[MOBY-dev] Re: parseMobyData

[Rebecca Ernst]

Hi Eddie, Mark, Pieter, Tom and others!

The problem No.1 (Collections in parsemobydata) is solved resp. it 
didn't exist.
As for every other service or scavenger Taverna decomposes the object 
into simples! (this is true for Taverna versions up to 1.1 and for 1.3. 
Not for the 1.2 release though but here Eddie has a bugfix via CVS)
The reason we believed it is a collection problem is that parsing of one 
service output failed which gives back collections.
Now we digged into it and found that Taverna doesn't have a problem with 
the object being a collection: the problem was that the service is 
registered as giving back simples but gives back collections. In 
contrast to gbrowse Taverna obviously only decomposes collections when 
it expects them to be there.

We had a look at the second problem (primitives in moby-objects) and 
think that your suggestion with further ports giving access to the 
primitives would solve the problem. If we got it right this would 
replace the 'parseMobyData' scavenger completely - is that right?


Cheers,
Rebecca and Dirk








Edward Kawas wrote:

>Hi Rebecca,
>
>I was unaware of those issues, mainly because I didn't touch
>that widget and I left it as is for compatibility reasons. 
>
>Also, I think that I could add support for parsing
>collections. Given a collection, return a list of whatever
>that widget returns.
>
>Moreover, you and Pieter have been talking about retrieving
>the string (and most likely integers, floats, etc) from the
>objects. Pieter went as far to say that he creates
>processors to do that for him. Do you think that it would be
>worthwhile to add another port to processors that contain
>the 'primitives' so that you can retrieve them? 
>
>For example, imagine that you are using a processor blastDB
>that performs a blast search on some database and returns
>the blast results in xml. In Moby, this would be a data type
>called text-xml (I think). Would it be useful to also have
>an output port that contains only the xml text in it?
>
>Let me know what you think. Most likely, you have a better
>idea. Tell it to me and I will see what I can do.
>
>Eddie
>
>  
>
>>-----Original Message-----
>>From: Rebecca Ernst [mailto:rebecca.ernst at gsf.de]
>>Sent: Wednesday, November 02, 2005 4:33 AM
>>To: Edward Kawas
>>Cc: mobydev
>>Subject: parseMobyData
>>
>>Hi Eddie!
>>
>>I had another look into Taverna to see if our workflows
>>now run
>>correctly but found two problems of parseMobyData.
>>The first problem is that parseMobyData can't deal with
>>collections (it
>>never could) the second is that it also can't deal with
>>the new object
>>stucture (e.g. a string object containing a string now) as
>>it only
>>checks the first layer content and never goes into the
>>additional string.
>>Do you know of these problems and if so - are there any
>>plans for fixing it?
>>
>>Cheers,
>>Rebecca
>>    
>>
>
>
>
>  
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de