From markw at illuminae.com  Fri Jun  1 12:23:01 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 01 Jun 2007 09:23:01 -0700
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <E7E914B8-1377-43B5-9CBF-70BBF36085A1@wur.nl>
References: <C781839E63F2A140A7928F015DBBA650024410FC@HERMES>
	<op.ts68cqnfnbznux@personalpc>
	<E7E914B8-1377-43B5-9CBF-70BBF36085A1@wur.nl>
Message-ID: <op.ts83snz3nbznux@personalpc>

Ah!  Yes, that's likely the cause.

We had problems last week at TIGR also using an older version of  
SOAP::Lite.  I should update the Makefile to ensure that it is properly  
listing .69 as a requirement...  luckily, SOAP::Lite no longer attempts to  
upgrade your Perl installation when it installs itself  :-)

M




On Thu, 31 May 2007 12:01:29 -0700, Pieter Neerincx  
<Pieter.Neerincx at wur.nl> wrote:

> Hi,
>
> I also didn't see this specific case before, but it looks like a
> double encoded CDATA section. We've had problems with double encoded
> stuff before due to the way some versions of SOAP::Lite were handling
> encoding/decoding. If you are running SOAP::Lite < 0.69 please
> upgrade to 0.69. If you are running something more recent please let
> us know. Might be a new S::L peculiarity in that case...
>
> Cheers,
>
> Pi
>
>
> On  31 May 2007, at 18:06, Mark Wilkinson wrote:
>
>> Never seen that error before...
>>
>> perhaps check that your LibXML C libraries are up-to-date?  They
>> are used
>> by the XML::LibXML module that Moby uses for XML parsing.
>>
>> M
>>
>>
>>
>> On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI)
>> <L.Barboza at cgiar.org> wrote:
>>
>>> I have already got and installed the biomoby code in the server. Then
>>> running the "make test" give me this result:
>>>
>>>
>>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>>>
>>> t/Central.....................ok
>>>
>>>
>>> t/Client-Central..............ok 22/0:7: parser error : Sequence
>>> ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>>  at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> t/Client-Central..............ok 23/0# Looks like your test died just
>>> after 23.
>>>
>>> t/Client-Central..............dubious
>>>
>>>
>>>         Test returned status 255 (wstat 65280, 0xff00)
>>>
>>>         after all the subtests completed successfully
>>>
>>> t/Client-CollectionArticle....ok
>>>
>>>
>>> t/Client-OntologyServer.......ok
>>>
>>>
>>> t/Client-Registration.........ok
>>>
>>>
>>> t/Client-SecondaryArticle.....ok
>>>
>>>
>>> t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>>  at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> # Looks like your test died just after 2.
>>>
>>> t/Client-Service..............dubious
>>>
>>>
>>>         Test returned status 255 (wstat 65280, 0xff00)
>>>
>>>         after all the subtests completed successfully
>>>
>>> t/Client-ServiceInstance......ok
>>>
>>>
>>> t/Client-SimpleArticle........ok
>>>
>>>
>>> t/CommonSubs..................ok
>>>
>>>
>>> t/Config......................skipped
>>>
>>>         all skipped: Required only when you have your own local MOBY
>>> Central
>>>
>>> t/CrossReference..............ok
>>>
>>>
>>> t/Template....................ok
>>>
>>>
>>> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> -------
>>>
>>> t/Client-Central.t  255 65280    23    0   0.00%  ??
>>>
>>> t/Client-Service.t  255 65280     2    0   0.00%  ??
>>>
>>> 1 test skipped.
>>>
>>> Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00%
>>> okay.
>>>
>>> make: *** [test_dynamic] Error 255
>>>
>>> lbarboza at cropwiki:/usr/local/moby-live/Perl$ <MOBYRegistration>
>>>
>>> -bash: syntax error near unexpected token `newline'
>>>
>>>
>>>
>>> I am using perl v5.8.4. pls help
>>>
>>>
>>> thanks
>>>
>>>
>>> Lord  Hendrix A. Barbozax`
>>>
>>> Programmer - Web Services
>>>
>>> Crop Research Informatics Laboratory (CRIL)
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
>> --
>> --
>> Mark Wilkinson
>> Assistant Professor, Dept. Medical Genetics
>> University of British Columbia
>> PI Bioinformatics
>> iCAPTURE Centre, St. Paul's Hospital
>> Tel:  604 682 2344 x62129
>> Fax:  604 806 9274
>>
>> ***CONFIDENTIALITY NOTICE***
>> This electronic message is intended only for the use of the
>> addressee and
>> may contain information that is privileged and confidential.  Any
>> dissemination, distribution or copying of this communication by
>> unauthorized individuals is strictly prohibited. If you have
>> received this
>> communication in error, please notify the sender immediately by reply
>> e-mail and delete the original and all copies from your system.
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
>
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> phone:  0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> -------------------------------------------------------------
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From markw at illuminae.com  Sun Jun  3 21:32:46 2007
From: markw at illuminae.com (mark wilkinson)
Date: Mon, 4 Jun 2007 01:32:46 +0000 GMT
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
Message-ID: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>

Well, we just had a meeting of the core jMoby developers here in Vancouver.  The *intent* of the meeting was to consolidate the various Java toolkits, or at least to decide on a unified "face" to present to the world on the Java side of Moby, since there is a lot of overlap between the functionality of the various Java libraries (and increasingly on the Perl side as well) which makes it difficult for newcomers to navigate through what they are supposed to do.

But...

The meeting was hijacked!  The hijackers were Martin, Ivan, Paul and Me :-)

We ended-up discussing the core API, particularly in light of the recent deprecation of RPC encoding in SOAP (which is what Moby has used since the beginning)

You can browse the minutes of the meeting by clicking on the "General" blog category on the right hand column of the homepage.  There is a list of the 4 core API changes we are planning to implement, as well as the broader discussion of why we want to do this, and who is responsible for each one.  There is a TODO list of ~30 items that have been assigned to individuals at the meeting, but anyone in the Moby community is welcome to help in areas where they have specific expertise!

One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!

Best wishes everyone!!

Moby-on!

Mark

--
Mark Wilkinson
...on the road!


From L.Barboza at cgiar.org  Mon Jun  4 02:05:43 2007
From: L.Barboza at cgiar.org (Barboza, Lord Hendrix (IRRI))
Date: Mon, 4 Jun 2007 14:05:43 +0800
Subject: [MOBY-dev]  help: local registry installation
Message-ID: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>

Hi,

Before I do an update of my SOAP::Lite to .69 this morning, I've updated
the code first using "cvs update -dP" since I've received an email from
eddie Kawas stating that there was a bug in the repository code and it
is already fixed. So I tried it first and fortunately it gives a
successful result. Do I still have to update Soap::Lite for future use? 

Thanks for all the ideas and help. 

 

Lord  Hendrix A. Barboza

Programmer - Web Services

Crop Research Informatics Laboratory (CRIL)

 



From Pieter.Neerincx at wur.nl  Mon Jun  4 05:00:57 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Mon, 04 Jun 2007 11:00:57 +0200
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
References: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
Message-ID: <9E38D5BE-51ED-4B3B-A707-8E882ABED318@wur.nl>

Hi,

What version are you currently running? S::L 0.60 has been the  
official "stable" release for a very long time (released February  
2004). It's rather outdated, but don't fix something if it ain't  
broke. If you do upgrade, go straight to 0.69 and skip the 0.60 <  
releases < 0.69, they are all beta and have severe known issues. 0.69  
is probably not perfect either (it's labeled "** UNAUTHORIZED RELEASE  
**" on CPAN), but so far I haven't had problems with this one.

Fortunately BioMOBY only requires rather basic functionality from  
S::L. If you use S::L for more complex things like for example  
sending SOAP attachments, you'll see issues with all versions :(.

Cheers,

Pi


On  04 Jun 2007, at 08:05, Barboza, Lord Hendrix ((IRRI)) wrote:

> Hi,
>
> Before I do an update of my SOAP::Lite to .69 this morning, I've  
> updated
> the code first using "cvs update -dP" since I've received an email  
> from
> eddie Kawas stating that there was a bug in the repository code and it
> is already fixed. So I tried it first and fortunately it gives a
> successful result. Do I still have to update Soap::Lite for future  
> use?
>
> Thanks for all the ideas and help.
>
>
>
> Lord  Hendrix A. Barboza
>
> Programmer - Web Services
>
> Crop Research Informatics Laboratory (CRIL)
>
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------------------------------------------------------
Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034

Dreijenlaan 3
6703 HA Wageningen
The Netherlands

phone:  0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
mail: pieter.neerincx at wur.nl
skype: pieter.online
-------------------------------------------------------------



From gordonp at ucalgary.ca  Mon Jun  4 10:50:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 04 Jun 2007 08:50:36 -0600
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
In-Reply-To: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
References: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
Message-ID: <466426BC.3070101@ucalgary.ca>

Hi all,

While I appreciate Mark's plaudits, he has stolen a bit of my thunder :-)

My Seahawk manuscript should be published on-line in the next couple of 
weeks (it is now "accepted in principle" by the journal),
and in preparation for that, I am making some minor but critical updates 
to the applet so it does not overload MobyCentral
as more people use it. I'll post to the mailing lists when this "public" 
version is ready.  I will also setup somewhere where bugs can be
formally lodged by users.  This way I can be sure to fix them promptly!

The "auto-mobyfication" of any Web form is, alas, not part of Seahawk 
yet.  While I have done prototyping of this (and hence the
convincing screenshots Mark saw), it is a few months away from going 
into the public version.  Nevertheless, it is my primary focus
now and I am keen to unleash it on the world!

Regards,

Paul
> One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!
>
> Best wishes everyone!!
>
> Moby-on!
>
> Mark
>
> --
> Mark Wilkinson
> ...on the road!
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,46636ce88021640413918!
>
>
>
>   


From gordonp at ucalgary.ca  Mon Jun  4 10:50:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 04 Jun 2007 08:50:36 -0600
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
In-Reply-To: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
References: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
Message-ID: <466426BC.3070101@ucalgary.ca>

Hi all,

While I appreciate Mark's plaudits, he has stolen a bit of my thunder :-)

My Seahawk manuscript should be published on-line in the next couple of 
weeks (it is now "accepted in principle" by the journal),
and in preparation for that, I am making some minor but critical updates 
to the applet so it does not overload MobyCentral
as more people use it. I'll post to the mailing lists when this "public" 
version is ready.  I will also setup somewhere where bugs can be
formally lodged by users.  This way I can be sure to fix them promptly!

The "auto-mobyfication" of any Web form is, alas, not part of Seahawk 
yet.  While I have done prototyping of this (and hence the
convincing screenshots Mark saw), it is a few months away from going 
into the public version.  Nevertheless, it is my primary focus
now and I am keen to unleash it on the world!

Regards,

Paul
> One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!
>
> Best wishes everyone!!
>
> Moby-on!
>
> Mark
>
> --
> Mark Wilkinson
> ...on the road!
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,46636ce88021640413918!
>
>
>
>   


From markw at illuminae.com  Mon Jun  4 15:52:24 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 04 Jun 2007 12:52:24 -0700
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
References: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
Message-ID: <op.ttexhmqonbznux@homecomp>

It depends on which version of SOAP::Lite you have now... but I would  
recommend that you update if you possibly can, since there have been a lot  
of troublesome bugs in earlier versions of SOAP::Lite (or at least,  
incompatibilities with the Java libraries)

M



On Sun, 03 Jun 2007 23:05:43 -0700, Barboza, Lord Hendrix (IRRI)  
<L.Barboza at cgiar.org> wrote:

> Hi,
>
> Before I do an update of my SOAP::Lite to .69 this morning, I've updated
> the code first using "cvs update -dP" since I've received an email from
> eddie Kawas stating that there was a bug in the repository code and it
> is already fixed. So I tried it first and fortunately it gives a
> successful result. Do I still have to update Soap::Lite for future use?
>
> Thanks for all the ideas and help.
>
>
> Lord  Hendrix A. Barboza
>
> Programmer - Web Services
>
> Crop Research Informatics Laboratory (CRIL)
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From groscurt at mpiz-koeln.mpg.de  Wed Jun  6 08:13:24 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 6 Jun 2007 14:13:24 +0200
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
Message-ID: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>

Hi everyone,

after the developer meeting at Vancouver the suggestion came up to introduce 
you to the idea and features of the Moby Synchronization process, so everyone 
can contribute ideas and recommendations on that.

I decided against writing all the information in the list because of the 
amount of information, so I ask you all to have a look at the following files

http://bioinfo.mpiz-koeln.mpg.de/moby_sync/README.txt
http://bioinfo.mpiz-koeln.mpg.de/moby_sync/MOBYSync_config.txt

which contain the essentiel information about the project (the README is badly 
copied from the rdfagent *g).

Please write recommendations, errors and all the other stuff so I can think 
about that :-)

Best greetings from Germany and thanks again for the wonderful meeting in 
Vancouver !

Andreas

PS: During the development of the process i encountered some errors, I also 
like to discuss...

The registration of some services fails because of two errors mainly:

- Registration Failed During INPUT Article Registration: Input Simples and 	
collections are required to have an articleName as of API version 0.86

- Problem with reading XML input: org.xml.sax.SAXParseException: The character 
sequence "]]>" must not appear in content unless used to mark the end of a 
CDATA section.

how to handle this errors ? Where do they emerge from and so on ?


