From jerzyo at genesilico.pl Mon Sep 1 06:01:45 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 01 Sep 2008 12:01:45 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
Message-ID: <48BBBD89.6020803@genesilico.pl>
Hello
I am searchng for a java class representing a BioMoby workflow:
I found some classes that represent connections:
datatype -> service
service -> datatype
datatype -> datatype
in org.biomoby.client.
(There is even a class for drawing graphs using graphviz, but
unfortunately without datatype -> datatype connections.)
I do not find find any class that these connections gathers them
together as a workflow and enables execution of this workflow given some
inputs.
Does such class exist in jMoby? Or should I run my workflows using
Taverna libraries (How should I do it)?
If it does not exist I will probably write it but maybe somebody is
already doing it.
Jerzy Orlowski
From serr at ac.uma.es Mon Sep 1 06:10:53 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Mon, 01 Sep 2008 12:10:53 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBD89.6020803@genesilico.pl>
References: <48BBBD89.6020803@genesilico.pl>
Message-ID: <48BBBFAD.7060401@ac.uma.es>
Hello Jerzy
Unfortunately, moby can not handle workflows by itself for now. Normally
you use taverna for building workflows.
I'm trying to learn how to use Taverna libraries to run workflows. There
is a taverna class (workflowlauncher or similar) available in the web
page for taverna, but I couldn't make it work.
I'm also very interesting in this topic.
Greetings, Sergio
Jerzy Orlowski wrote:
> Hello
>
> I am searchng for a java class representing a BioMoby workflow:
>
> I found some classes that represent connections:
> datatype -> service
> service -> datatype
> datatype -> datatype
> in org.biomoby.client.
> (There is even a class for drawing graphs using graphviz, but
> unfortunately without datatype -> datatype connections.)
>
> I do not find find any class that these connections gathers them
> together as a workflow and enables execution of this workflow given
> some inputs.
>
> Does such class exist in jMoby? Or should I run my workflows using
> Taverna libraries (How should I do it)?
> If it does not exist I will probably write it but maybe somebody is
> already doing it.
>
> Jerzy Orlowski
>
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de Mon Sep 1 06:44:58 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Mon, 01 Sep 2008 12:44:58 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBFAD.7060401@ac.uma.es>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
Message-ID: <48BBC7AA.2060002@mpiz-koeln.mpg.de>
Hi Sergio,
if you follow the mail list correspondance of the taverna list
http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results
you will find the same question with answer and links to your problem.
best
andreas
Sergio Ramirez Ramirez wrote:
> Hello Jerzy
>
> Unfortunately, moby can not handle workflows by itself for now.
> Normally you use taverna for building workflows.
> I'm trying to learn how to use Taverna libraries to run workflows.
> There is a taverna class (workflowlauncher or similar) available in
> the web page for taverna, but I couldn't make it work.
>
> I'm also very interesting in this topic.
> Greetings, Sergio
>
> Jerzy Orlowski wrote:
>> Hello
>>
>> I am searchng for a java class representing a BioMoby workflow:
>>
>> I found some classes that represent connections:
>> datatype -> service
>> service -> datatype
>> datatype -> datatype
>> in org.biomoby.client.
>> (There is even a class for drawing graphs using graphviz, but
>> unfortunately without datatype -> datatype connections.)
>>
>> I do not find find any class that these connections gathers them
>> together as a workflow and enables execution of this workflow given
>> some inputs.
>>
>> Does such class exist in jMoby? Or should I run my workflows using
>> Taverna libraries (How should I do it)?
>> If it does not exist I will probably write it but maybe somebody is
>> already doing it.
>>
>> Jerzy Orlowski
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From serr at ac.uma.es Mon Sep 1 07:15:17 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Mon, 01 Sep 2008 13:15:17 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBC7AA.2060002@mpiz-koeln.mpg.de>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
<48BBC7AA.2060002@mpiz-koeln.mpg.de>
Message-ID: <48BBCEC5.1070505@ac.uma.es>
Thank you very much
Best Sergio.
Andreas Groscurth wrote:
> Hi Sergio,
>
> if you follow the mail list correspondance of the taverna list
>
> http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results
>
>
> you will find the same question with answer and links to your problem.
>
> best
> andreas
>
> Sergio Ramirez Ramirez wrote:
>> Hello Jerzy
>>
>> Unfortunately, moby can not handle workflows by itself for now.
>> Normally you use taverna for building workflows.
>> I'm trying to learn how to use Taverna libraries to run workflows.
>> There is a taverna class (workflowlauncher or similar) available in
>> the web page for taverna, but I couldn't make it work.
>>
>> I'm also very interesting in this topic.
>> Greetings, Sergio
>>
>> Jerzy Orlowski wrote:
>>> Hello
>>>
>>> I am searchng for a java class representing a BioMoby workflow:
>>>
>>> I found some classes that represent connections:
>>> datatype -> service
>>> service -> datatype
>>> datatype -> datatype
>>> in org.biomoby.client.
>>> (There is even a class for drawing graphs using graphviz, but
>>> unfortunately without datatype -> datatype connections.)
>>>
>>> I do not find find any class that these connections gathers them
>>> together as a workflow and enables execution of this workflow given
>>> some inputs.
>>>
>>> Does such class exist in jMoby? Or should I run my workflows using
>>> Taverna libraries (How should I do it)?
>>> If it does not exist I will probably write it but maybe somebody is
>>> already doing it.
>>>
>>> Jerzy Orlowski
>>>
>>> _______________________________________________
>>> 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 MichaelGerlich at gmx.de Wed Sep 3 05:17:42 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Wed, 3 Sep 2008 11:17:42 +0200
Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters
Message-ID: <000001c90da5$eb498a40$c1dc9ec0$@de>
Hi all,
I'm working on a simple java app (client) that calls some Biomoby services I
wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist"
registered under authority "ipb-halle.de" takes additional 2 secondary
parameters that modify its query behavior and the resulting number of
outputs.
Now when I try to add both secondary parameters to the input, the service
call fails with the following message:
Exception in thread "main" org.biomoby.shared.MobyException: Service
get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but
takes 2 (query 1). Extra secondary parameters must have been specified
at
org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java
:928)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275)
at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86)
My code is like that:
Central worker = new CentralImpl();
templateService = new MobyService("get_DBLinks_From_Peaklist", authority);
// authority = "ipb-halle.de"
validServices = worker.findService(templateService);
comp = new MobyDataComposite(new MobyDataType("MSPeakRel"));
comp.put("relInt", new MobyDataInt(999));
comp.put("mz", new MobyDataFloat(273.069));
MobyDataSecondaryInstance[] secParams = new
MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length];
for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) {
secParams[i] = new MobyDataSecondaryInstance(new
MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()),
validServices[0].getSecondaryInputs()[i].getDefaultValue()); }
mr.setService(validServices[0]);
mr.setInput(comp);
mr.setSecondaryInput(secParams);
System.out.println(mr.invokeService().toString());
The setSecondaryInput() function takes an array that consists of all
parameters and applies them to all inputs. Now there are 2 parameters and an
array of length 2 - with the default values for both parameters (I defined
default values for both parameters).
Some hints what I'm doing wrong?
Another question - my input is of type MSPeakRel and is defined as
collection. How do I manage to add multiple inputs - in this case, they
would represent a complete peaklist of (m/z value, relative intensity) for
querying a database?
Best wishes,
Michael
From jason.e.stewart at gmail.com Mon Sep 8 07:06:59 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 8 Sep 2008 16:36:59 +0530
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
Message-ID: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
Hey Moby-devs,
The version of SOAP::Lite in CVS claims to support Document/literal
encoding - I need help determing if this support is sufficient. Can
you look this over?
=head3 DOCUMENT/LITERAL
SOAP web services using the document/literal message encoding are usually
described by some Web Service Definition. Our web service has the following
WSDL description:
The XML message (inside the SOAP Envelope) look like this:
KutterMartinHello Martin Kutter!
You can call this web service with the following client code:
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->call("sayHello",
SOAP::Data->name('name')->value( 'Kutter' ),
SOAP::Data->name('givenName')->value('Martin'),
);
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
=head2 Differences between the implementations
You may have noticed that there's no between the rpc/literal
and the document/literal example's implementation. In fact, from SOAP::Lite's
point of view, the only differences between rpc/literal and document/literal
that parameters are always named.
In our example, the rpc/literal variant already used named parameters (by
using a single complexType only as positional parameter), so there's no
difference at all.
The differences would have been bigger if the rpc/literal example had used
more than one positional parameter, but this is quite unlikely to happen in
the future: Current interoperability standards (like the WS-I basic profile)
mandate the use of a single complexType as only parameter in rpc/literal
calls.
-- snip --
Help me on this one - is this valid? Is it sufficient for what MOBY
and the rest of the Perl world needs? I suggest that I test this claim
against:
* perl SOAP::Lite client = axis Java server
* java client = perl SOAP::Lite server
I could use some suggestions for how to make these tests useful.
Cheers, jas.
From edward.kawas at gmail.com Mon Sep 8 11:16:08 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 8 Sep 2008 08:16:08 -0700
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
In-Reply-To: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
Message-ID: <48c541bc.2a528c0a.2895.3efe@mx.google.com>
Hi Jason,
One of the problems that I have with soap lite and trying to perform doc/lit
requests/responses is the inability to use attributes in the request.
Since that statement doesn't make too much sense (to some it might have ;-),
I will provide an example:
I modified the wsdl that you sent to include an attribute in the givenName
element, so that a request now looks like:
Joe BlowJoe
The server side code is simply:
sub sayHello {
SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) );
}
So all that I am doing is dumping whatever is sent to the server.
The response is
$VAR1 = [ 'HelloWorld', 'Joe Blow',
'Joe' ];
I do believe that this is one of the biggest stumbling blocks so far.
Because numerous Moby api calls use attributes. One such example is the
retrieveService call.
My dispatcher code is below!
Eddie
------ CODE START -----
#!/usr/bin/perl -w
# _________________________________________________________________
use SOAP::Transport::HTTP;
if ($ENV{REQUEST_METHOD} eq "GET") {
if (lc($ENV{QUERY_STRING} || "") eq "wsdl") {
require CGI;
my $q = CGI->new();
my $wsdl = HelloWorld::wsdl();
my $c = length($wsdl);
print $q->header(-type=>'application/xml',-Content-length=>$c);
print "$wsdl";
}
} else {
my $x = new SOAP::Transport::HTTP::CGI;
$x->dispatch_to('/var/www/cgi-bin', 'HelloWorld');
$x->handle;
}
package HelloWorld;
use Data::Dumper;
sub sayHello {
SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) );
}
sub wsdl {
return <
EOF
}
1;
------ CODE END ------
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jason Stewart
Sent: September-08-08 4:07 AM
To: Core developer announcements
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
Hey Moby-devs,
The version of SOAP::Lite in CVS claims to support Document/literal
encoding - I need help determing if this support is sufficient. Can
you look this over?
=head3 DOCUMENT/LITERAL
SOAP web services using the document/literal message encoding are usually
described by some Web Service Definition. Our web service has the following
WSDL description:
The XML message (inside the SOAP Envelope) look like this:
KutterMartinHello Martin Kutter!
You can call this web service with the following client code:
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->call("sayHello",
SOAP::Data->name('name')->value( 'Kutter' ),
SOAP::Data->name('givenName')->value('Martin'),
);
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
=head2 Differences between the implementations
You may have noticed that there's no between the rpc/literal
and the document/literal example's implementation. In fact, from
SOAP::Lite's
point of view, the only differences between rpc/literal and document/literal
that parameters are always named.
In our example, the rpc/literal variant already used named parameters (by
using a single complexType only as positional parameter), so there's no
difference at all.
The differences would have been bigger if the rpc/literal example had used
more than one positional parameter, but this is quite unlikely to happen in
the future: Current interoperability standards (like the WS-I basic profile)
mandate the use of a single complexType as only parameter in rpc/literal
calls.
-- snip --
Help me on this one - is this valid? Is it sufficient for what MOBY
and the rest of the Perl world needs? I suggest that I test this claim
against:
* perl SOAP::Lite client = axis Java server
* java client = perl SOAP::Lite server
I could use some suggestions for how to make these tests useful.
Cheers, jas.
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From jason.e.stewart at gmail.com Mon Sep 8 12:00:18 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 8 Sep 2008 21:30:18 +0530
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
In-Reply-To: <48c541bc.2a528c0a.2895.3efe@mx.google.com>
References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
<48c541bc.2a528c0a.2895.3efe@mx.google.com>
Message-ID: <41c1ade50809080900l4d681b02m7962f04e81310421@mail.gmail.com>
Hey Eddie,
On Mon, Sep 8, 2008 at 8:46 PM, Edward Kawas wrote:
> One of the problems that I have with soap lite and trying to perform doc/lit
> requests/responses is the inability to use attributes in the request.
OK. I've sent this off as a query to the SOAP-Lite dev list - I'll see
what they have to say.
Either there is an intended workaround or it needs to be implemented.
Thanks. jas.
From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 08:11:10 2008
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Wed, 10 Sep 2008 14:11:10 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
Message-ID: <48C7B95E.4080903@avignon.inra.fr>
Hi,
We have a problem with dashboard. We unregistered and re-registred our
services (with some changes), but after reloading the service list we
don't see these services in the list and our authority is missing.
We tried to delete manually our cache and to restart the dashboard
several time. We tried to reload or update every thing without changes
(which obviously make sense).
Does it link in any way to experimental "big bang" this morning in Geneve ?
Any other ideas ?
Thanks,
Regards,
Dominique
From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 08:23:31 2008
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Wed, 10 Sep 2008 14:23:31 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7B95E.4080903@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
Message-ID: <48C7BC43.70008@avignon.inra.fr>
Dominique Jeannin a ?crit :
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in
> Geneve ?
> Any other ideas ?
>
Does anyone see our services named Solstis_getDatasetDescFromKeyword on
avilin05.avignon.inra.fr ?
From all our tests we cannot...
Thanks,
Regards,
Dominique
From groscurt at mpiz-koeln.mpg.de Wed Sep 10 08:47:29 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 10 Sep 2008 14:47:29 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7BC43.70008@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7BC43.70008@avignon.inra.fr>
Message-ID: <48C7C1E1.1030406@mpiz-koeln.mpg.de>
Hi Dominique,
i do find it in the dashboard on the test central and via a simple moby
java test.
I had the same issue some days ago that changes (like service
(de)registration) could not be shown in dashboard, whatever i did to
it... My solution was then to use someonelse moby checkout and this
dashboard :(
Hope someone knows about that and knows a general solution
Andreas
Dominique Jeannin wrote:
> Dominique Jeannin a ?crit :
>> Hi,
>>
>> We have a problem with dashboard. We unregistered and re-registred
>> our services (with some changes), but after reloading the service
>> list we don't see these services in the list and our authority is
>> missing.
>> We tried to delete manually our cache and to restart the dashboard
>> several time. We tried to reload or update every thing without
>> changes (which obviously make sense).
>>
>> Does it link in any way to experimental "big bang" this morning in
>> Geneve ?
>> Any other ideas ?
>>
> Does anyone see our services named Solstis_getDatasetDescFromKeyword
> on avilin05.avignon.inra.fr ?
> From all our tests we cannot...
>
> Thanks,
> Regards,
>
> Dominique
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From py at pingoured.fr Wed Sep 10 08:49:19 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 14:49:19 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7B95E.4080903@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
Message-ID: <48C7C24F.3050709@pingoured.fr>
Dominique Jeannin wrote:
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in Geneve ?
> Any other ideas ?
More informations on the problem:
While doing an "Update" on all (Services, datatypes...) we have the
following error:
===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8 sequence.
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========
While on the other when doing a "Reload" all, we do not have any error
but we still can't see our services nor authority.
Regards,
Pierre
From edward.kawas at gmail.com Wed Sep 10 09:12:10 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 06:12:10 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7C24F.3050709@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
Message-ID: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Hi,
I am trying to reproduce your problems, but I cannot. I am not seeing any
SOAP exceptions and I don't see your service either.
The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
tried to use non utf8 characters in my soap message.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-10-08 5:49 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Dominique Jeannin wrote:
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in Geneve
?
> Any other ideas ?
More informations on the problem:
While doing an "Update" on all (Services, datatypes...) we have the
following error:
===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8 sequence.
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========
While on the other when doing a "Reload" all, we do not have any error
but we still can't see our services nor authority.
Regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From py at pingoured.fr Wed Sep 10 09:31:33 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 15:31:33 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Message-ID: <48C7CC35.6090803@pingoured.fr>
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
Strange since Andreas seems to see it as well as another person that
contacted us off-list.
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
What surprise us the most is that two of our services that we did not
change (Solstis_getProjet and dom_test2) are not shown either.
The whole authority avilin05.avignon.inra.fr seems to have disappeared...
We will try by deleting jMoby and re-downloading it from the CVS.
Hope that fix the problem
Thanks for your help,
Regards,
Pierre
From edward.kawas at gmail.com Wed Sep 10 09:33:30 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 06:33:30 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7CC35.6090803@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
<48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
<48C7CC35.6090803@pingoured.fr>
Message-ID: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
I also forgot to mention that I also tried looking for your services in the
database that backs the registry and failed to find 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 Pierre-Yves Chibon
Sent: September-10-08 6:32 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
Strange since Andreas seems to see it as well as another person that
contacted us off-list.
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
What surprise us the most is that two of our services that we did not
change (Solstis_getProjet and dom_test2) are not shown either.
The whole authority avilin05.avignon.inra.fr seems to have disappeared...
We will try by deleting jMoby and re-downloading it from the CVS.
Hope that fix the problem
Thanks for your help,
Regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From py at pingoured.fr Wed Sep 10 09:47:47 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 15:47:47 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C7D003.3070903@pingoured.fr>
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find it!
This is weird because the registration seems to work (cf below)
Could you check Solstis_getProject ? We did not change that one normally.
Thanks for your help,
Regards,
Pierre
../jMoby/build/run/run-cmdline-client -e
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl -uri
http://bioinfo.icapture.ubc.ca/MOBY/Central -call registerService
'mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
'
Calling method 'registerService' with the input from 'mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
':
mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
--------------
0
From groscurt at mpiz-koeln.mpg.de Wed Sep 10 09:53:13 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 10 Sep 2008 15:53:13 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C7D149.1020308@mpiz-koeln.mpg.de>
So basically its not there anymore but i can see it in dashboard ? then
my cache is old.
My problem was not even based on the encoding problem. I set a different
cache location and did reload/update and everything. I didnt get any
SOAP error, but still the service i registered didnt show up.
If i queried the central via the jmoby api and looked explictly for my
service i found it...
dont know if and how this error might be reproducable :(
Best
andreas
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find 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 Pierre-Yves Chibon
> Sent: September-10-08 6:32 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Problem with dashboard to list services
>
> Edward Kawas wrote:
>
>> Hi,
>>
>> I am trying to reproduce your problems, but I cannot. I am not seeing any
>> SOAP exceptions and I don't see your service either.
>>
>
> Strange since Andreas seems to see it as well as another person that
> contacted us off-list.
>
>
>> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
>> tried to use non utf8 characters in my soap message.
>>
>>
>
> What surprise us the most is that two of our services that we did not
> change (Solstis_getProjet and dom_test2) are not shown either.
>
> The whole authority avilin05.avignon.inra.fr seems to have disappeared...
>
>
> We will try by deleting jMoby and re-downloading it from the CVS.
> Hope that fix the problem
>
> Thanks for your help,
> Regards,
>
> Pierre
> _______________________________________________
> 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
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From jason.e.stewart at gmail.com Wed Sep 10 10:28:16 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 10 Sep 2008 19:58:16 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
Message-ID: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
Hey Eddie,
So I dug a bit on the server side and this is what I found.
If your server class subclasses from SOAP::Server::Parameters, the
method will get an extra parameter of type SOAP::SOM which gives
access to all the request information. That object contains a lot of
methods for searching the soap envelope - but it converts all the data
it finds into a SOAP::Data instance - which throws away all attributes
not located at the root of the data being returned. For example if the
XML looked like this:
Joe BlowJoe
and we did a query like $root = $som->dataof('//Body'), then $root
would be the soap:Body and we would see all of the sub-elements but
not their attributes. Only if we do $gn = $som->dataof('//givenName')
do we actually get the givenName element with the middlename attribute
still intact.
But the $som object has all the information in an internal hash table
- both as a hash table representation of the entire message and the
HTTP::Request object with the original XML.
