to change the dynamic Central lookup 
policy (which goes through biomoby.org) to change from returning one 
server to returning a list of servers.  Pretty simple, but still has a 
single point of failure, now at biomoby.org.  Dynamic Central lookup is 
disabled by default unless a connection to Central fails, so maybe it's 
not such a big deal (unless moby.ucalgary.ca AND biomoby.org in Boston 
(or wherever) fail at the same time).

The other (robust) option is to have an LSID that points to a document 
listing the servers.  The resolution protocol allows for redundant data 
serving in theory, but we'd need to set up moby as a "proper" authority 
that goes in the lsid.org DNSPTR records.

-Paul

Heiko Schoof wrote:
> Hi,
> we have implemented synchronization of moby centrals. But it needs 
> some testing under production conditions. Read-only should work fine. 
> So if anyone is willing and able to host an alternative 
> moby-central... we are in the process of setting one up, and could 
> possibly act as European mirror. But I need to discuss this with 
> Andreas first, and see in what time scale this is feasible.
> Has anyone else been experimenting with the synchronization code from 
> Andreas?
>
> What would then be missing is the implementation for a fall-back in 
> the client libraries, I think. In effect, the ability to give a second 
> moby-central, which is used if connections to the primary fail.
>
> Best, Heiko
>
> On 12.06.2008, at 09:41, sneumann wrote:
>
>> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>>> someone killed it again ;-(
>>
>> Hi,
>>
>> wouldn't that be the time to call for redundancy for moby-central ?
>> Either some read-only secondary server which keeps
>> at least the services running if the primary is unreachable,
>>
>> or even a full-blown anycast a la Root-DNS servers
>> with synchronized backend-something for the registry database ?
>>
>> Or has that already been discussed and dismissed ?
>>
>> 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
>>
>> _______________________________________________
>> 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
>
> !DSPAM:60005,4850f8cc10950795412468!
>
>
>


From gordonp at ucalgary.ca  Thu Jun 12 17:20:49 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 12 Jun 2008 11:20:49 -0600
Subject: [MOBY-dev] BioMoby central dead...
In-Reply-To: <485158BA.2070802@ucalgary.ca>
References: <op.ucavjynqnbznux@mark.ubic.ca>	<4d93f07c0806051730v65f404a9n9f453fec2d60b628@mail.gmail.com>	<484E415D.9080600@mpiz-koeln.mpg.de>	<op.ucjb4ff6nbznux@mark.ubic.ca>	<484E841F.4070008@mpiz-koeln.mpg.de>	<op.ucjcobhznbznux@mark.ubic.ca>	<485006FC.3060003@mpiz-koeln.mpg.de>	<1213256466.16760.251.camel@lathan.ipb-sub.ipb-halle.de>	<B0932FEE-0608-4F74-ADF7-E8CEDD7C48C4@mpiz-koeln.mpg.de>
	<485158BA.2070802@ucalgary.ca>
Message-ID: <48515AF1.9050704@ucalgary.ca>

Actually, I lied. It's even easier.  If the LSID for the list of 
centrals is urn:lsid:biomoby.org:... we can just add lower priority LSID 
data servers to the biomoby.org SRV records for 
_lsid._tcp.biomoby.org...mirror LSID servers for Moby Central data. 

>
> The other (robust) option is to have an LSID that points to a document 
> listing the servers.  The resolution protocol allows for redundant 
> data serving in theory, but we'd need to set up moby as a "proper" 
> authority that goes in the lsid.org DNSPTR records.
>
> -Paul
>
> Heiko Schoof wrote:
>> Hi,
>> we have implemented synchronization of moby centrals. But it needs 
>> some testing under production conditions. Read-only should work fine. 
>> So if anyone is willing and able to host an alternative 
>> moby-central... we are in the process of setting one up, and could 
>> possibly act as European mirror. But I need to discuss this with 
>> Andreas first, and see in what time scale this is feasible.
>> Has anyone else been experimenting with the synchronization code from 
>> Andreas?
>>
>> What would then be missing is the implementation for a fall-back in 
>> the client libraries, I think. In effect, the ability to give a 
>> second moby-central, which is used if connections to the primary fail.
>>
>> Best, Heiko
>>
>> On 12.06.2008, at 09:41, sneumann wrote:
>>
>>> On Mi, 2008-06-11 at 19:10 +0200, Andreas Groscurth wrote:
>>>> someone killed it again ;-(
>>>
>>> Hi,
>>>
>>> wouldn't that be the time to call for redundancy for moby-central ?
>>> Either some read-only secondary server which keeps
>>> at least the services running if the primary is unreachable,
>>>
>>> or even a full-blown anycast a la Root-DNS servers
>>> with synchronized backend-something for the registry database ?
>>>
>>> Or has that already been discussed and dismissed ?
>>>
>>> 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
>>>
>>> _______________________________________________
>>> 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
>
> !DSPAM:60005,4851566410950685925024!
>
>
>


From markw at illuminae.com  Thu Jun 12 21:26:25 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 12 Jun 2008 14:26:25 -0700
Subject: [MOBY-dev] Apologies
Message-ID: <op.ucnm6by1nbznux@mark.ubic.ca>

Hi all,

It took most of the day today to fix the Dashboard WebStart from the  
biomoby.org homepage once I messed it up early this morning.  My apologies  
if you tried using it.  It's all fixed now!

Mark



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From groscurt at mpiz-koeln.mpg.de  Fri Jun 13 13:57:44 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 13 Jun 2008 15:57:44 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4851431d.1420720a.52bf.243d@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
Message-ID: <48527CD8.9060904@mpiz-koeln.mpg.de>

Hi,

just a short question about dead services.
I call some services with my aggregator, which are registered at the 
production central. Some of them always return and error and therefore 
arent useable at all.

E.g. getAREXGFPImageCollection from arexdb.org

if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
dead" - but on the "dead service" page it is not listed (and its dead 
for a longer time)

Also in the Java code in MobyService there are flags for the status of a 
service - but how to i find them out - after a findService call all 
service i retrieve have status 0 (unchecked).

So my questions/comment:

1. The dead service page does not show up all dead services.
2. How do I find out with JMoby if a service is dead ?

THX
Andreas


From edward.kawas at gmail.com  Fri Jun 13 14:04:52 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 13 Jun 2008 07:04:52 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48527CD8.9060904@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
Message-ID: <48527e8d.02578c0a.75ce.57f4@mx.google.com>

Hi Andreas,

The service seems to be up and running:
http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator (choose the service
provider from the drop down). I think that is why it isn't listed on the
dead services page.

I am not sure how to figure out if the service is dead in jMoby. Maybe the
easiest thing to do would be to add code into MobyService that actually
pings the service. But that should be better thought out. I know that the
RDF for services contains this information, but don't trust it. Ever since
we started caching, that information is no longer useful. Again, this value
should be removed or we should figure out how to ensure that this
information is valid.

Eddie




-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-13-08 6:58 AM
To: Core developer announcements
Subject: [MOBY-dev] Dead services and how to figure them out

Hi,

just a short question about dead services.
I call some services with my aggregator, which are registered at the 
production central. Some of them always return and error and therefore 
arent useable at all.

E.g. getAREXGFPImageCollection from arexdb.org

if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
dead" - but on the "dead service" page it is not listed (and its dead 
for a longer time)

Also in the Java code in MobyService there are flags for the status of a 
service - but how to i find them out - after a findService call all 
service i retrieve have status 0 (unchecked).

So my questions/comment:

1. The dead service page does not show up all dead services.
2. How do I find out with JMoby if a service is dead ?

THX
Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From Sebastien.Carrere at toulouse.inra.fr  Fri Jun 13 14:29:27 2008
From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere)
Date: Fri, 13 Jun 2008 16:29:27 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48527CD8.9060904@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
Message-ID: <48528447.7040807@toulouse.inra.fr>

Bonjour ,


Thanks Andreas to restart the discussion about DeadServices and cleaning 
the registry.
I encounter the same problem in Remora.
The DeadServices list provided  is not exhaustive as you say.

I launch every night a cleaner which do this thing:
- get all services registered in Mobycentral
- try to execute them with the perl command: eval 
{$service_instance->execute(XMLinputlist =>[[]])};

Here is my list of Dead services (Ihave got also list for the 3 past 
days for testRegistry and Inab registry) :
http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral

(Format is "service_name    auth_uri    registry_name    error_message")

Most of them are 404 or 500 errors.

If my test is correct, that means that around 10% of services are dead.
And here I cannot test if the returned message is well-formed (many 
changes happened since the birth of BioMOBY and maybe some services have 
not been updated), so it's at least 10%...

 From my point of view, this problem of dead/non-functionnal  services 
is really a critical one.
We develop tools based on web-services and we advice our users to use 
tools such as Taverna, Remora etc...
So if the basis (web-services) is not robust, we lost all our credibility.

We deploy here (Toulouse, France) procedures to test our services every 
night to ensure their availablity and stability.
I think it's time to currate the main registry.

What do you think about this ?

Sebastien




Andreas Groscurth wrote:
> Hi,
>
> just a short question about dead services.
> I call some services with my aggregator, which are registered at the 
> production central. Some of them always return and error and therefore 
> arent useable at all.
>
> E.g. getAREXGFPImageCollection from arexdb.org
>
> if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
> dead" - but on the "dead service" page it is not listed (and its dead 
> for a longer time)
>
> Also in the Java code in MobyService there are flags for the status of 
> a service - but how to i find them out - after a findService call all 
> service i retrieve have status 0 (unchecked).
>
> So my questions/comment:
>
> 1. The dead service page does not show up all dead services.
> 2. How do I find out with JMoby if a service is dead ?
>
> THX
> Andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------- next part --------------
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From M4o at gmx.de  Fri Jun 13 15:32:08 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Fri, 13 Jun 2008 17:32:08 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48528447.7040807@toulouse.inra.fr>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
	<48528447.7040807@toulouse.inra.fr>
Message-ID: <20080613153208.307160@gmx.net>

Hi,

In my opinion there are about three or more questions we should think of:

1. Who should test the Services?
2. Who should host the Deadservices list?
3. How the should the Services be test. Only with the Empty Moby "Ping" or should there be some real example Data. In the Last months i worked with the Moby Services often Services respond to an Moby "Ping" but doesn?t Work correctly due to DB Connection, or Configuration Errors. (Like a lot of the mips.gsf.de) .
3a. Maybe a central system or Mailing list where User could comment the Function of the Services or "complain" about the misuse of Datatypes would be useful (for the Users ;-) ) Sure every user could email the problem to the Authority but I think it would be helpful to centralize the comments.
4. How could the Perl and Java API access the Dead list and use the Informations.

My small suggestions:
1 and 2. The best and less traffic way would it be if the MOBY Central test the Services keeps the list.

3. If it is to complicated to test the Services with real example Data then there should be a system to complain about the service and add it to the dead list if it is not working correctly (like db connections errors for about a week).

4. There are already Methods in the jMoby Api which could be extended if there is a reliabil Dead Servcies List.

In my Opinion, the reliability and Quality of the MOBY Services in the NON Testing MOBY Central should be more important then the quantity. 
Because if a user doesn?t find a Service that does what he wants he maybe set up one by himself. But if there are a few services that should does what he wants but are non working that?s frustrating.

But these are just my 2 cents. 

Thanks for all the (fish) work you have done.