From martin.senger at gmail.com  Wed Jun  6 09:14:47 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 6 Jun 2007 14:14:47 +0100
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706061413.24492.groscurt@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0706060614x65421a2fw4e34c98e0124a421@mail.gmail.com>

> The registration of some services fails because of two errors mainly:


How was the registration done (with which tool)?

Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger

From markw at illuminae.com  Wed Jun  6 14:19:52 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 06 Jun 2007 11:19:52 -0700
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706061413.24492.groscurt@mpiz-koeln.mpg.de>
Message-ID: <op.ttiijeaonbznux@personalpc>

On Wed, 06 Jun 2007 05:13:24 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> - Registration Failed During INPUT Article Registration: Input Simples  
> and 	
> collections are required to have an articleName as of API version 0.86


I think this one is self-explanatory :-)



> - Problem with reading XML input: org.xml.sax.SAXParseException: The  
> character
> sequence "]]>" must not appear in content unless used to mark the end of  
> a
> CDATA section.

I believe this comes from running an older version of SOAP::Lite.  Eddie  
can likely confirm this diagnosis.

M




-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 

From edward.kawas at gmail.com  Wed Jun  6 16:20:43 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 6 Jun 2007 13:20:43 -0700
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <op.ttiijeaonbznux@personalpc>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org><200706061413.24492.groscurt@mpiz-koeln.mpg.de>
	<op.ttiijeaonbznux@personalpc>
Message-ID: <006601c7a878$303351c0$6400a8c0@notebook>

> I believe this comes from running an older version of SOAP::Lite.  Eddie
> can likely confirm this diagnosis.

I would have to see what it is the 'SyncAgent' ;-) is trying to do. Maybe
the XML is malformed.

Andreas, do you have any further information regarding this?

Thanks,

Eddie


From dmitry.repchevski at bsc.es  Thu Jun  7 04:52:11 2007
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Thu, 07 Jun 2007 10:52:11 +0200
Subject: [MOBY-dev] jMoby add a parameter into a message
Message-ID: <4667C73B.7050604@bsc.es>

Hello,

I'm making an xslt converter from jMoby ontology object to Perl ontology 
objects.
The idea is to convert moby XML message to Perl dumped format directly 
through xslt.

looking into jMoby code I found different basic moby types (i.e. 
MobyDataBoolean and MobyBoolean), but can't find a way to construct a 
message:

here is the code snip I have:

**************************************************
            MobyJob mj =  new MobyJob("sip_1_");
           
            AminoAcidSequence seq = new AminoAcidSequence();
            seq.setId("id");
            seq.setName("sequence");
            //seq.setNamespace();
            seq.set_SequenceString("aaaaaaaaaaaaaaaaaaaaa");
            seq.set_Length(new MobyInteger(20));
           
            mj.addData(seq);
           
            //mj.addDataElement(new )

            StringWriter writer = new StringWriter();
            XMLOutputter xo = new XMLOutputter();
            xo.setFormat(Format.getPrettyFormat());
            xo.output(mj.toXML(), writer);

**************************************************
Sure it's easy, but...

Thank you in advance,

Dmitry

From groscurt at mpiz-koeln.mpg.de  Fri Jun  8 08:21:04 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 8 Jun 2007 14:21:04 +0200
Subject: [MOBY-dev] Perl question
In-Reply-To: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
Message-ID: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>

Hiho,

because of the awesome perl hackers on the list.. I hope someone can help 
me....

I have the following Moby response

<?xml version="1.0" encoding="UTF-8"?>
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
  <moby:mobyContent>
    <moby:mobyData moby:queryID="sip_1_">
      <moby:Collection moby:articleName="pubmedID">
        <moby:Simple>
          <moby:Object moby:id="" moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
        </moby:Simple>
      </moby:Collection>
    </moby:mobyData>
  </moby:mobyContent>
</moby:MOBY>

and the following perl code

my $parser = XML::LibXML->new();
$parser->clean_namespaces( 1 );
my $doc = $parser->parse_string($resultXML);
my $root = $doc->getDocumentElement;

my @objectNodes = ();
# $outObjType = Object (!)
@objectNodes = $root->findnodes("//moby:$outObjType");
# deal with 'moby-less' xml tags:
@objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
my $resCnt = 0; # a result counter, used as default for file naming
# iterate over all result objects
foreach my $objectNode (@objectNodes) {
# create a filename and write the object to the cache directory

# if provider uses other namespaces (that is other
# than the start namespace of the application), get
# this and use it for cache file name
my ($ns,$id);
if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
     $ns = $objectNode->getAttributeNS('moby', 'namespace');
}
# deal with 'moby-less' attributes
elsif ( $objectNode->hasAttribute('namespace') ) {
  $ns = $objectNode->getAttribute('namespace');
}

as far as I understand this code (is from Dirks aggregator), it should parse 
the namespace of the element 'moby:Object'... but it doesnt.

I know nothing about LibXML and parsing xml in Perl.. so I was wondering, why 

if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
     $ns = $objectNode->getAttributeNS('moby', 'namespace');
}

is not working.

Any hints ?

Thanks
Andreas


From edward.kawas at gmail.com  Fri Jun  8 09:35:09 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 06:35:09 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <002301c7a9d1$d700a070$6400a8c0@notebook>

Hi Andreas,

So one of the problems is that getAttributeNS takes as argument a URI and
the attribute name.

However, that didn't fix the problem for you me.

So a quick hack would be to call getAttribute('moby:namespace');

Perhaps someone else knows why the 'right' way isn't working!

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 08, 2007 5:21 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Perl question
> 
> Hiho,
> 
> because of the awesome perl hackers on the list.. I hope someone can help
> me....
> 
> I have the following Moby response
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>   <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Collection moby:articleName="pubmedID">
>         <moby:Simple>
>           <moby:Object moby:id="" moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
>         </moby:Simple>
>       </moby:Collection>
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
> 
> and the following perl code
> 
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces( 1 );
> my $doc = $parser->parse_string($resultXML);
> my $root = $doc->getDocumentElement;
> 
> my @objectNodes = ();
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:$outObjType");
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> my $resCnt = 0; # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> # create a filename and write the object to the cache directory
> 
> # if provider uses other namespaces (that is other
> # than the start namespace of the application), get
> # this and use it for cache file name
> my ($ns,$id);
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> # deal with 'moby-less' attributes
> elsif ( $objectNode->hasAttribute('namespace') ) {
>   $ns = $objectNode->getAttribute('namespace');
> }
> 
> as far as I understand this code (is from Dirks aggregator), it should
> parse
> the namespace of the element 'moby:Object'... but it doesnt.
> 
> I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> why
> 
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> 
> is not working.
> 
> Any hints ?
> 
> Thanks
> Andreas
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Fri Jun  8 09:37:35 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 06:37:35 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>

Actually, I guess that I haven't had all my coffee yet, because the 'right'
way does work (but not if you include other stuff in the URI!)

Here is the code:

my $parser = XML::LibXML->new();
$parser->clean_namespaces(1);
my $doc  = $parser->parse_string($stuff);
my $root = $doc->getDocumentElement;

my @objectNodes = ();

# $outObjType = Object (!)
@objectNodes = $root->findnodes("//moby:Object");

# deal with 'moby-less' xml tags:
@objectNodes = $root->findnodes("//Object") unless @objectNodes;
my $resCnt = 0;

# a result counter, used as default for file naming
# iterate over all result objects
foreach my $objectNode (@objectNodes) {
	my ( $ns, $id );
	if ( $objectNode->hasAttributeNS( 'http://www.biomoby.org/moby',
'namespace' ) ) {
		$ns = $objectNode->getAttributeNS(
'http://www.biomoby.org/moby', 'namespace' );
			}
	elsif ( $objectNode->hasAttribute('namespace') ) {
		$ns = $objectNode->getAttribute('namespace');
	
	}
	print $ns;
}

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 08, 2007 5:21 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Perl question
> 
> Hiho,
> 
> because of the awesome perl hackers on the list.. I hope someone can help
> me....
> 
> I have the following Moby response
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>   <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Collection moby:articleName="pubmedID">
>         <moby:Simple>
>           <moby:Object moby:id="" moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
>         </moby:Simple>
>       </moby:Collection>
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
> 
> and the following perl code
> 
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces( 1 );
> my $doc = $parser->parse_string($resultXML);
> my $root = $doc->getDocumentElement;
> 
> my @objectNodes = ();
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:$outObjType");
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> my $resCnt = 0; # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> # create a filename and write the object to the cache directory
> 
> # if provider uses other namespaces (that is other
> # than the start namespace of the application), get
> # this and use it for cache file name
> my ($ns,$id);
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> # deal with 'moby-less' attributes
> elsif ( $objectNode->hasAttribute('namespace') ) {
>   $ns = $objectNode->getAttribute('namespace');
> }
> 
> as far as I understand this code (is from Dirks aggregator), it should
> parse
> the namespace of the element 'moby:Object'... but it doesnt.
> 
> I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> why
> 
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> 
> is not working.
> 
> Any hints ?
> 
> Thanks
> Andreas
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Fri Jun  8 13:14:49 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 08 Jun 2007 10:14:49 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <op.ttl4uzcinbznux@personalpc>

On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:


> <moby:Object moby:id="" moby:namespace="PMID_" />

that's an unusual namespace...  Where are you getting it from?

M

 


From markw at illuminae.com  Fri Jun  8 13:19:45 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 08 Jun 2007 10:19:45 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<002401c7a9d2$2d6b6df0$6400a8c0@notebook>
Message-ID: <op.ttl427b4nbznux@personalpc>

On Fri, 08 Jun 2007 06:37:35 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:


> does work (but not if you include other stuff in the URI!)

What "other stuff" do you mean??  Eddie is apparently just making up  
"other stuff" to stick into our URI's :-)

Please forgive him, he caught the illness that I had during the Moby  
meeting so he's as spaced-out as I was!

M
 

From gordonp at ucalgary.ca  Fri Jun  8 16:09:45 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 08 Jun 2007 14:09:45 -0600
Subject: [MOBY-dev] In Moby Central dead?
Message-ID: <4669B789.1030103@ucalgary.ca>

I can't ping it from the U of C. 

Maybe I killed it?

From edward.kawas at gmail.com  Fri Jun  8 16:16:42 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 13:16:42 -0700
Subject: [MOBY-dev] In Moby Central dead?
In-Reply-To: <4669B789.1030103@ucalgary.ca>
References: <4669B789.1030103@ucalgary.ca>
Message-ID: <009a01c7aa09$edf284f0$6400a8c0@notebook>

Works for me.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Paul Gordon
> Sent: Friday, June 08, 2007 1:10 PM
> To: Core developer announcements
> Subject: [MOBY-dev] In Moby Central dead?
> 
> I can't ping it from the U of C.
> 
> Maybe I killed it?
> _______________________________________________
> 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  Sat Jun  9 13:14:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Sat, 09 Jun 2007 11:14:36 -0600
Subject: [MOBY-dev] Object Ontology problem
Message-ID: <466ADFFC.40700@ucalgary.ca>

Hi folks (Mark or Eddie especially I guess),

Can we please correct the definition of DNASequenceWithGFFFeatures, it 
has a member without an article name!

  <owl:Class 
rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequenceWithGFFFeatures">
    <moby:has>
      <mobyObject:BasicGFFSequenceFeature>
        <moby:articleName xml:lang="en"><!-- Paul says there should be a 
name here... --></moby:articleName>
      </mobyObject:BasicGFFSequenceFeature>
    </moby:has>
    <rdfs:subClassOf>
      <owl:Class 
rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
    </rdfs:subClassOf>


From edward.kawas at gmail.com  Sat Jun  9 16:58:36 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Sat, 9 Jun 2007 13:58:36 -0700
Subject: [MOBY-dev] Object Ontology problem
In-Reply-To: <466ADFFC.40700@ucalgary.ca>
References: <466ADFFC.40700@ucalgary.ca>
Message-ID: <001b01c7aad8$f33fefe0$6400a8c0@notebook>

I will look into it. There are others out there, but thanks for pointing
that one 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 Paul Gordon
> Sent: Saturday, June 09, 2007 10:15 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Object Ontology problem
> 
> Hi folks (Mark or Eddie especially I guess),
> 
> Can we please correct the definition of DNASequenceWithGFFFeatures, it
> has a member without an article name!
> 
>   <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-
> S/Objects#DNASequenceWithGFFFeatures">
>     <moby:has>
>       <mobyObject:BasicGFFSequenceFeature>
>         <moby:articleName xml:lang="en"><!-- Paul says there should be a
> name here... --></moby:articleName>
>       </mobyObject:BasicGFFSequenceFeature>
>     </moby:has>
>     <rdfs:subClassOf>
>       <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
>     </rdfs:subClassOf>
> 
> _______________________________________________
> 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  Sun Jun 10 05:13:27 2007
From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de)
Date: Sun, 10 Jun 2007 11:13:27 +0200 (CEST)
Subject: [MOBY-dev] Perl question
In-Reply-To: <op.ttl4uzcinbznux@personalpc>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<op.ttl4uzcinbznux@personalpc>
Message-ID: <61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>

> On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>
>> <moby:Object moby:id="" moby:namespace="PMID_" />
>
> that's an unusual namespace...  Where are you getting it from?
>
> M
Its part of the Locus2Publications Service from Chris Wilks (tair)
registered at the test central....