What I don't understand is why when the dataof() method traverses the
internal hash table structure it throws away all the attributes not on
the root element being returned.
Also, I don't understand why there isn't a method that just returns
the content of the soap:Body element as plain XML - this should be the
default behavior for document/literal. I would like to see a call
something like $xml = $som->document();
Any thoughts of how I could make this interface most useful for MOBY
purposes? I will have to alter the internal SOAP::Lite code, and send
the patches to the maintainers.
Cheers, jas.
From jmfernandez at cnio.es Wed Sep 10 11:06:50 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Wed, 10 Sep 2008 17:06:50 +0200
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
Message-ID: <48C7E28A.6020203@cnio.es>
Hi Jason,
when we were developing the Perl MOBY::Async libraries we had the same
problem (we needed to access to the full input message), and we solved it
using custom deserializers fom WSRF::Lite package. Next sentences set-up them:
my $server = new SOAP::Transport::HTTP::CGI;
$server->serializer(WSRF::Serializer->new);
$server->deserializer(WSRF::Deserializer->new);
WSRF::Serializer and WSRF::Deserializer are subclasses of SOAP::Serializer
and SOAP::Deserializer, respectively. SOAP::Deserializer translates input SOAP
message into a SOAP::SOM instance. WSRF::Deserializer translates input SOAP
message into a WSRF::SOM instance, which is a SOAP::SOM instance plus a new
method called 'raw_xml'. This method returns the raw input message, which can
be parsed with XML::LibXML (for instance).
Hope this helps,
Jos? Mar?a
Jason Stewart wrote:
> Hey Eddie,
>
> So I dug a bit on the server side and this is what I found.
>
> If your server class subclasses from SOAP::Server::Parameters, the
> method will get an extra parameter of type SOAP::SOM which gives
> access to all the request information. That object contains a lot of
> methods for searching the soap envelope - but it converts all the data
> it finds into a SOAP::Data instance - which throws away all attributes
> not located at the root of the data being returned. For example if the
> XML looked like this:
>
>
>
> Joe Blow
> Joe
>
>
>
> and we did a query like $root = $som->dataof('//Body'), then $root
> would be the soap:Body and we would see all of the sub-elements but
> not their attributes. Only if we do $gn = $som->dataof('//givenName')
> do we actually get the givenName element with the middlename attribute
> still intact.
>
> But the $som object has all the information in an internal hash table
> - both as a hash table representation of the entire message and the
> HTTP::Request object with the original XML.
>
> What I don't understand is why when the dataof() method traverses the
> internal hash table structure it throws away all the attributes not on
> the root element being returned.
>
> Also, I don't understand why there isn't a method that just returns
> the content of the soap:Body element as plain XML - this should be the
> default behavior for document/literal. I would like to see a call
> something like $xml = $som->document();
>
> Any thoughts of how I could make this interface most useful for MOBY
> purposes? I will have to alter the internal SOAP::Lite code, and send
> the patches to the maintainers.
>
> Cheers, jas.
> _______________________________________________
> 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 martin.senger at gmail.com Wed Sep 10 14:28:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 11 Sep 2008 02:28:06 +0800
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7C24F.3050709@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
Message-ID: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
Martin
--
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
From edward.kawas at gmail.com Wed Sep 10 14:41:24 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 11:41:24 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
Message-ID: <48c814e0.14b48c0a.2f35.ffff9d83@mx.google.com>
So I haven't seen anything obvious in the description field for the services
from avilin05.avignon.inra.fr.
I am trying to track down the offending service and once it is found, I will
fix it. Then I will update the registry to use the utf8 patch that I coded
last month to solve this problem.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: September-10-08 11:28 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
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 edward.kawas at gmail.com Wed Sep 10 15:20:59 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 12:20:59 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
Message-ID: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
Okay, I found the culprit and I have fixed it. It was a the service
simpleTest under the authority mpiz-koeln.mpg.de.
I will also deploy patches to the test registry to see if we can trap these
errors in the future.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: September-10-08 11:28 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
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 gordonp at ucalgary.ca Wed Sep 10 15:35:11 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 10 Sep 2008 13:35:11 -0600
Subject: [MOBY-dev] Problems calling a Moby service with secondary
parameters
In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de>
References: <000001c90da5$eb498a40$c1dc9ec0$@de>
Message-ID: <48C8216F.8090801@ucalgary.ca>
Hi Michael,
Sorry for not getting back to you earlier. The problem is in the way to
create the secondary data instances. If you do a toString() on them,
you;ll see that they have a blank name based on the constructor you
used. The easiest way to use the default secondaries is with the
one-arg constructor, e.g.:
int i = 0;
for (MobySecondaryData param: service.getSecondaryInputs()) {
secParams[i++] = new MobyDataSecondaryInstance(param);
//auto-populates the instance with the template's default value
}
I'll add a check to MobyRequest that'll complain if you give blank or
duplicately named secondaries, which should make this mistake more
obvious to others in the future.
Regards,
Paul
P.S. I've also updated MobyDataComposite to handle put() for cases such
as your where the data type is not in the registry yet, facilitating
testing. Better yet though is to use the test registry in such cases.
Michael Gerlich wrote:
> Hi all,
>
> I'm working on a simple java app (client) that calls some Biomoby services I
> wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist"
> registered under authority "ipb-halle.de" takes additional 2 secondary
> parameters that modify its query behavior and the resulting number of
> outputs.
>
> Now when I try to add both secondary parameters to the input, the service
> call fails with the following message:
>
> Exception in thread "main" org.biomoby.shared.MobyException: Service
> get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but
> takes 2 (query 1). Extra secondary parameters must have been specified
> at
> org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java
> :928)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275)
> at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86)
>
>
> My code is like that:
>
> Central worker = new CentralImpl();
> templateService = new MobyService("get_DBLinks_From_Peaklist", authority);
> // authority = "ipb-halle.de"
> validServices = worker.findService(templateService);
>
> comp = new MobyDataComposite(new MobyDataType("MSPeakRel"));
> comp.put("relInt", new MobyDataInt(999));
> comp.put("mz", new MobyDataFloat(273.069));
>
> MobyDataSecondaryInstance[] secParams = new
> MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length];
> for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) {
> secParams[i] = new MobyDataSecondaryInstance(new
> MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()),
> validServices[0].getSecondaryInputs()[i].getDefaultValue()); }
>
> mr.setService(validServices[0]);
> mr.setInput(comp);
> mr.setSecondaryInput(secParams);
> System.out.println(mr.invokeService().toString());
>
>
>
> The setSecondaryInput() function takes an array that consists of all
> parameters and applies them to all inputs. Now there are 2 parameters and an
> array of length 2 - with the default values for both parameters (I defined
> default values for both parameters).
>
> Some hints what I'm doing wrong?
>
>
> Another question - my input is of type MSPeakRel and is defined as
> collection. How do I manage to add multiple inputs - in this case, they
> would represent a complete peaklist of (m/z value, relative intensity) for
> querying a database?
>
>
>
> Best wishes,
>
> Michael
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,48be578210950321565264!
>
>
>
>
From gordonp at ucalgary.ca Wed Sep 10 16:08:52 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 10 Sep 2008 14:08:52 -0600
Subject: [MOBY-dev] Java MobyRequest changes
In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de>
References: <000001c90da5$eb498a40$c1dc9ec0$@de>
Message-ID: <48C82954.5030507@ucalgary.ca>
Hi all,
If you use MobyRequest in your code, please note that setSecondaries()
now throws a MobyException in CVS. This is to help catch problems with
invalid secondary parameter values. You will need to ensure any call to
this method is now enclosed in a "try" block. Sorry for any
inconvenience this API change may cause.
Paul
From jason.e.stewart at gmail.com Thu Sep 11 00:14:54 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Thu, 11 Sep 2008 09:44:54 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <48C7E28A.6020203@cnio.es>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
<48C7E28A.6020203@cnio.es>
Message-ID: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
Hey Jose,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> when we were developing the Perl MOBY::Async libraries we had the
> same problem (we needed to access to the full input message), and we solved
> it using custom deserializers fom WSRF::Lite package.
Thanks, that's useful for MOBY users, definately.
I still think that it should be a functionality that is built into the
core of SOAP::Lite, though, especially since document/literal is the
standard encoding now. I will get a response from Martin, the current
maintainer of SOAP::Lite, and see what he thinks should be done.
Likewise, on the client side it should be made trivial to attach a
fragment of XML as the body of the soap message without any
interference from SOAP::Lite.
Any comments?
Thanks, jas.
From groscurt at mpiz-koeln.mpg.de Thu Sep 11 01:50:02 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Thu, 11 Sep 2008 07:50:02 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr>
<48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
<48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
Message-ID: <48C8B18A.7020401@mpiz-koeln.mpg.de>
ohoh - that was my service... at least kind of - i tested the problem we
discussed last time with the umlaut etc.
I'm sorry - i totally forgot that service :(
Andreas
Edward Kawas wrote:
> Okay, I found the culprit and I have fixed it. It was a the service
> simpleTest under the authority mpiz-koeln.mpg.de.
>
> I will also deploy patches to the test registry to see if we can trap these
> errors in the future.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
> Sent: September-10-08 11:28 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Problem with dashboard to list services
>
>
>> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
>>
> UTF-8
>
>> sequence.
>>
>
>
> This seems to be a re-occurrence of the same problem that we were solving
> couple of months ago with a service from Germany. In that case, the problem
> was caused by using non-ascii characters (such as German umlaut characters)
> in the service description. The problem was (and I guess still is, with your
> services) has two parts:
>
> First, jMoby (in Dashboard but also in any other usage og its libraries) may
> send a wrong Unicode characters. This is probably a bug in my libraries. I
> should fix it.
>
> Second, BioMoby central registry accepts wrong Unicode characters, stores
> them in its database and sends back them as an invalid XML. This should be
> fixed by Eddie or Mark I guess.
>
> If I am correct and your situation is indeed the one I am describing, it is
> a very dangerous situation because by registering a service with such
> description *all* jMoby users around the world will be affected (their
> Dashboards, for example, will not be able to reload or update anymore -
> until Eddie manually fixes the descriptions in the registry database; that's
> how he fixed it last time).
>
> Martin
>
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From py at pingoured.fr Thu Sep 11 03:45:30 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Thu, 11 Sep 2008 09:45:30 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C8CC9A.7050808@pingoured.fr>
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
From jason.e.stewart at gmail.com Thu Sep 11 04:54:10 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Thu, 11 Sep 2008 14:24:10 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <48C7E28A.6020203@cnio.es>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
<48C7E28A.6020203@cnio.es>
Message-ID: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
Hi Jose Maria,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> $server->serializer(WSRF::Serializer->new);
This code dies with a class not found error from Perl, I presume you
mean WSRF::WSRFSerializer->new?
Cheers, jas.
From edward.kawas at gmail.com Thu Sep 11 09:11:07 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 06:11:07 -0700
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es>
<41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
Message-ID: <48c918f9.27b38c0a.385f.ffffdcea@mx.google.com>
Hi Jason,
I like your thinking. I don?t have much experience with doc/lit services,
but I do feel that the additions that you have mentioned would probably be
best (and similar to what we have now for rpc/encoded).
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 Jason Stewart
Sent: September-10-08 9:15 PM
To: Core developer announcements
Subject: Re: [MOBY-dev] More info on SOAP::Lite document/literal
Hey Jose,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> when we were developing the Perl MOBY::Async libraries we had the
> same problem (we needed to access to the full input message), and we
solved
> it using custom deserializers fom WSRF::Lite package.
Thanks, that's useful for MOBY users, definately.
I still think that it should be a functionality that is built into the
core of SOAP::Lite, though, especially since document/literal is the
standard encoding now. I will get a response from Martin, the current
maintainer of SOAP::Lite, and see what he thinks should be done.
Likewise, on the client side it should be made trivial to attach a
fragment of XML as the body of the soap message without any
interference from SOAP::Lite.
Any comments?
Thanks, jas.
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From edward.kawas at gmail.com Thu Sep 11 09:15:49 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 06:15:49 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C8CC9A.7050808@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
<48C8CC9A.7050808@pingoured.fr>
Message-ID: <48c91a12.16538c0a.530a.ffffdd16@mx.google.com>
Yes, for some reason the file is not being generated properly. I am not sure
if this is a memory problem on the server or ...???
I noticed that yesterday, the RDF file is generated once properly and then
truncated the following times.
Hopefully I get this fixed soon,
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-11-08 12:46 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in
the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From jerzyo at genesilico.pl Thu Sep 11 10:22:09 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 11 Sep 2008 16:22:09 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
Message-ID: <48C92991.2000407@genesilico.pl>
Hi
I have several hundreds of workflows made up of BioMoby Services and
want to execute them all without opening any GUI.
I was looking for some solution over the internet and the think I came
across was using Taverna plugin and try to execute it programaticaly.
I have a few questions:
1. Is it the only way?
2. I found several tutorial tutorials on running saved workflow saved
in scufl language.
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
How do you one make a workflow step by step? like:
workflow.addProcesor(...)
workflow.addConnector(...)
...
workflow.execute()
and especially, how do one add BioMoby objects this way? Is there any
tutorial or do I have go though the API?
Best
Jerzy Orlowski
From edward.kawas at gmail.com Thu Sep 11 10:36:02 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 07:36:02 -0700
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92991.2000407@genesilico.pl>
References: <48C92991.2000407@genesilico.pl>
Message-ID: <48c92ce0.28d7720a.65e4.0366@mx.google.com>
Hi Jerzy,
You can execute workflows from the command line too if you have your input
file for the workflows handy.
If you want to create workflows programmatically, you will need to look at
the javadoc for the taverna source code.
You should probably explore the taverna website[1] and its manual[2] for
more information.
Eddie
[1] http://taverna.sourceforge.net/
[2] http://taverna.sourceforge.net/doc
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: September-11-08 7:22 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] Executing Moby Workflow straight from java
Hi
I have several hundreds of workflows made up of BioMoby Services and
want to execute them all without opening any GUI.
I was looking for some solution over the internet and the think I came
across was using Taverna plugin and try to execute it programaticaly.
I have a few questions:
1. Is it the only way?
2. I found several tutorial tutorials on running saved workflow saved
in scufl language.
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
How do you one make a workflow step by step? like:
workflow.addProcesor(...)
workflow.addConnector(...)
...
workflow.execute()
and especially, how do one add BioMoby objects this way? Is there any
tutorial or do I have go though the API?
Best
Jerzy Orlowski
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From jmfernandez at cnio.es Thu Sep 11 10:49:25 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Thu, 11 Sep 2008 16:49:25 +0200
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es>
<41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
Message-ID: <48C92FF5.5040405@cnio.es>
Hi Jason,
yes, you are right, it should be WSRF::WSRFSerializer. We have some pending
janitorial work on MOBY::Async, related to our usage of some namespace classes
which we do not own (WSRF::Serializer is one of those cases).
Best Regards,
Jos? Mar?a
Jason Stewart wrote:
> Hi Jose Maria,
>
> On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
> wrote:
>
>> $server->serializer(WSRF::Serializer->new);
>
> This code dies with a class not found error from Perl, I presume you
> mean WSRF::WSRFSerializer->new?
>
> Cheers, jas.
>
> _______________________________________________
> 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 Thu Sep 11 10:38:49 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Thu, 11 Sep 2008 16:38:49 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92991.2000407@genesilico.pl>
References: <48C92991.2000407@genesilico.pl>
Message-ID: <48C92D79.9010706@ac.uma.es>
Hello Jerzy
I had the same problem that you.
I have got it to work by browsing deep in the Taverna code. I cannot
give you many sample code because I'm trying to organize all the code
tries and examples that I have.
But I can give you some comments:
For build a workflow model the class is:
org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new
ScuflModel();
This class contains the methods that you mention addProcessor ...
For run I'm using freeflow, because taverna classes and raven are a
"little" tricky. The classes:
uk.ac.soton.itinnovation.freefluo.main.Engine or
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
can help you.
I hope this little details help you to begin. If you have more detailed
questions I will be very happy of help you.
Best regards,
Sergio
Jerzy Orlowski wrote:
> Hi
>
> I have several hundreds of workflows made up of BioMoby Services and
> want to execute them all without opening any GUI.
>
> I was looking for some solution over the internet and the think I came
> across was using Taverna plugin and try to execute it programaticaly.
> I have a few questions:
>
> 1. Is it the only way?
>
> 2. I found several tutorial tutorials on running saved workflow saved
> in scufl language.
> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>
> How do you one make a workflow step by step? like:
>
> workflow.addProcesor(...)
> workflow.addConnector(...)
> ...
> workflow.execute()
>
> and especially, how do one add BioMoby objects this way? Is there any
> tutorial or do I have go though the API?
>
> Best
>
> Jerzy Orlowski
>
> _______________________________________________
> 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 gordonp at ucalgary.ca Thu Sep 11 11:10:13 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 11 Sep 2008 09:10:13 -0600
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92D79.9010706@ac.uma.es>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
Message-ID: <48C934D5.50700@ucalgary.ca>
I think whoever has a headless Taverna workflow creation and/or
enactment working should put examples up in the Java developer's section
of the Moby Web site...I believe the myExperiment people also have a
headless workflow enactment engine working now...anyone from there on
this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in
the BioWEP software. So many people are doing this, but no good sample
code is easily available, especially for Moby services...
Sergio Ramirez Ramirez wrote:
> Hello Jerzy
>
> I had the same problem that you.
>
> I have got it to work by browsing deep in the Taverna code. I cannot
> give you many sample code because I'm trying to organize all the code
> tries and examples that I have.
>
> But I can give you some comments:
>
> For build a workflow model the class is:
> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new
> ScuflModel();
> This class contains the methods that you mention addProcessor ...
>
> For run I'm using freeflow, because taverna classes and raven are a
> "little" tricky. The classes:
> uk.ac.soton.itinnovation.freefluo.main.Engine or
> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
> can help you.
>
> I hope this little details help you to begin. If you have more
> detailed questions I will be very happy of help you.
>
> Best regards,
> Sergio
>
> Jerzy Orlowski wrote:
>> Hi
>>
>> I have several hundreds of workflows made up of BioMoby Services and
>> want to execute them all without opening any GUI.
>>
>> I was looking for some solution over the internet and the think I
>> came across was using Taverna plugin and try to execute it
>> programaticaly.
>> I have a few questions:
>>
>> 1. Is it the only way?
>>
>> 2. I found several tutorial tutorials on running saved workflow
>> saved in scufl language.
>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>
>>
>> How do you one make a workflow step by step? like:
>>
>> workflow.addProcesor(...)
>> workflow.addConnector(...)
>> ...
>> workflow.execute()
>>
>> and especially, how do one add BioMoby objects this way? Is there any
>> tutorial or do I have go though the API?
>>
>> Best
>>
>> Jerzy Orlowski
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
>
From serr at ac.uma.es Thu Sep 11 11:23:30 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Thu, 11 Sep 2008 17:23:30 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C934D5.50700@ucalgary.ca>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca>
Message-ID: <48C937F2.3030708@ac.uma.es>
Here there is my small contribution, just the two methods that I use for
run a workflow.
Hope it can help to someone
Paul Gordon wrote:
> I think whoever has a headless Taverna workflow creation and/or
> enactment working should put examples up in the Java developer's
> section of the Moby Web site...I believe the myExperiment people also
> have a headless workflow enactment engine working now...anyone from
> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
> enactor in the BioWEP software. So many people are doing this, but no
> good sample code is easily available, especially for Moby services...
>
> Sergio Ramirez Ramirez wrote:
>> Hello Jerzy
>>
>> I had the same problem that you.
>>
>> I have got it to work by browsing deep in the Taverna code. I cannot
>> give you many sample code because I'm trying to organize all the code
>> tries and examples that I have.
>>
>> But I can give you some comments:
>>
>> For build a workflow model the class is:
>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>> new ScuflModel();
>> This class contains the methods that you mention addProcessor ...
>>
>> For run I'm using freeflow, because taverna classes and raven are a
>> "little" tricky. The classes:
>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>> can help you.
>>
>> I hope this little details help you to begin. If you have more
>> detailed questions I will be very happy of help you.
>>
>> Best regards,
>> Sergio
>>
>> Jerzy Orlowski wrote:
>>> Hi
>>>
>>> I have several hundreds of workflows made up of BioMoby Services and
>>> want to execute them all without opening any GUI.
>>>
>>> I was looking for some solution over the internet and the think I
>>> came across was using Taverna plugin and try to execute it
>>> programaticaly.
>>> I have a few questions:
>>>
>>> 1. Is it the only way?
