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

[Pieter Neerincx]

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
>>>
>>> _______________________________________________
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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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>
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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