Moritz



-------- Original-Nachricht --------
> Datum: Fri, 13 Jun 2008 16:29:27 +0200
> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Bonjour ,
> 
> 
> Thanks Andreas to restart the discussion about DeadServices and cleaning 
> the registry.
> I encounter the same problem in Remora.
> The DeadServices list provided  is not exhaustive as you say.
> 
> I launch every night a cleaner which do this thing:
> - get all services registered in Mobycentral
> - try to execute them with the perl command: eval 
> {$service_instance->execute(XMLinputlist =>[[]])};
> 
> Here is my list of Dead services (Ihave got also list for the 3 past 
> days for testRegistry and Inab registry) :
> http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral
> 
> (Format is "service_name    auth_uri    registry_name    error_message")
> 
> Most of them are 404 or 500 errors.
> 
> If my test is correct, that means that around 10% of services are dead.
> And here I cannot test if the returned message is well-formed (many 
> changes happened since the birth of BioMOBY and maybe some services have 
> not been updated), so it's at least 10%...
> 
>  From my point of view, this problem of dead/non-functionnal  services 
> is really a critical one.
> We develop tools based on web-services and we advice our users to use 
> tools such as Taverna, Remora etc...
> So if the basis (web-services) is not robust, we lost all our credibility.
> 
> We deploy here (Toulouse, France) procedures to test our services every 
> night to ensure their availablity and stability.
> I think it's time to currate the main registry.
> 
> What do you think about this ?
> 
> Sebastien
> 
> 
> 
> 
> Andreas Groscurth wrote:
> > Hi,
> >
> > just a short question about dead services.
> > I call some services with my aggregator, which are registered at the 
> > production central. Some of them always return and error and therefore 
> > arent useable at all.
> >
> > E.g. getAREXGFPImageCollection from arexdb.org
> >
> > if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
> > dead" - but on the "dead service" page it is not listed (and its dead 
> > for a longer time)
> >
> > Also in the Java code in MobyService there are flags for the status of 
> > a service - but how to i find them out - after a findService call all 
> > service i retrieve have status 0 (unchecked).
> >
> > So my questions/comment:
> >
> > 1. The dead service page does not show up all dead services.
> > 2. How do I find out with JMoby if a service is dead ?
> >
> > THX
> > Andreas
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger


From gordonp at ucalgary.ca  Fri Jun 13 15:48:15 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 13 Jun 2008 09:48:15 -0600
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080613153208.307160@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>
Message-ID: <485296BF.8010303@ucalgary.ca>

Hi all,

I'll respond to several posts at once:

1. There is a list of dead services at Moby Central, but it is not used 
by default in the jMoby API, and it's not part of the formal API. 
http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
2. There is a mechanism to flag services in MobyService, but it does not 
do the checking itself.  For an example of ping checking and flagging 
based on the aforementioned URL, see 
ca.ucalgary.seahawk.services.MobyClient and search for "MobyService.ALIVE".
3. We decided at the Hackathon in February to introduce service test 
cases in the service metadata (retrievable by LSID resolution), but I'm 
not sure if that made it into the documentation.  Mark?  I'll add 
support for this jMoby if someone points me to the docs.

Cheers,

Paul

M4o at gmx.de wrote:
> Hi,
>
> In my opinion there are about three or more questions we should think of:
>
> 1. Who should test the Services?
> 2. Who should host the Deadservices list?
> 3. How the should the Services be test. Only with the Empty Moby "Ping" or should there be some real example Data. In the Last months i worked with the Moby Services often Services respond to an Moby "Ping" but doesn?t Work correctly due to DB Connection, or Configuration Errors. (Like a lot of the mips.gsf.de) .
> 3a. Maybe a central system or Mailing list where User could comment the Function of the Services or "complain" about the misuse of Datatypes would be useful (for the Users ;-) ) Sure every user could email the problem to the Authority but I think it would be helpful to centralize the comments.
> 4. How could the Perl and Java API access the Dead list and use the Informations.
>
> My small suggestions:
> 1 and 2. The best and less traffic way would it be if the MOBY Central test the Services keeps the list.
>
> 3. If it is to complicated to test the Services with real example Data then there should be a system to complain about the service and add it to the dead list if it is not working correctly (like db connections errors for about a week).
>
> 4. There are already Methods in the jMoby Api which could be extended if there is a reliabil Dead Servcies List.
>
> In my Opinion, the reliability and Quality of the MOBY Services in the NON Testing MOBY Central should be more important then the quantity. 
> Because if a user doesn?t find a Service that does what he wants he maybe set up one by himself. But if there are a few services that should does what he wants but are non working that?s frustrating.
>
> But these are just my 2 cents. 
>
> Thanks for all the (fish) work you have done.
>
> Moritz
>
>
>
> -------- Original-Nachricht --------
>   
>> Datum: Fri, 13 Jun 2008 16:29:27 +0200
>> Von: Sebastien Carrere <Sebastien.Carrere at toulouse.inra.fr>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Bonjour ,
>>
>>
>> Thanks Andreas to restart the discussion about DeadServices and cleaning 
>> the registry.
>> I encounter the same problem in Remora.
>> The DeadServices list provided  is not exhaustive as you say.
>>
>> I launch every night a cleaner which do this thing:
>> - get all services registered in Mobycentral
>> - try to execute them with the perl command: eval 
>> {$service_instance->execute(XMLinputlist =>[[]])};
>>
>> Here is my list of Dead services (Ihave got also list for the 3 past 
>> days for testRegistry and Inab registry) :
>> http://lipm-bioinfo.toulouse.inra.fr/remora/sessions/blacklist.mobycentral
>>
>> (Format is "service_name    auth_uri    registry_name    error_message")
>>
>> Most of them are 404 or 500 errors.
>>
>> If my test is correct, that means that around 10% of services are dead.
>> And here I cannot test if the returned message is well-formed (many 
>> changes happened since the birth of BioMOBY and maybe some services have 
>> not been updated), so it's at least 10%...
>>
>>  From my point of view, this problem of dead/non-functionnal  services 
>> is really a critical one.
>> We develop tools based on web-services and we advice our users to use 
>> tools such as Taverna, Remora etc...
>> So if the basis (web-services) is not robust, we lost all our credibility.
>>
>> We deploy here (Toulouse, France) procedures to test our services every 
>> night to ensure their availablity and stability.
>> I think it's time to currate the main registry.
>>
>> What do you think about this ?
>>
>> Sebastien
>>
>>
>>
>>
>> Andreas Groscurth wrote:
>>     
>>> Hi,
>>>
>>> just a short question about dead services.
>>> I call some services with my aggregator, which are registered at the 
>>> production central. Some of them always return and error and therefore 
>>> arent useable at all.
>>>
>>> E.g. getAREXGFPImageCollection from arexdb.org
>>>
>>> if i ping it in dashboard it tells me "getAREXGFPImageCollection is 
>>> dead" - but on the "dead service" page it is not listed (and its dead 
>>> for a longer time)
>>>
>>> Also in the Java code in MobyService there are flags for the status of 
>>> a service - but how to i find them out - after a findService call all 
>>> service i retrieve have status 0 (unchecked).
>>>
>>> So my questions/comment:
>>>
>>> 1. The dead service page does not show up all dead services.
>>> 2. How do I find out with JMoby if a service is dead ?
>>>
>>> THX
>>> Andreas
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>       
>
>   


From markw at illuminae.com  Fri Jun 13 16:18:09 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 13 Jun 2008 09:18:09 -0700
Subject: [MOBY-dev] Fwd:  Unit testing of BioMoby Services
In-Reply-To: <op.t700xervnbznux@dd0710001l.icapture.ubc.ca>
References: <op.t700xervnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <op.uco2dkjmnbznux@dd0710001l.icapture.ubc.ca>

In response to the current discussion on automated testing of Moby  
services, I'm re-posting this email.

YES!  It needs to go into the formal API documentation.  My bad!  In the  
end, it became quite difficult to do the unit testing in perl because of  
the lack of support for OWL-RDF in Perl, so hopefully someone from the  
Java world will pick-up this ball and create the application that does it?

M



------- Forwarded message -------
From: "Mark Wilkinson" <markw at illuminae.com>
To: "moby Core developer announcements" <moby-dev at lists.open-bio.org>
Cc:
Subject: [MOBY-dev] Unit testing of BioMoby Services
Date: Fri, 14 Mar 2008 15:04:16 -0700

Hi all,

During the hackathon I was working on the OWL classes and predicates we
need for the ability to create unit tests in the Service metadata coming
  from the Service provider.  I just finished working things out with the
myGrid team, and here are the predicates and classes we have agreed on:

Namespace:  http://www.mygrid.org.uk/mygrid-moby-service#

Class:  #unitTest
usage:  can have one or more unitTests per service #operation


ObjectProperty:	#hasUnitTest
	domain:	#operation
	range:	#unitTest

DatatypeProperty:	#exampleInput
	domain:		#unitTest
	range:		xsd#string
	content:	the full SOAP payload XML of an invocation message
	
DatatypeProperty:	#validOutputXML
	domain:		#unitTest
	range:		xsd#string
	content:	the full SOAP payload of the associated output message

DatatypeProperty:	#validREGEX
	domain:		#unitTest
	range:		xsd#string
	content:	a regular expression that should match against the output SOAP
Payload of this unitTest

DatatypeProperty:	#validXPath
	domain:		#unitTest
	range:		xsd#string
	content:	an XPath expression that should match against the output SOAP
Payload of this unitTest


An example can be seen in the antirrhinum.net,getDragonAlleleLocus
service, whose signature RDF is available here:
http://moby.ucalgary.ca/signatures/antirrhinum.rdf

I'm almost finished writing a little Perl script that will go through and
test the services based on the Unit Test data - I'll put it in the CVS as
soon as it's done.

Cheers all!

Mark



-- 
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 edward.kawas at gmail.com  Mon Jun 16 17:36:50 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 16 Jun 2008 10:36:50 -0700
Subject: [MOBY-dev] sending data by reference
Message-ID: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>

Greetings all!

I remember that some time ago (Feb), we had a discussion on sending data by
reference and in fact agreed to some sort of mechanism, but I don't recall
the details. Does anyone else remember the specifics?

Thanks!

Eddie



From jmfernandez at cnio.es  Mon Jun 16 18:02:56 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Mon, 16 Jun 2008 20:02:56 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
Message-ID: <4856AAD0.50800@cnio.es>

Hi Eddie and everybody,
	AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were going to use 
XInclude for sending data by reference. We also talked about the need to 
create a "moby" URI protocol to specify the way to get referenced information 
reachable calling a MOBY service, and the need to negotiate between client and 
service the kind of reference protocols they share (i.e. they understand).

	If I have forgotten some detail, you are welcome to complement/correct my answer!

	Best Regards,
		Jos? Mar?a

Edward Kawas wrote:
> Greetings all!
> 
> I remember that some time ago (Feb), we had a discussion on sending data by
> reference and in fact agreed to some sort of mechanism, but I don't recall
> the details. Does anyone else remember the specifics?
> 
> Thanks!
> 
> Eddie
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

Jos? Mar?a Fern?ndez Gonz?lez
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinform?tica
Biolog?a Estructural y Biocomputaci?n	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncol?gicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)

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From serr at ac.uma.es  Tue Jun 17 06:41:02 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Tue, 17 Jun 2008 08:41:02 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
	<4856AAD0.50800@cnio.es>
Message-ID: <48575C7E.5040402@ac.uma.es>

Hello everybody,

I'm very interested in this theme.
I will truly appreciate if someone can sent me some examples of how the 
xml message will look.