>>>
>>> 2. I found several tutorial tutorials on running saved workflow
>>> saved in scufl language.
>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>
>>>
>>> How do you one make a workflow step by step? like:
>>>
>>> workflow.addProcesor(...)
>>> workflow.addConnector(...)
>>> ...
>>> workflow.execute()
>>>
>>> and especially, how do one add BioMoby objects this way? Is there
>>> any tutorial or do I have go though the API?
>>>
>>> Best
>>>
>>> Jerzy Orlowski
>>>
>>> _______________________________________________
>>> 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
>
--
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
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From jmfernandez at cnio.es Thu Sep 11 11:49:29 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Thu, 11 Sep 2008 17:49:29 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C937F2.3030708@ac.uma.es>
References: <48C92991.2000407@genesilico.pl>
<48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca>
<48C937F2.3030708@ac.uma.es>
Message-ID: <48C93E09.3030107@cnio.es>
Hi everybody,
as Sergio *should* know, we have at INB IWWE&M, which means 'Interactive Web
Workflow Enactor and Manager'. It is able to host workflows, workflow examples
with documentation, do web workflow enactions, and take and store workflow
enaction snapshots.
Next days we are going to have a Trac server with is going to host the source
code and development of IWWE&M.
Best Regards,
Jos? Mar?a
Sergio Ramirez Ramirez wrote:
> Here there is my small contribution, just the two methods that I use for
> run a workflow.
> Hope it can help to someone
>
> Paul Gordon wrote:
>> I think whoever has a headless Taverna workflow creation and/or
>> enactment working should put examples up in the Java developer's
>> section of the Moby Web site...I believe the myExperiment people also
>> have a headless workflow enactment engine working now...anyone from
>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>> enactor in the BioWEP software. So many people are doing this, but no
>> good sample code is easily available, especially for Moby services...
>>
>> Sergio Ramirez Ramirez wrote:
>>> Hello Jerzy
>>>
>>> I had the same problem that you.
>>>
>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>> give you many sample code because I'm trying to organize all the code
>>> tries and examples that I have.
>>>
>>> But I can give you some comments:
>>>
>>> For build a workflow model the class is:
>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>> new ScuflModel();
>>> This class contains the methods that you mention addProcessor ...
>>>
>>> For run I'm using freeflow, because taverna classes and raven are a
>>> "little" tricky. The classes:
>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>> can help you.
>>>
>>> I hope this little details help you to begin. If you have more
>>> detailed questions I will be very happy of help you.
>>>
>>> Best regards,
>>> Sergio
>>>
>>> Jerzy Orlowski wrote:
>>>> Hi
>>>>
>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>> want to execute them all without opening any GUI.
>>>>
>>>> I was looking for some solution over the internet and the think I
>>>> came across was using Taverna plugin and try to execute it
>>>> programaticaly.
>>>> I have a few questions:
>>>>
>>>> 1. Is it the only way?
>>>>
>>>> 2. I found several tutorial tutorials on running saved workflow
>>>> saved in scufl language.
>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>
>>>>
>>>> How do you one make a workflow step by step? like:
>>>>
>>>> workflow.addProcesor(...)
>>>> workflow.addConnector(...)
>>>> ...
>>>> workflow.execute()
>>>>
>>>> and especially, how do one add BioMoby objects this way? Is there
>>>> any tutorial or do I have go though the API?
>>>>
>>>> Best
>>>>
>>>> Jerzy Orlowski
>>>>
>>>> _______________________________________________
>>>> 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
--
"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 alanrw at cs.man.ac.uk Thu Sep 11 11:25:18 2008
From: alanrw at cs.man.ac.uk (Alan Williams)
Date: Thu, 11 Sep 2008 16:25:18 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C934D5.50700@ucalgary.ca>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca>
Message-ID: <48C9385E.8060209@cs.man.ac.uk>
Paul Gordon wrote:
> I think whoever has a headless Taverna workflow creation and/or
> enactment working should put examples up in the Java developer's section
> of the Moby Web site...I believe the myExperiment people also have a
> headless workflow enactment engine working now...anyone from there on
> this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in
> the BioWEP software. So many people are doing this, but no good sample
> code is easily available, especially for Moby services...
If by headless you mean without the UI, then there is a WorkflowLauncher
that enacts a Taverna workflow. The source code (written by the myGrid
team) can be downloaded from
http://prdownloads.sourceforge.net/taverna/workflowlauncher-0.1.2.zip?download
It may not what you need as it reads in a pre-existing Taverna
workflow - it does not create one programmatically.
You can also execute a Taverna workflow on a remote machine see
myExperiment can run the workflow you are looking at on a Taverna remote
execution engine. (You will, of course, need to have the right
authorization to get at a given remote enactor.)
I'm rather confused as to what people are trying to do. Could someone
give a use case? I'll probably have to get Katy Wolstencroft to explain
the biology for me :-)
Alan R Williams (currently the support hat wearer for Taverna)
From jason at bioteam.net Thu Sep 11 21:54:46 2008
From: jason at bioteam.net (jason)
Date: Fri, 12 Sep 2008 09:54:46 +0800
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Message-ID: <48C9CBE6.7010808@bioteam.net>
Hi, all
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
>
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
Part of the Moby code use String manipulation to parse and generate Xml
message instead of using a standard of XML parsing/writing.
The invalid byte could be related to this. I saw this error in another
project. Xml message generated by String concatenation could cause many
unexpected XML parsing error.
> Eddie
>
>
>
From soiland-reyes at cs.manchester.ac.uk Fri Sep 12 04:46:03 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Fri, 12 Sep 2008 09:46:03 +0100
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBFAD.7060401@ac.uma.es>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
Message-ID:
On Mon, Sep 1, 2008 at 11:10, Sergio Ramirez Ramirez wrote:
> Unfortunately, moby can not handle workflows by itself for now. Normally you
> use taverna for building workflows.
> I'm trying to learn how to use Taverna libraries to run workflows. There is
> a taverna class (workflowlauncher or similar) available in the web page for
> taverna, but I couldn't make it work.
Hi, also check out
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram.html
If you can't make it work - do please send us an email about what kind
of error message you get or what doesn't work - so we can improve it.
Note that if you run this within a container like Tomcat (instead of
standalone, which should work) you might run into issues recently
uncovered, there's a workaround described here:
http://markmail.org/search/?q=taverna-hackers+globus#query:taverna-hackers%20globus+page:1+mid:leq2tlx3adyekssq+state:results
I recommend signing up to the taverna-hackers mailing list for any
further questions and issues you might run into - we're happy to help!
http://taverna.sourceforge.net/lists
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From edward.kawas at gmail.com Fri Sep 12 09:41:51 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 12 Sep 2008 06:41:51 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C8CC9A.7050808@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
<48C8CC9A.7050808@pingoured.fr>
Message-ID: <48ca71b0.2a528c0a.282c.ffffba33@mx.google.com>
Hi All,
The problem now should be all fixed. I recently created a patch to avoid
this non utf8 mess and deployed it on the test registry; moreover, the RDF
shouldn't cause problems with Dashboard.
Let me know how things work out,
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-11-08 12:46 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in
the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From edward.kawas at gmail.com Thu Sep 18 13:08:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 18 Sep 2008 10:08:21 -0700
Subject: [MOBY-dev] FWD: Making SOAP::Lite painlessly support
document-literal encoding
In-Reply-To: <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry>
References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com><48d26bbb.27b38c0a.32a5.ffff9576@mx.google.com>
<146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry>
Message-ID: <48d28b06.1cbd720a.50af.ffff83bc@mx.google.com>
Just to keep everyone on the list in the know ...
Eddie
--------------------
From: "Ed Kawas"
Date: Thu, 18 Sep 2008 07:54:49
To: 'Jason Stewart'; 'Mark';
'Martin Kutter';
Subject: RE: Making SOAP::Lite painlessly support document-literal encoding
Hi Jason,
I like the fact that you hand off the XML document to the server service
developer. Also the ability of the client to just attach a document looks
good too. I wonder how other toolkits do it? I am pretty sure that if the
soap envelope was compatible with other toolkits and all I could do was
get/set the XML document, I would definitely start using S::L for doc/lit
services.
Eddie
-----Original Message-----
From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
Sent: September-18-08 1:40 AM
To: Mark; Martin Kutter; soaplite-devel at lists.sf.net; Ed Kawas
Subject: Making SOAP::Lite painlessly support document-literal encoding
Hey All,
So I've been doing a lot of digging through the codebase understanding
how doc/lit could be used at the moment, and I find that the ease of
use that S::L provides for rpc/enc is not matched in it's doc/lit
support. I don't think it would take very much effort to enable simple
support for doc/lit on both the client and the server - but very
likely there would be issues with compatibility with Java and .NET
implementations that would have to be worked out.
For me the major difference is that a client wanting to use a doc/lit
service wants to simply attach a pre-produced XML payload to the soap
message - and the server wants to retrieve that message - WITHOUT ANY
INTERFERENCE FROM SOAP::LIT.
so we have:
-- begin of client.pl 8< --
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
my $xml =<KutterMartinHello Martin Kutter!
XML
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->document($xml)->call("sayHello");
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
-- end of client.pl --
-- begin server.pl 8< --
package HelloWorld;
use SOAP::Lite;
use base qw(SOAP::Server::Document);
sub sayHello {
my $self = shift;
my $doc = shift;
my $som = shift;
my $ret_val = some_processing_method($doc);
return $ret_val;
}
-- end of server.pl --
The client builds an XML document inserts it into the request using
the document() method on the SOAP object.
The client subclasses from SOAP::Server::Document so it gets the XML
payload as the second argument on the stack, processes it somehow, and
returns an XML payload back to the client.
feedback?
Cheers, jas.
From jason.e.stewart at gmail.com Fri Sep 19 04:02:49 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 19 Sep 2008 13:32:49 +0530
Subject: [MOBY-dev] Making SOAP::Lite painlessly support
document-literal encoding
In-Reply-To: <1221760547.9975.19.camel@cyclops>
References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com>
<1221760547.9975.19.camel@cyclops>
Message-ID: <41c1ade50809190102n16ee2f2fh94dd0da1d7dc9e@mail.gmail.com>
Hey All,
I like your suggestions Martin.
I think the namespace SOAP::Lite::Server::Document is definitely the way to go.
I support the idea of using a SOAP::Data object in addition to an XML
scalar as the value for either the client or the server.
I will make a patch and some test cases and send them to the list.
Cheers, jas.
On Thu, Sep 18, 2008 at 11:25 PM, Martin Kutter
wrote:
> Hi Jason,
>
> forcing the server developer to create XML may or may not be a good
> idea, depending on it's complexity.
>
> How about making the proposed SOAP::Server::Document a bit more DWIM by
> accepting either a scalar (which is supposed to be plain XML) or a
> SOAP::Data object?
>
> This would ease migration for existing web services which want to move
> to SOAP::Server::Document
>
> Maybe SOAP::Lite::Server::Document would be the more appropriate name -
> the use of the SOAP namespace has provoked numerous errors on CPAN, so
> SOAP::Lite is a better namespace for new modules.
>
> Thanks for your ideas,
>
> Martin
>
> Am Donnerstag, den 18.09.2008, 14:10 +0530 schrieb Jason Stewart:
>> Hey All,
>>
>> So I've been doing a lot of digging through the codebase understanding
>> how doc/lit could be used at the moment, and I find that the ease of
>> use that S::L provides for rpc/enc is not matched in it's doc/lit
>> support. I don't think it would take very much effort to enable simple
>> support for doc/lit on both the client and the server - but very
>> likely there would be issues with compatibility with Java and .NET
>> implementations that would have to be worked out.
>>
>> For me the major difference is that a client wanting to use a doc/lit
>> service wants to simply attach a pre-produced XML payload to the soap
>> message - and the server wants to retrieve that message - WITHOUT ANY
>> INTERFERENCE FROM SOAP::LIT.
>>
>> so we have:
>>
>> -- begin of client.pl 8< --
>>
>> use SOAP::Lite;
>> my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
>>
>> my $xml =<>
>> Kutter
>> Martin
>>
>>
>>
>> Hello Martin Kutter!
>>
>> XML
>>
>> $soap->on_action( sub { "urn:HelloWorld#sayHello" });
>> $soap->autotype(0);
>> $soap->default_ns('urn:HelloWorld');
>>
>> my $som = $soap->document($xml)->call("sayHello");
>>
>> die $som->fault->{ faultstring } if ($som->fault);
>> print $som->result, "\n";
>>
>> -- end of client.pl --
>>
>> -- begin server.pl 8< --
>>
>> package HelloWorld;
>> use SOAP::Lite;
>>
>> use base qw(SOAP::Server::Document);
>>
>> sub sayHello {
>> my $self = shift;
>> my $doc = shift;
>> my $som = shift;
>>
>> my $ret_val = some_processing_method($doc);
>> return $ret_val;
>> }
>>
>> -- end of server.pl --
>>
>> The client builds an XML document inserts it into the request using
>> the document() method on the SOAP object.
>>
>> The client subclasses from SOAP::Server::Document so it gets the XML
>> payload as the second argument on the stack, processes it somehow, and
>> returns an XML payload back to the client.
>>
>> feedback?
>>
>> Cheers, jas.
>>
>
>
From jason.e.stewart at gmail.com Fri Sep 19 05:29:46 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 19 Sep 2008 14:59:46 +0530
Subject: [MOBY-dev] moby doc-lit services.
In-Reply-To: <48D411EB.2080606@bsc.es>
References: <48D32B1C.3050304@bsc.es>
<41c1ade50809190044l124fcf63h52e728402f4a4de3@mail.gmail.com>
<48D411EB.2080606@bsc.es>
Message-ID: <41c1ade50809190229me6e597arb728754a03ab9eb7@mail.gmail.com>
Hey Dmitry,
I agree with your suggestion as to the "right" way to do it.
I am less concerned with the WSDL, from my current understanding of
MOBY (which is very weak I am afraid) the WSDL is almost useless,
MOBY-enabled clients will have to be aware of how to deserialize data
types that they handle using their own libraries or libraries bundled
with MOBY.
Originally I thought MOBY would rely heavily on XML Schemas to define
their data types, and that would be the core - but since that isn't
how things are done, I don't see much use in the WSDL. I'd like to
know if I am understanding this incorrectly.
Cheers, jas.
On Sat, Sep 20, 2008 at 2:26 AM, Dmitry Repchevsky
wrote:
> Hi Jason,
>
>> Mark has asked me to modify SOAP::Lite in order to better support doc/lit
>> services in general...
>
> This is a good news, because my concern was that you are going to do a sort
> of hack - make a common schema for all services,
> something like a "" and pass a Moby message inside...
>
> What I suggested to do (and this is the "right" way to do in java) is to
> pass all the MobyMessage inside a soap message:
> Something like:
>
>
>
>
>
>
>
>
>
> ns1:id=""
> ns1:namespace="">AGHFJHGDKHGJKADGHJGDJH
>
>
>
>
>
>
>
>
> This way there is no problem as it is a STANDARD Moby XML inside a SOAP
> .
>
> The problem is that you need to attach a XML Schema to your WSDL (if you
> wish a "real" web-service")
> Such a schema could be divided in two parts:
>
> 1. Static (common for all moby doc/lit services) that contains Moby specific
> schema (MobySimple, MobyContent....):
>
> ******************************************************************************************************************************
>
> version="1.0"
> targetNamespace="http://www.biomoby.org/moby"
>
> xmlns:xs="http://www.w3.org/2001/XMLSchema"
>
> xmlns="http://www.biomoby.org/moby" >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> maxOccurs="unbounded"/>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ******************************************************************************************************************************
>
> 2. Moby Datatypes specific one - that one depends of the ontology types used
> by service...
> In extreme case you can put the same scheme representing ALL the ontology
> (not generate it for every service, but generate it once for the ontology
> and use for every service).
> You can even put an EXTERNAL reference to it (for example make a servlet
> that dynamically generates it from the ontology). This way it will be always
> updated.
>
> Cheers,
>
> Dmitry
>
>
>
>
> Jason Stewart wrote:
>>
>> Hi Dmitry,
>>
>> On Fri, Sep 19, 2008 at 10:01 AM, Dmitry Repchevsky
>> wrote:
>>
>>
>>>
>>> My name is Dmitry and I am a developer in Spanish National Institute of
>>> Bioinformatics.
>>> We just have finished an informal meeting with Mark Wilkinson and he
>>> suggested to contact you about moby document/literal services...
>>>
>>> I have my own implementation of it based on XML Schema and I would like
>>> to
>>> know the way you are implementing it.
>>>
>>
>> Mark has asked me to modify SOAP::Lite in order to better support
>> doc/lit services in general, not just for MOBY.
>>
>> I'd love to hear more about how you do things.
>>
>> Currently, I'm in discussion with the SOAP::Lite developer group how
>> to modify the core of S::L in order to better handle doc/lit.
>>
>> Cheers, jas.
>>
>>
>
>
From jerzyo at genesilico.pl Wed Sep 24 11:55:58 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Wed, 24 Sep 2008 17:55:58 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C937F2.3030708@ac.uma.es>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
Message-ID: <48DA630E.6050901@genesilico.pl>
Hi
I am trying to use your code, but I get strange erros like:
The constructor EngineImpl(EngineConfiguration) is undefined
Perhaps I am working on different versions of the code (some from
taverna, some from ogasadai and some from freefluo).
Where can I find source code or javadoc for
uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
I cannot find in anywhere on the web....
Jerzy
Sergio Ramirez Ramirez wrote:
> Here there is my small contribution, just the two methods that I use for
> run a workflow.
> Hope it can help to someone
>
> Paul Gordon wrote:
>> I think whoever has a headless Taverna workflow creation and/or
>> enactment working should put examples up in the Java developer's
>> section of the Moby Web site...I believe the myExperiment people also
>> have a headless workflow enactment engine working now...anyone from
>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>> enactor in the BioWEP software. So many people are doing this, but no
>> good sample code is easily available, especially for Moby services...
>>
>> Sergio Ramirez Ramirez wrote:
>>> Hello Jerzy
>>>
>>> I had the same problem that you.
>>>
>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>> give you many sample code because I'm trying to organize all the code
>>> tries and examples that I have.
>>>
>>> But I can give you some comments:
>>>
>>> For build a workflow model the class is:
>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>> new ScuflModel();
>>> This class contains the methods that you mention addProcessor ...
>>>
>>> For run I'm using freeflow, because taverna classes and raven are a
>>> "little" tricky. The classes:
>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>> can help you.
>>>
>>> I hope this little details help you to begin. If you have more
>>> detailed questions I will be very happy of help you.
>>>
>>> Best regards,
>>> Sergio
>>>
>>> Jerzy Orlowski wrote:
>>>> Hi
>>>>
>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>> want to execute them all without opening any GUI.
>>>>
>>>> I was looking for some solution over the internet and the think I
>>>> came across was using Taverna plugin and try to execute it
>>>> programaticaly.
>>>> I have a few questions:
>>>>
>>>> 1. Is it the only way?
>>>>
>>>> 2. I found several tutorial tutorials on running saved workflow
>>>> saved in scufl language.
>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>
>>>>
>>>> How do you one make a workflow step by step? like:
>>>>
>>>> workflow.addProcesor(...)
>>>> workflow.addConnector(...)
>>>> ...
>>>> workflow.execute()
>>>>
>>>> and especially, how do one add BioMoby objects this way? Is there
>>>> any tutorial or do I have go though the API?
>>>>
>>>> Best
>>>>
>>>> Jerzy Orlowski
>>>>
>>>> _______________________________________________
>>>> 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 Sep 24 12:31:14 2008
From: groscurt at mpiz-koeln.mpg.de (groscurt)
Date: Wed, 24 Sep 2008 18:31:14 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA630E.6050901@genesilico.pl>
Message-ID:
Hi,
i would really encourage you to use the taverna mailing list for issues
concerning taverna. As some people here have strong experience with it, i
think its way better to ask the people working with it and developing it
directly.
Cheers
Andreas
----------------original message-----------------
From: "Jerzy Orlowski" jerzyo at genesilico.pl
To: moby-dev at lists.open-bio.org
Date: Wed, 24 Sep 2008 17:55:58 +0200
-------------------------------------------------
> Hi
>
> I am trying to use your code, but I get strange erros like:
>
> The constructor EngineImpl(EngineConfiguration) is undefined
>
> Perhaps I am working on different versions of the code (some from
> taverna, some from ogasadai and some from freefluo).