From groscurt at mpiz-koeln.mpg.de  Mon Jun 11 05:49:30 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Mon, 11 Jun 2007 11:49:30 +0200
Subject: [MOBY-dev] Perl question
In-Reply-To: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<002401c7a9d2$2d6b6df0$6400a8c0@notebook>
Message-ID: <200706111149.30222.groscurt@mpiz-koeln.mpg.de>

Awesome :-)

works fine.. thanks for that

Andreas

On Friday 08 June 2007 15:37, Edward Kawas wrote:
> Actually, I guess that I haven't had all my coffee yet, because the 'right'
> way does work (but not if you include other stuff in the URI!)
>
> Here is the code:
>
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces(1);
> my $doc  = $parser->parse_string($stuff);
> my $root = $doc->getDocumentElement;
>
> my @objectNodes = ();
>
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:Object");
>
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//Object") unless @objectNodes;
> my $resCnt = 0;
>
> # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> 	my ( $ns, $id );
> 	if ( $objectNode->hasAttributeNS( 'http://www.biomoby.org/moby',
> 'namespace' ) ) {
> 		$ns = $objectNode->getAttributeNS(
> 'http://www.biomoby.org/moby', 'namespace' );
> 			}
> 	elsif ( $objectNode->hasAttribute('namespace') ) {
> 		$ns = $objectNode->getAttribute('namespace');
>
> 	}
> 	print $ns;
> }
>
> Eddie
>
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> > Sent: Friday, June 08, 2007 5:21 AM
> > To: moby-dev at lists.open-bio.org
> > Subject: [MOBY-dev] Perl question
> >
> > Hiho,
> >
> > because of the awesome perl hackers on the list.. I hope someone can help
> > me....
> >
> > I have the following Moby response
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
> >   <moby:mobyContent>
> >     <moby:mobyData moby:queryID="sip_1_">
> >       <moby:Collection moby:articleName="pubmedID">
> >         <moby:Simple>
> >           <moby:Object moby:id="" moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >       </moby:Collection>
> >     </moby:mobyData>
> >   </moby:mobyContent>
> > </moby:MOBY>
> >
> > and the following perl code
> >
> > my $parser = XML::LibXML->new();
> > $parser->clean_namespaces( 1 );
> > my $doc = $parser->parse_string($resultXML);
> > my $root = $doc->getDocumentElement;
> >
> > my @objectNodes = ();
> > # $outObjType = Object (!)
> > @objectNodes = $root->findnodes("//moby:$outObjType");
> > # deal with 'moby-less' xml tags:
> > @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> > my $resCnt = 0; # a result counter, used as default for file naming
> > # iterate over all result objects
> > foreach my $objectNode (@objectNodes) {
> > # create a filename and write the object to the cache directory
> >
> > # if provider uses other namespaces (that is other
> > # than the start namespace of the application), get
> > # this and use it for cache file name
> > my ($ns,$id);
> > if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
> >      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> > }
> > # deal with 'moby-less' attributes
> > elsif ( $objectNode->hasAttribute('namespace') ) {
> >   $ns = $objectNode->getAttribute('namespace');
> > }
> >
> > as far as I understand this code (is from Dirks aggregator), it should
> > parse
> > the namespace of the element 'moby:Object'... but it doesnt.
> >
> > I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> > why
> >
> > if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
> >      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> > }
> >
> > is not working.
> >
> > Any hints ?
> >
> > Thanks
> > Andreas
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447


From gordonp at ucalgary.ca  Mon Jun 11 10:51:01 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 11 Jun 2007 08:51:01 -0600
Subject: [MOBY-dev] Seahawk Testing
Message-ID: <466D6155.7070905@ucalgary.ca>

Hello fellow MOBYers,

I've posted an update of the Seahawk applet to:

http://moby.ucalgary.ca/seahawk

I fixed several small bugs, and added the capability to specify a 
different central registry (using the new "Preferences" dialog box).
If you choose a different MOBY central, I suggest you close your browser 
and restart Seahawk.
If you get a chance, please check it out and let me know of any bugs you 
find, before we start unleashing MOBY virgins on it in
the next couple of weeks. 
I am hoping (as Mark alluded to last week) that Seahawk can help the 
less technically inclined than us actually use MOBY to its
full potential.  Brief overview of some features:

-Zero install (signed applet)
-Data creation by highlighting (see the Help file)
-Drag and drop support (e.g. drag sample data from the API specification 
from your Web browser onto Seahawk).  I use this a lot.
-Secondary and multiple-primary parameter support
-Hierarchical service selection menus
-Support for "asynchronous" services, in the Spanish style :-)
-A moby data clipboard
-Exports browsing history as SCUFL (read: Taverna) workflow
-Multiple tabs, for concurrent service execution
-Open source:  its all in the Java MOBY CVS

Near-future features:
-Web-forms as MOBY Services: wrapping-by-example
-Sidebar with Favorites and Suggestions

Happy MOBYing!

Paul

P.S. The Seahawk JAR file 
(http://moby.ucalgary.ca/seahawk/java/seahawk.jar) can also be used 
directly as an application, i.e.: java -jar seahawk.jar
If there is demand, I will create an InstallAnywhere package for it.

From markw at illuminae.com  Tue Jun 12 11:52:50 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 12 Jun 2007 08:52:50 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<op.ttl4uzcinbznux@personalpc>
	<61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <op.tttfqc0tnbznux@personalpc>

Ah, OK.  that namespace doesn't exist in the "real" registry, so I was a  
bit concerned.

M


On Sun, 10 Jun 2007 02:13:27 -0700, <groscurt at mpiz-koeln.mpg.de> wrote:

>> On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>
>>> <moby:Object moby:id="" moby:namespace="PMID_" />
>>
>> that's an unusual namespace...  Where are you getting it from?
>>
>> M
> Its part of the Locus2Publications Service from Chris Wilks (tair)
> registered at the test central....
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From edward.kawas at gmail.com  Thu Jun 14 13:02:50 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 14 Jun 2007 10:02:50 -0700
Subject: [MOBY-dev] Object Ontology problem
In-Reply-To: <466ADFFC.40700@ucalgary.ca>
References: <466ADFFC.40700@ucalgary.ca>
Message-ID: <008401c7aea5$d74049e0$6400a8c0@notebook>

I have fixed this datatype on mobycentral. I gave it an articlename of
'feature'.

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 Paul Gordon
> Sent: Saturday, June 09, 2007 10:15 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Object Ontology problem
> 
> Hi folks (Mark or Eddie especially I guess),
> 
> Can we please correct the definition of DNASequenceWithGFFFeatures, it
> has a member without an article name!
> 
>   <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-
> S/Objects#DNASequenceWithGFFFeatures">
>     <moby:has>
>       <mobyObject:BasicGFFSequenceFeature>
>         <moby:articleName xml:lang="en"><!-- Paul says there should be a
> name here... --></moby:articleName>
>       </mobyObject:BasicGFFSequenceFeature>
>     </moby:has>
>     <rdfs:subClassOf>
>       <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
>     </rdfs:subClassOf>
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Tue Jun 19 11:40:02 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 19 Jun 2007 08:40:02 -0700
Subject: [MOBY-dev] Making the clients more obvious
Message-ID: <op.tt6ds2d7nbznux@personalpc>

Hiya,

There was a criticizm during the last meeting that one of the reasons that  
the website "sucks" is that it was too hard to find the Moby browsers so  
that people could get in and start using Moby.

I just tweaked the homepage so that it is easier to get to the Moby  
browsers.

Let me know if this is better, or if there could still be improvements.

M



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 

From gordonp at ucalgary.ca  Thu Jun 21 15:48:38 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 21 Jun 2007 13:48:38 -0600
Subject: [MOBY-dev] Seahawk JAR availability
Message-ID: <467AD616.2010806@ucalgary.ca>

Hi everyone,

I noticed in my server error logs that some people have been trying to 
download the Seahawk JAR file (for development purposes, I suppose) from 
its old URL. 
I found the incorrect link in the jMOBY docs and updated it to point to 
the correct URL.  Sorry for any inconvenience!

Regards,

Paul

From markw at illuminae.com  Fri Jun 22 13:03:58 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 22 Jun 2007 10:03:58 -0700
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
Message-ID: <op.tub1owwgnbznux@personalpc>

Hi all,

One of the TODO's that was assigned to me was the task of getting MOBY  
Central prepared for multi-lingual support.  I've been investigating how  
to do this, and it looks like it is going to be a bit of a blocker.

According to the XML specification, the xml:lang attribute is supposed to  
apply to the node it is in, and any sub-node until another xml:lang  
attribute is encountered.  Unfortunately, most of the XML parsing  
libraries in Perl do not even notice the xml:lang attribute as "special",  
so you only have access to it as a normal attribute in the node where it  
is included.

There is one XML parsing library in Perl that does keep track of this  
attribute (XML::LibXML::Reader); however that is not available on Windows  
using ActiveState's Perl and PPM, which is what most Windows users will be  
using, I suspect.. (though I know it is possible to use Cygwin also).  I  
also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
some odd modules that you can't get anywhere else, but it isn't there  
either.

So... I guess there are several possibilities:

1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
as part of Moby

1a)  we modify XML::LibXML such that it does recognize and make note of  
this attribute, and contribute that back to the authors

2)  I re-code Moby such that it traverses back up the XML tree looking for  
the last xml:lang attribute for every node that has content.

3)  We put an additional constraint on the rules of XML, requiring that  
the xml:lang attribute must be present in the same node in which the  
multilingul content is present.

4)  ??? give up :-)


Can someone have a quick look at how well xml:lang is supported on the  
Java side, since that will help us make the decision on what to do.  If it  
isn't supported in the Java libraries either, then maybe #3 is the only  
rational (ugly) solution?

M




-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 

From gordonp at ucalgary.ca  Fri Jun 22 14:05:16 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 22 Jun 2007 12:05:16 -0600
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
In-Reply-To: <op.tub1owwgnbznux@personalpc>
References: <op.tub1owwgnbznux@personalpc>
Message-ID: <467C0F5C.2080907@ucalgary.ca>

Just throwing this out there:

I like option 3 (requiring xml:lang in the description tags).  It may 
seem like a kludge, but we decided that the
multilinguality is only supported at the description level in MOBY, 
right?  We assume that all other fields (such as
object name) are opaque tokens in the ontology, and these tokens happen 
to mostly be in semi-intelligible English.
I don't think we want to start supporting synonyms for object names yet, 
as this would require quite a bit of work.
Maybe in MOBY 1.5? :-)

An analogy might be sheet music.  Everyone who reads music knows the 
instruction keywords, which happen to be in Italian
(like biologists usually know key concepts in English, as well as their 
native tongue).  In the short term, option 3
sounds reasonable to me.
> Hi all,
>
> One of the TODO's that was assigned to me was the task of getting MOBY  
> Central prepared for multi-lingual support.  I've been investigating how  
> to do this, and it looks like it is going to be a bit of a blocker.
>
> According to the XML specification, the xml:lang attribute is supposed to  
> apply to the node it is in, and any sub-node until another xml:lang  
> attribute is encountered.  Unfortunately, most of the XML parsing  
> libraries in Perl do not even notice the xml:lang attribute as "special",  
> so you only have access to it as a normal attribute in the node where it  
> is included.
>
> There is one XML parsing library in Perl that does keep track of this  
> attribute (XML::LibXML::Reader); however that is not available on Windows  
> using ActiveState's Perl and PPM, which is what most Windows users will be  
> using, I suspect.. (though I know it is possible to use Cygwin also).  I  
> also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
> some odd modules that you can't get anywhere else, but it isn't there  
> either.
>
> So... I guess there are several possibilities:
>
> 1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
> as part of Moby
>
> 1a)  we modify XML::LibXML such that it does recognize and make note of  
> this attribute, and contribute that back to the authors
>
> 2)  I re-code Moby such that it traverses back up the XML tree looking for  
> the last xml:lang attribute for every node that has content.
>
> 3)  We put an additional constraint on the rules of XML, requiring that  
> the xml:lang attribute must be present in the same node in which the  
> multilingul content is present.
>
> 4)  ??? give up :-)
>
>
> Can someone have a quick look at how well xml:lang is supported on the  
> Java side, since that will help us make the decision on what to do.  If it  
> isn't supported in the Java libraries either, then maybe #3 is the only  
> rational (ugly) solution?
>
> M
>
>
>
>
>   


From gordonp at ucalgary.ca  Fri Jun 22 14:05:16 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 22 Jun 2007 12:05:16 -0600
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
In-Reply-To: <op.tub1owwgnbznux@personalpc>
References: <op.tub1owwgnbznux@personalpc>
Message-ID: <467C0F5C.2080907@ucalgary.ca>

Just throwing this out there:

I like option 3 (requiring xml:lang in the description tags).  It may 
seem like a kludge, but we decided that the
multilinguality is only supported at the description level in MOBY, 
right?  We assume that all other fields (such as
object name) are opaque tokens in the ontology, and these tokens happen 
to mostly be in semi-intelligible English.
I don't think we want to start supporting synonyms for object names yet, 
as this would require quite a bit of work.
Maybe in MOBY 1.5? :-)