Thanks in advance.
Sergio

Jos? Mar?a Fern?ndez Gonz?lez wrote:
> Hi Eddie and everybody,
>     AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were 
> going to use XInclude for sending data by reference. We also talked 
> about the need to create a "moby" URI protocol to specify the way to 
> get referenced information reachable calling a MOBY service, and the 
> need to negotiate between client and service the kind of reference 
> protocols they share (i.e. they understand).
>
>     If I have forgotten some detail, you are welcome to 
> complement/correct my answer!
>
>     Best Regards,
>         Jos? Mar?a
>
> Edward Kawas wrote:
>> Greetings all!
>>
>> I remember that some time ago (Feb), we had a discussion on sending 
>> data by
>> reference and in fact agreed to some sort of mechanism, but I don't 
>> recall
>> the details. Does anyone else remember the specifics?
>>
>> Thanks!
>>
>> Eddie
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>

-- 
Sergio Ram?rez Ram?rez
Instituto Nacional de Bioinform?tica (INB)
Integrated Bioinformatics Node (GNV-5)
Dpto. de Arquitectura de Computadores
Campus Universitario de Teatinos, despacho 2.3.9a
29071 M?laga (Spain) +34 95 213 3387


"Short-term decisions tend to fail in the long-term."
            Frank Herbert, God Emperor of Dune 



From dmitry.repchevski at bsc.es  Tue Jun 17 10:43:47 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Tue, 17 Jun 2008 12:43:47 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856AAD0.50800@cnio.es>
Message-ID: <48579563.3090303@bsc.es>

Doesn't we already have WSRF references?

I mean that they uniquely reference the resource that not necessary must 
be accessed from the same service that called "asynchronous" service.

Actually this is what WSRF is about - persistence rather than asynchrony.
We can use WS Addressing (as we do now) in the same way as for 
asynchronous services...
We can look also into WS-Naming specification from Open Grid consorcium 
(GDF-109.pdf).
The latest becomes the standard to reference webservices in a 
distributed world...

I am not sure how to include it into current Moby message... IMHO we 
desperately need a doc/lit schema based services to move forward (by the 
way, any news about Perl?).

I am going to rise all these question in INB meeting in Valencia 13-15 
of July.

Best regards,

Dmitry


From groscurt at mpiz-koeln.mpg.de  Tue Jun 17 12:17:27 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 17 Jun 2008 14:17:27 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <485296BF.8010303@ucalgary.ca>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>
	<485296BF.8010303@ucalgary.ca>
Message-ID: <4857AB57.8010203@mpiz-koeln.mpg.de>

Paul Gordon wrote:
> Hi all,
>
> I'll respond to several posts at once:
>
> 1. There is a list of dead services at Moby Central, but it is not 
> used by default in the jMoby API, and it's not part of the formal API. 
> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
thanks for the link - but for me it stops at

moby.ucalgary.ca

what about the other authorities ?

Thanks
andreas


From serr at ac.uma.es  Tue Jun 17 12:21:28 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Tue, 17 Jun 2008 14:21:28 +0200
Subject: [MOBY-dev] sending data by reference
In-Reply-To: <4856AAD0.50800@cnio.es>
References: <4856a4c3.14b48c0a.2c62.fffff42f@mx.google.com>
	<4856AAD0.50800@cnio.es>
Message-ID: <4857AC48.4070803@ac.uma.es>

Hello everybody,

I'm very interested in this theme.
I will truly appreciate if someone can sent me some examples of how the
xml message will look.

Thanks in advance.
Sergio

Jos? Mar?a Fern?ndez Gonz?lez wrote:
> Hi Eddie and everybody,
>     AFAICR from our "mini-meeting" at BioHackathon in Tokyo, we were 
> going to use XInclude for sending data by reference. We also talked 
> about the need to create a "moby" URI protocol to specify the way to 
> get referenced information reachable calling a MOBY service, and the 
> need to negotiate between client and service the kind of reference 
> protocols they share (i.e. they understand).
>
>     If I have forgotten some detail, you are welcome to 
> complement/correct my answer!
>
>     Best Regards,
>         Jos? Mar?a
>
> Edward Kawas wrote:
>> Greetings all!
>>
>> I remember that some time ago (Feb), we had a discussion on sending 
>> data by
>> reference and in fact agreed to some sort of mechanism, but I don't 
>> recall
>> the details. Does anyone else remember the specifics?
>>
>> Thanks!
>>
>> Eddie
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>

-- 
Sergio Ram?rez Ram?rez
Instituto Nacional de Bioinform?tica (INB)
Integrated Bioinformatics Node (GNV-5)
Dpto. de Arquitectura de Computadores
Campus Universitario de Teatinos, despacho 2.3.9a
29071 M?laga (Spain) +34 95 213 3387


"Short-term decisions tend to fail in the long-term."
            Frank Herbert, God Emperor of Dune




From M4o at gmx.de  Tue Jun 17 12:30:59 2008
From: M4o at gmx.de (M4o at gmx.de)
Date: Tue, 17 Jun 2008 14:30:59 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857AB57.8010203@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>
Message-ID: <20080617123059.152780@gmx.net>

Hi all,

Andreas maybe try a reload.
For me it works for all auths.

In my Tool I use the adress with param: http://moby.ucalgary.ca/moby/ValidateService?getDeadServices

Maybe it is possible to extend the testing of the VaildateService function.

Moritz

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> An: Core developer announcements <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Paul Gordon wrote:
> > Hi all,
> >
> > I'll respond to several posts at once:
> >
> > 1. There is a list of dead services at Moby Central, but it is not 
> > used by default in the jMoby API, and it's not part of the formal API. 
> > http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> thanks for the link - but for me it stops at
> 
> moby.ucalgary.ca
> 
> what about the other authorities ?
> 
> Thanks
> andreas
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger


From groscurt at mpiz-koeln.mpg.de  Tue Jun 17 12:40:04 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 17 Jun 2008 14:40:04 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617123059.152780@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>
	<20080617123059.152780@gmx.net>
Message-ID: <4857B0A4.2000005@mpiz-koeln.mpg.de>

weird..

also with deleting the browser cache - i only get the list to

moby.ucalgary.ca


regardlessly with or without param :(

andreas

M4o at gmx.de wrote:
> Hi all,
>
> Andreas maybe try a reload.
> For me it works for all auths.
>
> In my Tool I use the adress with param: http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
>
> Maybe it is possible to extend the testing of the VaildateService function.
>
> Moritz
>
> -------- Original-Nachricht --------
>   
>> Datum: Tue, 17 Jun 2008 14:17:27 +0200
>> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Paul Gordon wrote:
>>     
>>> Hi all,
>>>
>>> I'll respond to several posts at once:
>>>
>>> 1. There is a list of dead services at Moby Central, but it is not 
>>> used by default in the jMoby API, and it's not part of the formal API. 
>>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
>>>       
>> thanks for the link - but for me it stops at
>>
>> moby.ucalgary.ca
>>
>> what about the other authorities ?
>>
>> Thanks
>> andreas
>> _______________________________________________
>> 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  Tue Jun 17 14:01:45 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 07:01:45 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857B0A4.2000005@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
Message-ID: <4857c3de.1cba720a.3b23.5d4f@mx.google.com>

I get the same behaviour ... I am looking into it!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-17-08 5:40 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

weird..

also with deleting the browser cache - i only get the list to

moby.ucalgary.ca


regardlessly with or without param :(

andreas

M4o at gmx.de wrote:
> Hi all,
>
> Andreas maybe try a reload.
> For me it works for all auths.
>
> In my Tool I use the adress with param:
http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
>
> Maybe it is possible to extend the testing of the VaildateService
function.
>
> Moritz
>
> -------- Original-Nachricht --------
>   
>> Datum: Tue, 17 Jun 2008 14:17:27 +0200
>> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
>> An: Core developer announcements <moby-dev at lists.open-bio.org>
>> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
>>     
>
>   
>> Paul Gordon wrote:
>>     
>>> Hi all,
>>>
>>> I'll respond to several posts at once:
>>>
>>> 1. There is a list of dead services at Moby Central, but it is not 
>>> used by default in the jMoby API, and it's not part of the formal API. 
>>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
>>>       
>> thanks for the link - but for me it stops at
>>
>> moby.ucalgary.ca
>>
>> what about the other authorities ?
>>
>> Thanks
>> andreas
>> _______________________________________________
>> 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 M4o at gmx.de  Tue Jun 17 14:45:21 2008
From: M4o at gmx.de (Moritz W)
Date: Tue, 17 Jun 2008 16:45:21 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857c3de.1cba720a.3b23.5d4f@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
Message-ID: <20080617144521.97370@gmx.net>

That's strange... 
I tried under my windows maschine with ie and firefox.
And also under a linux box with lynx:
Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt

Wget doesn't work (maybe wrong my wrong/missing params):
linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
--16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
           => `ValidateService'
Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
Connecting to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
HTTP Anforderung gesendet, warte auf Antwort... 200 OK
L??nge: nicht spezifiziert [text/plain]
ValidateService: Keine Berechtigung

I attached my result.

Hope my tests make sense...

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:01:45 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> I get the same behaviour ... I am looking into it!
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas
> Groscurth
> Sent: June-17-08 5:40 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> weird..
> 
> also with deleting the browser cache - i only get the list to
> 
> moby.ucalgary.ca
> 
> 
> regardlessly with or without param :(
> 
> andreas
> 
> M4o at gmx.de wrote:
> > Hi all,
> >
> > Andreas maybe try a reload.
> > For me it works for all auths.
> >
> > In my Tool I use the adress with param:
> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> >
> > Maybe it is possible to extend the testing of the VaildateService
> function.
> >
> > Moritz
> >
> > -------- Original-Nachricht --------
> >   
> >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> >>     
> >
> >   
> >> Paul Gordon wrote:
> >>     
> >>> Hi all,
> >>>
> >>> I'll respond to several posts at once:
> >>>
> >>> 1. There is a list of dead services at Moby Central, but it is not 
> >>> used by default in the jMoby API, and it's not part of the formal API.
> >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> >>>       
> >> thanks for the link - but for me it stops at
> >>
> >> moby.ucalgary.ca
> >>
> >> what about the other authorities ?
> >>
> >> Thanks
> >> andreas
> >> _______________________________________________
> >> 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

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
-------------- next part --------------

    The following are services, sorted by Service Provider, have been identified as "dead" by the MOBY Service Testing agent.
      
      A "dead" service is one that does not respond correctly to a MOBY "ping"; where a correct "ping" request/response is:
      
      REQUEST
      
            <MOBY>
            	<mobyContent></mobyContent>
            </MOBY>
      
      RESPONSE
      
            <MOBY>
            	<mobyContent></mobyContent>
            </MOBY>
      
      The status of all services is tested hourly, and is recorded in the 
      LSID metadata for each service as a boolean value in the RDF tag
       "isAlive", which may be used by client software to filter-out
       non-functional services.