>
> Where can I find source code or javadoc for
> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
>
> I cannot find in anywhere on the web....
>
> Jerzy
>
>
> Sergio Ramirez Ramirez wrote:
>> Here there is my small contribution, just the two methods that I use for
>> run a workflow.
>> Hope it can help to someone
>>
>> Paul Gordon wrote:
>>> I think whoever has a headless Taverna workflow creation and/or
>>> enactment working should put examples up in the Java developer's
>>> section of the Moby Web site...I believe the myExperiment people also
>>> have a headless workflow enactment engine working now...anyone from
>>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>>> enactor in the BioWEP software. So many people are doing this, but no
>>> good sample code is easily available, especially for Moby services...
>>>
>>> Sergio Ramirez Ramirez wrote:
>>>> Hello Jerzy
>>>>
>>>> I had the same problem that you.
>>>>
>>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>>> give you many sample code because I'm trying to organize all the code
>>>> tries and examples that I have.
>>>>
>>>> But I can give you some comments:
>>>>
>>>> For build a workflow model the class is:
>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>>> new ScuflModel();
>>>> This class contains the methods that you mention addProcessor ...
>>>>
>>>> For run I'm using freeflow, because taverna classes and raven are a
>>>> "little" tricky. The classes:
>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>> can help you.
>>>>
>>>> I hope this little details help you to begin. If you have more
>>>> detailed questions I will be very happy of help you.
>>>>
>>>> Best regards,
>>>> Sergio
>>>>
>>>> Jerzy Orlowski wrote:
>>>>> Hi
>>>>>
>>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>>> want to execute them all without opening any GUI.
>>>>>
>>>>> I was looking for some solution over the internet and the think I
>>>>> came across was using Taverna plugin and try to execute it
>>>>> programaticaly.
>>>>> I have a few questions:
>>>>>
>>>>> 1. Is it the only way?
>>>>>
>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>> saved in scufl language.
>>>>>
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>
>>>>>
>>>>>
>>>>> How do you one make a workflow step by step? like:
>>>>>
>>>>> workflow.addProcesor(...)
>>>>> workflow.addConnector(...)
>>>>> ...
>>>>> workflow.execute()
>>>>>
>>>>> and especially, how do one add BioMoby objects this way? Is there
>>>>> any tutorial or do I have go though the API?
>>>>>
>>>>> Best
>>>>>
>>>>> Jerzy Orlowski
>>>>>
>>>>> _______________________________________________
>>>>> 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 soiland-reyes at cs.manchester.ac.uk Thu Sep 25 05:54:47 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Thu, 25 Sep 2008 10:54:47 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA630E.6050901@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl>
Message-ID:
On Wed, Sep 24, 2008 at 16:55, Jerzy Orlowski wrote:
I suggest as well to move the discussion to the taverna-hackers list (
http://taverna.sourceforge.net/lists )
> I am trying to use your code, but I get strange erros like:
>
> The constructor EngineImpl(EngineConfiguration) is undefined
>
> Perhaps I am working on different versions of the code (some from taverna,
> some from ogasadai and some from freefluo).
If you want to be sure to get it to work with Taverna 1.7.1, use
http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo/NO-VERSION/freefluo-NO-VERSION.jar
and http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1/freefluo-taverna-exts-1.7.1.jar
The other projects are likely to have code in either too new or too old version.
> Where can I find source code or javadoc for
> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
Note that this version of Freefluo was never released officially by
the Freefluo project, but it can be checked out from their CVS using a
date range.
Look at the thread of http://markmail.org/message/dnrqdicmbzbfjjl5 if
you really want to build Freefluo from source.
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From jerzyo at genesilico.pl Thu Sep 25 06:22:02 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 25 Sep 2008 12:22:02 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA6624.7040806@uma.es>
References: <48C92991.2000407@genesilico.pl>
<48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca>
<48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl>
<48DA6624.7040806@uma.es>
Message-ID: <48DB664A.6030305@genesilico.pl>
I keep trying, but I cannot find anywhere a jar with
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
I have an impression that freefluo is outdated
----------------------------------------------------------------------
uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error
with configuration named tavernaClassNotFound for WorkflowParser
implementation:
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108)
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64)
at org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84)
at org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11)
Caused by: java.lang.ClassNotFoundException:
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102)
... 3 more
------------------------------------------------------------------------
Jerzyo
Sergio Ramirez Ramirez wrote:
> Hi Jerzy
>
> I see you cannot got to resolve the problem.
>
> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel;
>
> Maybe is what you need. to built your own workflow.
>
> Keep me informed ;) and good luck.
>
> Jerzy Orlowski wrote:
>> Hi
>>
>> I am trying to use your code, but I get strange erros like:
>>
>> The constructor EngineImpl(EngineConfiguration) is undefined
>>
>> Perhaps I am working on different versions of the code (some from
>> taverna, some from ogasadai and some from freefluo).
>>
>> Where can I find source code or javadoc for
>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other
>> classes?
>>
>> I cannot find in anywhere on the web....
>>
>> Jerzy
>>
>>
>> Sergio Ramirez Ramirez wrote:
>>> Here there is my small contribution, just the two methods that I use
>>> for run a workflow.
>>> Hope it can help to someone
>>>
>>> Paul Gordon wrote:
>>>> I think whoever has a headless Taverna workflow creation and/or
>>>> enactment working should put examples up in the Java developer's
>>>> section of the Moby Web site...I believe the myExperiment people
>>>> also have a headless workflow enactment engine working now...anyone
>>>> from there on this list? Also, Paolo Romano in Italy has a headless
>>>> SCUFL enactor in the BioWEP software. So many people are doing this,
>>>> but no good sample code is easily available, especially for Moby
>>>> services...
>>>>
>>>> Sergio Ramirez Ramirez wrote:
>>>>> Hello Jerzy
>>>>>
>>>>> I had the same problem that you.
>>>>>
>>>>> I have got it to work by browsing deep in the Taverna code. I
>>>>> cannot give you many sample code because I'm trying to organize all
>>>>> the code tries and examples that I have.
>>>>>
>>>>> But I can give you some comments:
>>>>>
>>>>> For build a workflow model the class is:
>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>>>> new ScuflModel();
>>>>> This class contains the methods that you mention addProcessor ...
>>>>>
>>>>> For run I'm using freeflow, because taverna classes and raven are a
>>>>> "little" tricky. The classes:
>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>>> can help you.
>>>>>
>>>>> I hope this little details help you to begin. If you have more
>>>>> detailed questions I will be very happy of help you.
>>>>>
>>>>> Best regards,
>>>>> Sergio
>>>>>
>>>>> Jerzy Orlowski wrote:
>>>>>> Hi
>>>>>>
>>>>>> I have several hundreds of workflows made up of BioMoby Services
>>>>>> and want to execute them all without opening any GUI.
>>>>>>
>>>>>> I was looking for some solution over the internet and the think I
>>>>>> came across was using Taverna plugin and try to execute it
>>>>>> programaticaly.
>>>>>> I have a few questions:
>>>>>>
>>>>>> 1. Is it the only way?
>>>>>>
>>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>>> saved in scufl language.
>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>>
>>>>>>
>>>>>> How do you one make a workflow step by step? like:
>>>>>>
>>>>>> workflow.addProcesor(...)
>>>>>> workflow.addConnector(...)
>>>>>> ...
>>>>>> workflow.execute()
>>>>>>
>>>>>> and especially, how do one add BioMoby objects this way? Is there
>>>>>> any tutorial or do I have go though the API?
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Jerzy Orlowski
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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 jerzyo at genesilico.pl Fri Sep 26 04:28:48 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Fri, 26 Sep 2008 10:28:48 +0200
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
Message-ID: <48DC9D40.5030604@genesilico.pl>
Hi
I think there is one important option missing in BioMoby plugins in Taverna.
Suppose I have a MobyService that returns an AminoAcidSequence. I want
to extract the sequence on my AminAcidSequence (it is a String object)
and use it as input for another MobyServices that eats String as its input.
The only way I can do it now is to use a Parser which decomposes
AminoAcidSequence to basic types and then construct my String from these
basic elements
(namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns,aminoacid_'SequenceString',aminoacid_'SequenceString'_id
and aminoacid_'SequenceString'_ns).
This is not very difficult in this case, but imagine what would happen
if I parse an object which is composed of for example
WieghtedAminoSequences and try to get AminoAcidSequence out of it...
In fact current BioMobyObjectProcessors are processors for constructing
MobyObjects (with basic types as input ports and composite types as
output ports). There should be another type of
BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects
(with composite types as input ports and basic types as output ports).
Please inform me if such option already exists somewhere and I missed it.
Jerzy Orlowski
From edward.kawas at gmail.com Fri Sep 26 08:16:20 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 26 Sep 2008 05:16:20 -0700
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
In-Reply-To: <48DC9D40.5030604@genesilico.pl>
References: <48DC9D40.5030604@genesilico.pl>
Message-ID: <48dcd299.1bbc720a.76c6.ffffb9d8@mx.google.com>
Hi Jerzy,
That option is indeed unavailable. It can be something that we add in the
future.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: September-26-08 1:29 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
Hi
I think there is one important option missing in BioMoby plugins in Taverna.
Suppose I have a MobyService that returns an AminoAcidSequence. I want
to extract the sequence on my AminAcidSequence (it is a String object)
and use it as input for another MobyServices that eats String as its input.
The only way I can do it now is to use a Parser which decomposes
AminoAcidSequence to basic types and then construct my String from these
basic elements
(namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns
,aminoacid_'SequenceString',aminoacid_'SequenceString'_id
and aminoacid_'SequenceString'_ns).
This is not very difficult in this case, but imagine what would happen
if I parse an object which is composed of for example
WieghtedAminoSequences and try to get AminoAcidSequence out of it...
In fact current BioMobyObjectProcessors are processors for constructing
MobyObjects (with basic types as input ports and composite types as
output ports). There should be another type of
BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects
(with composite types as input ports and basic types as output ports).
Please inform me if such option already exists somewhere and I missed it.
Jerzy Orlowski
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From soiland-reyes at cs.manchester.ac.uk Fri Sep 26 09:39:14 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Fri, 26 Sep 2008 14:39:14 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DB664A.6030305@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es>
<48DB664A.6030305@genesilico.pl>
Message-ID:
On Thu, Sep 25, 2008 at 11:22, Jerzy Orlowski wrote:
> I keep trying, but I cannot find anywhere a jar with
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
: stain at mira ~/.m2/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1;unzip
-t freefluo-taverna-exts-1.7.1.jar
Archive: freefluo-taverna-exts-1.7.1.jar
testing: META-INF/ OK
testing: META-INF/MANIFEST.MF OK
testing: uk/ OK
testing: uk/ac/ OK
testing: uk/ac/soton/ OK
testing: uk/ac/soton/itinnovation/ OK
testing: uk/ac/soton/itinnovation/freefluo/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaDataHandler.class
OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaScuflModelParser.class
OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaWorkflowInstance.class
OK
No errors detected in compressed data of freefluo-taverna-exts-1.7.1.jar.
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From srramirez at uma.es Thu Sep 25 06:29:18 2008
From: srramirez at uma.es (Sergio Ramirez Ramirez)
Date: Thu, 25 Sep 2008 12:29:18 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DB664A.6030305@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es>
<48DB664A.6030305@genesilico.pl>
Message-ID: <48DB67FE.4000507@uma.es>
Yes, you are right but taverna still using it in the core.
If you download the entire src of taverna you will find a jar file:
taverna-workbench with that class
If you couldn't find it, just tell me and I will sent it to you
Best regards, Sergio
Jerzy Orlowski wrote:
> I keep trying, but I cannot find anywhere a jar with
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
>
> I have an impression that freefluo is outdated
>
> ----------------------------------------------------------------------
> uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error
> with configuration named tavernaClassNotFound for WorkflowParser
> implementation:
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108)
>
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64)
>
> at
> org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84)
> at
> org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11)
> Caused by: java.lang.ClassNotFoundException:
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
> at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102)
>
> ... 3 more
> ------------------------------------------------------------------------
>
> Jerzyo
>
>
>
> Sergio Ramirez Ramirez wrote:
>> Hi Jerzy
>>
>> I see you cannot got to resolve the problem.
>>
>> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel;
>>
>> Maybe is what you need. to built your own workflow.
>>
>> Keep me informed ;) and good luck.
>>
>> Jerzy Orlowski wrote:
>>> Hi
>>>
>>> I am trying to use your code, but I get strange erros like:
>>>
>>> The constructor EngineImpl(EngineConfiguration) is undefined
>>>
>>> Perhaps I am working on different versions of the code (some from
>>> taverna, some from ogasadai and some from freefluo).
>>>
>>> Where can I find source code or javadoc for
>>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other
>>> classes?
>>>
>>> I cannot find in anywhere on the web....
>>>
>>> Jerzy
>>>
>>>
>>> Sergio Ramirez Ramirez wrote:
>>>> Here there is my small contribution, just the two methods that I
>>>> use for run a workflow.
>>>> Hope it can help to someone
>>>>
>>>> Paul Gordon wrote:
>>>>> I think whoever has a headless Taverna workflow creation and/or
>>>>> enactment working should put examples up in the Java developer's
>>>>> section of the Moby Web site...I believe the myExperiment people
>>>>> also have a headless workflow enactment engine working
>>>>> now...anyone from there on this list? Also, Paolo Romano in Italy
>>>>> has a headless SCUFL enactor in the BioWEP software. So many
>>>>> people are doing this, but no good sample code is easily
>>>>> available, especially for Moby services...
>>>>>
>>>>> Sergio Ramirez Ramirez wrote:
>>>>>> Hello Jerzy
>>>>>>
>>>>>> I had the same problem that you.
>>>>>>
>>>>>> I have got it to work by browsing deep in the Taverna code. I
>>>>>> cannot give you many sample code because I'm trying to organize
>>>>>> all the code tries and examples that I have.
>>>>>>
>>>>>> But I can give you some comments:
>>>>>>
>>>>>> For build a workflow model the class is:
>>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model
>>>>>> = new ScuflModel();
>>>>>> This class contains the methods that you mention addProcessor ...
>>>>>>
>>>>>> For run I'm using freeflow, because taverna classes and raven are
>>>>>> a "little" tricky. The classes:
>>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>>>> can help you.
>>>>>>
>>>>>> I hope this little details help you to begin. If you have more
>>>>>> detailed questions I will be very happy of help you.
>>>>>>
>>>>>> Best regards,
>>>>>> Sergio
>>>>>>
>>>>>> Jerzy Orlowski wrote:
>>>>>>> Hi
>>>>>>>
>>>>>>> I have several hundreds of workflows made up of BioMoby Services
>>>>>>> and want to execute them all without opening any GUI.
>>>>>>>
>>>>>>> I was looking for some solution over the internet and the think
>>>>>>> I came across was using Taverna plugin and try to execute it
>>>>>>> programaticaly.
>>>>>>> I have a few questions:
>>>>>>>
>>>>>>> 1. Is it the only way?
>>>>>>>
>>>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>>>> saved in scufl language.
>>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>>>
>>>>>>>
>>>>>>> How do you one make a workflow step by step? like:
>>>>>>>
>>>>>>> workflow.addProcesor(...)
>>>>>>> workflow.addConnector(...)
>>>>>>> ...
>>>>>>> workflow.execute()
>>>>>>>
>>>>>>> and especially, how do one add BioMoby objects this way? Is
>>>>>>> there any tutorial or do I have go though the API?
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>> Jerzy Orlowski
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> MOBY-dev mailing list
>>>>>>> MOBY-dev at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>
>>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
--
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 jerzyo at genesilico.pl Mon Sep 1 10:01:45 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Mon, 01 Sep 2008 12:01:45 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
Message-ID: <48BBBD89.6020803@genesilico.pl>
Hello
I am searchng for a java class representing a BioMoby workflow:
I found some classes that represent connections:
datatype -> service
service -> datatype
datatype -> datatype
in org.biomoby.client.
(There is even a class for drawing graphs using graphviz, but
unfortunately without datatype -> datatype connections.)
I do not find find any class that these connections gathers them
together as a workflow and enables execution of this workflow given some
inputs.
Does such class exist in jMoby? Or should I run my workflows using
Taverna libraries (How should I do it)?
If it does not exist I will probably write it but maybe somebody is
already doing it.
Jerzy Orlowski
From serr at ac.uma.es Mon Sep 1 10:10:53 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Mon, 01 Sep 2008 12:10:53 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBD89.6020803@genesilico.pl>
References: <48BBBD89.6020803@genesilico.pl>
Message-ID: <48BBBFAD.7060401@ac.uma.es>
Hello Jerzy
Unfortunately, moby can not handle workflows by itself for now. Normally
you use taverna for building workflows.
I'm trying to learn how to use Taverna libraries to run workflows. There
is a taverna class (workflowlauncher or similar) available in the web
page for taverna, but I couldn't make it work.
I'm also very interesting in this topic.
Greetings, Sergio
Jerzy Orlowski wrote:
> Hello
>
> I am searchng for a java class representing a BioMoby workflow:
>
> I found some classes that represent connections:
> datatype -> service
> service -> datatype
> datatype -> datatype
> in org.biomoby.client.
> (There is even a class for drawing graphs using graphviz, but
> unfortunately without datatype -> datatype connections.)
>
> I do not find find any class that these connections gathers them
> together as a workflow and enables execution of this workflow given
> some inputs.
>
> Does such class exist in jMoby? Or should I run my workflows using
> Taverna libraries (How should I do it)?
> If it does not exist I will probably write it but maybe somebody is
> already doing it.
>
> Jerzy Orlowski
>
> _______________________________________________
> 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 groscurt at mpiz-koeln.mpg.de Mon Sep 1 10:44:58 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Mon, 01 Sep 2008 12:44:58 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBFAD.7060401@ac.uma.es>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
Message-ID: <48BBC7AA.2060002@mpiz-koeln.mpg.de>
Hi Sergio,
if you follow the mail list correspondance of the taverna list
http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results
you will find the same question with answer and links to your problem.
best
andreas
Sergio Ramirez Ramirez wrote:
> Hello Jerzy
>
> Unfortunately, moby can not handle workflows by itself for now.
> Normally you use taverna for building workflows.
> I'm trying to learn how to use Taverna libraries to run workflows.
> There is a taverna class (workflowlauncher or similar) available in
> the web page for taverna, but I couldn't make it work.
>
> I'm also very interesting in this topic.
> Greetings, Sergio
>
> Jerzy Orlowski wrote:
>> Hello
>>
>> I am searchng for a java class representing a BioMoby workflow:
>>
>> I found some classes that represent connections:
>> datatype -> service
>> service -> datatype
>> datatype -> datatype
>> in org.biomoby.client.
>> (There is even a class for drawing graphs using graphviz, but
>> unfortunately without datatype -> datatype connections.)
>>
>> I do not find find any class that these connections gathers them
>> together as a workflow and enables execution of this workflow given
>> some inputs.
>>
>> Does such class exist in jMoby? Or should I run my workflows using
>> Taverna libraries (How should I do it)?
>> If it does not exist I will probably write it but maybe somebody is
>> already doing it.
>>
>> Jerzy Orlowski
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From serr at ac.uma.es Mon Sep 1 11:15:17 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Mon, 01 Sep 2008 13:15:17 +0200
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBC7AA.2060002@mpiz-koeln.mpg.de>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
<48BBC7AA.2060002@mpiz-koeln.mpg.de>
Message-ID: <48BBCEC5.1070505@ac.uma.es>
Thank you very much
Best Sergio.
Andreas Groscurth wrote:
> Hi Sergio,
>
> if you follow the mail list correspondance of the taverna list
>
> http://markmail.org/message/x5vtct5hbovnj3zy#query:%22anika%20joecker%22+page:1+mid:ko2eo5moj6atnoeu+state:results
>
>
> you will find the same question with answer and links to your problem.
>
> best
> andreas
>
> Sergio Ramirez Ramirez wrote:
>> Hello Jerzy
>>
>> Unfortunately, moby can not handle workflows by itself for now.
>> Normally you use taverna for building workflows.
>> I'm trying to learn how to use Taverna libraries to run workflows.
>> There is a taverna class (workflowlauncher or similar) available in
>> the web page for taverna, but I couldn't make it work.
>>
>> I'm also very interesting in this topic.
>> Greetings, Sergio
>>
>> Jerzy Orlowski wrote:
>>> Hello
>>>
>>> I am searchng for a java class representing a BioMoby workflow:
>>>
>>> I found some classes that represent connections:
>>> datatype -> service
>>> service -> datatype
>>> datatype -> datatype
>>> in org.biomoby.client.
