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

[Pieter Neerincx]

Hi Eddie,

On 11-Oct-2005, at 6:58 AM, Edward Kawas wrote:

> Hi Pieter,
>
> I uploaded 2 new files. I am not sure if your bug is fixed,
> but I thought that I would let you know. I have made new
> additions and I modified some of the xml parsing, so while I
> haven't worked on your bug, it may be fixed (or made worse
> ;-).

Well just tested the new versions and to be honest it kind of made it  
really bad :( I can not get any output anymore from any BioMOBY  
service. So I switched back to the previous versions of the *.jar  
files you had uploaded and apart from the missing articleName  
attribute things work again :).

>
> By the way, do you think that you could send me a workflow
> whenever you notice something fishy?

Sure. You mean the workflow saved as a scufl xml file I assume. Will  
do that in the future, but, in this case just try any BioMOBY  
service. Maybe some other files got updated as well in your  
development version apart from the 2 uploaded files...

Cheers,

Pieter

>
> Thanks,
>
> Eddie
>
> http://bioinfo.icapture.ubc.ca/ekawas/jars/taverna-1.3.jar
> http://bioinfo.icapture.ubc.ca/ekawas/jars/jmoby.jar
>
>
>> -----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: Friday, October 07, 2005 10:25 AM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] Taverna plugin bug?: elements
>> missing in BioMOBYobjects
>>
>> Hi Eddie,
>>
>> Sorry, I cheered premature :(. For one of my services I
>> use the
>> articleName attribute of two String objects to know which
>> one
>> contains which data. Hence I have something like:
>>
>> <SomeObject id="" namespace="some.ns">
>>      <String id="" namespace="another.ns"
>> articleName="this.one">
>>          Bla bla
>>      </String>
>>      <String id="" namespace="another.ns"
>> articleName="the.other.one">
>>          Alb alb
>>      </String>
>> <SomeObject>
>>
>> The Object my service receives in Taverna lacks the
>> articleName
>> attributes for it's String childs :(. Hence it becomes
>> this:
>>
>> <SomeObject id="" namespace="some.ns">
>>      <String id="" namespace="another.ns">
>>          Bla bla
>>      </String>
>>      <String id="" namespace="another.ns">
>>          Alb alb
>>      </String>
>> <SomeObject>
>>
>> Looks like the fix introduced a new bug as well...
>>
>> Pieter
>>
>> On  07Oct2005, at 11:30, Pieter Neerincx wrote:
>>
>>
>>> 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
>>>>
>>>>
>>
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>>
>
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