	CDK.SF.NET
		CalculateAccurateMass

	ab.wur.nl
		MetwareGetExperimentRaw
		random_number
		xcmsFindPeaks

	arabidopsis.info
		getArabidopsisImageByNASCinsertNumber
		getArabidopsisImageByNASCstockCode

	arexdb.org
		getGOCollection

	asrp.cgrb.oregonstate.edu
		ASRP_miRNA_target_in_AGI
		ASRP_smallRNA_hit_in_IGR_downstream_of_AGI
		ASRP_smallRNA_hit_in_IGR_upstream_of_AGI
		ASRP_smallRNA_sequence_from_chromosomal_AGI

	bibiserv.techfak.uni-bielefeld.de
		RNAShapes_ConsensusShapes
		RNAShapes_Sampling
		RNAShapes_ShapeFolding
		RNAShapes_ShapeProbabilities
		RNAShapes_SuboptimalShapeFolding

	bioassist.nl
		BioAssistSequenceSorter

	bioinfo.cipf.es
		displayDifferentialExpressionTest
		runDifferentialExpressionTest

	bioinfo.icapture.ubc.ca
		GeneticMap2GFF
		getGoTerm
		getGoTermAssociations
		RetrieveGOFromKeywords

	bioinfo.mpimp-golm.mpg.de
		getTrypticPeptideSequenceByAGI

	biomoby.renci.org
		AntiGenic
		BackTranAmbig
		BackTranSeq
		Banana
		Biosed
		Blast
		Btwisted
		Cai
		Chaos
		Charge
		Checktrans
		Chips
		Clustalw
		Codcmp
		CompSeq
		Cons
		Consense
		CPGPlot
		CPGReport
		Cusp
		DeGapSeq
		DescSeq
		DiffSeq
		DNAComp
		DNADist
		DNAPars
		DNAPenny
		DotMatcher
		DotPath
		Dottup
		Drawgram
		Drawtree
		DReg
		EInverted
		Emowse
		EQuickTandem
		Est2Genome
		ETandem
		ExtractBlastReportSequences
		ExtractFeat
		ExtractSeq
		Fitch
		Freak
		FuzzNuc
		FuzzPro
		FuzzTran
		Garnier
		Geecee
		GetOrf
		HelixTurnHelix
		Iep
		InfoAlign
		IsNucleotideSequence
		IsoChore
		Kitsch
		Listor
		LookupSequence
		MakeNucSeq
		MakeProtSeq
		MarScan
		MaskFeat
		Matcher
		MegaMerger
		Merger
		MSBAR
		Needle
		Neighbor
		NewCPGReport
		NewCPGSeek
		NotSeq
		Octanol
		OddComp
		Palindrome
		PatMatDB
		PatMatMotifs
		PepCoil
		PepInfo
		PepNet
		PepStats
		PepWheel
		PepWindow
		PepWindowAll
		PlotCon
		PlotOrf
		PolyDot
		PrettyPlot
		PrettySeq
		ProtDist
		ProtPars
		Recoder
		RegisterAminoAcidSequence
		RegisterNucleotideSequence
		RegisterSequence
		RevSeq
		SeqMatchAll
		SeqRetSplit
		ShowAlign
		ShowFeat
		ShowOrf
		ShowSeq
		SigCleave
		Splitter
		Stretcher
		SuperMatcher
		Syco
		TFScan
		TranSeq
		TrimEST
		TrimSeq
		Union
		Water
		Wobble
		WordCount
		WordMatch

	bioserv.rpbs.jussieu.fr
		ASA
		ASAfromPDBid
		Automat
		BasicBuilder
		Clustalw
		CysPred
		ExtractTurn
		HBonds
		HCA
		Jnet
		Mead_PKa
		Mead_Pot
		NetAsa
		PredAcc
		PSea
		psiBlast
		psiPred
		Stride
		Substitution

	bioweb.pasteur.fr
		Melting

	ccgb.umn.edu
		GI2ScientificName
		MtKeyword

	ccrc.uga.edu
		ccrctest

	cshl.edu
		getArabidoposisAMIRNA

	heaven.mshri.on.ca
		GridService

	imb.uq.edu.au
		IMB_Get_MaximallyRepresentativeCluster

	inblosam.com
		extractGeneProteinNames

	itdinges.mine.nu
		Echo
		helloWorld

	llama.med.harvard.edu
		CCSBHI1
		CorrelatedCoexpression
		GavinSpoke
		Giot
		Harbison
		Ito2001
		Johnson
		LCI
		LeeTF
		Phosphorylome
		Shyamsundar
		Stelzl
		Su
		Tong2004
		Uetz
		Zhang

	metnetdb.org
		getMetNetComments
		getMetNetPathways

	migale.jouy.inra.fr
		Water

	mips.gsf.de
		BlastFastaVsArabiProteincoding
		BlastRawSeqVsArabiContigs
		BlastRawSeqVsArabiProteincoding
		getCosBBHForGene
		MIPSBlast
		MIPSBlastBetterE13
		MIPSBlastXML
		MIPSBlastXMLClickableImage

	mncn.csic.es
		getCoordinatesOfTaxon

	moby.ucalgary.ca
		ABIChromatogramToDNASequence
		ReverseComplementSequence
		TrimSequenceEndsOfAmbiguities
		TrimSequencePolyATail
		TrimSequenceVector


From edward.kawas at gmail.com  Tue Jun 17 14:46:47 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 07:46:47 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617144521.97370@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
	<20080617144521.97370@gmx.net>
Message-ID: <4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>

Yeah, some results are there, but like andreas mentioned ealier, the list
stops at moby.ucalgary.ca.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 7:45 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

That's strange... 
I tried under my windows maschine with ie and firefox.
And also under a linux box with lynx:
Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt

Wget doesn't work (maybe wrong my wrong/missing params):
linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
--16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
           => `ValidateService'
Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80 Connecting
to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
HTTP Anforderung gesendet, warte auf Antwort... 200 OK
L??nge: nicht spezifiziert [text/plain]
ValidateService: Keine Berechtigung

I attached my result.

Hope my tests make sense...

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:01:45 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> I get the same behaviour ... I am looking into it!
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> Groscurth
> Sent: June-17-08 5:40 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> weird..
> 
> also with deleting the browser cache - i only get the list to
> 
> moby.ucalgary.ca
> 
> 
> regardlessly with or without param :(
> 
> andreas
> 
> M4o at gmx.de wrote:
> > Hi all,
> >
> > Andreas maybe try a reload.
> > For me it works for all auths.
> >
> > In my Tool I use the adress with param:
> http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> >
> > Maybe it is possible to extend the testing of the VaildateService
> function.
> >
> > Moritz
> >
> > -------- Original-Nachricht --------
> >   
> >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> >>     
> >
> >   
> >> Paul Gordon wrote:
> >>     
> >>> Hi all,
> >>>
> >>> I'll respond to several posts at once:
> >>>
> >>> 1. There is a list of dead services at Moby Central, but it is not 
> >>> used by default in the jMoby API, and it's not part of the formal API.
> >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> >>>       
> >> thanks for the link - but for me it stops at
> >>
> >> moby.ucalgary.ca
> >>
> >> what about the other authorities ?
> >>
> >> Thanks
> >> andreas
> >> _______________________________________________
> >> 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

--
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
downloaden: http://www.gmx.net/de/go/browser




From M4o at gmx.de  Tue Jun 17 15:16:13 2008
From: M4o at gmx.de (Moritz W)
Date: Tue, 17 Jun 2008 17:16:13 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>
	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
Message-ID: <20080617151613.198390@gmx.net>

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser


From edward.kawas at gmail.com  Tue Jun 17 15:18:14 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 08:18:14 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617151613.198390@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
Message-ID: <4857d5cc.08b38c0a.6aec.265a@mx.google.com>

No problem, I actually misread it a few times too!

Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 8:16 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev




From duncan.hull at cs.man.ac.uk  Tue Jun 17 15:30:12 2008
From: duncan.hull at cs.man.ac.uk (Duncan Hull)
Date: Tue, 17 Jun 2008 16:30:12 +0100
Subject: [MOBY-dev] BioMOBY gets fishy
In-Reply-To: <4857d5cc.08b38c0a.6aec.265a@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>
	<4857d5cc.08b38c0a.6aec.265a@mx.google.com>
Message-ID: <4857D884.4090609@cs.man.ac.uk>

Hello

Just spotted this, might be of interest...

http://pubmed.gov/18554176

FishMap: A Community Resource for Zebrafish Genomics (uses BioMOBY)

via the biomoby feed
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0vWF7uqpQRiVaiVbzYGm2HeVCqdj2BZfCXLbzPc6TZj

-- 
Duncan Hull
http://duncan.hull.name
+44 (0) 161 306 5138



From markw at illuminae.com  Tue Jun 17 18:15:45 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 17 Jun 2008 11:15:45 -0700
Subject: [MOBY-dev] BioMOBY gets fishy
In-Reply-To: <4857D884.4090609@cs.man.ac.uk>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>
	<485127d8.25bb720a.622e.0d84@mx.google.com>
	<48512862.7030104@mpiz-koeln.mpg.de>
	<4851431d.1420720a.52bf.243d@mx.google.com>
	<48527CD8.9060904@mpiz-koeln.mpg.de>
	<48528447.7040807@toulouse.inra.fr>
	<20080613153208.307160@gmx.net> <485296BF.8010303@ucalgary.ca>
	<4857AB57.8010203@mpiz-koeln.mpg.de>
	<20080617123059.152780@gmx.net>
	<4857B0A4.2000005@mpiz-koeln.mpg.de>
	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>
	<20080617144521.97370@gmx.net>
	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
	<4857d5cc.08b38c0a.6aec.265a@mx.google.com>
	<4857D884.4090609@cs.man.ac.uk>
Message-ID: <op.ucwnojdqnbznux@mark.ubic.ca>

Cool :-)

Thanks Dull Hunk!

M


On Tue, 17 Jun 2008 08:30:12 -0700, Duncan Hull <duncan.hull at cs.man.ac.uk>  
wrote:

> Hello
>
> Just spotted this, might be of interest...
>
> http://pubmed.gov/18554176
>
> FishMap: A Community Resource for Zebrafish Genomics (uses BioMOBY)
>
> via the biomoby feed
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0vWF7uqpQRiVaiVbzYGm2HeVCqdj2BZfCXLbzPc6TZj
>



-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre



From edward.kawas at gmail.com  Tue Jun 17 20:53:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 17 Jun 2008 13:53:01 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <20080617151613.198390@gmx.net>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>
	<20080617151613.198390@gmx.net>
Message-ID: <48582444.22ba720a.14d5.ffffda5d@mx.google.com>

Okay, it works again.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
Sent: June-17-08 8:16 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Sorry for that...
I misread andreas post... :(

-------- Original-Nachricht --------
> Datum: Tue, 17 Jun 2008 07:46:47 -0700
> Von: "Edward Kawas" <edward.kawas at gmail.com>
> An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> Betreff: Re: [MOBY-dev] Dead services and how to figure them out