>>> (There is even a class for drawing graphs using graphviz, but
>>> unfortunately without datatype -> datatype connections.)
>>>
>>> I do not find find any class that these connections gathers them
>>> together as a workflow and enables execution of this workflow given
>>> some inputs.
>>>
>>> Does such class exist in jMoby? Or should I run my workflows using
>>> Taverna libraries (How should I do it)?
>>> If it does not exist I will probably write it but maybe somebody is
>>> already doing it.
>>>
>>> Jerzy Orlowski
>>>
>>> _______________________________________________
>>> 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 MichaelGerlich at gmx.de Wed Sep 3 09:17:42 2008
From: MichaelGerlich at gmx.de (Michael Gerlich)
Date: Wed, 3 Sep 2008 11:17:42 +0200
Subject: [MOBY-dev] Problems calling a Moby service with secondary parameters
Message-ID: <000001c90da5$eb498a40$c1dc9ec0$@de>
Hi all,
I'm working on a simple java app (client) that calls some Biomoby services I
wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist"
registered under authority "ipb-halle.de" takes additional 2 secondary
parameters that modify its query behavior and the resulting number of
outputs.
Now when I try to add both secondary parameters to the input, the service
call fails with the following message:
Exception in thread "main" org.biomoby.shared.MobyException: Service
get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but
takes 2 (query 1). Extra secondary parameters must have been specified
at
org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java
:928)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282)
at
org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275)
at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86)
My code is like that:
Central worker = new CentralImpl();
templateService = new MobyService("get_DBLinks_From_Peaklist", authority);
// authority = "ipb-halle.de"
validServices = worker.findService(templateService);
comp = new MobyDataComposite(new MobyDataType("MSPeakRel"));
comp.put("relInt", new MobyDataInt(999));
comp.put("mz", new MobyDataFloat(273.069));
MobyDataSecondaryInstance[] secParams = new
MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length];
for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) {
secParams[i] = new MobyDataSecondaryInstance(new
MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()),
validServices[0].getSecondaryInputs()[i].getDefaultValue()); }
mr.setService(validServices[0]);
mr.setInput(comp);
mr.setSecondaryInput(secParams);
System.out.println(mr.invokeService().toString());
The setSecondaryInput() function takes an array that consists of all
parameters and applies them to all inputs. Now there are 2 parameters and an
array of length 2 - with the default values for both parameters (I defined
default values for both parameters).
Some hints what I'm doing wrong?
Another question - my input is of type MSPeakRel and is defined as
collection. How do I manage to add multiple inputs - in this case, they
would represent a complete peaklist of (m/z value, relative intensity) for
querying a database?
Best wishes,
Michael
From jason.e.stewart at gmail.com Mon Sep 8 11:06:59 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 8 Sep 2008 16:36:59 +0530
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
Message-ID: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
Hey Moby-devs,
The version of SOAP::Lite in CVS claims to support Document/literal
encoding - I need help determing if this support is sufficient. Can
you look this over?
=head3 DOCUMENT/LITERAL
SOAP web services using the document/literal message encoding are usually
described by some Web Service Definition. Our web service has the following
WSDL description:
The XML message (inside the SOAP Envelope) look like this:
KutterMartinHello Martin Kutter!
You can call this web service with the following client code:
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->call("sayHello",
SOAP::Data->name('name')->value( 'Kutter' ),
SOAP::Data->name('givenName')->value('Martin'),
);
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
=head2 Differences between the implementations
You may have noticed that there's no between the rpc/literal
and the document/literal example's implementation. In fact, from SOAP::Lite's
point of view, the only differences between rpc/literal and document/literal
that parameters are always named.
In our example, the rpc/literal variant already used named parameters (by
using a single complexType only as positional parameter), so there's no
difference at all.
The differences would have been bigger if the rpc/literal example had used
more than one positional parameter, but this is quite unlikely to happen in
the future: Current interoperability standards (like the WS-I basic profile)
mandate the use of a single complexType as only parameter in rpc/literal
calls.
-- snip --
Help me on this one - is this valid? Is it sufficient for what MOBY
and the rest of the Perl world needs? I suggest that I test this claim
against:
* perl SOAP::Lite client = axis Java server
* java client = perl SOAP::Lite server
I could use some suggestions for how to make these tests useful.
Cheers, jas.
From edward.kawas at gmail.com Mon Sep 8 15:16:08 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 8 Sep 2008 08:16:08 -0700
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
In-Reply-To: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
Message-ID: <48c541bc.2a528c0a.2895.3efe@mx.google.com>
Hi Jason,
One of the problems that I have with soap lite and trying to perform doc/lit
requests/responses is the inability to use attributes in the request.
Since that statement doesn't make too much sense (to some it might have ;-),
I will provide an example:
I modified the wsdl that you sent to include an attribute in the givenName
element, so that a request now looks like:
Joe BlowJoe
The server side code is simply:
sub sayHello {
SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) );
}
So all that I am doing is dumping whatever is sent to the server.
The response is
$VAR1 = [ 'HelloWorld', 'Joe Blow',
'Joe' ];
I do believe that this is one of the biggest stumbling blocks so far.
Because numerous Moby api calls use attributes. One such example is the
retrieveService call.
My dispatcher code is below!
Eddie
------ CODE START -----
#!/usr/bin/perl -w
# _________________________________________________________________
use SOAP::Transport::HTTP;
if ($ENV{REQUEST_METHOD} eq "GET") {
if (lc($ENV{QUERY_STRING} || "") eq "wsdl") {
require CGI;
my $q = CGI->new();
my $wsdl = HelloWorld::wsdl();
my $c = length($wsdl);
print $q->header(-type=>'application/xml',-Content-length=>$c);
print "$wsdl";
}
} else {
my $x = new SOAP::Transport::HTTP::CGI;
$x->dispatch_to('/var/www/cgi-bin', 'HelloWorld');
$x->handle;
}
package HelloWorld;
use Data::Dumper;
sub sayHello {
SOAP::Data->name('sayHelloResult')->value( Dumper(\@_) );
}
sub wsdl {
return <
EOF
}
1;
------ CODE END ------
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jason Stewart
Sent: September-08-08 4:07 AM
To: Core developer announcements
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
Hey Moby-devs,
The version of SOAP::Lite in CVS claims to support Document/literal
encoding - I need help determing if this support is sufficient. Can
you look this over?
=head3 DOCUMENT/LITERAL
SOAP web services using the document/literal message encoding are usually
described by some Web Service Definition. Our web service has the following
WSDL description:
The XML message (inside the SOAP Envelope) look like this:
KutterMartinHello Martin Kutter!
You can call this web service with the following client code:
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->call("sayHello",
SOAP::Data->name('name')->value( 'Kutter' ),
SOAP::Data->name('givenName')->value('Martin'),
);
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
=head2 Differences between the implementations
You may have noticed that there's no between the rpc/literal
and the document/literal example's implementation. In fact, from
SOAP::Lite's
point of view, the only differences between rpc/literal and document/literal
that parameters are always named.
In our example, the rpc/literal variant already used named parameters (by
using a single complexType only as positional parameter), so there's no
difference at all.
The differences would have been bigger if the rpc/literal example had used
more than one positional parameter, but this is quite unlikely to happen in
the future: Current interoperability standards (like the WS-I basic profile)
mandate the use of a single complexType as only parameter in rpc/literal
calls.
-- snip --
Help me on this one - is this valid? Is it sufficient for what MOBY
and the rest of the Perl world needs? I suggest that I test this claim
against:
* perl SOAP::Lite client = axis Java server
* java client = perl SOAP::Lite server
I could use some suggestions for how to make these tests useful.
Cheers, jas.
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
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From jason.e.stewart at gmail.com Mon Sep 8 16:00:18 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 8 Sep 2008 21:30:18 +0530
Subject: [MOBY-dev] SOAP::Lite claims support for document/literal
In-Reply-To: <48c541bc.2a528c0a.2895.3efe@mx.google.com>
References: <41c1ade50809080406w6dfc7774ha275ecf11c7a8b6c@mail.gmail.com>
<48c541bc.2a528c0a.2895.3efe@mx.google.com>
Message-ID: <41c1ade50809080900l4d681b02m7962f04e81310421@mail.gmail.com>
Hey Eddie,
On Mon, Sep 8, 2008 at 8:46 PM, Edward Kawas wrote:
> One of the problems that I have with soap lite and trying to perform doc/lit
> requests/responses is the inability to use attributes in the request.
OK. I've sent this off as a query to the SOAP-Lite dev list - I'll see
what they have to say.
Either there is an intended workaround or it needs to be implemented.
Thanks. jas.
From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 12:11:10 2008
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Wed, 10 Sep 2008 14:11:10 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
Message-ID: <48C7B95E.4080903@avignon.inra.fr>
Hi,
We have a problem with dashboard. We unregistered and re-registred our
services (with some changes), but after reloading the service list we
don't see these services in the list and our authority is missing.
We tried to delete manually our cache and to restart the dashboard
several time. We tried to reload or update every thing without changes
(which obviously make sense).
Does it link in any way to experimental "big bang" this morning in Geneve ?
Any other ideas ?
Thanks,
Regards,
Dominique
From Dominique.Jeannin at avignon.inra.fr Wed Sep 10 12:23:31 2008
From: Dominique.Jeannin at avignon.inra.fr (Dominique Jeannin)
Date: Wed, 10 Sep 2008 14:23:31 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7B95E.4080903@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
Message-ID: <48C7BC43.70008@avignon.inra.fr>
Dominique Jeannin a ?crit :
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in
> Geneve ?
> Any other ideas ?
>
Does anyone see our services named Solstis_getDatasetDescFromKeyword on
avilin05.avignon.inra.fr ?
From all our tests we cannot...
Thanks,
Regards,
Dominique
From groscurt at mpiz-koeln.mpg.de Wed Sep 10 12:47:29 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 10 Sep 2008 14:47:29 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7BC43.70008@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7BC43.70008@avignon.inra.fr>
Message-ID: <48C7C1E1.1030406@mpiz-koeln.mpg.de>
Hi Dominique,
i do find it in the dashboard on the test central and via a simple moby
java test.
I had the same issue some days ago that changes (like service
(de)registration) could not be shown in dashboard, whatever i did to
it... My solution was then to use someonelse moby checkout and this
dashboard :(
Hope someone knows about that and knows a general solution
Andreas
Dominique Jeannin wrote:
> Dominique Jeannin a ?crit :
>> Hi,
>>
>> We have a problem with dashboard. We unregistered and re-registred
>> our services (with some changes), but after reloading the service
>> list we don't see these services in the list and our authority is
>> missing.
>> We tried to delete manually our cache and to restart the dashboard
>> several time. We tried to reload or update every thing without
>> changes (which obviously make sense).
>>
>> Does it link in any way to experimental "big bang" this morning in
>> Geneve ?
>> Any other ideas ?
>>
> Does anyone see our services named Solstis_getDatasetDescFromKeyword
> on avilin05.avignon.inra.fr ?
> From all our tests we cannot...
>
> Thanks,
> Regards,
>
> Dominique
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From py at pingoured.fr Wed Sep 10 12:49:19 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 14:49:19 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7B95E.4080903@avignon.inra.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
Message-ID: <48C7C24F.3050709@pingoured.fr>
Dominique Jeannin wrote:
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in Geneve ?
> Any other ideas ?
More informations on the problem:
While doing an "Update" on all (Services, datatypes...) we have the
following error:
===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8 sequence.
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========
While on the other when doing a "Reload" all, we do not have any error
but we still can't see our services nor authority.
Regards,
Pierre
From edward.kawas at gmail.com Wed Sep 10 13:12:10 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 06:12:10 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7C24F.3050709@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
Message-ID: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Hi,
I am trying to reproduce your problems, but I cannot. I am not seeing any
SOAP exceptions and I don't see your service either.
The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
tried to use non utf8 characters in my soap message.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-10-08 5:49 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Dominique Jeannin wrote:
> Hi,
>
> We have a problem with dashboard. We unregistered and re-registred our
> services (with some changes), but after reloading the service list we
> don't see these services in the list and our authority is missing.
> We tried to delete manually our cache and to restart the dashboard
> several time. We tried to reload or update every thing without changes
> (which obviously make sense).
>
> Does it link in any way to experimental "big bang" this morning in Geneve
?
> Any other ideas ?
More informations on the problem:
While doing an "Update" on all (Services, datatypes...) we have the
following error:
===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8 sequence.
Fault code:
{http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========
While on the other when doing a "Reload" all, we do not have any error
but we still can't see our services nor authority.
Regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From py at pingoured.fr Wed Sep 10 13:31:33 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 15:31:33 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Message-ID: <48C7CC35.6090803@pingoured.fr>
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
Strange since Andreas seems to see it as well as another person that
contacted us off-list.
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
What surprise us the most is that two of our services that we did not
change (Solstis_getProjet and dom_test2) are not shown either.
The whole authority avilin05.avignon.inra.fr seems to have disappeared...
We will try by deleting jMoby and re-downloading it from the CVS.
Hope that fix the problem
Thanks for your help,
Regards,
Pierre
From edward.kawas at gmail.com Wed Sep 10 13:33:30 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 06:33:30 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7CC35.6090803@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr>
<48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
<48C7CC35.6090803@pingoured.fr>
Message-ID: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
I also forgot to mention that I also tried looking for your services in the
database that backs the registry and failed to find 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 Pierre-Yves Chibon
Sent: September-10-08 6:32 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
Strange since Andreas seems to see it as well as another person that
contacted us off-list.
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
What surprise us the most is that two of our services that we did not
change (Solstis_getProjet and dom_test2) are not shown either.
The whole authority avilin05.avignon.inra.fr seems to have disappeared...
We will try by deleting jMoby and re-downloading it from the CVS.
Hope that fix the problem
Thanks for your help,
Regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From py at pingoured.fr Wed Sep 10 13:47:47 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Wed, 10 Sep 2008 15:47:47 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C7D003.3070903@pingoured.fr>
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find it!
This is weird because the registration seems to work (cf below)
Could you check Solstis_getProject ? We did not change that one normally.
Thanks for your help,
Regards,
Pierre
../jMoby/build/run/run-cmdline-client -e
http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl -uri
http://bioinfo.icapture.ubc.ca/MOBY/Central -call registerService
'mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
'
Calling method 'registerService' with the input from 'mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
':
mobySolstis_getDatasetDescFromKeywordgetDatasetavilin05.avignon.inra.frhttp://avilin05/axis/services/Solstis_getDatasetDescFromKeywordjean-paul.bouchet at avignon.inra.fr1String
--------------
0
From groscurt at mpiz-koeln.mpg.de Wed Sep 10 13:53:13 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 10 Sep 2008 15:53:13 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C7D149.1020308@mpiz-koeln.mpg.de>
So basically its not there anymore but i can see it in dashboard ? then
my cache is old.
My problem was not even based on the encoding problem. I set a different
cache location and did reload/update and everything. I didnt get any
SOAP error, but still the service i registered didnt show up.
If i queried the central via the jmoby api and looked explictly for my
service i found it...
dont know if and how this error might be reproducable :(
Best
andreas
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find 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 Pierre-Yves Chibon
> Sent: September-10-08 6:32 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Problem with dashboard to list services
>
> Edward Kawas wrote:
>
>> Hi,
>>
>> I am trying to reproduce your problems, but I cannot. I am not seeing any
>> SOAP exceptions and I don't see your service either.
>>
>
> Strange since Andreas seems to see it as well as another person that
> contacted us off-list.
>
>
>> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
>> tried to use non utf8 characters in my soap message.
>>
>>
>
> What surprise us the most is that two of our services that we did not
> change (Solstis_getProjet and dom_test2) are not shown either.
>
> The whole authority avilin05.avignon.inra.fr seems to have disappeared...
>
>
> We will try by deleting jMoby and re-downloading it from the CVS.
> Hope that fix the problem
>
> Thanks for your help,
> Regards,
>
> Pierre
> _______________________________________________
> 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
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From jason.e.stewart at gmail.com Wed Sep 10 14:28:16 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 10 Sep 2008 19:58:16 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
Message-ID: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
Hey Eddie,
So I dug a bit on the server side and this is what I found.
If your server class subclasses from SOAP::Server::Parameters, the
method will get an extra parameter of type SOAP::SOM which gives
access to all the request information. That object contains a lot of
methods for searching the soap envelope - but it converts all the data
it finds into a SOAP::Data instance - which throws away all attributes
not located at the root of the data being returned. For example if the
XML looked like this:
Joe BlowJoe
and we did a query like $root = $som->dataof('//Body'), then $root
would be the soap:Body and we would see all of the sub-elements but
not their attributes. Only if we do $gn = $som->dataof('//givenName')
do we actually get the givenName element with the middlename attribute
still intact.
But the $som object has all the information in an internal hash table
- both as a hash table representation of the entire message and the
HTTP::Request object with the original XML.
What I don't understand is why when the dataof() method traverses the
internal hash table structure it throws away all the attributes not on
the root element being returned.
Also, I don't understand why there isn't a method that just returns
the content of the soap:Body element as plain XML - this should be the
default behavior for document/literal. I would like to see a call
something like $xml = $som->document();
Any thoughts of how I could make this interface most useful for MOBY
purposes? I will have to alter the internal SOAP::Lite code, and send
the patches to the maintainers.
Cheers, jas.
From jmfernandez at cnio.es Wed Sep 10 15:06:50 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Wed, 10 Sep 2008 17:06:50 +0200
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
Message-ID: <48C7E28A.6020203@cnio.es>
Hi Jason,
when we were developing the Perl MOBY::Async libraries we had the same
problem (we needed to access to the full input message), and we solved it
using custom deserializers fom WSRF::Lite package. Next sentences set-up them:
my $server = new SOAP::Transport::HTTP::CGI;
$server->serializer(WSRF::Serializer->new);
$server->deserializer(WSRF::Deserializer->new);
WSRF::Serializer and WSRF::Deserializer are subclasses of SOAP::Serializer
and SOAP::Deserializer, respectively. SOAP::Deserializer translates input SOAP
message into a SOAP::SOM instance. WSRF::Deserializer translates input SOAP
message into a WSRF::SOM instance, which is a SOAP::SOM instance plus a new
method called 'raw_xml'. This method returns the raw input message, which can
be parsed with XML::LibXML (for instance).
Hope this helps,
Jos? Mar?a
Jason Stewart wrote:
> Hey Eddie,
>
> So I dug a bit on the server side and this is what I found.
>
> If your server class subclasses from SOAP::Server::Parameters, the
> method will get an extra parameter of type SOAP::SOM which gives
> access to all the request information. That object contains a lot of
> methods for searching the soap envelope - but it converts all the data
> it finds into a SOAP::Data instance - which throws away all attributes
> not located at the root of the data being returned. For example if the
> XML looked like this:
>
>
>
> Joe Blow
> Joe
>
>
>
> and we did a query like $root = $som->dataof('//Body'), then $root
> would be the soap:Body and we would see all of the sub-elements but
> not their attributes. Only if we do $gn = $som->dataof('//givenName')
> do we actually get the givenName element with the middlename attribute
> still intact.
>
> But the $som object has all the information in an internal hash table
> - both as a hash table representation of the entire message and the
> HTTP::Request object with the original XML.
>
> What I don't understand is why when the dataof() method traverses the
> internal hash table structure it throws away all the attributes not on
> the root element being returned.
>
> Also, I don't understand why there isn't a method that just returns
> the content of the soap:Body element as plain XML - this should be the
> default behavior for document/literal. I would like to see a call
> something like $xml = $som->document();
>
> Any thoughts of how I could make this interface most useful for MOBY
> purposes? I will have to alter the internal SOAP::Lite code, and send
> the patches to the maintainers.
>
> Cheers, jas.
> _______________________________________________
> 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 martin.senger at gmail.com Wed Sep 10 18:28:06 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 11 Sep 2008 02:28:06 +0800
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C7C24F.3050709@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
Message-ID: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
Martin
--
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
From edward.kawas at gmail.com Wed Sep 10 18:41:24 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 11:41:24 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
Message-ID: <48c814e0.14b48c0a.2f35.ffff9d83@mx.google.com>
So I haven't seen anything obvious in the description field for the services
from avilin05.avignon.inra.fr.
