Dear Pantelis, All,

chung wrote:
> On Fri, 2009-12-18 at 11:59 +0200, Nina Jeliazkova wrote:
>   
>> Dear Pantelis, All,
>>
>> chung wrote:
>>     
>>> However...
>>>
>>> * When building a new model, the service has to generate a new feature
>>> that will be used as a pointer to the predictions made by this model. Is
>>> this operation implemented?
>>>
>>>   
>>>       
>> Provided we don't have currently API for creating new features (these
>> are more or less embedded in datasets), there are two options I can
>> think of:
>>
>> 1) Extend the API to include Feature creation (independent of a
>> dataset), e.g. /feature POST rdf-representation-of-a-feature  (similar
>> to feature_definition POST in API 1.0)
>>
>>     
>
> The current version of the API (see
> http://opentox.org/dev/apis/api-1.1/Feature ) includes that operation.
> The client posts an RDF representation and creates a new feature URI.
>
>   
OK.   This is now  implemented in
http://ambit.uni-plovdiv.bg:8080/ambit2/feature .   POST any RDF
representation of a Feature object, as specified in opentox.owl with
application/rdf+xml , or text/n3 content type to create  a new feature.
>> 2) Embed the RDF representation of the new feature into the RDF
>> representation of the dataset, which is then POST-ed to a dataset service. 
>>
>> e.g. if a feature is described with triples  and there is no feature
>> URI, the dataset service will assume a new feature is to be created;
>>
>>     
>
> That's also a solution, but the embedded feature will not be globally
> accessible. I think the first solution is better. 
>
>   
I was assuming the dataset service will create a feature with globally
accessible URI.   This also could be used with
http://ambit.uni-plovdiv.bg:8080/ambit2/dataset
<http://ambit.uni-plovdiv.bg:8080/ambit2/feature>

To create a dataset, post an RDF representation of a dataset to
http://ambit.uni-plovdiv.bg:8080/ambit2/dataset
<http://ambit.uni-plovdiv.bg:8080/ambit2/feature> with content-type   
application/rdf+xml , or text/n3.
>   
>> In fact the two options are not mutually exclusive, with the first more
>> generic and the later requiring a single POST call to the dataset
>> service, instead of two (one for feature creation  and one for posting a
>> dataset).
>>
>>     
>
> Indeed in the first case we need two requests but the feature creation
> will not be very time consuming and the Content-length the client has to
> post is not that big, so I think the first option is not prohibitive. 
>
>   
>> Are there any preferences?
>>
>>     
>
> I'm in favor of the first solution. So if there are no objections I
> think we should proceed this way (because we're running out of time...)
>
>   
OK, please test any of the above.


After several trials and errors, I finally managed to use an ambit
dataset to create MLR model, as specified here
https://opentox.ntua.gr/index.php?p=guide

It seems the NTUA algorithm service expects parameters dataset_uri and
target to be within the posted content, rather than in the URL (my
initial assumption).  Do we have this specified in the API ? 

It would help with troubleshooting if in case of missing input the
service return client_error_bad_request with some explanation, than
internal server error (500).

Here is the successful call
1) curl -X POST -d
'dataset_uri=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/30&target=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12913'
http://opentox.ntua.gr:3000/algorithm/mlr

The dataset itself is a copy of |http://opentox.ntua.gr/ds.rdf, created
via POSTing its RDF/XMLrepresentation to
|http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/

2)Unsuccessful call  - here the dataset contains not only numerical, but
also string columns.