An analogy might be sheet music.  Everyone who reads music knows the 
instruction keywords, which happen to be in Italian
(like biologists usually know key concepts in English, as well as their 
native tongue).  In the short term, option 3
sounds reasonable to me.
> Hi all,
>
> One of the TODO's that was assigned to me was the task of getting MOBY  
> Central prepared for multi-lingual support.  I've been investigating how  
> to do this, and it looks like it is going to be a bit of a blocker.
>
> According to the XML specification, the xml:lang attribute is supposed to  
> apply to the node it is in, and any sub-node until another xml:lang  
> attribute is encountered.  Unfortunately, most of the XML parsing  
> libraries in Perl do not even notice the xml:lang attribute as "special",  
> so you only have access to it as a normal attribute in the node where it  
> is included.
>
> There is one XML parsing library in Perl that does keep track of this  
> attribute (XML::LibXML::Reader); however that is not available on Windows  
> using ActiveState's Perl and PPM, which is what most Windows users will be  
> using, I suspect.. (though I know it is possible to use Cygwin also).  I  
> also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
> some odd modules that you can't get anywhere else, but it isn't there  
> either.
>
> So... I guess there are several possibilities:
>
> 1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
> as part of Moby
>
> 1a)  we modify XML::LibXML such that it does recognize and make note of  
> this attribute, and contribute that back to the authors
>
> 2)  I re-code Moby such that it traverses back up the XML tree looking for  
> the last xml:lang attribute for every node that has content.
>
> 3)  We put an additional constraint on the rules of XML, requiring that  
> the xml:lang attribute must be present in the same node in which the  
> multilingul content is present.
>
> 4)  ??? give up :-)
>
>
> Can someone have a quick look at how well xml:lang is supported on the  
> Java side, since that will help us make the decision on what to do.  If it  
> isn't supported in the Java libraries either, then maybe #3 is the only  
> rational (ugly) solution?
>
> M
>
>
>
>
>   


From gordonp at ucalgary.ca  Mon Jun 25 15:42:58 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 25 Jun 2007 13:42:58 -0600
Subject: [MOBY-dev] FYI: A Calgary company uses the MOBY moniker too...
Message-ID: <46801AC2.1090907@ucalgary.ca>

Luckily they are pages, not services :-)

www.*moby**pages*.com

From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 06:14:24 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 12:14:24 +0200
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <467AD616.2010806@ucalgary.ca>
References: <467AD616.2010806@ucalgary.ca>
Message-ID: <200706291214.25053.groscurt@mpiz-koeln.mpg.de>

Hi all,

in Dirks code of the aggregator he has its own findeService workaround 
implementation with the following comment:

  # This is a workaround for a missing feature of MOBY::Central->findService,
  # namely the lacking expansion of objects to leaves direction for the output
  # side.
  # As soon as this is implemented in MOBY::Central, this should be used
  # directly, that is, this method here (and the whole module...) becomes 
  # redundant.

I just wanted to know whether this is still an issue, not anymore or not even 
at all has been any issue :-)

Thanks
Andreas

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447


From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 09:05:27 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 15:05:27 +0200
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <200706291214.25053.groscurt@mpiz-koeln.mpg.de>
References: <467AD616.2010806@ucalgary.ca>
	<200706291214.25053.groscurt@mpiz-koeln.mpg.de>
Message-ID: <200706291505.27668.groscurt@mpiz-koeln.mpg.de>

Hi all again,

I couldnt find anything about this, so I hope you can help me with this simple 
one:

Actually I only want to find services with specific informations, e.g. I want 
to find all services with a specific input or output namespace and so on.

I fail by creating a service with my needs.

The way I thought of doing it is to create a Central instance and call the 
findService method with a MobyService as parameter. 
My current problem is how to tell the Mobyservice which inputs it has to 
consume ?

E.g. how to tell that I want an GenBank identifier as input ? 

The MobyService has the method setInput, which requires MobyData... and i 
couldnt get any connection from MobyData to MobyObject (to set the namespace 
then to GenBank or whatsoever).

So how can I tell the service which MobyObjects I want to use or how can I 
find services with a given input and / or ouput ?

Thanks
obedient Andreas

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447


From edward.kawas at gmail.com  Fri Jun 29 09:09:21 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 29 Jun 2007 06:09:21 -0700
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <200706291505.27668.groscurt@mpiz-koeln.mpg.de>
References: <467AD616.2010806@ucalgary.ca><200706291214.25053.groscurt@mpiz-koeln.mpg.de>
	<200706291505.27668.groscurt@mpiz-koeln.mpg.de>
Message-ID: <001701c7ba4e$b5d2e060$6400a8c0@notebook>

Hi Andreas,

Hopefully this helps you out!
	CentralImpl central = new CentralImpl();
	MobyService s = new MobyService();
	s.setCategory("");
	MobyDataObject data = new MobyDataObject("");
	data.setDataType(new MobyDataType("Object"));
	data.addNamespace(new MobyNamespace("NCBI_gi"));
	MobyDataObjectSet set = new MobyDataObjectSet("");
	set.add(data);
	s.addOutput((set));
	MobyService[] services = central.findService(s,null,true,false);

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 29, 2007 6:05 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Another Java API question
> 
> Hi all again,
> 
> I couldnt find anything about this, so I hope you can help me with this
> simple
> one:
> 
> Actually I only want to find services with specific informations, e.g. I
> want
> to find all services with a specific input or output namespace and so on.
> 
> I fail by creating a service with my needs.
> 
> The way I thought of doing it is to create a Central instance and call the
> findService method with a MobyService as parameter.
> My current problem is how to tell the Mobyservice which inputs it has to
> consume ?
> 
> E.g. how to tell that I want an GenBank identifier as input ?
> 
> The MobyService has the method setInput, which requires MobyData... and i
> couldnt get any connection from MobyData to MobyObject (to set the
> namespace
> then to GenBank or whatsoever).
> 
> So how can I tell the service which MobyObjects I want to use or how can I
> find services with a given input and / or ouput ?
> 
> Thanks
> obedient Andreas
> 
> --
> Andreas Groscurth
> Diplom Bioinformatik - PhD Student
> Max Planck Institute for Plant Breeding Research
> Carl-von-Linn?-Weg 10
> 50829 Cologne
> Germany
> E-mail: ? ?groscurt at mpiz-koeln.mpg.de
> Phone: ? ?+49(0)221-5062-447
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From haase_dirk at web.de  Fri Jun 29 09:32:19 2007
From: haase_dirk at web.de (Dirk Haase)
Date: Fri, 29 Jun 2007 15:32:19 +0200
Subject: [MOBY-dev] Question MobyCentral API
Message-ID: <1140939448@web.de>

Hi Andreas,

> Hi all,
> 
> in Dirks code of the aggregator he has its own findeService workaround 
> implementation with the following comment:
> 
>   # This is a workaround for a missing feature of MOBY::Central->findService,
>   # namely the lacking expansion of objects to leaves direction for the output
>   # side.
>   # As soon as this is implemented in MOBY::Central, this should be used
>   # directly, that is, this method here (and the whole module...) becomes 
>   # redundant.
> 
> I just wanted to know whether this is still an issue, not anymore or not even 
> at all has been any issue :-)

It WAS an issue... But if I remember correctly, I submitted the according changes
to the CVS in February and the new code was also deployed on MOBY Central.
Mark, Eddie, please correct me if I'm wrong.

Best,
dirk

From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 10:06:21 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 16:06:21 +0200
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <001701c7ba4e$b5d2e060$6400a8c0@notebook>
References: <467AD616.2010806@ucalgary.ca>
	<200706291505.27668.groscurt@mpiz-koeln.mpg.de>
	<001701c7ba4e$b5d2e060$6400a8c0@notebook>
Message-ID: <200706291606.21798.groscurt@mpiz-koeln.mpg.de>

Thanks eddie the code is working !

I even figured out how to retrieve service which does not need a collection as 
input :-)

Thanks
Andreas

On Friday 29 June 2007 15:09, Edward Kawas wrote:
> Hi Andreas,
>
> Hopefully this helps you out!
> 	CentralImpl central = new CentralImpl();
> 	MobyService s = new MobyService();
> 	s.setCategory("");
> 	MobyDataObject data = new MobyDataObject("");
> 	data.setDataType(new MobyDataType("Object"));
> 	data.addNamespace(new MobyNamespace("NCBI_gi"));
> 	MobyDataObjectSet set = new MobyDataObjectSet("");
> 	set.add(data);
> 	s.addOutput((set));
> 	MobyService[] services = central.findService(s,null,true,false);
>
> Eddie
>
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> > Sent: Friday, June 29, 2007 6:05 AM
> > To: Core developer announcements
> > Subject: [MOBY-dev] Another Java API question
> >
> > Hi all again,
> >
> > I couldnt find anything about this, so I hope you can help me with this
> > simple
> > one:
> >
> > Actually I only want to find services with specific informations, e.g. I
> > want
> > to find all services with a specific input or output namespace and so on.
> >
> > I fail by creating a service with my needs.
> >
> > The way I thought of doing it is to create a Central instance and call
> > the findService method with a MobyService as parameter.
> > My current problem is how to tell the Mobyservice which inputs it has to
> > consume ?
> >
> > E.g. how to tell that I want an GenBank identifier as input ?
> >
> > The MobyService has the method setInput, which requires MobyData... and i
> > couldnt get any connection from MobyData to MobyObject (to set the
> > namespace
> > then to GenBank or whatsoever).
> >
> > So how can I tell the service which MobyObjects I want to use or how can
> > I find services with a given input and / or ouput ?
> >
> > Thanks
> > obedient Andreas
> >
> > --
> > Andreas Groscurth
> > Diplom Bioinformatik - PhD Student
> > Max Planck Institute for Plant Breeding Research
> > Carl-von-Linn?-Weg 10
> > 50829 Cologne
> > Germany
> > E-mail: ? ?groscurt at mpiz-koeln.mpg.de
> > Phone: ? ?+49(0)221-5062-447
> >
> > _______________________________________________
> > 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

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447


From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 10:10:37 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 16:10:37 +0200
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <1140939448@web.de>
References: <1140939448@web.de>
Message-ID: <200706291610.37515.groscurt@mpiz-koeln.mpg.de>

Hi dirk,

nice to see you still on the list :-)

I currently try to find out why the correct automatic discovery of services 
fails on our local system, so I thought if this is not an issue anymore it 
can be removed and the error searches continue ;-)

best
andreas

On Friday 29 June 2007 15:32, Dirk Haase wrote:
> Hi Andreas,
>
> > Hi all,
> >
> > in Dirks code of the aggregator he has its own findeService workaround
> > implementation with the following comment:
> >
> >   # This is a workaround for a missing feature of
> > MOBY::Central->findService, # namely the lacking expansion of objects to
> > leaves direction for the output # side.
> >   # As soon as this is implemented in MOBY::Central, this should be used
> >   # directly, that is, this method here (and the whole module...) becomes
> >   # redundant.
> >
> > I just wanted to know whether this is still an issue, not anymore or not
> > even at all has been any issue :-)
>
> It WAS an issue... But if I remember correctly, I submitted the according
> changes to the CVS in February and the new code was also deployed on MOBY
> Central. Mark, Eddie, please correct me if I'm wrong.
>
> Best,
> dirk
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447


From markw at illuminae.com  Fri Jun 29 10:22:38 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 29 Jun 2007 07:22:38 -0700
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <1140939448@web.de>
References: <1140939448@web.de>
Message-ID: <op.tuosv5eznbznux@homecomp>

On Fri, 29 Jun 2007 06:32:19 -0700, Dirk Haase <haase_dirk at web.de> wrote:


> It WAS an issue... But if I remember correctly, I submitted the  
> according changes
> to the CVS in February and the new code was also deployed on MOBY  
> Central.
> Mark, Eddie, please correct me if I'm wrong.


I believe that is correct, but I haven't tried to test it.

M

From markw at illuminae.com  Fri Jun  1 16:23:01 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 01 Jun 2007 09:23:01 -0700
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <E7E914B8-1377-43B5-9CBF-70BBF36085A1@wur.nl>
References: <C781839E63F2A140A7928F015DBBA650024410FC@HERMES>
	<op.ts68cqnfnbznux@personalpc>
	<E7E914B8-1377-43B5-9CBF-70BBF36085A1@wur.nl>
Message-ID: <op.ts83snz3nbznux@personalpc>

Ah!  Yes, that's likely the cause.