I am trying to track down the offending service and once it is found, I will
fix it. Then I will update the registry to use the utf8 patch that I coded
last month to solve this problem.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: September-10-08 11:28 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
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 edward.kawas at gmail.com Wed Sep 10 19:20:59 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 10 Sep 2008 12:20:59 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
Message-ID: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
Okay, I found the culprit and I have fixed it. It was a the service
simpleTest under the authority mpiz-koeln.mpg.de.
I will also deploy patches to the test registry to see if we can trap these
errors in the future.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: September-10-08 11:28 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
UTF-8
> sequence.
This seems to be a re-occurrence of the same problem that we were solving
couple of months ago with a service from Germany. In that case, the problem
was caused by using non-ascii characters (such as German umlaut characters)
in the service description. The problem was (and I guess still is, with your
services) has two parts:
First, jMoby (in Dashboard but also in any other usage og its libraries) may
send a wrong Unicode characters. This is probably a bug in my libraries. I
should fix it.
Second, BioMoby central registry accepts wrong Unicode characters, stores
them in its database and sends back them as an invalid XML. This should be
fixed by Eddie or Mark I guess.
If I am correct and your situation is indeed the one I am describing, it is
a very dangerous situation because by registering a service with such
description *all* jMoby users around the world will be affected (their
Dashboards, for example, will not be able to reload or update anymore -
until Eddie manually fixes the descriptions in the registry database; that's
how he fixed it last time).
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 gordonp at ucalgary.ca Wed Sep 10 19:35:11 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 10 Sep 2008 13:35:11 -0600
Subject: [MOBY-dev] Problems calling a Moby service with secondary
parameters
In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de>
References: <000001c90da5$eb498a40$c1dc9ec0$@de>
Message-ID: <48C8216F.8090801@ucalgary.ca>
Hi Michael,
Sorry for not getting back to you earlier. The problem is in the way to
create the secondary data instances. If you do a toString() on them,
you;ll see that they have a blank name based on the constructor you
used. The easiest way to use the default secondaries is with the
one-arg constructor, e.g.:
int i = 0;
for (MobySecondaryData param: service.getSecondaryInputs()) {
secParams[i++] = new MobyDataSecondaryInstance(param);
//auto-populates the instance with the template's default value
}
I'll add a check to MobyRequest that'll complain if you give blank or
duplicately named secondaries, which should make this mistake more
obvious to others in the future.
Regards,
Paul
P.S. I've also updated MobyDataComposite to handle put() for cases such
as your where the data type is not in the registry yet, facilitating
testing. Better yet though is to use the test registry in such cases.
Michael Gerlich wrote:
> Hi all,
>
> I'm working on a simple java app (client) that calls some Biomoby services I
> wrote (for JUnit testing). One of these, "get_DBLinks_From_Peaklist"
> registered under authority "ipb-halle.de" takes additional 2 secondary
> parameters that modify its query behavior and the resulting number of
> outputs.
>
> Now when I try to add both secondary parameters to the input, the service
> call fails with the following message:
>
> Exception in thread "main" org.biomoby.shared.MobyException: Service
> get_DBLinks_From_Peaklist was provided 1 secondary input parameter(s), but
> takes 2 (query 1). Extra secondary parameters must have been specified
> at
> org.biomoby.client.MobyRequest.convertMOBYDataToMOBYRequest(MobyRequest.java
> :928)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:302)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:282)
> at
> org.biomoby.client.MobyRequest.invokeService(MobyRequest.java:275)
> at test.Moby_JUnit_Tests.main(Moby_JUnit_Tests.java:86)
>
>
> My code is like that:
>
> Central worker = new CentralImpl();
> templateService = new MobyService("get_DBLinks_From_Peaklist", authority);
> // authority = "ipb-halle.de"
> validServices = worker.findService(templateService);
>
> comp = new MobyDataComposite(new MobyDataType("MSPeakRel"));
> comp.put("relInt", new MobyDataInt(999));
> comp.put("mz", new MobyDataFloat(273.069));
>
> MobyDataSecondaryInstance[] secParams = new
> MobyDataSecondaryInstance[validServices[0].getSecondaryInputs().length];
> for (int i = 0; i < validServices[0].getSecondaryInputs().length; i++) {
> secParams[i] = new MobyDataSecondaryInstance(new
> MobySecondaryData(validServices[0].getSecondaryInputs()[i].getDataType()),
> validServices[0].getSecondaryInputs()[i].getDefaultValue()); }
>
> mr.setService(validServices[0]);
> mr.setInput(comp);
> mr.setSecondaryInput(secParams);
> System.out.println(mr.invokeService().toString());
>
>
>
> The setSecondaryInput() function takes an array that consists of all
> parameters and applies them to all inputs. Now there are 2 parameters and an
> array of length 2 - with the default values for both parameters (I defined
> default values for both parameters).
>
> Some hints what I'm doing wrong?
>
>
> Another question - my input is of type MSPeakRel and is defined as
> collection. How do I manage to add multiple inputs - in this case, they
> would represent a complete peaklist of (m/z value, relative intensity) for
> querying a database?
>
>
>
> Best wishes,
>
> Michael
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,48be578210950321565264!
>
>
>
>
From gordonp at ucalgary.ca Wed Sep 10 20:08:52 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 10 Sep 2008 14:08:52 -0600
Subject: [MOBY-dev] Java MobyRequest changes
In-Reply-To: <000001c90da5$eb498a40$c1dc9ec0$@de>
References: <000001c90da5$eb498a40$c1dc9ec0$@de>
Message-ID: <48C82954.5030507@ucalgary.ca>
Hi all,
If you use MobyRequest in your code, please note that setSecondaries()
now throws a MobyException in CVS. This is to help catch problems with
invalid secondary parameter values. You will need to ensure any call to
this method is now enclosed in a "try" block. Sorry for any
inconvenience this API change may cause.
Paul
From jason.e.stewart at gmail.com Thu Sep 11 04:14:54 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Thu, 11 Sep 2008 09:44:54 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <48C7E28A.6020203@cnio.es>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
<48C7E28A.6020203@cnio.es>
Message-ID: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
Hey Jose,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> when we were developing the Perl MOBY::Async libraries we had the
> same problem (we needed to access to the full input message), and we solved
> it using custom deserializers fom WSRF::Lite package.
Thanks, that's useful for MOBY users, definately.
I still think that it should be a functionality that is built into the
core of SOAP::Lite, though, especially since document/literal is the
standard encoding now. I will get a response from Martin, the current
maintainer of SOAP::Lite, and see what he thinks should be done.
Likewise, on the client side it should be made trivial to attach a
fragment of XML as the body of the soap message without any
interference from SOAP::Lite.
Any comments?
Thanks, jas.
From groscurt at mpiz-koeln.mpg.de Thu Sep 11 05:50:02 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Thu, 11 Sep 2008 07:50:02 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr>
<48C7C24F.3050709@pingoured.fr> <4d93f07c0809101128h1e6f3fabs6552b8b566c2a280@mail.gmail.com>
<48c81e2a.16538c0a.5326.ffffb815@mx.google.com>
Message-ID: <48C8B18A.7020401@mpiz-koeln.mpg.de>
ohoh - that was my service... at least kind of - i tested the problem we
discussed last time with the umlaut etc.
I'm sorry - i totally forgot that service :(
Andreas
Edward Kawas wrote:
> Okay, I found the culprit and I have fixed it. It was a the service
> simpleTest under the authority mpiz-koeln.mpg.de.
>
> I will also deploy patches to the test registry to see if we can trap these
> errors in the future.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
> Sent: September-10-08 11:28 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Problem with dashboard to list services
>
>
>> Fault string: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte
>>
> UTF-8
>
>> sequence.
>>
>
>
> This seems to be a re-occurrence of the same problem that we were solving
> couple of months ago with a service from Germany. In that case, the problem
> was caused by using non-ascii characters (such as German umlaut characters)
> in the service description. The problem was (and I guess still is, with your
> services) has two parts:
>
> First, jMoby (in Dashboard but also in any other usage og its libraries) may
> send a wrong Unicode characters. This is probably a bug in my libraries. I
> should fix it.
>
> Second, BioMoby central registry accepts wrong Unicode characters, stores
> them in its database and sends back them as an invalid XML. This should be
> fixed by Eddie or Mark I guess.
>
> If I am correct and your situation is indeed the one I am describing, it is
> a very dangerous situation because by registering a service with such
> description *all* jMoby users around the world will be affected (their
> Dashboards, for example, will not be able to reload or update anymore -
> until Eddie manually fixes the descriptions in the registry database; that's
> how he fixed it last time).
>
> Martin
>
>
--
=====================================================
Dipl. Bioinf. Andreas Groscurth
Bioinformatics Software Developer
Plant Computational Biology group
Max-Planck Institute for plant breeding research
Carl-von-Linne Weg 10
50829 Cologne
Germany
+49(0) 221 5062449
=====================================================
From py at pingoured.fr Thu Sep 11 07:45:30 2008
From: py at pingoured.fr (Pierre-Yves Chibon)
Date: Thu, 11 Sep 2008 09:45:30 +0200
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr>
<48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
Message-ID: <48C8CC9A.7050808@pingoured.fr>
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
From jason.e.stewart at gmail.com Thu Sep 11 08:54:10 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Thu, 11 Sep 2008 14:24:10 +0530
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <48C7E28A.6020203@cnio.es>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com>
<48C7E28A.6020203@cnio.es>
Message-ID: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
Hi Jose Maria,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> $server->serializer(WSRF::Serializer->new);
This code dies with a class not found error from Perl, I presume you
mean WSRF::WSRFSerializer->new?
Cheers, jas.
From edward.kawas at gmail.com Thu Sep 11 13:11:07 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 06:11:07 -0700
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es>
<41c1ade50809102114h1a474e68j4bdfd262d27c5269@mail.gmail.com>
Message-ID: <48c918f9.27b38c0a.385f.ffffdcea@mx.google.com>
Hi Jason,
I like your thinking. I don?t have much experience with doc/lit services,
but I do feel that the additions that you have mentioned would probably be
best (and similar to what we have now for rpc/encoded).
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 Jason Stewart
Sent: September-10-08 9:15 PM
To: Core developer announcements
Subject: Re: [MOBY-dev] More info on SOAP::Lite document/literal
Hey Jose,
On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
wrote:
> when we were developing the Perl MOBY::Async libraries we had the
> same problem (we needed to access to the full input message), and we
solved
> it using custom deserializers fom WSRF::Lite package.
Thanks, that's useful for MOBY users, definately.
I still think that it should be a functionality that is built into the
core of SOAP::Lite, though, especially since document/literal is the
standard encoding now. I will get a response from Martin, the current
maintainer of SOAP::Lite, and see what he thinks should be done.
Likewise, on the client side it should be made trivial to attach a
fragment of XML as the body of the soap message without any
interference from SOAP::Lite.
Any comments?
Thanks, jas.
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From edward.kawas at gmail.com Thu Sep 11 13:15:49 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 06:15:49 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C8CC9A.7050808@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
<48C8CC9A.7050808@pingoured.fr>
Message-ID: <48c91a12.16538c0a.530a.ffffdd16@mx.google.com>
Yes, for some reason the file is not being generated properly. I am not sure
if this is a memory problem on the server or ...???
I noticed that yesterday, the RDF file is generated once properly and then
truncated the following times.
Hopefully I get this fixed soon,
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-11-08 12:46 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in
the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From jerzyo at genesilico.pl Thu Sep 11 14:22:09 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 11 Sep 2008 16:22:09 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
Message-ID: <48C92991.2000407@genesilico.pl>
Hi
I have several hundreds of workflows made up of BioMoby Services and
want to execute them all without opening any GUI.
I was looking for some solution over the internet and the think I came
across was using Taverna plugin and try to execute it programaticaly.
I have a few questions:
1. Is it the only way?
2. I found several tutorial tutorials on running saved workflow saved
in scufl language.
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
How do you one make a workflow step by step? like:
workflow.addProcesor(...)
workflow.addConnector(...)
...
workflow.execute()
and especially, how do one add BioMoby objects this way? Is there any
tutorial or do I have go though the API?
Best
Jerzy Orlowski
From edward.kawas at gmail.com Thu Sep 11 14:36:02 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 11 Sep 2008 07:36:02 -0700
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92991.2000407@genesilico.pl>
References: <48C92991.2000407@genesilico.pl>
Message-ID: <48c92ce0.28d7720a.65e4.0366@mx.google.com>
Hi Jerzy,
You can execute workflows from the command line too if you have your input
file for the workflows handy.
If you want to create workflows programmatically, you will need to look at
the javadoc for the taverna source code.
You should probably explore the taverna website[1] and its manual[2] for
more information.
Eddie
[1] http://taverna.sourceforge.net/
[2] http://taverna.sourceforge.net/doc
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: September-11-08 7:22 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] Executing Moby Workflow straight from java
Hi
I have several hundreds of workflows made up of BioMoby Services and
want to execute them all without opening any GUI.
I was looking for some solution over the internet and the think I came
across was using Taverna plugin and try to execute it programaticaly.
I have a few questions:
1. Is it the only way?
2. I found several tutorial tutorials on running saved workflow saved
in scufl language.
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
How do you one make a workflow step by step? like:
workflow.addProcesor(...)
workflow.addConnector(...)
...
workflow.execute()
and especially, how do one add BioMoby objects this way? Is there any
tutorial or do I have go though the API?
Best
Jerzy Orlowski
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From jmfernandez at cnio.es Thu Sep 11 14:49:25 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Thu, 11 Sep 2008 16:49:25 +0200
Subject: [MOBY-dev] More info on SOAP::Lite document/literal
In-Reply-To: <41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
References: <41c1ade50809100728q59f6722el57ed70d7cfd367be@mail.gmail.com> <48C7E28A.6020203@cnio.es>
<41c1ade50809110154sae5277ao23571a7203f7d3f9@mail.gmail.com>
Message-ID: <48C92FF5.5040405@cnio.es>
Hi Jason,
yes, you are right, it should be WSRF::WSRFSerializer. We have some pending
janitorial work on MOBY::Async, related to our usage of some namespace classes
which we do not own (WSRF::Serializer is one of those cases).
Best Regards,
Jos? Mar?a
Jason Stewart wrote:
> Hi Jose Maria,
>
> On Wed, Sep 10, 2008 at 8:36 PM, Jos? Mar?a Fern?ndez Gonz?lez
> wrote:
>
>> $server->serializer(WSRF::Serializer->new);
>
> This code dies with a class not found error from Perl, I presume you
> mean WSRF::WSRFSerializer->new?
>
> Cheers, jas.
>
> _______________________________________________
> 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)
**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
From serr at ac.uma.es Thu Sep 11 14:38:49 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Thu, 11 Sep 2008 16:38:49 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92991.2000407@genesilico.pl>
References: <48C92991.2000407@genesilico.pl>
Message-ID: <48C92D79.9010706@ac.uma.es>
Hello Jerzy
I had the same problem that you.
I have got it to work by browsing deep in the Taverna code. I cannot
give you many sample code because I'm trying to organize all the code
tries and examples that I have.
But I can give you some comments:
For build a workflow model the class is:
org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new
ScuflModel();
This class contains the methods that you mention addProcessor ...
For run I'm using freeflow, because taverna classes and raven are a
"little" tricky. The classes:
uk.ac.soton.itinnovation.freefluo.main.Engine or
org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
can help you.
I hope this little details help you to begin. If you have more detailed
questions I will be very happy of help you.
Best regards,
Sergio
Jerzy Orlowski wrote:
> Hi
>
> I have several hundreds of workflows made up of BioMoby Services and
> want to execute them all without opening any GUI.
>
> I was looking for some solution over the internet and the think I came
> across was using Taverna plugin and try to execute it programaticaly.
> I have a few questions:
>
> 1. Is it the only way?
>
> 2. I found several tutorial tutorials on running saved workflow saved
> in scufl language.
> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>
> How do you one make a workflow step by step? like:
>
> workflow.addProcesor(...)
> workflow.addConnector(...)
> ...
> workflow.execute()
>
> and especially, how do one add BioMoby objects this way? Is there any
> tutorial or do I have go though the API?
>
> Best
>
> Jerzy Orlowski
>
> _______________________________________________
> 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 gordonp at ucalgary.ca Thu Sep 11 15:10:13 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 11 Sep 2008 09:10:13 -0600
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C92D79.9010706@ac.uma.es>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
Message-ID: <48C934D5.50700@ucalgary.ca>
I think whoever has a headless Taverna workflow creation and/or
enactment working should put examples up in the Java developer's section
of the Moby Web site...I believe the myExperiment people also have a
headless workflow enactment engine working now...anyone from there on
this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in
the BioWEP software. So many people are doing this, but no good sample
code is easily available, especially for Moby services...
Sergio Ramirez Ramirez wrote:
> Hello Jerzy
>
> I had the same problem that you.
>
> I have got it to work by browsing deep in the Taverna code. I cannot
> give you many sample code because I'm trying to organize all the code
> tries and examples that I have.
>
> But I can give you some comments:
>
> For build a workflow model the class is:
> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model = new
> ScuflModel();
> This class contains the methods that you mention addProcessor ...
>
> For run I'm using freeflow, because taverna classes and raven are a
> "little" tricky. The classes:
> uk.ac.soton.itinnovation.freefluo.main.Engine or
> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
> can help you.
>
> I hope this little details help you to begin. If you have more
> detailed questions I will be very happy of help you.
>
> Best regards,
> Sergio
>
> Jerzy Orlowski wrote:
>> Hi
>>
>> I have several hundreds of workflows made up of BioMoby Services and
>> want to execute them all without opening any GUI.
>>
>> I was looking for some solution over the internet and the think I
>> came across was using Taverna plugin and try to execute it
>> programaticaly.
>> I have a few questions:
>>
>> 1. Is it the only way?
>>
>> 2. I found several tutorial tutorials on running saved workflow
>> saved in scufl language.
>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>
>>
>> How do you one make a workflow step by step? like:
>>
>> workflow.addProcesor(...)
>> workflow.addConnector(...)
>> ...
>> workflow.execute()
>>
>> and especially, how do one add BioMoby objects this way? Is there any
>> tutorial or do I have go though the API?
>>
>> Best
>>
>> Jerzy Orlowski
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>
>
From serr at ac.uma.es Thu Sep 11 15:23:30 2008
From: serr at ac.uma.es (Sergio Ramirez Ramirez)
Date: Thu, 11 Sep 2008 17:23:30 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C934D5.50700@ucalgary.ca>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca>
Message-ID: <48C937F2.3030708@ac.uma.es>
Here there is my small contribution, just the two methods that I use for
run a workflow.
Hope it can help to someone
Paul Gordon wrote:
> I think whoever has a headless Taverna workflow creation and/or
> enactment working should put examples up in the Java developer's
> section of the Moby Web site...I believe the myExperiment people also
> have a headless workflow enactment engine working now...anyone from
> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
> enactor in the BioWEP software. So many people are doing this, but no
> good sample code is easily available, especially for Moby services...
>
> Sergio Ramirez Ramirez wrote:
>> Hello Jerzy
>>
>> I had the same problem that you.
>>
>> I have got it to work by browsing deep in the Taverna code. I cannot
>> give you many sample code because I'm trying to organize all the code
>> tries and examples that I have.
>>
>> But I can give you some comments:
>>
>> For build a workflow model the class is:
>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>> new ScuflModel();
>> This class contains the methods that you mention addProcessor ...
>>
>> For run I'm using freeflow, because taverna classes and raven are a
>> "little" tricky. The classes:
>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>> can help you.
>>
>> I hope this little details help you to begin. If you have more
>> detailed questions I will be very happy of help you.
>>
>> Best regards,
>> Sergio
>>
>> Jerzy Orlowski wrote:
>>> Hi
>>>
>>> I have several hundreds of workflows made up of BioMoby Services and
>>> want to execute them all without opening any GUI.
>>>
>>> I was looking for some solution over the internet and the think I
>>> came across was using Taverna plugin and try to execute it
>>> programaticaly.
>>> I have a few questions:
>>>
>>> 1. Is it the only way?
>>>
>>> 2. I found several tutorial tutorials on running saved workflow
>>> saved in scufl language.
>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>
>>>
>>> How do you one make a workflow step by step? like:
>>>
>>> workflow.addProcesor(...)
>>> workflow.addConnector(...)
>>> ...
>>> workflow.execute()
>>>
>>> and especially, how do one add BioMoby objects this way? Is there
>>> any tutorial or do I have go though the API?
