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We're not suggesting adding a "polling tool"; instead the suggestion was
that your "WSDL tool generator" generate the XML tool definition and a
wrapper script.

That wrapper script would handle whatever WSDL operation it was created
for, polling, and collection of results (ALL IN ONE). Since polling is a
WSDL specific operation as you say, this would solve that, as every
generated tool would have code to submit+poll+collect.


Conditionals and loops would generate /many/ "empty" jobs saying "your
results are not done yet", which would not lend themselves to inclusion
in workflows. galaxy workflow loops are probably not the best way to
solve this particular problem.

Additionally, If you write your WSDL tool generator in such a way that
the generated tools handles the entire process: from submission to
retrieval of results, then they could be used in workflows and used with
the existing infrastructure, and jobs down the line could depend on the
output of your generated tools.

Cheers,
Eric

On 03/06/2014 08:25 AM, Michael E. Cotterell wrote:
> The tool is generic. This means that it is supposed to work (and does work) 
> with any WSDL. In the described use case, one of the operations/“generated 
> tools" already serves as a polling tool: it takes a unique id and requests a 
> result from the web service, then the web service either returns the results 
> or returns a message indicating that the results are not ready. 
> Conditionals/Loops would be a perfect way to solve this.
> 
> 
> If we added a polling tool like you described, then that tool would need to 
> Web service specific since not all web service adhere to the same naming 
> conventions and level of asynchrony.  
> 
> Sincerely,
> Michael E. Cotterell
> 
> Ph.D. Student in Computer Science, University of Georgia
> Instructor of Record, Graduate RA & TA, University of Georgia
> Department Liaison, CS Graduate Student Association, University of Georgia
> mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
> mepc...@uga.edu (mailto:mepc...@uga.edu)
> m...@cs.uga.edu (mailto:m...@cs.uga.edu)
> http://michaelcotterell.com/
> 
> 
> On Thursday, March 6, 2014 at 9:17 AM, Peter Cock wrote:
> 
>> On Thu, Mar 6, 2014 at 2:12 PM, Michael E. Cotterell
>> <mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)> wrote:
>>> While I agree that would work, the tool I'm working with generates
>>> tools for web operations in a generic fashion. That is, you provide
>>> it a WDSL and a list of operations you want from that WSDL, and
>>> then tool XML files are generated for each of those operations.
>>  
>>  
>>  
>> So could your "WDSL Galaxy Tool Factory" also produce a wrapper
>> script to go with the Galaxy Tool XML, where the wrapper script
>> handles polling the service with the unique identifier assigned by
>> the service?
>>  
>> Peter  
> 
> 

- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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