ambit:/home/nina# curl -X POST -d
'dataset_uri=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6&target=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'
http://opentox.ntua.gr:3000/algorithm/mlr -v
* About to connect() to opentox.ntua.gr port 3000 (#0)
*   Trying 147.102.82.32... connected
* Connected to opentox.ntua.gr (147.102.82.32) port 3000 (#0)
> POST /algorithm/mlr HTTP/1.1
> User-Agent: curl/7.18.2 (x86_64-pc-linux-gnu) libcurl/7.18.2
OpenSSL/0.9.8g zlib/1.2.3.3 libidn/1.8 libssh2/0.18
> Host: opentox.ntua.gr:3000
> Accept: */*
> Content-Length: 122
> Content-Type: application/x-www-form-urlencoded
>
< HTTP/1.1 500 empty String
< Content-Type: text/html; charset=ISO-8859-1
< Content-Length: 284
< Date: Sun, 20 Dec 2009 23:09:53 GMT
< Server: Noelios-Restlet/2.0m3
< Connection: close
<
<html>
<head>
   <title>Status page</title>
</head>
<body>
<h3>empty String</h3><p>You can get technical details <a
href="http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html#sec10.5.1">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>
* Closing connection #0

3)  Unsuccessful call:
If the dataset URI contains query parameters (in this case specifying to
include only 3 numerical features),  I am not sure if it is parsed
correctly by the NTUA service, or feature_uris[] parameter is perceived
as a separate one to the dataset_uri parameter. The entire dataset URI
should read:
 'dataset_uri=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6?feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11938&feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'

The entire (unsuccessful) call :
ambit:/home/nina# curl -X POST -d
'dataset_uri=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6?feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11938&feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951&target=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'
http://opentox.ntua.gr:3000/algorithm/mlr -v

* About to connect() to opentox.ntua.gr port 3000 (#0)
*   Trying 147.102.82.32... connected
* Connected to opentox.ntua.gr (147.102.82.32) port 3000 (#0)
> POST /algorithm/mlr HTTP/1.1
> User-Agent: curl/7.18.2 (x86_64-pc-linux-gnu) libcurl/7.18.2
OpenSSL/0.9.8g zlib/1.2.3.3 libidn/1.8 libssh2/0.18
> Host: opentox.ntua.gr:3000
> Accept: */*
> Content-Length: 329
> Content-Type: application/x-www-form-urlencoded
>
< HTTP/1.1 500 empty String

4)Unsuccessful call  (same as above, but with dataset_uri URL encoded)

ambit:/home/nina# curl -X POST -d
'dataset_uri=http%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Fdataset%2F6%3Ffeature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F11938%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F11947%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F11951&target=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'
http://opentox.ntua.gr:3000/algorithm/mlr -v
* About to connect() to opentox.ntua.gr port 3000 (#0)
*   Trying 147.102.82.32... connected
* Connected to opentox.ntua.gr (147.102.82.32) port 3000 (#0)
> POST /algorithm/mlr HTTP/1.1
> User-Agent: curl/7.18.2 (x86_64-pc-linux-gnu) libcurl/7.18.2
OpenSSL/0.9.8g zlib/1.2.3.3 libidn/1.8 libssh2/0.18
> Host: opentox.ntua.gr:3000
> Accept: */*
> Content-Length: 409
> Content-Type: application/x-www-form-urlencoded
>
< HTTP/1.1 500 For input string: "NC"

Most important question so far is - is the way of specifying parameters
as asciii data content and using syntax like below agreed and sufficient?

    dataset_uri=aaaa&target=bbbbb 

Do the services expect these parameter values to be URL encoded -
otherwise it is impossible to use e.g. URIs with query parameters.

Best regards,
Nina

> Best Regards
> Pantelis
>
>   
>>> * When a client posts a dataset on a model to make a prediction, then
>>> the service generates a new dataset which (according to the API) should
>>> be posted to a dataset service. Is this operation available?
>>>   
>>>       
>> ambit services accept SDF datasets on POST currently, and RDF upload
>> will be available later today (if everything works right).
>>     
>>> * How can I calculate a feature value for a certain compound URI? Is
>>> there an example (e.g. curl command)?
>>>
>>>   
>>>       
>> Perhaps we need "compound_uri" parameter for algorithm API, similar to 
>> Model API ?   
>>
>> AFAIK TUM are developing descriptor calculation service, it will make
>> sense to synchronize parameter names.
>>
>> Hope this helps,
>> Nina
>>
>>
>>     
>>> Best Regards,
>>> Pantelis
>>>
>>> _______________________________________________
>>> 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
>>
>>     
>
>