We had problems last week at TIGR also using an older version of  
SOAP::Lite.  I should update the Makefile to ensure that it is properly  
listing .69 as a requirement...  luckily, SOAP::Lite no longer attempts to  
upgrade your Perl installation when it installs itself  :-)

M




On Thu, 31 May 2007 12:01:29 -0700, Pieter Neerincx  
<Pieter.Neerincx at wur.nl> wrote:

> Hi,
>
> I also didn't see this specific case before, but it looks like a
> double encoded CDATA section. We've had problems with double encoded
> stuff before due to the way some versions of SOAP::Lite were handling
> encoding/decoding. If you are running SOAP::Lite < 0.69 please
> upgrade to 0.69. If you are running something more recent please let
> us know. Might be a new S::L peculiarity in that case...
>
> Cheers,
>
> Pi
>
>
> On  31 May 2007, at 18:06, Mark Wilkinson wrote:
>
>> Never seen that error before...
>>
>> perhaps check that your LibXML C libraries are up-to-date?  They
>> are used
>> by the XML::LibXML module that Moby uses for XML parsing.
>>
>> M
>>
>>
>>
>> On Wed, 30 May 2007 20:12:32 -0700, Barboza, Lord Hendrix (IRRI)
>> <L.Barboza at cgiar.org> wrote:
>>
>>> I have already got and installed the biomoby code in the server. Then
>>> running the "make test" give me this result:
>>>
>>>
>>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>>>
>>> t/Central.....................ok
>>>
>>>
>>> t/Client-Central..............ok 22/0:7: parser error : Sequence
>>> ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>>  at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> t/Client-Central..............ok 23/0# Looks like your test died just
>>> after 23.
>>>
>>> t/Client-Central..............dubious
>>>
>>>
>>>         Test returned status 255 (wstat 65280, 0xff00)
>>>
>>>         after all the subtests completed successfully
>>>
>>> t/Client-CollectionArticle....ok
>>>
>>>
>>> t/Client-OntologyServer.......ok
>>>
>>>
>>> t/Client-Registration.........ok
>>>
>>>
>>> t/Client-SecondaryArticle.....ok
>>>
>>>
>>> t/Client-Service..............ok 2/0:7: parser error : Sequence ']]>'
>>> not allowed in content
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : internal error
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>> :7: parser error : Extra content at the end of the document
>>>
>>> ]]>]]></message>
>>>
>>>    ^
>>>
>>>  at /usr/local/moby-live/Perl/blib/lib/MOBY/Client/Central.pm line
>>> 2107
>>>
>>> # Looks like your test died just after 2.
>>>
>>> t/Client-Service..............dubious
>>>
>>>
>>>         Test returned status 255 (wstat 65280, 0xff00)
>>>
>>>         after all the subtests completed successfully
>>>
>>> t/Client-ServiceInstance......ok
>>>
>>>
>>> t/Client-SimpleArticle........ok
>>>
>>>
>>> t/CommonSubs..................ok
>>>
>>>
>>> t/Config......................skipped
>>>
>>>         all skipped: Required only when you have your own local MOBY
>>> Central
>>>
>>> t/CrossReference..............ok
>>>
>>>
>>> t/Template....................ok
>>>
>>>
>>> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
>>>
>>> ---------------------------------------------------------------------
>>> ---
>>> -------
>>>
>>> t/Client-Central.t  255 65280    23    0   0.00%  ??
>>>
>>> t/Client-Service.t  255 65280     2    0   0.00%  ??
>>>
>>> 1 test skipped.
>>>
>>> Failed 2/13 test scripts, 84.62% okay. 0/235 subtests failed, 100.00%
>>> okay.
>>>
>>> make: *** [test_dynamic] Error 255
>>>
>>> lbarboza at cropwiki:/usr/local/moby-live/Perl$ <MOBYRegistration>
>>>
>>> -bash: syntax error near unexpected token `newline'
>>>
>>>
>>>
>>> I am using perl v5.8.4. pls help
>>>
>>>
>>> thanks
>>>
>>>
>>> Lord  Hendrix A. Barbozax`
>>>
>>> Programmer - Web Services
>>>
>>> Crop Research Informatics Laboratory (CRIL)
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
>> --
>> --
>> Mark Wilkinson
>> Assistant Professor, Dept. Medical Genetics
>> University of British Columbia
>> PI Bioinformatics
>> iCAPTURE Centre, St. Paul's Hospital
>> Tel:  604 682 2344 x62129
>> Fax:  604 806 9274
>>
>> ***CONFIDENTIALITY NOTICE***
>> This electronic message is intended only for the use of the
>> addressee and
>> may contain information that is privileged and confidential.  Any
>> dissemination, distribution or copying of this communication by
>> unauthorized individuals is strictly prohibited. If you have
>> received this
>> communication in error, please notify the sender immediately by reply
>> e-mail and delete the original and all copies from your system.
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> -------------------------------------------------------------
> Wageningen University and Research centre (WUR)
> Laboratory of Bioinformatics
> Transitorium (building 312) room 1034
>
> Dreijenlaan 3
> 6703 HA Wageningen
> The Netherlands
>
> phone:  0317-483 060
> fax: 0317-483 584
> mobile: 06-143 66 783
> mail: pieter.neerincx at wur.nl
> skype: pieter.online
> -------------------------------------------------------------
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 



From markw at illuminae.com  Mon Jun  4 01:32:46 2007
From: markw at illuminae.com (mark wilkinson)
Date: Mon, 4 Jun 2007 01:32:46 +0000 GMT
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
Message-ID: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>

Well, we just had a meeting of the core jMoby developers here in Vancouver.  The *intent* of the meeting was to consolidate the various Java toolkits, or at least to decide on a unified "face" to present to the world on the Java side of Moby, since there is a lot of overlap between the functionality of the various Java libraries (and increasingly on the Perl side as well) which makes it difficult for newcomers to navigate through what they are supposed to do.

But...

The meeting was hijacked!  The hijackers were Martin, Ivan, Paul and Me :-)

We ended-up discussing the core API, particularly in light of the recent deprecation of RPC encoding in SOAP (which is what Moby has used since the beginning)

You can browse the minutes of the meeting by clicking on the "General" blog category on the right hand column of the homepage.  There is a list of the 4 core API changes we are planning to implement, as well as the broader discussion of why we want to do this, and who is responsible for each one.  There is a TODO list of ~30 items that have been assigned to individuals at the meeting, but anyone in the Moby community is welcome to help in areas where they have specific expertise!

One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!

Best wishes everyone!!

Moby-on!

Mark

--
Mark Wilkinson
...on the road!



From L.Barboza at cgiar.org  Mon Jun  4 06:05:43 2007
From: L.Barboza at cgiar.org (Barboza, Lord Hendrix (IRRI))
Date: Mon, 4 Jun 2007 14:05:43 +0800
Subject: [MOBY-dev]  help: local registry installation
Message-ID: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>

Hi,

Before I do an update of my SOAP::Lite to .69 this morning, I've updated
the code first using "cvs update -dP" since I've received an email from
eddie Kawas stating that there was a bug in the repository code and it
is already fixed. So I tried it first and fortunately it gives a
successful result. Do I still have to update Soap::Lite for future use? 

Thanks for all the ideas and help. 

 

Lord  Hendrix A. Barboza

Programmer - Web Services

Crop Research Informatics Laboratory (CRIL)

 




From Pieter.Neerincx at wur.nl  Mon Jun  4 09:00:57 2007
From: Pieter.Neerincx at wur.nl (Pieter Neerincx)
Date: Mon, 04 Jun 2007 11:00:57 +0200
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
References: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
Message-ID: <9E38D5BE-51ED-4B3B-A707-8E882ABED318@wur.nl>

Hi,

What version are you currently running? S::L 0.60 has been the  
official "stable" release for a very long time (released February  
2004). It's rather outdated, but don't fix something if it ain't  
broke. If you do upgrade, go straight to 0.69 and skip the 0.60 <  
releases < 0.69, they are all beta and have severe known issues. 0.69  
is probably not perfect either (it's labeled "** UNAUTHORIZED RELEASE  
**" on CPAN), but so far I haven't had problems with this one.

Fortunately BioMOBY only requires rather basic functionality from  
S::L. If you use S::L for more complex things like for example  
sending SOAP attachments, you'll see issues with all versions :(.

Cheers,

Pi


On  04 Jun 2007, at 08:05, Barboza, Lord Hendrix ((IRRI)) wrote:

> Hi,
>
> Before I do an update of my SOAP::Lite to .69 this morning, I've  
> updated
> the code first using "cvs update -dP" since I've received an email  
> from
> eddie Kawas stating that there was a bug in the repository code and it
> is already fixed. So I tried it first and fortunately it gives a
> successful result. Do I still have to update Soap::Lite for future  
> use?
>
> Thanks for all the ideas and help.
>
>
>
> Lord  Hendrix A. Barboza
>
> Programmer - Web Services
>
> Crop Research Informatics Laboratory (CRIL)
>
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-------------------------------------------------------------
Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034

Dreijenlaan 3
6703 HA Wageningen
The Netherlands

phone:  0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
mail: pieter.neerincx at wur.nl
skype: pieter.online
-------------------------------------------------------------




From gordonp at ucalgary.ca  Mon Jun  4 14:50:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 04 Jun 2007 08:50:36 -0600
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
In-Reply-To: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
References: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
Message-ID: <466426BC.3070101@ucalgary.ca>

Hi all,

While I appreciate Mark's plaudits, he has stolen a bit of my thunder :-)

My Seahawk manuscript should be published on-line in the next couple of 
weeks (it is now "accepted in principle" by the journal),
and in preparation for that, I am making some minor but critical updates 
to the applet so it does not overload MobyCentral
as more people use it. I'll post to the mailing lists when this "public" 
version is ready.  I will also setup somewhere where bugs can be
formally lodged by users.  This way I can be sure to fix them promptly!

The "auto-mobyfication" of any Web form is, alas, not part of Seahawk 
yet.  While I have done prototyping of this (and hence the
convincing screenshots Mark saw), it is a few months away from going 
into the public version.  Nevertheless, it is my primary focus
now and I am keen to unleash it on the world!

Regards,

Paul
> One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!
>
> Best wishes everyone!!
>
> Moby-on!
>
> Mark
>
> --
> Mark Wilkinson
> ...on the road!
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,46636ce88021640413918!
>
>
>
>   



From gordonp at ucalgary.ca  Mon Jun  4 14:50:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 04 Jun 2007 08:50:36 -0600
Subject: [MOBY-dev] The hijacked jMoby meeting in Vancouver
In-Reply-To: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
References: <1671640238-1180920829-cardhu_blackberry.rim.net-1514-@engine08-cell01>
Message-ID: <466426BC.3070101@ucalgary.ca>

Hi all,

While I appreciate Mark's plaudits, he has stolen a bit of my thunder :-)

My Seahawk manuscript should be published on-line in the next couple of 
weeks (it is now "accepted in principle" by the journal),
and in preparation for that, I am making some minor but critical updates 
to the applet so it does not overload MobyCentral
as more people use it. I'll post to the mailing lists when this "public" 
version is ready.  I will also setup somewhere where bugs can be
formally lodged by users.  This way I can be sure to fix them promptly!

The "auto-mobyfication" of any Web form is, alas, not part of Seahawk 
yet.  While I have done prototyping of this (and hence the
convincing screenshots Mark saw), it is a few months away from going 
into the public version.  Nevertheless, it is my primary focus
now and I am keen to unleash it on the world!

Regards,

Paul
> One of the most exciting developments was Paul Gordon's presentation of his SeaHawk Moby client.  Access to Moby from any web browsing session, and the auto-mobyfication of any web resource!  Absolutely amazing!!!  The usefulness of Moby is about to explode!!!!!!  We should all pay close attention to this client and utilize it/extend it as best we can as it is (IMO) the most powerful client we have seen so far!
>
> Best wishes everyone!!
>
> Moby-on!
>
> Mark
>
> --
> Mark Wilkinson
> ...on the road!
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,46636ce88021640413918!
>
>
>
>   



From markw at illuminae.com  Mon Jun  4 19:52:24 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 04 Jun 2007 12:52:24 -0700
Subject: [MOBY-dev] help: local registry installation
In-Reply-To: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
References: <C781839E63F2A140A7928F015DBBA650024413DC@HERMES>
Message-ID: <op.ttexhmqonbznux@homecomp>

It depends on which version of SOAP::Lite you have now... but I would  
recommend that you update if you possibly can, since there have been a lot  
of troublesome bugs in earlier versions of SOAP::Lite (or at least,  
incompatibilities with the Java libraries)

M



On Sun, 03 Jun 2007 23:05:43 -0700, Barboza, Lord Hendrix (IRRI)  
<L.Barboza at cgiar.org> wrote:

> Hi,
>
> Before I do an update of my SOAP::Lite to .69 this morning, I've updated
> the code first using "cvs update -dP" since I've received an email from
> eddie Kawas stating that there was a bug in the repository code and it
> is already fixed. So I tried it first and fortunately it gives a
> successful result. Do I still have to update Soap::Lite for future use?
>
> Thanks for all the ideas and help.
>
>
> Lord  Hendrix A. Barboza
>
> Programmer - Web Services
>
> Crop Research Informatics Laboratory (CRIL)
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From groscurt at mpiz-koeln.mpg.de  Wed Jun  6 12:13:24 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Wed, 6 Jun 2007 14:13:24 +0200
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
Message-ID: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>

Hi everyone,

after the developer meeting at Vancouver the suggestion came up to introduce 
you to the idea and features of the Moby Synchronization process, so everyone 
can contribute ideas and recommendations on that.

I decided against writing all the information in the list because of the 
amount of information, so I ask you all to have a look at the following files

http://bioinfo.mpiz-koeln.mpg.de/moby_sync/README.txt
http://bioinfo.mpiz-koeln.mpg.de/moby_sync/MOBYSync_config.txt

which contain the essentiel information about the project (the README is badly 
copied from the rdfagent *g).

Please write recommendations, errors and all the other stuff so I can think 
about that :-)

Best greetings from Germany and thanks again for the wonderful meeting in 
Vancouver !

Andreas

PS: During the development of the process i encountered some errors, I also 
like to discuss...

The registration of some services fails because of two errors mainly:

- Registration Failed During INPUT Article Registration: Input Simples and 	
collections are required to have an articleName as of API version 0.86

- Problem with reading XML input: org.xml.sax.SAXParseException: The character 
sequence "]]>" must not appear in content unless used to mark the end of a 
CDATA section.

how to handle this errors ? Where do they emerge from and so on ?



From martin.senger at gmail.com  Wed Jun  6 13:14:47 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 6 Jun 2007 14:14:47 +0100
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706061413.24492.groscurt@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0706060614x65421a2fw4e34c98e0124a421@mail.gmail.com>

> The registration of some services fails because of two errors mainly:


How was the registration done (with which tool)?

Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger


From markw at illuminae.com  Wed Jun  6 18:19:52 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 06 Jun 2007 11:19:52 -0700
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <200706061413.24492.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706061413.24492.groscurt@mpiz-koeln.mpg.de>
Message-ID: <op.ttiijeaonbznux@personalpc>

On Wed, 06 Jun 2007 05:13:24 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:

> - Registration Failed During INPUT Article Registration: Input Simples  
> and 	
> collections are required to have an articleName as of API version 0.86


I think this one is self-explanatory :-)



> - Problem with reading XML input: org.xml.sax.SAXParseException: The  
> character
> sequence "]]>" must not appear in content unless used to mark the end of  
> a
> CDATA section.

I believe this comes from running an older version of SOAP::Lite.  Eddie  
can likely confirm this diagnosis.

M




-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
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From edward.kawas at gmail.com  Wed Jun  6 20:20:43 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 6 Jun 2007 13:20:43 -0700
Subject: [MOBY-dev] Moby Synchronization
In-Reply-To: <op.ttiijeaonbznux@personalpc>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org><200706061413.24492.groscurt@mpiz-koeln.mpg.de>
	<op.ttiijeaonbznux@personalpc>
Message-ID: <006601c7a878$303351c0$6400a8c0@notebook>

> I believe this comes from running an older version of SOAP::Lite.  Eddie
> can likely confirm this diagnosis.

I would have to see what it is the 'SyncAgent' ;-) is trying to do. Maybe
the XML is malformed.

Andreas, do you have any further information regarding this?

Thanks,

Eddie



From dmitry.repchevski at bsc.es  Thu Jun  7 08:52:11 2007
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Thu, 07 Jun 2007 10:52:11 +0200
Subject: [MOBY-dev] jMoby add a parameter into a message
Message-ID: <4667C73B.7050604@bsc.es>

Hello,

I'm making an xslt converter from jMoby ontology object to Perl ontology 
objects.
The idea is to convert moby XML message to Perl dumped format directly 
through xslt.

looking into jMoby code I found different basic moby types (i.e. 
MobyDataBoolean and MobyBoolean), but can't find a way to construct a 
message:

here is the code snip I have:

**************************************************
            MobyJob mj =  new MobyJob("sip_1_");
           
            AminoAcidSequence seq = new AminoAcidSequence();
            seq.setId("id");
            seq.setName("sequence");
            //seq.setNamespace();
            seq.set_SequenceString("aaaaaaaaaaaaaaaaaaaaa");
            seq.set_Length(new MobyInteger(20));
           
            mj.addData(seq);
           
            //mj.addDataElement(new )

            StringWriter writer = new StringWriter();
            XMLOutputter xo = new XMLOutputter();
            xo.setFormat(Format.getPrettyFormat());
            xo.output(mj.toXML(), writer);

**************************************************
Sure it's easy, but...

Thank you in advance,

Dmitry


From groscurt at mpiz-koeln.mpg.de  Fri Jun  8 12:21:04 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 8 Jun 2007 14:21:04 +0200
Subject: [MOBY-dev] Perl question
In-Reply-To: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
Message-ID: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>

Hiho,

because of the awesome perl hackers on the list.. I hope someone can help 
me....

I have the following Moby response

<?xml version="1.0" encoding="UTF-8"?>
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
  <moby:mobyContent>
    <moby:mobyData moby:queryID="sip_1_">
      <moby:Collection moby:articleName="pubmedID">
        <moby:Simple>
          <moby:Object moby:id="" moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
        </moby:Simple>
        <moby:Simple>
          <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
        </moby:Simple>
      </moby:Collection>
    </moby:mobyData>
  </moby:mobyContent>
</moby:MOBY>

and the following perl code

my $parser = XML::LibXML->new();
$parser->clean_namespaces( 1 );
my $doc = $parser->parse_string($resultXML);
my $root = $doc->getDocumentElement;

my @objectNodes = ();
# $outObjType = Object (!)
@objectNodes = $root->findnodes("//moby:$outObjType");
# deal with 'moby-less' xml tags:
@objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
my $resCnt = 0; # a result counter, used as default for file naming
# iterate over all result objects
foreach my $objectNode (@objectNodes) {
# create a filename and write the object to the cache directory

# if provider uses other namespaces (that is other
# than the start namespace of the application), get
# this and use it for cache file name
my ($ns,$id);
if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
     $ns = $objectNode->getAttributeNS('moby', 'namespace');
}
# deal with 'moby-less' attributes
elsif ( $objectNode->hasAttribute('namespace') ) {
  $ns = $objectNode->getAttribute('namespace');
}

as far as I understand this code (is from Dirks aggregator), it should parse 
the namespace of the element 'moby:Object'... but it doesnt.

I know nothing about LibXML and parsing xml in Perl.. so I was wondering, why 

if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
     $ns = $objectNode->getAttributeNS('moby', 'namespace');
}

is not working.

Any hints ?

Thanks
Andreas



From edward.kawas at gmail.com  Fri Jun  8 13:35:09 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 06:35:09 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <002301c7a9d1$d700a070$6400a8c0@notebook>

Hi Andreas,

So one of the problems is that getAttributeNS takes as argument a URI and
the attribute name.

However, that didn't fix the problem for you me.

So a quick hack would be to call getAttribute('moby:namespace');

Perhaps someone else knows why the 'right' way isn't working!

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 08, 2007 5:21 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Perl question
> 
> Hiho,
> 
> because of the awesome perl hackers on the list.. I hope someone can help
> me....
> 
> I have the following Moby response
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>   <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Collection moby:articleName="pubmedID">
>         <moby:Simple>
>           <moby:Object moby:id="" moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
>         </moby:Simple>
>       </moby:Collection>
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
> 
> and the following perl code
> 
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces( 1 );
> my $doc = $parser->parse_string($resultXML);
> my $root = $doc->getDocumentElement;
> 
> my @objectNodes = ();
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:$outObjType");
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> my $resCnt = 0; # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> # create a filename and write the object to the cache directory
> 
> # if provider uses other namespaces (that is other
> # than the start namespace of the application), get
> # this and use it for cache file name
> my ($ns,$id);
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> # deal with 'moby-less' attributes
> elsif ( $objectNode->hasAttribute('namespace') ) {
>   $ns = $objectNode->getAttribute('namespace');
> }
> 
> as far as I understand this code (is from Dirks aggregator), it should
> parse
> the namespace of the element 'moby:Object'... but it doesnt.
> 
> I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> why
> 
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> 
> is not working.
> 
> Any hints ?
> 
> Thanks
> Andreas
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Fri Jun  8 13:37:35 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 06:37:35 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>

Actually, I guess that I haven't had all my coffee yet, because the 'right'
way does work (but not if you include other stuff in the URI!)

Here is the code:

my $parser = XML::LibXML->new();
$parser->clean_namespaces(1);
my $doc  = $parser->parse_string($stuff);
my $root = $doc->getDocumentElement;

my @objectNodes = ();

# $outObjType = Object (!)
@objectNodes = $root->findnodes("//moby:Object");

# deal with 'moby-less' xml tags:
@objectNodes = $root->findnodes("//Object") unless @objectNodes;
my $resCnt = 0;

# a result counter, used as default for file naming
# iterate over all result objects
foreach my $objectNode (@objectNodes) {
	my ( $ns, $id );
	if ( $objectNode->hasAttributeNS( 'http://www.biomoby.org/moby',
'namespace' ) ) {
		$ns = $objectNode->getAttributeNS(
'http://www.biomoby.org/moby', 'namespace' );
			}
	elsif ( $objectNode->hasAttribute('namespace') ) {
		$ns = $objectNode->getAttribute('namespace');
	
	}
	print $ns;
}

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 08, 2007 5:21 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Perl question
> 
> Hiho,
> 
> because of the awesome perl hackers on the list.. I hope someone can help
> me....
> 
> I have the following Moby response
> 
> <?xml version="1.0" encoding="UTF-8"?>
> <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>   <moby:mobyContent>
>     <moby:mobyData moby:queryID="sip_1_">
>       <moby:Collection moby:articleName="pubmedID">
>         <moby:Simple>
>           <moby:Object moby:id="" moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
>         </moby:Simple>
>         <moby:Simple>
>           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
>         </moby:Simple>
>       </moby:Collection>
>     </moby:mobyData>
>   </moby:mobyContent>
> </moby:MOBY>
> 
> and the following perl code
> 
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces( 1 );
> my $doc = $parser->parse_string($resultXML);
> my $root = $doc->getDocumentElement;
> 
> my @objectNodes = ();
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:$outObjType");
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> my $resCnt = 0; # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> # create a filename and write the object to the cache directory
> 
> # if provider uses other namespaces (that is other
> # than the start namespace of the application), get
> # this and use it for cache file name
> my ($ns,$id);
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> # deal with 'moby-less' attributes
> elsif ( $objectNode->hasAttribute('namespace') ) {
>   $ns = $objectNode->getAttribute('namespace');
> }
> 
> as far as I understand this code (is from Dirks aggregator), it should
> parse
> the namespace of the element 'moby:Object'... but it doesnt.
> 
> I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> why
> 
> if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
>      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> }
> 
> is not working.
> 
> Any hints ?
> 
> Thanks
> Andreas
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Fri Jun  8 17:14:49 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 08 Jun 2007 10:14:49 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <200706081421.04962.groscurt@mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
Message-ID: <op.ttl4uzcinbznux@personalpc>

On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth  
<groscurt at mpiz-koeln.mpg.de> wrote:


> <moby:Object moby:id="" moby:namespace="PMID_" />

that's an unusual namespace...  Where are you getting it from?

M

 



From markw at illuminae.com  Fri Jun  8 17:19:45 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 08 Jun 2007 10:19:45 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<002401c7a9d2$2d6b6df0$6400a8c0@notebook>
Message-ID: <op.ttl427b4nbznux@personalpc>

On Fri, 08 Jun 2007 06:37:35 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:


> does work (but not if you include other stuff in the URI!)

What "other stuff" do you mean??  Eddie is apparently just making up  
"other stuff" to stick into our URI's :-)

Please forgive him, he caught the illness that I had during the Moby  
meeting so he's as spaced-out as I was!

M
 


From gordonp at ucalgary.ca  Fri Jun  8 20:09:45 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 08 Jun 2007 14:09:45 -0600
Subject: [MOBY-dev] In Moby Central dead?
Message-ID: <4669B789.1030103@ucalgary.ca>

I can't ping it from the U of C. 

Maybe I killed it?


From edward.kawas at gmail.com  Fri Jun  8 20:16:42 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 8 Jun 2007 13:16:42 -0700
Subject: [MOBY-dev] In Moby Central dead?
In-Reply-To: <4669B789.1030103@ucalgary.ca>
References: <4669B789.1030103@ucalgary.ca>
Message-ID: <009a01c7aa09$edf284f0$6400a8c0@notebook>

Works for me.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Paul Gordon
> Sent: Friday, June 08, 2007 1:10 PM
> To: Core developer announcements
> Subject: [MOBY-dev] In Moby Central dead?
> 
> I can't ping it from the U of C.
> 
> Maybe I killed it?
> _______________________________________________
> 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  Sat Jun  9 17:14:36 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Sat, 09 Jun 2007 11:14:36 -0600
Subject: [MOBY-dev] Object Ontology problem
Message-ID: <466ADFFC.40700@ucalgary.ca>

Hi folks (Mark or Eddie especially I guess),

Can we please correct the definition of DNASequenceWithGFFFeatures, it 
has a member without an article name!

  <owl:Class 
rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequenceWithGFFFeatures">
    <moby:has>
      <mobyObject:BasicGFFSequenceFeature>
        <moby:articleName xml:lang="en"><!-- Paul says there should be a 
name here... --></moby:articleName>
      </mobyObject:BasicGFFSequenceFeature>
    </moby:has>
    <rdfs:subClassOf>
      <owl:Class 
rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
    </rdfs:subClassOf>



From edward.kawas at gmail.com  Sat Jun  9 20:58:36 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Sat, 9 Jun 2007 13:58:36 -0700
Subject: [MOBY-dev] Object Ontology problem
In-Reply-To: <466ADFFC.40700@ucalgary.ca>
References: <466ADFFC.40700@ucalgary.ca>
Message-ID: <001b01c7aad8$f33fefe0$6400a8c0@notebook>

I will look into it. There are others out there, but thanks for pointing
that one 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 Paul Gordon
> Sent: Saturday, June 09, 2007 10:15 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Object Ontology problem
> 
> Hi folks (Mark or Eddie especially I guess),
> 
> Can we please correct the definition of DNASequenceWithGFFFeatures, it
> has a member without an article name!
> 
>   <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-
> S/Objects#DNASequenceWithGFFFeatures">
>     <moby:has>
>       <mobyObject:BasicGFFSequenceFeature>
>         <moby:articleName xml:lang="en"><!-- Paul says there should be a
> name here... --></moby:articleName>
>       </mobyObject:BasicGFFSequenceFeature>
>     </moby:has>
>     <rdfs:subClassOf>
>       <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
>     </rdfs:subClassOf>
> 
> _______________________________________________
> 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  Sun Jun 10 09:13:27 2007
From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de)
Date: Sun, 10 Jun 2007 11:13:27 +0200 (CEST)
Subject: [MOBY-dev] Perl question
In-Reply-To: <op.ttl4uzcinbznux@personalpc>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<op.ttl4uzcinbznux@personalpc>
Message-ID: <61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>

> On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth
> <groscurt at mpiz-koeln.mpg.de> wrote:
>
>
>> <moby:Object moby:id="" moby:namespace="PMID_" />
>
> that's an unusual namespace...  Where are you getting it from?
>
> M
Its part of the Locus2Publications Service from Chris Wilks (tair)
registered at the test central....