> Yeah, some results are there, but like andreas mentioned ealier, the list
> stops at moby.ucalgary.ca.
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Moritz W
> Sent: June-17-08 7:45 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
> 
> That's strange... 
> I tried under my windows maschine with ie and firefox.
> And also under a linux box with lynx:
> Umgeleitet nach file://localhost/tmp/XXXXnGKM8O/L27195-776TMP.txt
> 
> Wget doesn't work (maybe wrong my wrong/missing params):
> linux03 /> wget http://moby.ucalgary.ca/moby/ValidateService
> --16:40:40--  http://moby.ucalgary.ca/moby/ValidateService
>            => `ValidateService'
> Aufl??sen des Hostnamen ??moby.ucalgary.ca??.... 136.159.169.80
> Connecting
> to moby.ucalgary.ca|136.159.169.80|:80... verbunden.
> HTTP Anforderung gesendet, warte auf Antwort... 200 OK
> L??nge: nicht spezifiziert [text/plain]
> ValidateService: Keine Berechtigung
> 
> I attached my result.
> 
> Hope my tests make sense...
> 
> -------- Original-Nachricht --------
> > Datum: Tue, 17 Jun 2008 07:01:45 -0700
> > Von: "Edward Kawas" <edward.kawas at gmail.com>
> > An: "\'Core developer announcements\'" <moby-dev at lists.open-bio.org>
> > Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> 
> > I get the same behaviour ... I am looking into it!
> > 
> > Eddie
> > 
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas 
> > Groscurth
> > Sent: June-17-08 5:40 AM
> > To: Core developer announcements
> > Subject: Re: [MOBY-dev] Dead services and how to figure them out
> > 
> > weird..
> > 
> > also with deleting the browser cache - i only get the list to
> > 
> > moby.ucalgary.ca
> > 
> > 
> > regardlessly with or without param :(
> > 
> > andreas
> > 
> > M4o at gmx.de wrote:
> > > Hi all,
> > >
> > > Andreas maybe try a reload.
> > > For me it works for all auths.
> > >
> > > In my Tool I use the adress with param:
> > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices
> > >
> > > Maybe it is possible to extend the testing of the VaildateService
> > function.
> > >
> > > Moritz
> > >
> > > -------- Original-Nachricht --------
> > >   
> > >> Datum: Tue, 17 Jun 2008 14:17:27 +0200
> > >> Von: Andreas Groscurth <groscurt at mpiz-koeln.mpg.de>
> > >> An: Core developer announcements <moby-dev at lists.open-bio.org>
> > >> Betreff: Re: [MOBY-dev] Dead services and how to figure them out
> > >>     
> > >
> > >   
> > >> Paul Gordon wrote:
> > >>     
> > >>> Hi all,
> > >>>
> > >>> I'll respond to several posts at once:
> > >>>
> > >>> 1. There is a list of dead services at Moby Central, but it is not 
> > >>> used by default in the jMoby API, and it's not part of the formal
> API.
> > >>> http://moby.ucalgary.ca/moby/ValidateService. Eddie, should it be?
> > >>>       
> > >> thanks for the link - but for me it stops at
> > >>
> > >> moby.ucalgary.ca
> > >>
> > >> what about the other authorities ?
> > >>
> > >> Thanks
> > >> andreas
> > >> _______________________________________________
> > >> 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
> 
> --
> Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten Browser-Versionen
> downloaden: http://www.gmx.net/de/go/browser
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Ist Ihr Browser Vista-kompatibel? Jetzt die neuesten 
Browser-Versionen downloaden: http://www.gmx.net/de/go/browser
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev




From groscurt at mpiz-koeln.mpg.de  Wed Jun 18 13:10:21 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 18 Jun 2008 15:10:21 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48582444.22ba720a.14d5.ffffda5d@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>
	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>
Message-ID: <4859093D.4050800@mpiz-koeln.mpg.de>

Hi,

thanks for that it works....

one question i have about that - two of our services are marked as dead:

mpiz-koeln.mpg.de
	buildMultipleAlignmentWithMAFFT
	RPSBlast

and I'm wondering why ?

i tested them with the contract I know... giving an empty input should 
return an empty output.
They return an error message if no input is given - so this could be the 
reason, but all our other services do the same and they are not marked 
as dead ? so what is the base of this decision ?

now i'm also confused :D

Andreas

Edward Kawas wrote:
> Okay, it works again.
>
> Eddie
>



From edward.kawas at gmail.com  Wed Jun 18 13:14:01 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 18 Jun 2008 06:14:01 -0700
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <4859093D.4050800@mpiz-koeln.mpg.de>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>
	<4859093D.4050800@mpiz-koeln.mpg.de>
Message-ID: <48590a1a.1f588c0a.0b64.1fcf@mx.google.com>

Hi Andreas,

If you go to http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and
enter the service details, you will see what the service tester sees.

The first service in your list seems to return a page that starts with
'syntax error ...'

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
Sent: June-18-08 6:10 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Dead services and how to figure them out

Hi,

thanks for that it works....

one question i have about that - two of our services are marked as dead:

mpiz-koeln.mpg.de
	buildMultipleAlignmentWithMAFFT
	RPSBlast

and I'm wondering why ?

i tested them with the contract I know... giving an empty input should 
return an empty output.
They return an error message if no input is given - so this could be the 
reason, but all our other services do the same and they are not marked 
as dead ? so what is the base of this decision ?

now i'm also confused :D

Andreas

Edward Kawas wrote:
> Okay, it works again.
>
> Eddie
>

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From groscurt at mpiz-koeln.mpg.de  Wed Jun 18 13:26:39 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 18 Jun 2008 15:26:39 +0200
Subject: [MOBY-dev] Dead services and how to figure them out
In-Reply-To: <48590a1a.1f588c0a.0b64.1fcf@mx.google.com>
References: <4850BC9D.8090800@mpiz-koeln.mpg.de>	<485127d8.25bb720a.622e.0d84@mx.google.com>	<48512862.7030104@mpiz-koeln.mpg.de>	<4851431d.1420720a.52bf.243d@mx.google.com>	<48527CD8.9060904@mpiz-koeln.mpg.de>	<48528447.7040807@toulouse.inra.fr>	<20080613153208.307160@gmx.net>	<485296BF.8010303@ucalgary.ca>	<4857AB57.8010203@mpiz-koeln.mpg.de>	<20080617123059.152780@gmx.net>	<4857B0A4.2000005@mpiz-koeln.mpg.de>	<4857c3de.1cba720a.3b23.5d4f@mx.google.com>	<20080617144521.97370@gmx.net>	<4857ce6c.27b38c0a.4888.ffffdb07@mx.google.com>	<20080617151613.198390@gmx.net>	<48582444.22ba720a.14d5.ffffda5d@mx.google.com>	<4859093D.4050800@mpiz-koeln.mpg.de>
	<48590a1a.1f588c0a.0b64.1fcf@mx.google.com>
Message-ID: <48590D0F.6020404@mpiz-koeln.mpg.de>

Mistake on our side (they are registered on a host which is not visible 
to the outside....).... as usual - you did a good job ;-)

thanks
Andreas

Edward Kawas wrote:
> Hi Andreas,
>
> If you go to http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator and
> enter the service details, you will see what the service tester sees.
>
> The first service in your list seems to return a page that starts with
> 'syntax error ...'
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: June-18-08 6:10 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Dead services and how to figure them out
>
> Hi,
>
> thanks for that it works....
>
> one question i have about that - two of our services are marked as dead:
>
> mpiz-koeln.mpg.de
> 	buildMultipleAlignmentWithMAFFT
> 	RPSBlast
>
> and I'm wondering why ?
>
> i tested them with the contract I know... giving an empty input should 
> return an empty output.
> They return an error message if no input is given - so this could be the 
> reason, but all our other services do the same and they are not marked 
> as dead ? so what is the base of this decision ?
>
> now i'm also confused :D
>
> Andreas
>
> Edward Kawas wrote:
>   
>> Okay, it works again.
>>
>> Eddie
>>
>>     
>
> _______________________________________________
> 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 jflo at imim.es  Wed Jun 18 15:36:05 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 17:36:05 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
Message-ID: <48592B65.2030704@imim.es>

Hello everybody,

I have a "problem" with dashboard, when I "generate datatypes" I see a 
list of 630 datatypes, inside this list it appears text-xml, 
text-formatted, text_xml and text_formatted, but when I check the 
content of the jar, that is generated, it contains the text_ classes but 
not the text- ones.

In my jmoby project (eclipse) I can see that the datatypes that I create 
appear there, so I understand that I have the latest version of the list 
of datatypes, between them I cannot see the text- versions I just see 
the text_

Anyone has an idea about what can I do to have access to the text- 
objects? Am I missing something?

Thanks in advance,
j


From edward.kawas at gmail.com  Wed Jun 18 15:50:29 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 18 Jun 2008 08:50:29 -0700
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592B65.2030704@imim.es>
References: <48592B65.2030704@imim.es>
Message-ID: <48592ec7.1cbc720a.21de.1ac4@mx.google.com>

Hi Judith,

In java, '-' is a reserved token and so dashboard probably replaces it with
an '_'.

Martin can tell you for sure how it works.

Eddie



-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
Sent: June-18-08 8:36 AM
To: Core developer announcements
Subject: [MOBY-dev] dashboard problem generating datatypes

Hello everybody,

I have a "problem" with dashboard, when I "generate datatypes" I see a 
list of 630 datatypes, inside this list it appears text-xml, 
text-formatted, text_xml and text_formatted, but when I check the 
content of the jar, that is generated, it contains the text_ classes but 
not the text- ones.

In my jmoby project (eclipse) I can see that the datatypes that I create 
appear there, so I understand that I have the latest version of the list 
of datatypes, between them I cannot see the text- versions I just see 
the text_

Anyone has an idea about what can I do to have access to the text- 
objects? Am I missing something?

Thanks in advance,
j
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From jflo at imim.es  Wed Jun 18 16:02:55 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 18:02:55 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592ec7.1cbc720a.21de.1ac4@mx.google.com>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
Message-ID: <485931AF.5080300@imim.es>

Hi,
But the generated moby message contains also text_xml objects and not 
text-xml... :(
j

Edward Kawas wrote:
> Hi Judith,
>
> In java, '-' is a reserved token and so dashboard probably replaces it with
> an '_'.
>
> Martin can tell you for sure how it works.
>
> Eddie
>
>
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
> Sent: June-18-08 8:36 AM
> To: Core developer announcements
> Subject: [MOBY-dev] dashboard problem generating datatypes
>
> Hello everybody,
>
> I have a "problem" with dashboard, when I "generate datatypes" I see a 
> list of 630 datatypes, inside this list it appears text-xml, 
> text-formatted, text_xml and text_formatted, but when I check the 
> content of the jar, that is generated, it contains the text_ classes but 
> not the text- ones.
>
> In my jmoby project (eclipse) I can see that the datatypes that I create 
> appear there, so I understand that I have the latest version of the list 
> of datatypes, between them I cannot see the text- versions I just see 
> the text_
>
> Anyone has an idea about what can I do to have access to the text- 
> objects? Am I missing something?
>
> Thanks in advance,
> j
> _______________________________________________
> 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 martin.senger at gmail.com  Wed Jun 18 16:58:59 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 00:58:59 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48592B65.2030704@imim.es>
References: <48592B65.2030704@imim.es>
Message-ID: <4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>

> I have a "problem" with dashboard, when I "generate datatypes" I see a list
> of 630 datatypes, inside this list it appears text-xml, text-formatted,
> text_xml and text_formatted, but when I check the content of the jar, that
> is generated, it contains the text_ classes but not the text- ones.


MoSeS generator changes dashes to underscore. Which means that both Moby
data types text-plain and text_plain are represented by only one class. You
cannot distinguish them. However, MoSeS and Dashboard know what moby data
type is expected by a service and send a correct type (text-plain, or
text_plain). I forgot already how it is done, but it seems to work fine (you
can try - in Dashboard - to generate XML input, for example for a service
TestService and you will se there text-plain object.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From markw at illuminae.com  Wed Jun 18 17:00:58 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 18 Jun 2008 10:00:58 -0700
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>
References: <48592B65.2030704@imim.es>
	<4d93f07c0806180958x6db97f2dua6f4317cc1ffe2f8@mail.gmail.com>
Message-ID: <op.ucyevwkrnbznux@dd0710001l.icapture.ubc.ca>

I think we should curate the ontology... are there still services that use  
both nodes?

