Hi Nina,

I have created a basic ontology for the Maxtox model. Could please go
through it briefly when you have the time - and suggest improvements as well
as how we can fit this into the existing Ontology of Opentox. Just
indications will do (I understand you are already under a deadline
pressure...)

I have just started learning protege so a few concepts may have gone awry. I
have tried my best to get the gist of our prediction system into the
attached ontology.

Thanks in advance

Cheers
Surajit

On Tue, Feb 2, 2010 at 11:45 AM, Nina Jeliazkova <nina at acad.bg> wrote:

>  Hi Surajit,
>
>
> surajit ray wrote:
>
> Hi Nina,
>
>  Are we officially supposed to use the restlet2 m7 ?
>
>  The library and particular release are choice of the developer, so the
> answer is - it is up to you.
>
>  At this point I have few questions about this interaction
> a) Once a time consuming calculation is over - should the server notify an
> attached client about the result OR just sit with the data at a specified
> URL till it is fetched by the client ?
>
> The client sends GET requests and verifies if the result is ready (200 OK).
> Have a look at the API  at  http://opentox.org/dev/apis/api-1.1/AsyncTask
>
> When returning 303 (redirect) for an uncomplete task and making use of
> Refresh field, it is very easy to implement browser -like client to
> periodically check the task status. Browsers will automatically try to fetch
> the content after time interval, specified in Refresh:
>
>  (In the REST interface is it allowable for the server to contact a
> connected client ?)
>
> No.  REST is using HTTP protocol for communication and there is no any
> notion of an "attached" client.  The client sends GET/PUT/POST/DELETE
> request, receives an answer and there is no permanent between them after the
> response is sent.
> Unless you implement your client to behave as server as well, there is no
> way of server to tell the client anything, besides answering client request.
>
>  b) Should the server identify the client requesting the computation and
> authenticate before delivering the data OR give it to any client requesting
> the URI of the predicted/computed values ?
>
> We've decided to postpone everything, concerning authentication and
> authorization after the end of February, and currently all the services are
> open to everybody (I know it sounds scary :)
>
>  c) How long should the computed values be retained on the server OR
> should there be REST interface for destroying (and hence freeing up
> resources) a set of computed values ?
>
> It depends on your implementation.
>
> For example ambit services store everything in a database and keep the
> results forever, unless a delete operation is performed on specific
> resource.  REST way of deleting a resource is sending DELETE request
> (instead of POST or PUT, which are generaly for create/update).  For most of
> OpenTox resources DELETE operation is defined in the API (see wiki), but not
> everybody has implemented the full set of the API.
>
> d) Should there be an "account" like system for every client on the server
>
> See answer in (b).
>
> ? If yes - should the data generated by a client be attached to that
> "account" or available to all ?
>
> There might be public and private data, but at this moment we consider
> everything is public and will decide on details after finalizing
> deliverables at the end of this month.
>
>  Should the computed data persist indefinitely in each of these "accounts"
> ?
>
>  Again, it depends on your implementation.
>
> Best regards,
> Nina
>
>  Cheers
> Surajit
>
> On Tue, Feb 2, 2010 at 3:31 AM, Nina Jeliazkova <nina at acad.bg> wrote:
>
>> Hi Pantelis,
>>
>> There is a standard Java class java.util.concurrent.ExecutorService ; it
>> could be configured to work as a pool of fixed or variable number of
>> threads.
>>
>> There is a Restlet TaskService , which is wraps the ExecutorService.
>> I've found it behaved weird and switched to the standard Java class.
>>
>> You might look at ambit code at
>>
>>
>> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-www/src/main/java/ambit2/rest/AmbitApplication.java
>>
>> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-www/src/main/java/ambit2/rest/task
>>
>> For each asynchronous task, it creates a Callable class, which returns
>> Reference. Each tasks has an unique identifier (UUID) and the set of
>> tasks is stored in a ConcurrentMap. There is a timer, which removes
>> completed tasks few hours after completion.
>>
>> Hope this helps,
>> Nina
>>
>>
>> chung wrote:
>> > Hi Nina,
>> >  I'm trying to make some improvements on the services so except for the
>> > migration from restlet2 m3 to m7 I was thinking of introducing some
>> > execution pool (e.g. an ExecutorService or -why not- something
>> > 'homemade') and establish a queue for the incoming requests (especially
>> > those characterized as time-consuming and memory-consuming ones). This
>> > way I will be able to manage all running tasks on the server and make
>> > some performance improvements I hope. Is there some standard way of
>> > doing this? Could you suggest some executor or some utility to manage
>> > the running threads and do you know if there is some way to specify the
>> > maximum number of running threads for Restlet?
>> >
>> > Best Regards,
>> > Pantelis
>> >
>> >
>> > On Tue, 2010-01-26 at 14:21 +0200, Nina Jeliazkova wrote:
>> >
>> >> Hello All,
>> >>
>> >> Following the data type discussions and proposal earlier this month,
>> now
>> >> support for NumericFeature and NominalFeature are implemented in IDEA
>> >> services.
>> >>
>> >> Please note all features are explicitly declared to be subclass of
>> >> ot:Feature as well. While this is redundant and can be derived from the
>> >> ontology with a help of a reasoner, it does make the client
>> >> implementation somewhat easier.
>> >>
>> >> Examples from CPDBAS dataset at
>> >> http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/9
>> >>
>> >> <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12122>
>> >>       a       ot:Feature , ot:NominalFeature ;
>> >>       dc:identifier
>> >> "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12122"^^xsd:anyURI ;
>> >>       dc:title "ActivityOutcome_CPDBAS_SingleCellCall" ;
>> >>       ot:acceptValue "inactive" , "active" ;
>> >>       ot:hasSource
>> >> <http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11847> ;
>> >>       ot:units "" ;
>> >>       =       ot:ActivityOutcome_CPDBAS_SingleCellCall .
>> >>
>> >>
>> >> <http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12124>
>> >>       a       ot:Feature , ot:NumericFeature ;
>> >>       dc:identifier
>> >> "http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12124"^^xsd:anyURI ;
>> >>       dc:title "STRUCTURE_MolecularWeight" ;
>> >>       ot:hasSource
>> >> <http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11847> ;
>> >>       ot:units "" ;
>> >>       =       ot:STRUCTURE_MolecularWeight .
>> >>
>> >>
>> >> Bug reports are of course welcome at the usual place
>> >>
>> >> http://sourceforge.net/tracker/?group_id=191756
>> >>
>> >> Best regards,
>> >> Nina
>> >>
>> >>>
>> >>>
>> >>>>
>> >>>>
>> >>> 1) Feature data types:
>> >>> Proposal (based on Pantelis suggestions and Protege guide) at
>> >>> http://opentox.org/data/documents/development/RDF%20files/Datatypes.
>> >>> Updated opentox.owl at
>> >>>
>> http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/view
>> >>>
>> >>>
>> >>>
>> >> _______________________________________________
>> >> Development mailing list
>> >> Development at opentox.org
>> >> http://www.opentox.org/mailman/listinfo/development
>> >>
>> >>
>> >
>> >
>> > _______________________________________________
>> > Development mailing list
>> > Development at opentox.org
>> > http://www.opentox.org/mailman/listinfo/development
>> >
>>
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>
>
>
>
> --
> Surajit Ray
> Partner
> www.rareindianart.com
>
>
>


-- 
Surajit Ray
Partner
www.rareindianart.com
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