From groscurt at mpiz-koeln.mpg.de  Mon Jun 11 09:49:30 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Mon, 11 Jun 2007 11:49:30 +0200
Subject: [MOBY-dev] Perl question
In-Reply-To: <002401c7a9d2$2d6b6df0$6400a8c0@notebook>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<002401c7a9d2$2d6b6df0$6400a8c0@notebook>
Message-ID: <200706111149.30222.groscurt@mpiz-koeln.mpg.de>

Awesome :-)

works fine.. thanks for that

Andreas

On Friday 08 June 2007 15:37, Edward Kawas wrote:
> Actually, I guess that I haven't had all my coffee yet, because the 'right'
> way does work (but not if you include other stuff in the URI!)
>
> Here is the code:
>
> my $parser = XML::LibXML->new();
> $parser->clean_namespaces(1);
> my $doc  = $parser->parse_string($stuff);
> my $root = $doc->getDocumentElement;
>
> my @objectNodes = ();
>
> # $outObjType = Object (!)
> @objectNodes = $root->findnodes("//moby:Object");
>
> # deal with 'moby-less' xml tags:
> @objectNodes = $root->findnodes("//Object") unless @objectNodes;
> my $resCnt = 0;
>
> # a result counter, used as default for file naming
> # iterate over all result objects
> foreach my $objectNode (@objectNodes) {
> 	my ( $ns, $id );
> 	if ( $objectNode->hasAttributeNS( 'http://www.biomoby.org/moby',
> 'namespace' ) ) {
> 		$ns = $objectNode->getAttributeNS(
> 'http://www.biomoby.org/moby', 'namespace' );
> 			}
> 	elsif ( $objectNode->hasAttribute('namespace') ) {
> 		$ns = $objectNode->getAttribute('namespace');
>
> 	}
> 	print $ns;
> }
>
> Eddie
>
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> > Sent: Friday, June 08, 2007 5:21 AM
> > To: moby-dev at lists.open-bio.org
> > Subject: [MOBY-dev] Perl question
> >
> > Hiho,
> >
> > because of the awesome perl hackers on the list.. I hope someone can help
> > me....
> >
> > I have the following Moby response
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
> >   <moby:mobyContent>
> >     <moby:mobyData moby:queryID="sip_1_">
> >       <moby:Collection moby:articleName="pubmedID">
> >         <moby:Simple>
> >           <moby:Object moby:id="" moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="7743940   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="9090879   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >         <moby:Simple>
> >           <moby:Object moby:id="9090880   " moby:namespace="PMID_" />
> >         </moby:Simple>
> >       </moby:Collection>
> >     </moby:mobyData>
> >   </moby:mobyContent>
> > </moby:MOBY>
> >
> > and the following perl code
> >
> > my $parser = XML::LibXML->new();
> > $parser->clean_namespaces( 1 );
> > my $doc = $parser->parse_string($resultXML);
> > my $root = $doc->getDocumentElement;
> >
> > my @objectNodes = ();
> > # $outObjType = Object (!)
> > @objectNodes = $root->findnodes("//moby:$outObjType");
> > # deal with 'moby-less' xml tags:
> > @objectNodes = $root->findnodes("//$outObjType") unless @objectNodes;
> > my $resCnt = 0; # a result counter, used as default for file naming
> > # iterate over all result objects
> > foreach my $objectNode (@objectNodes) {
> > # create a filename and write the object to the cache directory
> >
> > # if provider uses other namespaces (that is other
> > # than the start namespace of the application), get
> > # this and use it for cache file name
> > my ($ns,$id);
> > if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
> >      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> > }
> > # deal with 'moby-less' attributes
> > elsif ( $objectNode->hasAttribute('namespace') ) {
> >   $ns = $objectNode->getAttribute('namespace');
> > }
> >
> > as far as I understand this code (is from Dirks aggregator), it should
> > parse
> > the namespace of the element 'moby:Object'... but it doesnt.
> >
> > I know nothing about LibXML and parsing xml in Perl.. so I was wondering,
> > why
> >
> > if ( $objectNode->hasAttributeNS('moby', 'namespace') ) {
> >      $ns = $objectNode->getAttributeNS('moby', 'namespace');
> > }
> >
> > is not working.
> >
> > Any hints ?
> >
> > Thanks
> > Andreas
> >
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447



From gordonp at ucalgary.ca  Mon Jun 11 14:51:01 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 11 Jun 2007 08:51:01 -0600
Subject: [MOBY-dev] Seahawk Testing
Message-ID: <466D6155.7070905@ucalgary.ca>

Hello fellow MOBYers,

I've posted an update of the Seahawk applet to:

http://moby.ucalgary.ca/seahawk

I fixed several small bugs, and added the capability to specify a 
different central registry (using the new "Preferences" dialog box).
If you choose a different MOBY central, I suggest you close your browser 
and restart Seahawk.
If you get a chance, please check it out and let me know of any bugs you 
find, before we start unleashing MOBY virgins on it in
the next couple of weeks. 
I am hoping (as Mark alluded to last week) that Seahawk can help the 
less technically inclined than us actually use MOBY to its
full potential.  Brief overview of some features:

-Zero install (signed applet)
-Data creation by highlighting (see the Help file)
-Drag and drop support (e.g. drag sample data from the API specification 
from your Web browser onto Seahawk).  I use this a lot.
-Secondary and multiple-primary parameter support
-Hierarchical service selection menus
-Support for "asynchronous" services, in the Spanish style :-)
-A moby data clipboard
-Exports browsing history as SCUFL (read: Taverna) workflow
-Multiple tabs, for concurrent service execution
-Open source:  its all in the Java MOBY CVS

Near-future features:
-Web-forms as MOBY Services: wrapping-by-example
-Sidebar with Favorites and Suggestions

Happy MOBYing!

Paul

P.S. The Seahawk JAR file 
(http://moby.ucalgary.ca/seahawk/java/seahawk.jar) can also be used 
directly as an application, i.e.: java -jar seahawk.jar
If there is demand, I will create an InstallAnywhere package for it.


From markw at illuminae.com  Tue Jun 12 15:52:50 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 12 Jun 2007 08:52:50 -0700
Subject: [MOBY-dev] Perl question
In-Reply-To: <61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>
References: <mailman.487.1180970312.2714.moby-dev@lists.open-bio.org>
	<200706081421.04962.groscurt@mpiz-koeln.mpg.de>
	<op.ttl4uzcinbznux@personalpc>
	<61444.89.52.167.215.1181466807.squirrel@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <op.tttfqc0tnbznux@personalpc>

Ah, OK.  that namespace doesn't exist in the "real" registry, so I was a  
bit concerned.

M


On Sun, 10 Jun 2007 02:13:27 -0700, <groscurt at mpiz-koeln.mpg.de> wrote:

>> On Fri, 08 Jun 2007 05:21:04 -0700, Andreas Groscurth
>> <groscurt at mpiz-koeln.mpg.de> wrote:
>>
>>
>>> <moby:Object moby:id="" moby:namespace="PMID_" />
>>
>> that's an unusual namespace...  Where are you getting it from?
>>
>> M
> Its part of the Locus2Publications Service from Chris Wilks (tair)
> registered at the test central....
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 



From edward.kawas at gmail.com  Thu Jun 14 17:02:50 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 14 Jun 2007 10:02:50 -0700
Subject: [MOBY-dev] Object Ontology problem
In-Reply-To: <466ADFFC.40700@ucalgary.ca>
References: <466ADFFC.40700@ucalgary.ca>
Message-ID: <008401c7aea5$d74049e0$6400a8c0@notebook>

I have fixed this datatype on mobycentral. I gave it an articlename of
'feature'.

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 Paul Gordon
> Sent: Saturday, June 09, 2007 10:15 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Object Ontology problem
> 
> Hi folks (Mark or Eddie especially I guess),
> 
> Can we please correct the definition of DNASequenceWithGFFFeatures, it
> has a member without an article name!
> 
>   <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-
> S/Objects#DNASequenceWithGFFFeatures">
>     <moby:has>
>       <mobyObject:BasicGFFSequenceFeature>
>         <moby:articleName xml:lang="en"><!-- Paul says there should be a
> name here... --></moby:articleName>
>       </mobyObject:BasicGFFSequenceFeature>
>     </moby:has>
>     <rdfs:subClassOf>
>       <owl:Class
> rdf:about="http://biomoby.org/RESOURCES/MOBY-S/Objects#DNASequence"/>
>     </rdfs:subClassOf>
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Tue Jun 19 15:40:02 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 19 Jun 2007 08:40:02 -0700
Subject: [MOBY-dev] Making the clients more obvious
Message-ID: <op.tt6ds2d7nbznux@personalpc>

Hiya,

There was a criticizm during the last meeting that one of the reasons that  
the website "sucks" is that it was too hard to find the Moby browsers so  
that people could get in and start using Moby.

I just tweaked the homepage so that it is easier to get to the Moby  
browsers.

Let me know if this is better, or if there could still be improvements.

M



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From gordonp at ucalgary.ca  Thu Jun 21 19:48:38 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 21 Jun 2007 13:48:38 -0600
Subject: [MOBY-dev] Seahawk JAR availability
Message-ID: <467AD616.2010806@ucalgary.ca>

Hi everyone,

I noticed in my server error logs that some people have been trying to 
download the Seahawk JAR file (for development purposes, I suppose) from 
its old URL. 
I found the incorrect link in the jMOBY docs and updated it to point to 
the correct URL.  Sorry for any inconvenience!

Regards,

Paul


From markw at illuminae.com  Fri Jun 22 17:03:58 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 22 Jun 2007 10:03:58 -0700
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
Message-ID: <op.tub1owwgnbznux@personalpc>

Hi all,

One of the TODO's that was assigned to me was the task of getting MOBY  
Central prepared for multi-lingual support.  I've been investigating how  
to do this, and it looks like it is going to be a bit of a blocker.

According to the XML specification, the xml:lang attribute is supposed to  
apply to the node it is in, and any sub-node until another xml:lang  
attribute is encountered.  Unfortunately, most of the XML parsing  
libraries in Perl do not even notice the xml:lang attribute as "special",  
so you only have access to it as a normal attribute in the node where it  
is included.

There is one XML parsing library in Perl that does keep track of this  
attribute (XML::LibXML::Reader); however that is not available on Windows  
using ActiveState's Perl and PPM, which is what most Windows users will be  
using, I suspect.. (though I know it is possible to use Cygwin also).  I  
also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
some odd modules that you can't get anywhere else, but it isn't there  
either.

So... I guess there are several possibilities:

1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
as part of Moby

1a)  we modify XML::LibXML such that it does recognize and make note of  
this attribute, and contribute that back to the authors

2)  I re-code Moby such that it traverses back up the XML tree looking for  
the last xml:lang attribute for every node that has content.

3)  We put an additional constraint on the rules of XML, requiring that  
the xml:lang attribute must be present in the same node in which the  
multilingul content is present.

4)  ??? give up :-)


Can someone have a quick look at how well xml:lang is supported on the  
Java side, since that will help us make the decision on what to do.  If it  
isn't supported in the Java libraries either, then maybe #3 is the only  
rational (ugly) solution?

M




-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From gordonp at ucalgary.ca  Fri Jun 22 18:05:16 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 22 Jun 2007 12:05:16 -0600
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
In-Reply-To: <op.tub1owwgnbznux@personalpc>
References: <op.tub1owwgnbznux@personalpc>
Message-ID: <467C0F5C.2080907@ucalgary.ca>

Just throwing this out there:

I like option 3 (requiring xml:lang in the description tags).  It may 
seem like a kludge, but we decided that the
multilinguality is only supported at the description level in MOBY, 
right?  We assume that all other fields (such as
object name) are opaque tokens in the ontology, and these tokens happen 
to mostly be in semi-intelligible English.
I don't think we want to start supporting synonyms for object names yet, 
as this would require quite a bit of work.
Maybe in MOBY 1.5? :-)

An analogy might be sheet music.  Everyone who reads music knows the 
instruction keywords, which happen to be in Italian
(like biologists usually know key concepts in English, as well as their 
native tongue).  In the short term, option 3
sounds reasonable to me.
> Hi all,
>
> One of the TODO's that was assigned to me was the task of getting MOBY  
> Central prepared for multi-lingual support.  I've been investigating how  
> to do this, and it looks like it is going to be a bit of a blocker.
>
> According to the XML specification, the xml:lang attribute is supposed to  
> apply to the node it is in, and any sub-node until another xml:lang  
> attribute is encountered.  Unfortunately, most of the XML parsing  
> libraries in Perl do not even notice the xml:lang attribute as "special",  
> so you only have access to it as a normal attribute in the node where it  
> is included.
>
> There is one XML parsing library in Perl that does keep track of this  
> attribute (XML::LibXML::Reader); however that is not available on Windows  
> using ActiveState's Perl and PPM, which is what most Windows users will be  
> using, I suspect.. (though I know it is possible to use Cygwin also).  I  
> also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
> some odd modules that you can't get anywhere else, but it isn't there  
> either.
>
> So... I guess there are several possibilities:
>
> 1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
> as part of Moby
>
> 1a)  we modify XML::LibXML such that it does recognize and make note of  
> this attribute, and contribute that back to the authors
>
> 2)  I re-code Moby such that it traverses back up the XML tree looking for  
> the last xml:lang attribute for every node that has content.
>
> 3)  We put an additional constraint on the rules of XML, requiring that  
> the xml:lang attribute must be present in the same node in which the  
> multilingul content is present.
>
> 4)  ??? give up :-)
>
>
> Can someone have a quick look at how well xml:lang is supported on the  
> Java side, since that will help us make the decision on what to do.  If it  
> isn't supported in the Java libraries either, then maybe #3 is the only  
> rational (ugly) solution?
>
> M
>
>
>
>
>   