M



On Wed, 18 Jun 2008 09:58:59 -0700, Martin Senger  
<martin.senger at gmail.com> wrote:

>> I have a "problem" with dashboard, when I "generate datatypes" I see a  
>> list
>> of 630 datatypes, inside this list it appears text-xml, text-formatted,
>> text_xml and text_formatted, but when I check the content of the jar,  
>> that
>> is generated, it contains the text_ classes but not the text- ones.
>
>
> MoSeS generator changes dashes to underscore. Which means that both Moby
> data types text-plain and text_plain are represented by only one class.  
> You
> cannot distinguish them. However, MoSeS and Dashboard know what moby data
> type is expected by a service and send a correct type (text-plain, or
> text_plain). I forgot already how it is done, but it seems to work fine  
> (you
> can try - in Dashboard - to generate XML input, for example for a service
> TestService and you will se there text-plain object.
>
> Martin
>



-- 
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 martin.senger at gmail.com  Wed Jun 18 17:10:13 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:10:13 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485931AF.5080300@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
Message-ID: <4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>

> But the generated moby message contains also text_xml objects and not
> text-xml...


Well, show me the message . Are you talking about a request or response?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From jflo at imim.es  Wed Jun 18 17:32:44 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 19:32:44 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
Message-ID: <485946BC.5090603@imim.es>

This is the message that I send to the service (it is a tcpmon capture 
with all the &lt; and &gt! changed to < and >):

<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope 
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" 
xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:runByoDyn 
soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" 
xmlns:ns1="http://biomoby.org/"><ns1:arg0 xsi:type="soapenc:string" 
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"><?xml 
version=&quot;1.0&quot; encoding=&quot;UTF-8&quot;?>
<moby:MOBY xmlns:moby=&quot;http://www.biomoby.org/moby>
  <moby:mobyContent>
    <moby:mobyData moby:queryID=&quot;job_0>
      <moby:Simple moby:articleName=&quot;input>
        <moby:*text_xml* moby:id=&quot;BIOMD0000000050.xml&quot; 
moby:namespace=&quot;text-xml>
          <moby:String moby:id=&quot;&quot; moby:namespace=&quot;&quot; 
moby:articleName=&quot;content>

BLA BLA LBA

    </moby:String>
        </moby:*text_xml*>
      </moby:Simple>
 
      <moby:Simple moby:articleName=&quot;parameters>
        <moby:*text_formatted* moby:id=&quot;runnerFile&quot; 
moby:namespace=&quot;text-formatted>
          <moby:String moby:id=&quot;&quot; moby:namespace=&quot;&quot; 
moby:articleName=&quot;content>


BLA BLA BLA

     </moby:String>
        </moby:*text_formatted*>
      </moby:Simple>
    </moby:mobyData>
  </moby:mobyContent>
</moby:MOBY>
S
 
</ns1:arg0></ns1:runByoDyn></soapenv:Body></soapenv:Envelope>

The service that i'm calling uses the text- objects...

Martin Senger wrote:
>> But the generated moby message contains also text_xml objects and not
>> text-xml...
>>     
>
>
> Well, show me the message . Are you talking about a request or response?
>
> Martin
>
>   


From martin.senger at gmail.com  Wed Jun 18 17:48:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:48:06 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485946BC.5090603@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
Message-ID: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>

> This is the message that I send to the service...


Which service it is? Do I have access to its description? Or perhaps even to
call it?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Wed Jun 18 17:48:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 01:48:06 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <485946BC.5090603@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
Message-ID: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>

> This is the message that I send to the service...


Which service it is? Do I have access to its description? Or perhaps even to
call it?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From judit.flo at gmail.com  Wed Jun 18 20:58:47 2008
From: judit.flo at gmail.com (Judith Flo)
Date: Wed, 18 Jun 2008 22:58:47 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
Message-ID: <48597707.1030505@imim.es>

The service is registered under the moby-dev repository, it is called 
runByoDyn, created by the auth inb.bsc.es


Martin Senger escribi?:
>> This is the message that I send to the service...
>>     
>
>
> Which service it is? Do I have access to its description? Or perhaps even to
> call it?
>
> Martin
>
>   


From jflo at imim.es  Wed Jun 18 21:00:38 2008
From: jflo at imim.es (Judith Flo)
Date: Wed, 18 Jun 2008 23:00:38 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
Message-ID: <48597776.1070804@imim.es>

The service is registered under the moby-dev repository, it is called
runByoDyn, created by the auth inb.bsc.es


Martin Senger escribi?:
>> This is the message that I send to the service...
>>     
>
>
> Which service it is? Do I have access to its description? Or perhaps even to
> call it?
>
> Martin
>
>   



--------
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Before printing this e-mail, please make certain it is absolutely necessary.
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Si no ??s la persona a la qual anava dirigida aquesta informaci??, si us 
plau, notifiqui immediatament l'enviament erroni al remitent i esborri 
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La informaci??n contenida en este mensaje y en cualquier fichero 
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remitente y borre el mensaje. Cualquier copia, divulgaci??n, 
distribuci??n o utilizaci??n no autorizada de este correo electr??nico y 
de sus adjuntos est?? prohibida en virtud de la legislaci??n vigente.

The information included in this e-mail and any attached files is 
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please notify the sender and delete this message immediately. 
Dissemination, forwarding or copying of this e-mail and 
its associated attachments is strictly prohibited in accordance with 
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--------



From martin.senger at gmail.com  Thu Jun 19 02:08:21 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 19 Jun 2008 10:08:21 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <48597776.1070804@imim.es>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
Message-ID: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>

> The service is registered under the moby-dev repository, it is called
> runByoDyn, created by the auth inb.bsc.es
>


Okay, I see the service now. And *it is clear now what is the problem*. The
service runByoDyn is an asynchronous service. And neither Dashboard nor
MoSeS have support for asynchronous services. I should be working on it, but
it is not there yet (not a priority in my current funding, unfortunately).
Bad luck for you, sorry.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From jflo at imim.es  Thu Jun 19 09:33:23 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 19 Jun 2008 11:33:23 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
Message-ID: <485A27E3.8000007@imim.es>

But I run it and got results using dashboard!

It returns a Zip_encoded object (base64), the service is async because 
there are some executions that takes lot of time and consume the 
timeout... But for "simple" executions it should return this zip_encoded 
object (in fact as I said, I test it and it works)

Does the dashboard use different libraries than moses (to generate the 
datatypes), I'm asking this to understand why my message is different 
(in terms of text_ objects) from the one that the dashboard generates...

(Sorry Martin, you'll receive this message twice, I don't know if there 
is someone in the list that can put some light on this...)

Martin Senger wrote:
>
> Okay, I see the service now. And *it is clear now what is the problem*. The
> service runByoDyn is an asynchronous service. And neither Dashboard nor
> MoSeS have support for asynchronous services. I should be working on it, but
> it is not there yet (not a priority in my current funding, unfortunately).
> Bad luck for you, sorry.
>
> Martin


From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 08:52:08 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 25 Jun 2008 10:52:08 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <485A27E3.8000007@imim.es>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es>
Message-ID: <48620738.7050103@mpiz-koeln.mpg.de>

Hi,

i dont know if i missed that somehow or if this is still an issue - but 
it came up here as currently biomoby.org is unavailable.

Is there a possibilty to use the cached ontologies for the jMoby API ?

My problem is that each time i start an application which e.g. calles a 
BioMoby service the datatype ontology and namespace ontology are fetched 
from http://biomoby.org.
Is it possible somehow to tell the API not to download it from the net 
but to use a local cache?

I'm not sure whether this was already a discussion before and i remember 
something about the Registry - but please give me some hints if and how 
this is possible ?

Thanks
andreas


From martin.senger at gmail.com  Wed Jun 25 08:59:45 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 16:59:45 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <48620738.7050103@mpiz-koeln.mpg.de>
References: <48592B65.2030704@imim.es>
	<48592ec7.1cbc720a.21de.1ac4@mx.google.com> <485931AF.5080300@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es> <48620738.7050103@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>

> My problem is that each time i start an application which e.g. calles a
> BioMoby service the datatype ontology and namespace ontology are fetched
> from http://biomoby.org.
> Is it possible somehow to tell the API not to download it from the net but
> to use a local cache?


For calling a service, you do not need any ontology at all - you just need
to know the service URL and what data type it expects.

Depending on the librray you are using, you can get even the information
that you do not need, from a local cache. Exactly the same way as Dashboard
does it. It uses
CentralDigestCachedImpl class (to access moby registry).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 09:41:56 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 25 Jun 2008 11:41:56 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
References: <48592B65.2030704@imim.es>	<48592ec7.1cbc720a.21de.1ac4@mx.google.com>
	<485931AF.5080300@imim.es>	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>	<485946BC.5090603@imim.es>	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>	<48597776.1070804@imim.es>	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>	<485A27E3.8000007@imim.es>
	<48620738.7050103@mpiz-koeln.mpg.de>
	<4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
Message-ID: <486212E4.2030304@mpiz-koeln.mpg.de>

thx martin,

but if i understand it correctly the CentralDigestCachedImpl does access 
a default moby registry and then caches it locally. What I'm interessted 
in is not to access any registry at all for getting the ontologies.
My sitatuation is that i query the moby central to find some services 
based on e.g. their input and output parameters. So I use 
MobyNames.getMobyNamespace("gi"); for example. This will download the 
ontgologies from biomoby.org.

So did i understand this wrong ? all classes will download the 
ontologies once and then some caches them ? this would mean that at 
start it will always download the ontologies ?

thx
andreas

Martin Senger wrote:
>> My problem is that each time i start an application which e.g. calles a
>> BioMoby service the datatype ontology and namespace ontology are fetched
>> from http://biomoby.org.
>> Is it possible somehow to tell the API not to download it from the net but
>> to use a local cache?
>>     
>
>
> For calling a service, you do not need any ontology at all - you just need
> to know the service URL and what data type it expects.
>
> Depending on the librray you are using, you can get even the information
> that you do not need, from a local cache. Exactly the same way as Dashboard
> does it. It uses
> CentralDigestCachedImpl class (to access moby registry).
>
> Martin
>
>   



From martin.senger at gmail.com  Wed Jun 25 10:54:43 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 18:54:43 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <486212E4.2030304@mpiz-koeln.mpg.de>
References: <48592B65.2030704@imim.es>
	<4d93f07c0806181010q70582ed7j6c9f56df80142a4d@mail.gmail.com>
	<485946BC.5090603@imim.es>
	<4d93f07c0806181048w444db921tbd7340d44889c5be@mail.gmail.com>
	<48597776.1070804@imim.es>
	<4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<485A27E3.8000007@imim.es> <48620738.7050103@mpiz-koeln.mpg.de>
	<4d93f07c0806250159n635a97f2t72acdef8a9a6bf63@mail.gmail.com>
	<486212E4.2030304@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>

> but if i understand it correctly the CentralDigestCachedImpl does access a
> default moby registry and then caches it locally.


