[MOBY-dev] Taverna plugin bug?: elements missing in BioMOBYobjects

Fri Oct 7 09:30:14 UTC 2005

Hi Eddie,

On 5-Oct-2005, at 2:52 AM, Edward Kawas wrote:

> Hi Pieter!
>
> I tracked down the bug and I fixed it (*fingers crossed*).
>
> I am placing 2 jar files at the following links that need to
> replace the ones in your /taverna-workbench-1.3/lib/
> directory:
> http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.jar
> http://bioinfo.icapture.ubc.ca/ekawas/jars/jmoby.jar
>
> Be sure to backup the 2 files you are about to replace, just
> in case!
>
> Then try out your workflows and let me know what happens.

I did some simple tests with the objects that failed previously and  
so far so good :)

Thanks for the quick fix!

>
> Also, if all is well, do you think that you could send me
> one of those workflows so I can use it as an example?

After a lot of trail and error playing with a local central I think  
it's about time I register my services and objects at the central  
Central as well. Will do so once the central Central databases are  
migrated to the new API...

Cheers,

Pi

> Thanks a lot,
>
> Eddie
>
>
>> -----Original Message-----
>> From: moby-dev-bounces at portal.open-bio.org [mailto:moby-
>> dev-bounces at portal.open-bio.org] On Behalf Of Pieter
>> Neerincx
>> Sent: Tuesday, October 04, 2005 9:04 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
>> missing in BioMOBYobjects
>>
>>
>> On 4-Oct-2005, at 5:12 PM, Edward Kawas wrote:
>>
>>
>>> No you are on to something! When I first created the
>>>
>> plugin,
>>
>>> I used a certain xml parser based on w3c dom. I had to
>>> switch to another parser and it seems that I was unaware
>>>
>> of
>>
>>> its limitations (getChildren only gets the direct
>>>
>> children
>>
>>> of an element).
>>>
>>> I will have this fixed fairly soon.
>>>
>>
>> I'm looking forward to "testdrive" it :)
>>
>> Thanks,
>>
>> Pieter
>>
>>
>>>
>>> Thanks,
>>>
>>> Eddie
>>>
>>>
>>>> -----Original Message-----
>>>> From: moby-dev-bounces at portal.open-bio.org
>>>>
>> [mailto:moby-
>>
>>>> dev-bounces at portal.open-bio.org] On Behalf Of Pieter
>>>> Neerincx
>>>> Sent: Tuesday, October 04, 2005 8:07 AM
>>>> To: Core developer announcements
>>>> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
>>>> missing in BioMOBYobjects
>>>>
>>>>
>>>> On 4-Oct-2005, at 3:44 PM, Edward Kawas wrote:
>>>>
>>>>
>>>>
>>>>>> moby:MOBY
>>>>>>      moby:Content
>>>>>>          moby:Data
>>>>>>              moby:Simple
>>>>>>                      moby:My_Child_Level_1B
>>>>>>                          moby:My_Child_Level_2A
>>>>>>                          moby:My_Child_Level_2B
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> Do you have an example of an object that has this type
>>>>>
>>>>>
>>>> of
>>>>
>>>>
>>>>> structure?
>>>>>
>>>>>
>>>>
>>>> Yes, try for example DnaSequenceHolder from the BioMOBY
>>>> Central.
>>>>
>>>> I have been running some other tests in the mean time
>>>>
>> and
>>
>>>> so far
>>>> almost every object I tried lacks child elements at
>>>>
>> level
>>
>>>> 2 or
>>>> further down. The only one that does have an element at
>>>> level 2 is
>>>> the BlastJob object I have in my local Central. This
>>>>
>> one
>>
>>>> has Strings,
>>>> Objects and a DataTime at level 2 or further down.
>>>> Everything is
>>>> missing except the DataTime primitive... I noticed that
>>>> hardly anyone
>>>> is using the DataTime primitive if I'm not the only one
>>>> using. It is
>>>> also hardly documented. Maybe it's just random noise in
>>>>
>> my
>>
>>>> testing or
>>>> maybe I'm onto something....
>>>>
>>>> If you want to try the BlastJob object my local
>>>>
>> registry
>>
>>>> should still
>>>> be accessible from outside at:
>>>> http://137.224.52.237/phenolink/biomoby/central/cgi-
>>>> bin/MOBY-Central.pl
>>>>
>>>> Hope this helps,
>>>>
>>>> Pi
>>>>
>>>>
>>>>
>>>>> Thanks,
>>>>>
>>>>> Eddie
>>>>>
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at biomoby.org
>>>>> http://www.biomoby.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
>>>> pieter.neerincx at wur.nl
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>>
>>>>
>>>
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>>>
>>>
>>
>>
>> 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
>> pieter.neerincx at wur.nl
>>
>>
>>
>> _______________________________________________
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>> http://www.biomoby.org/mailman/listinfo/moby-dev
>>
>
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> MOBY-dev at biomoby.org
> http://www.biomoby.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
pieter.neerincx at wur.nl