From gordonp at ucalgary.ca  Fri Jun 22 18:05:16 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 22 Jun 2007 12:05:16 -0600
Subject: [MOBY-dev] xml:lang  the story isn't pretty...
In-Reply-To: <op.tub1owwgnbznux@personalpc>
References: <op.tub1owwgnbznux@personalpc>
Message-ID: <467C0F5C.2080907@ucalgary.ca>

Just throwing this out there:

I like option 3 (requiring xml:lang in the description tags).  It may 
seem like a kludge, but we decided that the
multilinguality is only supported at the description level in MOBY, 
right?  We assume that all other fields (such as
object name) are opaque tokens in the ontology, and these tokens happen 
to mostly be in semi-intelligible English.
I don't think we want to start supporting synonyms for object names yet, 
as this would require quite a bit of work.
Maybe in MOBY 1.5? :-)

An analogy might be sheet music.  Everyone who reads music knows the 
instruction keywords, which happen to be in Italian
(like biologists usually know key concepts in English, as well as their 
native tongue).  In the short term, option 3
sounds reasonable to me.
> Hi all,
>
> One of the TODO's that was assigned to me was the task of getting MOBY  
> Central prepared for multi-lingual support.  I've been investigating how  
> to do this, and it looks like it is going to be a bit of a blocker.
>
> According to the XML specification, the xml:lang attribute is supposed to  
> apply to the node it is in, and any sub-node until another xml:lang  
> attribute is encountered.  Unfortunately, most of the XML parsing  
> libraries in Perl do not even notice the xml:lang attribute as "special",  
> so you only have access to it as a normal attribute in the node where it  
> is included.
>
> There is one XML parsing library in Perl that does keep track of this  
> attribute (XML::LibXML::Reader); however that is not available on Windows  
> using ActiveState's Perl and PPM, which is what most Windows users will be  
> using, I suspect.. (though I know it is possible to use Cygwin also).  I  
> also looked at the "theoryx" PPM repository in Winnipeg, which usually has  
> some odd modules that you can't get anywhere else, but it isn't there  
> either.
>
> So... I guess there are several possibilities:
>
> 1)  we attempt to compile XML::LibXML::Reader on Windows and distribute it  
> as part of Moby
>
> 1a)  we modify XML::LibXML such that it does recognize and make note of  
> this attribute, and contribute that back to the authors
>
> 2)  I re-code Moby such that it traverses back up the XML tree looking for  
> the last xml:lang attribute for every node that has content.
>
> 3)  We put an additional constraint on the rules of XML, requiring that  
> the xml:lang attribute must be present in the same node in which the  
> multilingul content is present.
>
> 4)  ??? give up :-)
>
>
> Can someone have a quick look at how well xml:lang is supported on the  
> Java side, since that will help us make the decision on what to do.  If it  
> isn't supported in the Java libraries either, then maybe #3 is the only  
> rational (ugly) solution?
>
> M
>
>
>
>
>   



From gordonp at ucalgary.ca  Mon Jun 25 19:42:58 2007
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 25 Jun 2007 13:42:58 -0600
Subject: [MOBY-dev] FYI: A Calgary company uses the MOBY moniker too...
Message-ID: <46801AC2.1090907@ucalgary.ca>

Luckily they are pages, not services :-)

www.*moby**pages*.com


From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 10:14:24 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 12:14:24 +0200
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <467AD616.2010806@ucalgary.ca>
References: <467AD616.2010806@ucalgary.ca>
Message-ID: <200706291214.25053.groscurt@mpiz-koeln.mpg.de>

Hi all,

in Dirks code of the aggregator he has its own findeService workaround 
implementation with the following comment:

  # This is a workaround for a missing feature of MOBY::Central->findService,
  # namely the lacking expansion of objects to leaves direction for the output
  # side.
  # As soon as this is implemented in MOBY::Central, this should be used
  # directly, that is, this method here (and the whole module...) becomes 
  # redundant.

I just wanted to know whether this is still an issue, not anymore or not even 
at all has been any issue :-)

Thanks
Andreas

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447



From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 13:05:27 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 15:05:27 +0200
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <200706291214.25053.groscurt@mpiz-koeln.mpg.de>
References: <467AD616.2010806@ucalgary.ca>
	<200706291214.25053.groscurt@mpiz-koeln.mpg.de>
Message-ID: <200706291505.27668.groscurt@mpiz-koeln.mpg.de>

Hi all again,

I couldnt find anything about this, so I hope you can help me with this simple 
one:

Actually I only want to find services with specific informations, e.g. I want 
to find all services with a specific input or output namespace and so on.

I fail by creating a service with my needs.

The way I thought of doing it is to create a Central instance and call the 
findService method with a MobyService as parameter. 
My current problem is how to tell the Mobyservice which inputs it has to 
consume ?

E.g. how to tell that I want an GenBank identifier as input ? 

The MobyService has the method setInput, which requires MobyData... and i 
couldnt get any connection from MobyData to MobyObject (to set the namespace 
then to GenBank or whatsoever).

So how can I tell the service which MobyObjects I want to use or how can I 
find services with a given input and / or ouput ?

Thanks
obedient Andreas

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447



From edward.kawas at gmail.com  Fri Jun 29 13:09:21 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 29 Jun 2007 06:09:21 -0700
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <200706291505.27668.groscurt@mpiz-koeln.mpg.de>
References: <467AD616.2010806@ucalgary.ca><200706291214.25053.groscurt@mpiz-koeln.mpg.de>
	<200706291505.27668.groscurt@mpiz-koeln.mpg.de>
Message-ID: <001701c7ba4e$b5d2e060$6400a8c0@notebook>

Hi Andreas,

Hopefully this helps you out!
	CentralImpl central = new CentralImpl();
	MobyService s = new MobyService();
	s.setCategory("");
	MobyDataObject data = new MobyDataObject("");
	data.setDataType(new MobyDataType("Object"));
	data.addNamespace(new MobyNamespace("NCBI_gi"));
	MobyDataObjectSet set = new MobyDataObjectSet("");
	set.add(data);
	s.addOutput((set));
	MobyService[] services = central.findService(s,null,true,false);

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> Sent: Friday, June 29, 2007 6:05 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Another Java API question
> 
> Hi all again,
> 
> I couldnt find anything about this, so I hope you can help me with this
> simple
> one:
> 
> Actually I only want to find services with specific informations, e.g. I
> want
> to find all services with a specific input or output namespace and so on.
> 
> I fail by creating a service with my needs.
> 
> The way I thought of doing it is to create a Central instance and call the
> findService method with a MobyService as parameter.
> My current problem is how to tell the Mobyservice which inputs it has to
> consume ?
> 
> E.g. how to tell that I want an GenBank identifier as input ?
> 
> The MobyService has the method setInput, which requires MobyData... and i
> couldnt get any connection from MobyData to MobyObject (to set the
> namespace
> then to GenBank or whatsoever).
> 
> So how can I tell the service which MobyObjects I want to use or how can I
> find services with a given input and / or ouput ?
> 
> Thanks
> obedient Andreas
> 
> --
> Andreas Groscurth
> Diplom Bioinformatik - PhD Student
> Max Planck Institute for Plant Breeding Research
> Carl-von-Linn?-Weg 10
> 50829 Cologne
> Germany
> E-mail: ? ?groscurt at mpiz-koeln.mpg.de
> Phone: ? ?+49(0)221-5062-447
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From haase_dirk at web.de  Fri Jun 29 13:32:19 2007
From: haase_dirk at web.de (Dirk Haase)
Date: Fri, 29 Jun 2007 15:32:19 +0200
Subject: [MOBY-dev] Question MobyCentral API
Message-ID: <1140939448@web.de>

Hi Andreas,

> Hi all,
> 
> in Dirks code of the aggregator he has its own findeService workaround 
> implementation with the following comment:
> 
>   # This is a workaround for a missing feature of MOBY::Central->findService,
>   # namely the lacking expansion of objects to leaves direction for the output
>   # side.
>   # As soon as this is implemented in MOBY::Central, this should be used
>   # directly, that is, this method here (and the whole module...) becomes 
>   # redundant.
> 
> I just wanted to know whether this is still an issue, not anymore or not even 
> at all has been any issue :-)

It WAS an issue... But if I remember correctly, I submitted the according changes
to the CVS in February and the new code was also deployed on MOBY Central.
Mark, Eddie, please correct me if I'm wrong.

Best,
dirk


From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 14:06:21 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 16:06:21 +0200
Subject: [MOBY-dev] Another Java API question
In-Reply-To: <001701c7ba4e$b5d2e060$6400a8c0@notebook>
References: <467AD616.2010806@ucalgary.ca>
	<200706291505.27668.groscurt@mpiz-koeln.mpg.de>
	<001701c7ba4e$b5d2e060$6400a8c0@notebook>
Message-ID: <200706291606.21798.groscurt@mpiz-koeln.mpg.de>

Thanks eddie the code is working !

I even figured out how to retrieve service which does not need a collection as 
input :-)

Thanks
Andreas

On Friday 29 June 2007 15:09, Edward Kawas wrote:
> Hi Andreas,
>
> Hopefully this helps you out!
> 	CentralImpl central = new CentralImpl();
> 	MobyService s = new MobyService();
> 	s.setCategory("");
> 	MobyDataObject data = new MobyDataObject("");
> 	data.setDataType(new MobyDataType("Object"));
> 	data.addNamespace(new MobyNamespace("NCBI_gi"));
> 	MobyDataObjectSet set = new MobyDataObjectSet("");
> 	set.add(data);
> 	s.addOutput((set));
> 	MobyService[] services = central.findService(s,null,true,false);
>
> Eddie
>
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth
> > Sent: Friday, June 29, 2007 6:05 AM
> > To: Core developer announcements
> > Subject: [MOBY-dev] Another Java API question
> >
> > Hi all again,
> >
> > I couldnt find anything about this, so I hope you can help me with this
> > simple
> > one:
> >
> > Actually I only want to find services with specific informations, e.g. I
> > want
> > to find all services with a specific input or output namespace and so on.
> >
> > I fail by creating a service with my needs.
> >
> > The way I thought of doing it is to create a Central instance and call
> > the findService method with a MobyService as parameter.
> > My current problem is how to tell the Mobyservice which inputs it has to
> > consume ?
> >
> > E.g. how to tell that I want an GenBank identifier as input ?
> >
> > The MobyService has the method setInput, which requires MobyData... and i
> > couldnt get any connection from MobyData to MobyObject (to set the
> > namespace
> > then to GenBank or whatsoever).
> >
> > So how can I tell the service which MobyObjects I want to use or how can
> > I find services with a given input and / or ouput ?
> >
> > Thanks
> > obedient Andreas
> >
> > --
> > Andreas Groscurth
> > Diplom Bioinformatik - PhD Student
> > Max Planck Institute for Plant Breeding Research
> > Carl-von-Linn?-Weg 10
> > 50829 Cologne
> > Germany
> > E-mail: ? ?groscurt at mpiz-koeln.mpg.de
> > Phone: ? ?+49(0)221-5062-447
> >
> > _______________________________________________
> > 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

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447



From groscurt at mpiz-koeln.mpg.de  Fri Jun 29 14:10:37 2007
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Fri, 29 Jun 2007 16:10:37 +0200
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <1140939448@web.de>
References: <1140939448@web.de>
Message-ID: <200706291610.37515.groscurt@mpiz-koeln.mpg.de>

Hi dirk,

nice to see you still on the list :-)

I currently try to find out why the correct automatic discovery of services 
fails on our local system, so I thought if this is not an issue anymore it 
can be removed and the error searches continue ;-)

best
andreas

On Friday 29 June 2007 15:32, Dirk Haase wrote:
> Hi Andreas,
>
> > Hi all,
> >
> > in Dirks code of the aggregator he has its own findeService workaround
> > implementation with the following comment:
> >
> >   # This is a workaround for a missing feature of
> > MOBY::Central->findService, # namely the lacking expansion of objects to
> > leaves direction for the output # side.
> >   # As soon as this is implemented in MOBY::Central, this should be used
> >   # directly, that is, this method here (and the whole module...) becomes
> >   # redundant.
> >
> > I just wanted to know whether this is still an issue, not anymore or not
> > even at all has been any issue :-)
>
> It WAS an issue... But if I remember correctly, I submitted the according
> changes to the CVS in February and the new code was also deployed on MOBY
> Central. Mark, Eddie, please correct me if I'm wrong.
>
> Best,
> dirk
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail: ? ?groscurt at mpiz-koeln.mpg.de
Phone: ? ?+49(0)221-5062-447



From markw at illuminae.com  Fri Jun 29 14:22:38 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 29 Jun 2007 07:22:38 -0700
Subject: [MOBY-dev] Question MobyCentral API
In-Reply-To: <1140939448@web.de>
References: <1140939448@web.de>
Message-ID: <op.tuosv5eznbznux@homecomp>

On Fri, 29 Jun 2007 06:32:19 -0700, Dirk Haase <haase_dirk at web.de> wrote:


> It WAS an issue... But if I remember correctly, I submitted the  
> according changes
> to the CVS in February and the new code was also deployed on MOBY  
> Central.
> Mark, Eddie, please correct me if I'm wrong.


I believe that is correct, but I haven't tried to test it.

M