Actually no. The class gets, in its constructor, a local directory where the
cached ontology are located, and uses it. Only if the cache is empty, it
tries to fill it.


> What I'm interessted in is not to access any registry at all for getting
> the ontologies.
> My sitatuation is that i query the moby central to find some services based
> on e.g. their input and output parameters.


The cache does not have the "find" method - we did not want to replicate the
whole registry's API. But because all ontologies are locally available, it
is easy to get them all (that's why the class is also called "digest",
because it provides the cumulative methods that the registry's API does not
provide in all cases) and iterate over them and make your search as you
wish.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From groscurt at mpiz-koeln.mpg.de  Wed Jun 25 11:28:55 2008
From: groscurt at mpiz-koeln.mpg.de (groscurt)
Date: Wed, 25 Jun 2008 13:28:55 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>
Message-ID: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>

this is an example code:

Central central = new CentralDigestCachedImpl(
"/home/pcb/groscurt/moby-live/Java/myCache" );
MobyService mobyService = new MobyService();
mobyService.setAuthority( "arabidopsis.org" );
mobyService.setName( "Locus2Publications" );
mobyService.setCategory( "" );
mobyService = central.findService( mobyService )[0];

MobyRequest mobyRequest = new MobyRequest( central );
mobyRequest.setService( mobyService );
mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );

running this starts to download the ontologies from biomoby.org. I guess the
handling of the MobyRequest stuff is the problem here - but how to solve
that ?

Best and thanks
andreas

----------------original message-----------------
From: "Martin Senger" martin.senger at gmail.com
To: "Core developer announcements" moby-dev at lists.open-bio.org
Date: Wed, 25 Jun 2008 18:54:43 +0800
-------------------------------------------------
>> but if i understand it correctly the CentralDigestCachedImpl does access
a
>> default moby registry and then caches it locally.
> 
> 
> Actually no. The class gets, in its constructor, a local directory where
the
> cached ontology are located, and uses it. Only if the cache is empty, it
> tries to fill it.
> 
> 
>> What I'm interessted in is not to access any registry at all for getting
>> the ontologies.
>> My sitatuation is that i query the moby central to find some services
based
>> on e.g. their input and output parameters.
> 
> 
> The cache does not have the "find" method - we did not want to replicate
the
> whole registry's API. But because all ontologies are locally available, it
> is easy to get them all (that's why the class is also called "digest",
> because it provides the cumulative methods that the registry's API does
not
> provide in all cases) and iterate over them and make your search as you
> wish.
> 
> Martin
> 
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 





From martin.senger at gmail.com  Wed Jun 25 12:42:08 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 25 Jun 2008 20:42:08 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <4d93f07c0806250354o64429eam564f68d2d09ca74a@mail.gmail.com>
	<83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0806250542w1c9bbed3h44567239cd83a6d5@mail.gmail.com>

> running this starts to download the ontologies from biomoby.org. I guess
> the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?


No idea, I do not use MobyRequest. It's rhe Paul's branche of jMoby...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From gordonp at ucalgary.ca  Wed Jun 25 14:20:30 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 25 Jun 2008 08:20:30 -0600
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4862542E.7050009@ucalgary.ca>

Hi Andreas,

I still need to update some of the code to use the new caching that 
Eddie implemented in February while we were in Japan.  I've been out of 
the Moby loop for a while, but starting this week I'll be able to start 
working on it again, so it should cache by default Real Soon Now(TM).

Paul

groscurt wrote:
> this is an example code:
>
> Central central = new CentralDigestCachedImpl(
> "/home/pcb/groscurt/moby-live/Java/myCache" );
> MobyService mobyService = new MobyService();
> mobyService.setAuthority( "arabidopsis.org" );
> mobyService.setName( "Locus2Publications" );
> mobyService.setCategory( "" );
> mobyService = central.findService( mobyService )[0];
>
> MobyRequest mobyRequest = new MobyRequest( central );
> mobyRequest.setService( mobyService );
> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );
>
> running this starts to download the ontologies from biomoby.org. I guess the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?
>
> Best and thanks
> andreas
>
> ----------------original message-----------------
> From: "Martin Senger" martin.senger at gmail.com
> To: "Core developer announcements" moby-dev at lists.open-bio.org
> Date: Wed, 25 Jun 2008 18:54:43 +0800
> -------------------------------------------------
>   
>>> but if i understand it correctly the CentralDigestCachedImpl does access
>>>       
> a
>   
>>> default moby registry and then caches it locally.
>>>       
>> Actually no. The class gets, in its constructor, a local directory where
>>     
> the
>   
>> cached ontology are located, and uses it. Only if the cache is empty, it
>> tries to fill it.
>>
>>
>>     
>>> What I'm interessted in is not to access any registry at all for getting
>>> the ontologies.
>>> My sitatuation is that i query the moby central to find some services
>>>       
> based
>   
>>> on e.g. their input and output parameters.
>>>       
>> The cache does not have the "find" method - we did not want to replicate
>>     
> the
>   
>> whole registry's API. But because all ontologies are locally available, it
>> is easy to get them all (that's why the class is also called "digest",
>> because it provides the cumulative methods that the registry's API does
>>     
> not
>   
>> provide in all cases) and iterate over them and make your search as you
>> wish.
>>
>> Martin
>>
>> -- 
>> Martin Senger
>> email: martin.senger at gmail.com,m.senger at cgiar.org
>> skype: martinsenger
>> _______________________________________________
>> 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
>
> !DSPAM:60005,48622972109501804129376!
>
>
>
>   


From dmitry.repchevski at bsc.es  Thu Jun 26 10:49:31 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Thu, 26 Jun 2008 12:49:31 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
Message-ID: <4863743B.3040909@bsc.es>

Hello Martin,
> Okay, I see the service now. And *it is clear now what is the problem*. The
> service runByoDyn is an asynchronous service. And neither Dashboard nor
> MoSeS have support for asynchronous services. I should be working on it, but
> it is not there yet (not a priority in my current funding, unfortunately).
> Bad luck for you, sorry.
When you mention Dashboard/MoSeS or JMoby?
Should we understand it that there is no java asynchrony planned for JMoby?

 > Judith:

You can try my library that supports asynchrony (if you need to call an 
asynchronous service from Java).
You can download it at http://inb.bsc.es/documents/java/index.html

I am going to talk about it in Valencia, but don't hesitate to write me 
if you will face some problem with it.

Dmitry



From martin.senger at gmail.com  Thu Jun 26 11:45:14 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 26 Jun 2008 19:45:14 +0800
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4863743B.3040909@bsc.es>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<4863743B.3040909@bsc.es>
Message-ID: <4d93f07c0806260445wbadd4davb22080e279282434@mail.gmail.com>

> When you mention Dashboard/MoSeS or JMoby?
> Should we understand it that there is no java asynchrony planned for JMoby?


It is planned.
M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From jflo at imim.es  Thu Jun 26 15:25:20 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 26 Jun 2008 17:25:20 +0200
Subject: [MOBY-dev] dashboard problem generating datatypes
In-Reply-To: <4863743B.3040909@bsc.es>
References: <4d93f07c0806181908v6abec37doe939969ef53183d1@mail.gmail.com>
	<4863743B.3040909@bsc.es>
Message-ID: <4863B4E0.7040503@imim.es>

Hi everyone,

I suppose that I'm confused about my problem with the text_ objects 
because noone has answered...

Anyway, I really need this "asynchronous thing" working and I can't wait 
:( --nor switch to perl--

I checked this library from Dmitry and I have to say that his job is 
really good, I changed my code and everything is working now! No 
problems with sync netiher async services!

Thanks Dmitry!
j


Dmitry Repchevsky wrote:
> Hello Martin,
>> Okay, I see the service now. And *it is clear now what is the 
>> problem*. The
>> service runByoDyn is an asynchronous service. And neither Dashboard nor
>> MoSeS have support for asynchronous services. I should be working on 
>> it, but
>> it is not there yet (not a priority in my current funding, 
>> unfortunately).
>> Bad luck for you, sorry.
> When you mention Dashboard/MoSeS or JMoby?
> Should we understand it that there is no java asynchrony planned for 
> JMoby?
>
> > Judith:
>
> You can try my library that supports asynchrony (if you need to call 
> an asynchronous service from Java).
> You can download it at http://inb.bsc.es/documents/java/index.html
>
> I am going to talk about it in Valencia, but don't hesitate to write 
> me if you will face some problem with it.
>
> Dmitry


From gordonp at ucalgary.ca  Thu Jun 26 15:44:09 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 26 Jun 2008 09:44:09 -0600
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <4863B949.9020204@ucalgary.ca>

Hi Andreas & Martin,

The issue is that you should really be calling

new MobyDataObject("AGI_LocusCode", "at4g30110", central)

on the last line of your example, but of course it's not your fault.  
The org.biomoby.shared.data package takes Registry as an optional 
argument for all of the constructors, and I had a mechanism that allowed 
you to associate a Registry object with a cache.  Because we are moving 
to a unified caching mechanism, the ideal solution from my perspective 
would be for Registry to become an interface, Central extends Registry, 
and all of the CentralImpls are children of the old Registry object 
(which becomes RegistryImpl).  Martin, would you have any objections if 
I did this?  I think the Registry -> Central hierarchy makes sense as 
you move from metadata to metadata+data.

Of course, if you wanted to use the default central endpoint and caching 
directory, the

new MobyDataObject("AGI_LocusCode", "at4g30110")

call would be all that is required under the new system.

Regards,

Paul

groscurt wrote:
> this is an example code:
>
> Central central = new CentralDigestCachedImpl(
> "/home/pcb/groscurt/moby-live/Java/myCache" );
> MobyService mobyService = new MobyService();
> mobyService.setAuthority( "arabidopsis.org" );
> mobyService.setName( "Locus2Publications" );
> mobyService.setCategory( "" );
> mobyService = central.findService( mobyService )[0];
>
> MobyRequest mobyRequest = new MobyRequest( central );
> mobyRequest.setService( mobyService );
> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", "at4g30110") );
>
> running this starts to download the ontologies from biomoby.org. I guess the
> handling of the MobyRequest stuff is the problem here - but how to solve
> that ?
>
> Best and thanks
> andreas
>
> ----------------original message-----------------
> From: "Martin Senger" martin.senger at gmail.com
> To: "Core developer announcements" moby-dev at lists.open-bio.org
> Date: Wed, 25 Jun 2008 18:54:43 +0800
> -------------------------------------------------
>   
>>> but if i understand it correctly the CentralDigestCachedImpl does access
>>>       
> a
>   
>>> default moby registry and then caches it locally.
>>>       
>> Actually no. The class gets, in its constructor, a local directory where
>>     
> the
>   
>> cached ontology are located, and uses it. Only if the cache is empty, it
>> tries to fill it.
>>
>>
>>     
>>> What I'm interessted in is not to access any registry at all for getting
>>> the ontologies.
>>> My sitatuation is that i query the moby central to find some services
>>>       
> based
>   
>>> on e.g. their input and output parameters.
>>>       
>> The cache does not have the "find" method - we did not want to replicate
>>     
> the
>   
>> whole registry's API. But because all ontologies are locally available, it
>> is easy to get them all (that's why the class is also called "digest",
>> because it provides the cumulative methods that the registry's API does
>>     
> not
>   
>> provide in all cases) and iterate over them and make your search as you
>> wish.
>>
>> Martin
>>
>> -- 
>> Martin Senger
>> email: martin.senger at gmail.com,m.senger at cgiar.org
>> skype: martinsenger
>> _______________________________________________
>> 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
>
> !DSPAM:60005,48622972109501804129376!
>
>
>
>   


From groscurt at mpiz-koeln.mpg.de  Fri Jun 27 07:04:22 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 27 Jun 2008 09:04:22 +0200
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <486490F6.7060706@mpiz-koeln.mpg.de>

Hi Paul,

as far as i can oversee that, this sounds quite reasonable for me. I was 
always wondered what a Central is if not a registry... so it sounds ok 
to make a connection between them programmatically. As long as this wont 
destroy current usage of the code - but that does not seems to be the 
case as you described it.