>>>
>>> Best
>>>
>>> Jerzy Orlowski
>>>
>>> _______________________________________________
>>> 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
>
--
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
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From jmfernandez at cnio.es Thu Sep 11 15:49:29 2008
From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Thu, 11 Sep 2008 17:49:29 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C937F2.3030708@ac.uma.es>
References: <48C92991.2000407@genesilico.pl>
<48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca>
<48C937F2.3030708@ac.uma.es>
Message-ID: <48C93E09.3030107@cnio.es>
Hi everybody,
as Sergio *should* know, we have at INB IWWE&M, which means 'Interactive Web
Workflow Enactor and Manager'. It is able to host workflows, workflow examples
with documentation, do web workflow enactions, and take and store workflow
enaction snapshots.
Next days we are going to have a Trac server with is going to host the source
code and development of IWWE&M.
Best Regards,
Jos? Mar?a
Sergio Ramirez Ramirez wrote:
> Here there is my small contribution, just the two methods that I use for
> run a workflow.
> Hope it can help to someone
>
> Paul Gordon wrote:
>> I think whoever has a headless Taverna workflow creation and/or
>> enactment working should put examples up in the Java developer's
>> section of the Moby Web site...I believe the myExperiment people also
>> have a headless workflow enactment engine working now...anyone from
>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>> enactor in the BioWEP software. So many people are doing this, but no
>> good sample code is easily available, especially for Moby services...
>>
>> Sergio Ramirez Ramirez wrote:
>>> Hello Jerzy
>>>
>>> I had the same problem that you.
>>>
>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>> give you many sample code because I'm trying to organize all the code
>>> tries and examples that I have.
>>>
>>> But I can give you some comments:
>>>
>>> For build a workflow model the class is:
>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>> new ScuflModel();
>>> This class contains the methods that you mention addProcessor ...
>>>
>>> For run I'm using freeflow, because taverna classes and raven are a
>>> "little" tricky. The classes:
>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>> can help you.
>>>
>>> I hope this little details help you to begin. If you have more
>>> detailed questions I will be very happy of help you.
>>>
>>> Best regards,
>>> Sergio
>>>
>>> Jerzy Orlowski wrote:
>>>> Hi
>>>>
>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>> want to execute them all without opening any GUI.
>>>>
>>>> I was looking for some solution over the internet and the think I
>>>> came across was using Taverna plugin and try to execute it
>>>> programaticaly.
>>>> I have a few questions:
>>>>
>>>> 1. Is it the only way?
>>>>
>>>> 2. I found several tutorial tutorials on running saved workflow
>>>> saved in scufl language.
>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>
>>>>
>>>> How do you one make a workflow step by step? like:
>>>>
>>>> workflow.addProcesor(...)
>>>> workflow.addConnector(...)
>>>> ...
>>>> workflow.execute()
>>>>
>>>> and especially, how do one add BioMoby objects this way? Is there
>>>> any tutorial or do I have go though the API?
>>>>
>>>> Best
>>>>
>>>> Jerzy Orlowski
>>>>
>>>> _______________________________________________
>>>> 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
--
"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)
**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
From alanrw at cs.man.ac.uk Thu Sep 11 15:25:18 2008
From: alanrw at cs.man.ac.uk (Alan Williams)
Date: Thu, 11 Sep 2008 16:25:18 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C934D5.50700@ucalgary.ca>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca>
Message-ID: <48C9385E.8060209@cs.man.ac.uk>
Paul Gordon wrote:
> I think whoever has a headless Taverna workflow creation and/or
> enactment working should put examples up in the Java developer's section
> of the Moby Web site...I believe the myExperiment people also have a
> headless workflow enactment engine working now...anyone from there on
> this list? Also, Paolo Romano in Italy has a headless SCUFL enactor in
> the BioWEP software. So many people are doing this, but no good sample
> code is easily available, especially for Moby services...
If by headless you mean without the UI, then there is a WorkflowLauncher
that enacts a Taverna workflow. The source code (written by the myGrid
team) can be downloaded from
http://prdownloads.sourceforge.net/taverna/workflowlauncher-0.1.2.zip?download
It may not what you need as it reads in a pre-existing Taverna
workflow - it does not create one programmatically.
You can also execute a Taverna workflow on a remote machine see
myExperiment can run the workflow you are looking at on a Taverna remote
execution engine. (You will, of course, need to have the right
authorization to get at a given remote enactor.)
I'm rather confused as to what people are trying to do. Could someone
give a use case? I'll probably have to get Katy Wolstencroft to explain
the biology for me :-)
Alan R Williams (currently the support hat wearer for Taverna)
From jason at bioteam.net Fri Sep 12 01:54:46 2008
From: jason at bioteam.net (jason)
Date: Fri, 12 Sep 2008 09:54:46 +0800
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48c7c7b5.26bc720a.7554.72fd@mx.google.com>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr>
<48c7c7b5.26bc720a.7554.72fd@mx.google.com>
Message-ID: <48C9CBE6.7010808@bioteam.net>
Hi, all
Edward Kawas wrote:
> Hi,
>
> I am trying to reproduce your problems, but I cannot. I am not seeing any
> SOAP exceptions and I don't see your service either.
>
> The last time I saw the Invalid byte 2 of 3-byte UTF-8 sequence was when I
> tried to use non utf8 characters in my soap message.
>
Part of the Moby code use String manipulation to parse and generate Xml
message instead of using a standard of XML parsing/writing.
The invalid byte could be related to this. I saw this error in another
project. Xml message generated by String concatenation could cause many
unexpected XML parsing error.
> Eddie
>
>
>
From soiland-reyes at cs.manchester.ac.uk Fri Sep 12 08:46:03 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Fri, 12 Sep 2008 09:46:03 +0100
Subject: [MOBY-dev] jmoby class for workflow. Does it exist?
In-Reply-To: <48BBBFAD.7060401@ac.uma.es>
References: <48BBBD89.6020803@genesilico.pl> <48BBBFAD.7060401@ac.uma.es>
Message-ID:
On Mon, Sep 1, 2008 at 11:10, Sergio Ramirez Ramirez wrote:
> Unfortunately, moby can not handle workflows by itself for now. Normally you
> use taverna for building workflows.
> I'm trying to learn how to use Taverna libraries to run workflows. There is
> a taverna class (workflowlauncher or similar) available in the web page for
> taverna, but I couldn't make it work.
Hi, also check out
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram.html
If you can't make it work - do please send us an email about what kind
of error message you get or what doesn't work - so we can improve it.
Note that if you run this within a container like Tomcat (instead of
standalone, which should work) you might run into issues recently
uncovered, there's a workaround described here:
http://markmail.org/search/?q=taverna-hackers+globus#query:taverna-hackers%20globus+page:1+mid:leq2tlx3adyekssq+state:results
I recommend signing up to the taverna-hackers mailing list for any
further questions and issues you might run into - we're happy to help!
http://taverna.sourceforge.net/lists
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From edward.kawas at gmail.com Fri Sep 12 13:41:51 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 12 Sep 2008 06:41:51 -0700
Subject: [MOBY-dev] Problem with dashboard to list services
In-Reply-To: <48C8CC9A.7050808@pingoured.fr>
References: <48C7B95E.4080903@avignon.inra.fr> <48C7C24F.3050709@pingoured.fr> <48c7c7b5.26bc720a.7554.72fd@mx.google.com> <48C7CC35.6090803@pingoured.fr> <48c7ccb5.1a36720a.780d.7ea7@mx.google.com>
<48C8CC9A.7050808@pingoured.fr>
Message-ID: <48ca71b0.2a528c0a.282c.ffffba33@mx.google.com>
Hi All,
The problem now should be all fixed. I recently created a patch to avoid
this non utf8 mess and deployed it on the test registry; moreover, the RDF
shouldn't cause problems with Dashboard.
Let me know how things work out,
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon
Sent: September-11-08 12:46 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Problem with dashboard to list services
Edward Kawas wrote:
> I also forgot to mention that I also tried looking for your services in
the
> database that backs the registry and failed to find it!
>
Few minutes after this email and after a couple of trials we have been
able to see our services again. What we observed is:
- avilin05.avignon.inra.fr appears in the second position in the /moses
generator/ panel while it was easily at the fourth or fifth position before.
- the list of services starting by the letter 's' (or S) seems to have
decrease dramatically now compare to earlier.
- when we try to reload or update our cache, or when we regenerate it
after removal when ends with the following error:
"rethrew: org.xml.sax.SAXParseException: XML document structures must
start and end within the same entity."
In the console I got the following error:
dashboard:
[Dashboard] 82708 [Thread-6] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 84375 [Thread-14] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 89602 [Thread-16] ERROR RDFDefaultErrorHandler - (line 46041
column 103): XML document structures must start and end within the same
entity.
[Dashboard] 100071 [Thread-15] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] 102828 [Thread-17] ERROR RDFDefaultErrorHandler - (line
46041 column 103): XML document structures must start and end within the
same entity.
[Dashboard] [Fatal Error] :-1:-1: Premature end of file.
It does not stop us from work so that's more for the report.
To us it would seems like something has gone wrong yesterday on the
server and a file has been corrupted ?
Thanks for your help,
Best regards,
Pierre
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From edward.kawas at gmail.com Thu Sep 18 17:08:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 18 Sep 2008 10:08:21 -0700
Subject: [MOBY-dev] FWD: Making SOAP::Lite painlessly support
document-literal encoding
In-Reply-To: <146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry>
References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com><48d26bbb.27b38c0a.32a5.ffff9576@mx.google.com>
<146344067-1221756917-cardhu_decombobulator_blackberry.rim.net-863784495-@bxe175.bisx.prod.on.blackberry>
Message-ID: <48d28b06.1cbd720a.50af.ffff83bc@mx.google.com>
Just to keep everyone on the list in the know ...
Eddie
--------------------
From: "Ed Kawas"
Date: Thu, 18 Sep 2008 07:54:49
To: 'Jason Stewart'; 'Mark';
'Martin Kutter';
Subject: RE: Making SOAP::Lite painlessly support document-literal encoding
Hi Jason,
I like the fact that you hand off the XML document to the server service
developer. Also the ability of the client to just attach a document looks
good too. I wonder how other toolkits do it? I am pretty sure that if the
soap envelope was compatible with other toolkits and all I could do was
get/set the XML document, I would definitely start using S::L for doc/lit
services.
Eddie
-----Original Message-----
From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
Sent: September-18-08 1:40 AM
To: Mark; Martin Kutter; soaplite-devel at lists.sf.net; Ed Kawas
Subject: Making SOAP::Lite painlessly support document-literal encoding
Hey All,
So I've been doing a lot of digging through the codebase understanding
how doc/lit could be used at the moment, and I find that the ease of
use that S::L provides for rpc/enc is not matched in it's doc/lit
support. I don't think it would take very much effort to enable simple
support for doc/lit on both the client and the server - but very
likely there would be issues with compatibility with Java and .NET
implementations that would have to be worked out.
For me the major difference is that a client wanting to use a doc/lit
service wants to simply attach a pre-produced XML payload to the soap
message - and the server wants to retrieve that message - WITHOUT ANY
INTERFERENCE FROM SOAP::LIT.
so we have:
-- begin of client.pl 8< --
use SOAP::Lite;
my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
my $xml =<KutterMartinHello Martin Kutter!
XML
$soap->on_action( sub { "urn:HelloWorld#sayHello" });
$soap->autotype(0);
$soap->default_ns('urn:HelloWorld');
my $som = $soap->document($xml)->call("sayHello");
die $som->fault->{ faultstring } if ($som->fault);
print $som->result, "\n";
-- end of client.pl --
-- begin server.pl 8< --
package HelloWorld;
use SOAP::Lite;
use base qw(SOAP::Server::Document);
sub sayHello {
my $self = shift;
my $doc = shift;
my $som = shift;
my $ret_val = some_processing_method($doc);
return $ret_val;
}
-- end of server.pl --
The client builds an XML document inserts it into the request using
the document() method on the SOAP object.
The client subclasses from SOAP::Server::Document so it gets the XML
payload as the second argument on the stack, processes it somehow, and
returns an XML payload back to the client.
feedback?
Cheers, jas.
From jason.e.stewart at gmail.com Fri Sep 19 08:02:49 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 19 Sep 2008 13:32:49 +0530
Subject: [MOBY-dev] Making SOAP::Lite painlessly support
document-literal encoding
In-Reply-To: <1221760547.9975.19.camel@cyclops>
References: <41c1ade50809180140i3f21fff9wd4170730bb6f7ec@mail.gmail.com>
<1221760547.9975.19.camel@cyclops>
Message-ID: <41c1ade50809190102n16ee2f2fh94dd0da1d7dc9e@mail.gmail.com>
Hey All,
I like your suggestions Martin.
I think the namespace SOAP::Lite::Server::Document is definitely the way to go.
I support the idea of using a SOAP::Data object in addition to an XML
scalar as the value for either the client or the server.
I will make a patch and some test cases and send them to the list.
Cheers, jas.
On Thu, Sep 18, 2008 at 11:25 PM, Martin Kutter
wrote:
> Hi Jason,
>
> forcing the server developer to create XML may or may not be a good
> idea, depending on it's complexity.
>
> How about making the proposed SOAP::Server::Document a bit more DWIM by
> accepting either a scalar (which is supposed to be plain XML) or a
> SOAP::Data object?
>
> This would ease migration for existing web services which want to move
> to SOAP::Server::Document
>
> Maybe SOAP::Lite::Server::Document would be the more appropriate name -
> the use of the SOAP namespace has provoked numerous errors on CPAN, so
> SOAP::Lite is a better namespace for new modules.
>
> Thanks for your ideas,
>
> Martin
>
> Am Donnerstag, den 18.09.2008, 14:10 +0530 schrieb Jason Stewart:
>> Hey All,
>>
>> So I've been doing a lot of digging through the codebase understanding
>> how doc/lit could be used at the moment, and I find that the ease of
>> use that S::L provides for rpc/enc is not matched in it's doc/lit
>> support. I don't think it would take very much effort to enable simple
>> support for doc/lit on both the client and the server - but very
>> likely there would be issues with compatibility with Java and .NET
>> implementations that would have to be worked out.
>>
>> For me the major difference is that a client wanting to use a doc/lit
>> service wants to simply attach a pre-produced XML payload to the soap
>> message - and the server wants to retrieve that message - WITHOUT ANY
>> INTERFERENCE FROM SOAP::LIT.
>>
>> so we have:
>>
>> -- begin of client.pl 8< --
>>
>> use SOAP::Lite;
>> my $soap = SOAP::Lite->new( proxy => 'http://localhost:80/helloworld.pl');
>>
>> my $xml =<>
>> Kutter
>> Martin
>>
>>
>>
>> Hello Martin Kutter!
>>
>> XML
>>
>> $soap->on_action( sub { "urn:HelloWorld#sayHello" });
>> $soap->autotype(0);
>> $soap->default_ns('urn:HelloWorld');
>>
>> my $som = $soap->document($xml)->call("sayHello");
>>
>> die $som->fault->{ faultstring } if ($som->fault);
>> print $som->result, "\n";
>>
>> -- end of client.pl --
>>
>> -- begin server.pl 8< --
>>
>> package HelloWorld;
>> use SOAP::Lite;
>>
>> use base qw(SOAP::Server::Document);
>>
>> sub sayHello {
>> my $self = shift;
>> my $doc = shift;
>> my $som = shift;
>>
>> my $ret_val = some_processing_method($doc);
>> return $ret_val;
>> }
>>
>> -- end of server.pl --
>>
>> The client builds an XML document inserts it into the request using
>> the document() method on the SOAP object.
>>
>> The client subclasses from SOAP::Server::Document so it gets the XML
>> payload as the second argument on the stack, processes it somehow, and
>> returns an XML payload back to the client.
>>
>> feedback?
>>
>> Cheers, jas.
>>
>
>
From jason.e.stewart at gmail.com Fri Sep 19 09:29:46 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 19 Sep 2008 14:59:46 +0530
Subject: [MOBY-dev] moby doc-lit services.
In-Reply-To: <48D411EB.2080606@bsc.es>
References: <48D32B1C.3050304@bsc.es>
<41c1ade50809190044l124fcf63h52e728402f4a4de3@mail.gmail.com>
<48D411EB.2080606@bsc.es>
Message-ID: <41c1ade50809190229me6e597arb728754a03ab9eb7@mail.gmail.com>
Hey Dmitry,
I agree with your suggestion as to the "right" way to do it.
I am less concerned with the WSDL, from my current understanding of
MOBY (which is very weak I am afraid) the WSDL is almost useless,
MOBY-enabled clients will have to be aware of how to deserialize data
types that they handle using their own libraries or libraries bundled
with MOBY.
Originally I thought MOBY would rely heavily on XML Schemas to define
their data types, and that would be the core - but since that isn't
how things are done, I don't see much use in the WSDL. I'd like to
know if I am understanding this incorrectly.
Cheers, jas.
On Sat, Sep 20, 2008 at 2:26 AM, Dmitry Repchevsky
wrote:
> Hi Jason,
>
>> Mark has asked me to modify SOAP::Lite in order to better support doc/lit
>> services in general...
>
> This is a good news, because my concern was that you are going to do a sort
> of hack - make a common schema for all services,
> something like a "" and pass a Moby message inside...
>
> What I suggested to do (and this is the "right" way to do in java) is to
> pass all the MobyMessage inside a soap message:
> Something like:
>
>
>
>
>
>
>
>
>
> ns1:id=""
> ns1:namespace="">AGHFJHGDKHGJKADGHJGDJH
>
>
>
>
>
>
>
>
> This way there is no problem as it is a STANDARD Moby XML inside a SOAP
> .
>
> The problem is that you need to attach a XML Schema to your WSDL (if you
> wish a "real" web-service")
> Such a schema could be divided in two parts:
>
> 1. Static (common for all moby doc/lit services) that contains Moby specific
> schema (MobySimple, MobyContent....):
>
> ******************************************************************************************************************************
>
> version="1.0"
> targetNamespace="http://www.biomoby.org/moby"
>
> xmlns:xs="http://www.w3.org/2001/XMLSchema"
>
> xmlns="http://www.biomoby.org/moby" >
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> maxOccurs="unbounded"/>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ******************************************************************************************************************************
>
> 2. Moby Datatypes specific one - that one depends of the ontology types used
> by service...
> In extreme case you can put the same scheme representing ALL the ontology
> (not generate it for every service, but generate it once for the ontology
> and use for every service).
> You can even put an EXTERNAL reference to it (for example make a servlet
> that dynamically generates it from the ontology). This way it will be always
> updated.
>
> Cheers,
>
> Dmitry
>
>
>
>
> Jason Stewart wrote:
>>
>> Hi Dmitry,
>>
>> On Fri, Sep 19, 2008 at 10:01 AM, Dmitry Repchevsky
>> wrote:
>>
>>
>>>
>>> My name is Dmitry and I am a developer in Spanish National Institute of
>>> Bioinformatics.
>>> We just have finished an informal meeting with Mark Wilkinson and he
>>> suggested to contact you about moby document/literal services...
>>>
>>> I have my own implementation of it based on XML Schema and I would like
>>> to
>>> know the way you are implementing it.
>>>
>>
>> Mark has asked me to modify SOAP::Lite in order to better support
>> doc/lit services in general, not just for MOBY.
>>
>> I'd love to hear more about how you do things.
>>
>> Currently, I'm in discussion with the SOAP::Lite developer group how
>> to modify the core of S::L in order to better handle doc/lit.
>>
>> Cheers, jas.
>>
>>
>
>
From jerzyo at genesilico.pl Wed Sep 24 15:55:58 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Wed, 24 Sep 2008 17:55:58 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48C937F2.3030708@ac.uma.es>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
Message-ID: <48DA630E.6050901@genesilico.pl>
Hi
I am trying to use your code, but I get strange erros like:
The constructor EngineImpl(EngineConfiguration) is undefined
Perhaps I am working on different versions of the code (some from
taverna, some from ogasadai and some from freefluo).
Where can I find source code or javadoc for
uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
I cannot find in anywhere on the web....
Jerzy
Sergio Ramirez Ramirez wrote:
> Here there is my small contribution, just the two methods that I use for
> run a workflow.
> Hope it can help to someone
>
> Paul Gordon wrote:
>> I think whoever has a headless Taverna workflow creation and/or
>> enactment working should put examples up in the Java developer's
>> section of the Moby Web site...I believe the myExperiment people also
>> have a headless workflow enactment engine working now...anyone from
>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>> enactor in the BioWEP software. So many people are doing this, but no
>> good sample code is easily available, especially for Moby services...
>>
>> Sergio Ramirez Ramirez wrote:
>>> Hello Jerzy
>>>
>>> I had the same problem that you.
