Hello Pantelis,
>>
>>
>
> I managed to create some features on the ambit server using the
> following curl command:
>
> curl -v -i -X POST -H 'Content-type:application/rdf+xml' -d '
> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
> xmlns:ot="http://www.opentox.org/api/1.1#"   
> xmlns:j.0="http://purl.org/net/nknouf/ns/bibtex#"   
> xmlns:owl="http://www.w3.org/2002/07/owl#"    
> xmlns:dc="http://purl.org/dc/elements/1.1/"    
> xmlns:xsd="http://www.w3.org/2001/XMLSchema#"    
> xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" >   
> <rdf:Description
> rdf:about="http://www.opentox.org/api/1.1#hasSource">     
> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>  
> </rdf:Description>  
> <rdf:Description rdf:about="http://www.opentox.org/api/1.1#units">    
> <rdf:type
> rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>  
> </rdf:Description>   
> <rdf:Description
> rdf:about="http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11889">   
> <rdfs:seeAlso>http://sth.com/feature/0</rdfs:seeAlso>    
> <dc:title>http://sth.com/feature/0</dc:title>     
> <dc:identifier
> rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11889</dc:identifier>  
>
> <rdf:type rdf:resource="http://purl.org/net/nknouf/ns/bibtex#Entry"/>   
> </rdf:Description>  
> <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Feature">    
> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>  
> </rdf:Description>  
> <rdf:Description
> rdf:about="http://purl.org/net/nknouf/ns/bibtex#Entry">    
> <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>  
> </rdf:Description>  
> <rdf:Description
> rdf:about="http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13001">    
> <dc:type>http://www.w3.org/2001/XMLSchema#string</dc:type>    
> <ot:hasSource
> rdf:resource="http://ambit.uni-plovdiv.bg:8080/ambit2/reference/11889"/>    
>
> <owl:sameAs>http://www.opentox.org/api/1.1#http://sth.com/feature/0</owl:sameAs>    
>
> <ot:units></ot:units>    
> <dc:title>http://sth.com/feature/0</dc:title>    
> <dc:identifier
> rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13001</dc:identifier>    
>
> <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Feature"/>  
> </rdf:Description> </rdf:RDF>'
> http://ambit.uni-plovdiv.bg:8080/ambit2/feature
>
> This generates a feature with a name I specify myself (that is
> http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13001 ). Is it
> possible that this name is
> automatically assigned by the service to the created feature resource?
>
No, you can't specify URI of the feature, it is generated
automatically.  dc:title will be retained though and accessible with
subsequent calls.  You will receive URI of the newly created feature
upon a successful call.  However, you could specify the feature is
owl:sameAs to a resource with arbitrary URI.

I am somewhat reluctant to allow creation of features with predefined
URIs ; one reason is it will be difficult to resolve in case more than
one client would like to create the same feature;would be better if the
link are established via ontologies.
>>
>> 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 ? 
>
> I think this is compliant with
> http://opentox.org/dev/apis/api-1.1/Model  (Is it?). I assume that the
> target is a parameter of the algorithm defined within the RDF
> representation of the algorithm.
> These parameters are provided within the posted content (-d
> 'dataset_uri=...&target=... ).
I have to check as well if it is compliant with the description from
http://opentox.org/dev/apis/api-1.1

    Parameters are posted with a
    "Content-Type:application/x-www-form-urlencoded" HTTP header.
    Parameter names are typed in *bold* letters in the API definitions.
    Square brackets (e.g. *compound_uris[]*) indicate that a list of
    arguments is expected.

>>
>> 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://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/
>
> This request fails in the case of svm models on opentox.ntua.gr but it
> works fine on my localhost. I will deploy the latest version and I
> think this will fix any bugs.
Yes, we haven't managed to create any other models than MLR via NTUA
service.
>>
>> 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://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"
>> <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
>
> The dataset http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6 does not
> contain purely numerical entries because they are declared to be of
> type xsd:string, so internally I handle these as strings, not as
> numbers. A modification of this dataset, changing these datatypes to
> xsd:double would fix this problem. However, I should return an
> explanatory message and a proper Status Code.
>
There is a mix of numeric and string entries.  I expected that you might
ignore the string entries (this is how I am going to proceed for a
clustering algorithm), but it might be better to return error code indeed.
> The text/x-arff representations you provide include some string and
> numeric declarations for the features of the dataset. So I think we
> should do something like that in the RDF.
Currently, I am using ,as you suggested , dc:type for the features (see
e.g. http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6) , but of course
we might decide to introduce something else.


<http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11946>
      a       ot:Feature ;
      dc:type "http://www.w3.org/2001/XMLSchema#double" .

<http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11950>
      a       ot:Feature ;
      dc:type "http://www.w3.org/2001/XMLSchema#double" .

<http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11948>
      a       ot:Feature ;
      dc:type "http://www.w3.org/2001/XMLSchema#string" .
>
> RDF representations, structurally, contain much more (meta)information
> about the objects they describe than ARFFs, so this piece of
> information in the text/x-arff (the datatype of each feature) IMHO has
> to be included in the RDF or at least - in order not to modify the RDF
> standards we adopted in API 1.1 - we should use proper XSD datatypes
> for every value. After all, its not 1^^double, 1^^string and
> 1^^nominal is not the same and won't (shouldn't) be handled the same
> way by a training algorithm.
Yes, especially for nominals, it would be better to introduce subclass
of Feature, rather than using XSD types for denoting the types.  I might
try to extend opentox.owl next days.
>>
>> 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/11938&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&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/11938&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&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://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
>
> I haven't implemented those feature_uris[]=... yet :-)
But in this case feature_uris[] are parameters to the ambit dataset
call, not to the http://opentox.ntua.gr:3000/algorithm/mlr  - the
problem is there is no way to say the dataset_uri is this entire one

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/11938&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris
<http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'

>>
>> 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 -
>
> As far as I know, you may use non-URL encoded parameters.
Yes, but I could not I specify as a value to dataset_uri= the following
line, without feature_uris[] being perceived as parameters of the
algorithm service call?

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/11938&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris
<http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11947&feature_uris>[]=http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11951'

>
>> otherwise it is impossible to use e.g. URIs with query parameters.
>
> I guess you can do that but I have to check this out.
>
ok
Best regards,
Nina
>
> Best Regards,
> Pantelis
>>
>> 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 <mailto:Development at opentox.org>
>>>>> http://www.opentox.org/mailman/listinfo/development
>>>>>   
>>>>>       
>>>>>           
>>>> _______________________________________________
>>>> Development mailing list
>>>> Development at opentox.org <mailto:Development at opentox.org>
>>>> http://www.opentox.org/mailman/listinfo/development
>>>>
>>>>     
>>>>         
>>>   
>>>       
>>
>