Looking forward for this :)

Andreas

Paul Gordon wrote:
> Hi Andreas & Martin,
>
> The issue is that you should really be calling
>
> new MobyDataObject("AGI_LocusCode", "at4g30110", central)
>
> on the last line of your example, but of course it's not your fault.  
> The org.biomoby.shared.data package takes Registry as an optional 
> argument for all of the constructors, and I had a mechanism that 
> allowed you to associate a Registry object with a cache.  Because we 
> are moving to a unified caching mechanism, the ideal solution from my 
> perspective would be for Registry to become an interface, Central 
> extends Registry, and all of the CentralImpls are children of the old 
> Registry object (which becomes RegistryImpl).  Martin, would you have 
> any objections if I did this?  I think the Registry -> Central 
> hierarchy makes sense as you move from metadata to metadata+data.
>
> Of course, if you wanted to use the default central endpoint and 
> caching directory, the
>
> new MobyDataObject("AGI_LocusCode", "at4g30110")
>
> call would be all that is required under the new system.
>
> Regards,
>
> Paul
>
> groscurt wrote:
>> this is an example code:
>>
>> Central central = new CentralDigestCachedImpl(
>> "/home/pcb/groscurt/moby-live/Java/myCache" );
>> MobyService mobyService = new MobyService();
>> mobyService.setAuthority( "arabidopsis.org" );
>> mobyService.setName( "Locus2Publications" );
>> mobyService.setCategory( "" );
>> mobyService = central.findService( mobyService )[0];
>>
>> MobyRequest mobyRequest = new MobyRequest( central );
>> mobyRequest.setService( mobyService );
>> mobyRequest.setInput( new MobyDataObject("AGI_LocusCode", 
>> "at4g30110") );
>>
>> running this starts to download the ontologies from biomoby.org. I 
>> guess the
>> handling of the MobyRequest stuff is the problem here - but how to solve
>> that ?
>>
>> Best and thanks
>> andreas
>>
>> ----------------original message-----------------
>> From: "Martin Senger" martin.senger at gmail.com
>> To: "Core developer announcements" moby-dev at lists.open-bio.org
>> Date: Wed, 25 Jun 2008 18:54:43 +0800
>> -------------------------------------------------
>>  
>>>> but if i understand it correctly the CentralDigestCachedImpl does 
>>>> access
>>>>       
>> a
>>  
>>>> default moby registry and then caches it locally.
>>>>       
>>> Actually no. The class gets, in its constructor, a local directory 
>>> where
>>>     
>> the
>>  
>>> cached ontology are located, and uses it. Only if the cache is 
>>> empty, it
>>> tries to fill it.
>>>
>>>
>>>    
>>>> What I'm interessted in is not to access any registry at all for 
>>>> getting
>>>> the ontologies.
>>>> My sitatuation is that i query the moby central to find some services
>>>>       
>> based
>>  
>>>> on e.g. their input and output parameters.
>>>>       
>>> The cache does not have the "find" method - we did not want to 
>>> replicate
>>>     
>> the
>>  
>>> whole registry's API. But because all ontologies are locally 
>>> available, it
>>> is easy to get them all (that's why the class is also called "digest",
>>> because it provides the cumulative methods that the registry's API does
>>>     
>> not
>>  
>>> provide in all cases) and iterate over them and make your search as you
>>> wish.
>>>
>>> Martin
>>>
>>> -- 
>>> Martin Senger
>>> email: martin.senger at gmail.com,m.senger at cgiar.org
>>> skype: martinsenger
>>> _______________________________________________
>>> 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
>>
>> !DSPAM:60005,48622972109501804129376!
>>
>>
>>
>>   
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From martin.senger at gmail.com  Mon Jun 30 03:14:09 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Mon, 30 Jun 2008 11:14:09 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <4d93f07c0806292014m310611f8ieba71594b9968d6d@mail.gmail.com>

> Central extends Registry...


Central already has constructors taking the registry. No need to change
anything - I think. But I cannot check it now, not being on my computer. I
will reply once again later.

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Mon Jun 30 18:19:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 1 Jul 2008 02:19:06 +0800
Subject: [MOBY-dev] jmoby using cached datatypes etc
In-Reply-To: <4863B949.9020204@ucalgary.ca>
References: <83d68e4c9eaa56d5c128499e4080196d@mpizmail.mpiz-koeln.mpg.de>
	<4863B949.9020204@ucalgary.ca>
Message-ID: <4d93f07c0806301119s6bf0fc71geee901bf51c223c9@mail.gmail.com>

> Because we are moving to a unified caching mechanism, the ideal solution
> from my perspective would be for Registry to become an interface


Sorry, Paul, but from my perspective, I would keep it as it is. The
CentralImpl has an ability (in constructors) to specify which registry to
talk to, and always had. If you wish to use it (and you should, but it is
jut my personal perspective) you should comply with it.

Cheers,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From andreas.groscurth at web.de  Mon Jun 30 14:53:54 2008
From: andreas.groscurth at web.de (Andreas Groscurthh)
Date: Mon, 30 Jun 2008 16:53:54 +0200
Subject: [MOBY-dev] question about mobycentral database
Message-ID: <4868F382.4000907@web.de>

Hi,

a short question about the database schema of mobycentral.

There are 2 databases (ofc among others) - mobyservice and mobycentral. 
mobyservice contains the table service and mobycentral service_instance.

If a service is registered - in which table is the information written ? 
in both ? and is then the service_instance_id from service_instance the 
same as service_id from service ? or is there another difference between 
these two tables ?

mhm ok - more than one question actually ;-)

Thanks
Andreas


From edward.kawas at gmail.com  Mon Jun 30 20:19:44 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 30 Jun 2008 13:19:44 -0700
Subject: [MOBY-dev] question about mobycentral database
In-Reply-To: <4868F382.4000907@web.de>
References: <4868F382.4000907@web.de>
Message-ID: <48693ff1.16538c0a.7690.1984@mx.google.com>

Hi Andreas,

The db mobycentral contains all the information for service instances, while
the db mobyservice contains information for service types.

When you register a new service instance, the information is kept in
mobycentral.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurthh
Sent: June-30-08 7:54 AM
To: Core developer announcements
Subject: [MOBY-dev] question about mobycentral database

Hi,

a short question about the database schema of mobycentral.

There are 2 databases (ofc among others) - mobyservice and mobycentral. 
mobyservice contains the table service and mobycentral service_instance.

If a service is registered - in which table is the information written ? 
in both ? and is then the service_instance_id from service_instance the 
same as service_id from service ? or is there another difference between 
these two tables ?

mhm ok - more than one question actually ;-)

Thanks
Andreas
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From martin.senger at gmail.com  Mon Jun 30 20:20:18 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 1 Jul 2008 04:20:18 +0800
Subject: [MOBY-dev] jMoby does not compile!
Message-ID: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>

Whoever committed it please rectify it.

Thanks,
Martin

compile:
    [javac] Compiling 348 source files to
/home/senger/moby-live/Java/build/classes
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/test/WSDLServiceTestCase.java:8:
cannot find symbol
    [javac] symbol  : class WSDLService
    [javac] location: package ca.ucalgary.services
    [javac] import ca.ucalgary.services.WSDLService;
    [javac]                             ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:406:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]     NodeList schemaElements =
wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:422:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]
if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI()))
&&
    [javac]                                       ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:436:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                     NodeList contentElements =
schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:440:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                             ((Element)
contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:443:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]                             NodeList attributeElements =
((Element)
restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,

[javac]
^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:465:
cannot find symbol
    [javac] symbol  : variable XSD_NAMESPACE
    [javac] location: class org.biomoby.shared.MobyPrefixResolver
    [javac]
if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
    [javac]                                                               ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:472:
cannot find symbol
    [javac] symbol  : method isLSID(java.lang.String)
    [javac] location: class org.biomoby.shared.LSIDResolver
    [javac]
if(lsidResolver.isLSID(schemaMapping)){
    [javac]                                                                ^
    [javac]
/home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:494:
cannot find symbol
    [javac] symbol  : method isLSID(java.lang.String)
    [javac] location: class org.biomoby.shared.LSIDResolver
    [javac]                 if(lsidResolver.isLSID(schemaMapping)){
    [javac]                                    ^
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.
    [javac] 9 errors



-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From gordonp at ucalgary.ca  Mon Jun 30 21:28:10 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 30 Jun 2008 15:28:10 -0600
Subject: [MOBY-dev] jMoby does not compile!
In-Reply-To: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>
References: <4d93f07c0806301320u228325demc590727eae84929@mail.gmail.com>
Message-ID: <48694FEA.3070107@ucalgary.ca>

Fixed now.  Sorry, I was in the middle of a string of commits and had to 
leave the office unexpectedly.  One argument for svn I suppose...

Martin Senger wrote:
> Whoever committed it please rectify it.
>
> Thanks,
> Martin
>
> compile:
>     [javac] Compiling 348 source files to
> /home/senger/moby-live/Java/build/classes
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/test/WSDLServiceTestCase.java:8:
> cannot find symbol
>     [javac] symbol  : class WSDLService
>     [javac] location: package ca.ucalgary.services
>     [javac] import ca.ucalgary.services.WSDLService;
>     [javac]                             ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:406:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]     NodeList schemaElements =
> wsdlRoot.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:422:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]
> if((MobyPrefixResolver.XSD_NAMESPACE.equals(schemaDefElement.getNamespaceURI()))
> &&
>     [javac]                                       ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:436:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                     NodeList contentElements =
> schemaDefElement.getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:440:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                             ((Element)
> contentElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:443:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]                             NodeList attributeElements =
> ((Element)
> restrictionElements.item(0)).getElementsByTagNameNS(MobyPrefixResolver.XSD_NAMESPACE,
>
> [javac]
> ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:465:
> cannot find symbol
>     [javac] symbol  : variable XSD_NAMESPACE
>     [javac] location: class org.biomoby.shared.MobyPrefixResolver
>     [javac]
> if((MobyPrefixResolver.XSD_NAMESPACE.equals(sde.getNamespaceURI())) &&
>     [javac]                                                               ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:472:
> cannot find symbol
>     [javac] symbol  : method isLSID(java.lang.String)
>     [javac] location: class org.biomoby.shared.LSIDResolver
>     [javac]
> if(lsidResolver.isLSID(schemaMapping)){
>     [javac]                                                                ^
>     [javac]
> /home/senger/moby-live/Java/src/main/ca/ucalgary/services/util/WSDLConfig.java:494:
> cannot find symbol
>     [javac] symbol  : method isLSID(java.lang.String)
>     [javac] location: class org.biomoby.shared.LSIDResolver
>     [javac]                 if(lsidResolver.isLSID(schemaMapping)){
>     [javac]                                    ^
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 9 errors
>
>
>
>