>>>
>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>> give you many sample code because I'm trying to organize all the code
>>> tries and examples that I have.
>>>
>>> But I can give you some comments:
>>>
>>> For build a workflow model the class is:
>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>> new ScuflModel();
>>> This class contains the methods that you mention addProcessor ...
>>>
>>> For run I'm using freeflow, because taverna classes and raven are a
>>> "little" tricky. The classes:
>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>> can help you.
>>>
>>> I hope this little details help you to begin. If you have more
>>> detailed questions I will be very happy of help you.
>>>
>>> Best regards,
>>> Sergio
>>>
>>> Jerzy Orlowski wrote:
>>>> Hi
>>>>
>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>> want to execute them all without opening any GUI.
>>>>
>>>> I was looking for some solution over the internet and the think I
>>>> came across was using Taverna plugin and try to execute it
>>>> programaticaly.
>>>> I have a few questions:
>>>>
>>>> 1. Is it the only way?
>>>>
>>>> 2. I found several tutorial tutorials on running saved workflow
>>>> saved in scufl language.
>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>
>>>>
>>>> How do you one make a workflow step by step? like:
>>>>
>>>> workflow.addProcesor(...)
>>>> workflow.addConnector(...)
>>>> ...
>>>> workflow.execute()
>>>>
>>>> and especially, how do one add BioMoby objects this way? Is there
>>>> any tutorial or do I have go though the API?
>>>>
>>>> Best
>>>>
>>>> Jerzy Orlowski
>>>>
>>>> _______________________________________________
>>>> 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 Sep 24 16:31:14 2008
From: groscurt at mpiz-koeln.mpg.de (groscurt)
Date: Wed, 24 Sep 2008 18:31:14 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA630E.6050901@genesilico.pl>
Message-ID:
Hi,
i would really encourage you to use the taverna mailing list for issues
concerning taverna. As some people here have strong experience with it, i
think its way better to ask the people working with it and developing it
directly.
Cheers
Andreas
----------------original message-----------------
From: "Jerzy Orlowski" jerzyo at genesilico.pl
To: moby-dev at lists.open-bio.org
Date: Wed, 24 Sep 2008 17:55:58 +0200
-------------------------------------------------
> Hi
>
> I am trying to use your code, but I get strange erros like:
>
> The constructor EngineImpl(EngineConfiguration) is undefined
>
> Perhaps I am working on different versions of the code (some from
> taverna, some from ogasadai and some from freefluo).
>
> Where can I find source code or javadoc for
> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
>
> I cannot find in anywhere on the web....
>
> Jerzy
>
>
> Sergio Ramirez Ramirez wrote:
>> Here there is my small contribution, just the two methods that I use for
>> run a workflow.
>> Hope it can help to someone
>>
>> Paul Gordon wrote:
>>> I think whoever has a headless Taverna workflow creation and/or
>>> enactment working should put examples up in the Java developer's
>>> section of the Moby Web site...I believe the myExperiment people also
>>> have a headless workflow enactment engine working now...anyone from
>>> there on this list? Also, Paolo Romano in Italy has a headless SCUFL
>>> enactor in the BioWEP software. So many people are doing this, but no
>>> good sample code is easily available, especially for Moby services...
>>>
>>> Sergio Ramirez Ramirez wrote:
>>>> Hello Jerzy
>>>>
>>>> I had the same problem that you.
>>>>
>>>> I have got it to work by browsing deep in the Taverna code. I cannot
>>>> give you many sample code because I'm trying to organize all the code
>>>> tries and examples that I have.
>>>>
>>>> But I can give you some comments:
>>>>
>>>> For build a workflow model the class is:
>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>>> new ScuflModel();
>>>> This class contains the methods that you mention addProcessor ...
>>>>
>>>> For run I'm using freeflow, because taverna classes and raven are a
>>>> "little" tricky. The classes:
>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>> can help you.
>>>>
>>>> I hope this little details help you to begin. If you have more
>>>> detailed questions I will be very happy of help you.
>>>>
>>>> Best regards,
>>>> Sergio
>>>>
>>>> Jerzy Orlowski wrote:
>>>>> Hi
>>>>>
>>>>> I have several hundreds of workflows made up of BioMoby Services and
>>>>> want to execute them all without opening any GUI.
>>>>>
>>>>> I was looking for some solution over the internet and the think I
>>>>> came across was using Taverna plugin and try to execute it
>>>>> programaticaly.
>>>>> I have a few questions:
>>>>>
>>>>> 1. Is it the only way?
>>>>>
>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>> saved in scufl language.
>>>>>
http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>
>>>>>
>>>>>
>>>>> How do you one make a workflow step by step? like:
>>>>>
>>>>> workflow.addProcesor(...)
>>>>> workflow.addConnector(...)
>>>>> ...
>>>>> workflow.execute()
>>>>>
>>>>> and especially, how do one add BioMoby objects this way? Is there
>>>>> any tutorial or do I have go though the API?
>>>>>
>>>>> Best
>>>>>
>>>>> Jerzy Orlowski
>>>>>
>>>>> _______________________________________________
>>>>> 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 soiland-reyes at cs.manchester.ac.uk Thu Sep 25 09:54:47 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Thu, 25 Sep 2008 10:54:47 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA630E.6050901@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl>
Message-ID:
On Wed, Sep 24, 2008 at 16:55, Jerzy Orlowski wrote:
I suggest as well to move the discussion to the taverna-hackers list (
http://taverna.sourceforge.net/lists )
> I am trying to use your code, but I get strange erros like:
>
> The constructor EngineImpl(EngineConfiguration) is undefined
>
> Perhaps I am working on different versions of the code (some from taverna,
> some from ogasadai and some from freefluo).
If you want to be sure to get it to work with Taverna 1.7.1, use
http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo/NO-VERSION/freefluo-NO-VERSION.jar
and http://www.mygrid.org.uk/maven/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1/freefluo-taverna-exts-1.7.1.jar
The other projects are likely to have code in either too new or too old version.
> Where can I find source code or javadoc for
> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other classes?
Note that this version of Freefluo was never released officially by
the Freefluo project, but it can be checked out from their CVS using a
date range.
Look at the thread of http://markmail.org/message/dnrqdicmbzbfjjl5 if
you really want to build Freefluo from source.
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From jerzyo at genesilico.pl Thu Sep 25 10:22:02 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Thu, 25 Sep 2008 12:22:02 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DA6624.7040806@uma.es>
References: <48C92991.2000407@genesilico.pl>
<48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca>
<48C937F2.3030708@ac.uma.es> <48DA630E.6050901@genesilico.pl>
<48DA6624.7040806@uma.es>
Message-ID: <48DB664A.6030305@genesilico.pl>
I keep trying, but I cannot find anywhere a jar with
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
I have an impression that freefluo is outdated
----------------------------------------------------------------------
uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error
with configuration named tavernaClassNotFound for WorkflowParser
implementation:
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108)
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64)
at org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84)
at org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11)
Caused by: java.lang.ClassNotFoundException:
uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
at
uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102)
... 3 more
------------------------------------------------------------------------
Jerzyo
Sergio Ramirez Ramirez wrote:
> Hi Jerzy
>
> I see you cannot got to resolve the problem.
>
> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel;
>
> Maybe is what you need. to built your own workflow.
>
> Keep me informed ;) and good luck.
>
> Jerzy Orlowski wrote:
>> Hi
>>
>> I am trying to use your code, but I get strange erros like:
>>
>> The constructor EngineImpl(EngineConfiguration) is undefined
>>
>> Perhaps I am working on different versions of the code (some from
>> taverna, some from ogasadai and some from freefluo).
>>
>> Where can I find source code or javadoc for
>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other
>> classes?
>>
>> I cannot find in anywhere on the web....
>>
>> Jerzy
>>
>>
>> Sergio Ramirez Ramirez wrote:
>>> Here there is my small contribution, just the two methods that I use
>>> for run a workflow.
>>> Hope it can help to someone
>>>
>>> Paul Gordon wrote:
>>>> I think whoever has a headless Taverna workflow creation and/or
>>>> enactment working should put examples up in the Java developer's
>>>> section of the Moby Web site...I believe the myExperiment people
>>>> also have a headless workflow enactment engine working now...anyone
>>>> from there on this list? Also, Paolo Romano in Italy has a headless
>>>> SCUFL enactor in the BioWEP software. So many people are doing this,
>>>> but no good sample code is easily available, especially for Moby
>>>> services...
>>>>
>>>> Sergio Ramirez Ramirez wrote:
>>>>> Hello Jerzy
>>>>>
>>>>> I had the same problem that you.
>>>>>
>>>>> I have got it to work by browsing deep in the Taverna code. I
>>>>> cannot give you many sample code because I'm trying to organize all
>>>>> the code tries and examples that I have.
>>>>>
>>>>> But I can give you some comments:
>>>>>
>>>>> For build a workflow model the class is:
>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model =
>>>>> new ScuflModel();
>>>>> This class contains the methods that you mention addProcessor ...
>>>>>
>>>>> For run I'm using freeflow, because taverna classes and raven are a
>>>>> "little" tricky. The classes:
>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>>> can help you.
>>>>>
>>>>> I hope this little details help you to begin. If you have more
>>>>> detailed questions I will be very happy of help you.
>>>>>
>>>>> Best regards,
>>>>> Sergio
>>>>>
>>>>> Jerzy Orlowski wrote:
>>>>>> Hi
>>>>>>
>>>>>> I have several hundreds of workflows made up of BioMoby Services
>>>>>> and want to execute them all without opening any GUI.
>>>>>>
>>>>>> I was looking for some solution over the internet and the think I
>>>>>> came across was using Taverna plugin and try to execute it
>>>>>> programaticaly.
>>>>>> I have a few questions:
>>>>>>
>>>>>> 1. Is it the only way?
>>>>>>
>>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>>> saved in scufl language.
>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>>
>>>>>>
>>>>>> How do you one make a workflow step by step? like:
>>>>>>
>>>>>> workflow.addProcesor(...)
>>>>>> workflow.addConnector(...)
>>>>>> ...
>>>>>> workflow.execute()
>>>>>>
>>>>>> and especially, how do one add BioMoby objects this way? Is there
>>>>>> any tutorial or do I have go though the API?
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Jerzy Orlowski
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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 jerzyo at genesilico.pl Fri Sep 26 08:28:48 2008
From: jerzyo at genesilico.pl (Jerzy Orlowski)
Date: Fri, 26 Sep 2008 10:28:48 +0200
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
Message-ID: <48DC9D40.5030604@genesilico.pl>
Hi
I think there is one important option missing in BioMoby plugins in Taverna.
Suppose I have a MobyService that returns an AminoAcidSequence. I want
to extract the sequence on my AminAcidSequence (it is a String object)
and use it as input for another MobyServices that eats String as its input.
The only way I can do it now is to use a Parser which decomposes
AminoAcidSequence to basic types and then construct my String from these
basic elements
(namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns,aminoacid_'SequenceString',aminoacid_'SequenceString'_id
and aminoacid_'SequenceString'_ns).
This is not very difficult in this case, but imagine what would happen
if I parse an object which is composed of for example
WieghtedAminoSequences and try to get AminoAcidSequence out of it...
In fact current BioMobyObjectProcessors are processors for constructing
MobyObjects (with basic types as input ports and composite types as
output ports). There should be another type of
BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects
(with composite types as input ports and basic types as output ports).
Please inform me if such option already exists somewhere and I missed it.
Jerzy Orlowski
From edward.kawas at gmail.com Fri Sep 26 12:16:20 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 26 Sep 2008 05:16:20 -0700
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
In-Reply-To: <48DC9D40.5030604@genesilico.pl>
References: <48DC9D40.5030604@genesilico.pl>
Message-ID: <48dcd299.1bbc720a.76c6.ffffb9d8@mx.google.com>
Hi Jerzy,
That option is indeed unavailable. It can be something that we add in the
future.
Eddie
-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jerzy Orlowski
Sent: September-26-08 1:29 AM
To: moby-dev at lists.open-bio.org
Subject: [MOBY-dev] decomposition of BioMoby Objects in Taverna
Hi
I think there is one important option missing in BioMoby plugins in Taverna.
Suppose I have a MobyService that returns an AminoAcidSequence. I want
to extract the sequence on my AminAcidSequence (it is a String object)
and use it as input for another MobyServices that eats String as its input.
The only way I can do it now is to use a Parser which decomposes
AminoAcidSequence to basic types and then construct my String from these
basic elements
(namespace,id,aminoacid_'Length',aminoacid_'Length'_id,aminoacid_'Length'_ns
,aminoacid_'SequenceString',aminoacid_'SequenceString'_id
and aminoacid_'SequenceString'_ns).
This is not very difficult in this case, but imagine what would happen
if I parse an object which is composed of for example
WieghtedAminoSequences and try to get AminoAcidSequence out of it...
In fact current BioMobyObjectProcessors are processors for constructing
MobyObjects (with basic types as input ports and composite types as
output ports). There should be another type of
BioMobyObjectDeconstructingProcessors for deconstructing MobyObjects
(with composite types as input ports and basic types as output ports).
Please inform me if such option already exists somewhere and I missed it.
Jerzy Orlowski
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev
From soiland-reyes at cs.manchester.ac.uk Fri Sep 26 13:39:14 2008
From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes)
Date: Fri, 26 Sep 2008 14:39:14 +0100
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DB664A.6030305@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es>
<48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es>
<48DB664A.6030305@genesilico.pl>
Message-ID:
On Thu, Sep 25, 2008 at 11:22, Jerzy Orlowski wrote:
> I keep trying, but I cannot find anywhere a jar with
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
: stain at mira ~/.m2/repository/uk/org/mygrid/resources/freefluo-taverna-exts/1.7.1;unzip
-t freefluo-taverna-exts-1.7.1.jar
Archive: freefluo-taverna-exts-1.7.1.jar
testing: META-INF/ OK
testing: META-INF/MANIFEST.MF OK
testing: uk/ OK
testing: uk/ac/ OK
testing: uk/ac/soton/ OK
testing: uk/ac/soton/itinnovation/ OK
testing: uk/ac/soton/itinnovation/freefluo/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/ OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaDataHandler.class
OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaScuflModelParser.class
OK
testing: uk/ac/soton/itinnovation/freefluo/exts/taverna/TavernaWorkflowInstance.class
OK
No errors detected in compressed data of freefluo-taverna-exts-1.7.1.jar.
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
From srramirez at uma.es Thu Sep 25 10:29:18 2008
From: srramirez at uma.es (Sergio Ramirez Ramirez)
Date: Thu, 25 Sep 2008 12:29:18 +0200
Subject: [MOBY-dev] Executing Moby Workflow straight from java
In-Reply-To: <48DB664A.6030305@genesilico.pl>
References: <48C92991.2000407@genesilico.pl> <48C92D79.9010706@ac.uma.es> <48C934D5.50700@ucalgary.ca> <48C937F2.3030708@ac.uma.es>
<48DA630E.6050901@genesilico.pl> <48DA6624.7040806@uma.es>
<48DB664A.6030305@genesilico.pl>
Message-ID: <48DB67FE.4000507@uma.es>
Yes, you are right but taverna still using it in the core.
If you download the entire src of taverna you will find a jar file:
taverna-workbench with that class
If you couldn't find it, just tell me and I will sent it to you
Best regards, Sergio
Jerzy Orlowski wrote:
> I keep trying, but I cannot find anywhere a jar with
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
>
> I have an impression that freefluo is outdated
>
> ----------------------------------------------------------------------
> uk.ac.soton.itinnovation.freefluo.conf.ConfigurationException: Error
> with configuration named tavernaClassNotFound for WorkflowParser
> implementation:
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:108)
>
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.(EngineConfigurationImpl.java:64)
>
> at
> org.genesilico.freeflow.FreeflowRunner.newEngine(FreeflowRunner.java:84)
> at
> org.genesilico.freeflow.FreeflowTester.main(FreeflowTester.java:11)
> Caused by: java.lang.ClassNotFoundException:
> uk.ac.soton.itinnovation.freefluo.exts.taverna.TavernaScuflModelParser
> at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> at
> uk.ac.soton.itinnovation.freefluo.conf.EngineConfigurationImpl.init(EngineConfigurationImpl.java:102)
>
> ... 3 more
> ------------------------------------------------------------------------
>
> Jerzyo
>
>
>
> Sergio Ramirez Ramirez wrote:
>> Hi Jerzy
>>
>> I see you cannot got to resolve the problem.
>>
>> Try to use this class: org.embl.ebi.escience.scufl.ScuflModel;
>>
>> Maybe is what you need. to built your own workflow.
>>
>> Keep me informed ;) and good luck.
>>
>> Jerzy Orlowski wrote:
>>> Hi
>>>
>>> I am trying to use your code, but I get strange erros like:
>>>
>>> The constructor EngineImpl(EngineConfiguration) is undefined
>>>
>>> Perhaps I am working on different versions of the code (some from
>>> taverna, some from ogasadai and some from freefluo).
>>>
>>> Where can I find source code or javadoc for
>>> uk/ac/soton/itinnovation/freefluo/main/EngineImpl.class and other
>>> classes?
>>>
>>> I cannot find in anywhere on the web....
>>>
>>> Jerzy
>>>
>>>
>>> Sergio Ramirez Ramirez wrote:
>>>> Here there is my small contribution, just the two methods that I
>>>> use for run a workflow.
>>>> Hope it can help to someone
>>>>
>>>> Paul Gordon wrote:
>>>>> I think whoever has a headless Taverna workflow creation and/or
>>>>> enactment working should put examples up in the Java developer's
>>>>> section of the Moby Web site...I believe the myExperiment people
>>>>> also have a headless workflow enactment engine working
>>>>> now...anyone from there on this list? Also, Paolo Romano in Italy
>>>>> has a headless SCUFL enactor in the BioWEP software. So many
>>>>> people are doing this, but no good sample code is easily
>>>>> available, especially for Moby services...
>>>>>
>>>>> Sergio Ramirez Ramirez wrote:
>>>>>> Hello Jerzy
>>>>>>
>>>>>> I had the same problem that you.
>>>>>>
>>>>>> I have got it to work by browsing deep in the Taverna code. I
>>>>>> cannot give you many sample code because I'm trying to organize
>>>>>> all the code tries and examples that I have.
>>>>>>
>>>>>> But I can give you some comments:
>>>>>>
>>>>>> For build a workflow model the class is:
>>>>>> org.embl.ebi.escience.scufl.ScuflModel, just do ScuflModel model
>>>>>> = new ScuflModel();
>>>>>> This class contains the methods that you mention addProcessor ...
>>>>>>
>>>>>> For run I'm using freeflow, because taverna classes and raven are
>>>>>> a "little" tricky. The classes:
>>>>>> uk.ac.soton.itinnovation.freefluo.main.Engine or
>>>>>> org.embl.ebi.escience.scufl.enactor.implementation.FreefluoEnactorProxy
>>>>>> can help you.
>>>>>>
>>>>>> I hope this little details help you to begin. If you have more
>>>>>> detailed questions I will be very happy of help you.
>>>>>>
>>>>>> Best regards,
>>>>>> Sergio
>>>>>>
>>>>>> Jerzy Orlowski wrote:
>>>>>>> Hi
>>>>>>>
>>>>>>> I have several hundreds of workflows made up of BioMoby Services
>>>>>>> and want to execute them all without opening any GUI.
>>>>>>>
>>>>>>> I was looking for some solution over the internet and the think
>>>>>>> I came across was using Taverna plugin and try to execute it
>>>>>>> programaticaly.
>>>>>>> I have a few questions:
>>>>>>>
>>>>>>> 1. Is it the only way?
>>>>>>>
>>>>>>> 2. I found several tutorial tutorials on running saved workflow
>>>>>>> saved in scufl language.
>>>>>>> http://www.mygrid.org.uk/usermanual1.7/executeworkflowprogram_source.html
>>>>>>>
>>>>>>>
>>>>>>> How do you one make a workflow step by step? like:
>>>>>>>
>>>>>>> workflow.addProcesor(...)
>>>>>>> workflow.addConnector(...)
>>>>>>> ...
>>>>>>> workflow.execute()
>>>>>>>
>>>>>>> and especially, how do one add BioMoby objects this way? Is
>>>>>>> there any tutorial or do I have go though the API?
>>>>>>>
>>>>>>> Best
>>>>>>>
>>>>>>> Jerzy Orlowski
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> MOBY-dev mailing list
>>>>>>> MOBY-dev at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>
>>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
--
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