On Mon, 2009-12-21 at 14:21 +0200, Nina Jeliazkova wrote:
> 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.

Yes, I totally agree on that but I did create features for which I
specified the URI. Could you give an example of how could one create a
new feature without specifying or suggesting its URI. What I do not
understand is what should I write instead of:

<rdf:Description
rdf:about="http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13001">    
...

> > > 
> > > 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://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://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
> > 
> > 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" .

I retrieve the type of each feature by picking an arbitrary value and
check its datatype, so I have to change that. I agree that we might have
to establish something better and more generic - maybe an extension of
XSD types (for example http://www.w3.org/TR/xmlschema11-2/ , section 4 )



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

Yes, you are right. I think an acceptable solution would be to create a
new dataset URI for that dataset or better parse the feature_uris
parameters (as well as other dataset related parameters) in the
algorithm service.

Best regards,
Pantelis

> > > 
> > > 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/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
> > > > > > http://www.opentox.org/mailman/listinfo/development
> > > > > >   
> > > > > >       
> > > > > >           
> > > > > _______________________________________________
> > > > > Development mailing list
> > > > > Development at opentox.org
> > > > > http://www.opentox.org/mailman/listinfo/development
> > > > > 
> > > > >     
> > > > >         
> > > > 
> > > >       
> > > 
> > 
>