Hi all,
   Following Barry's and Nina's suggestion about documentation of web
services and REST API so that (external) developers can understand and
use the existing applications and create their own, we have created an
integrated client, parsing, and RDF creation facility which is available
for download from http://github.com/alphaville/ToxOtis  . Take a look at
the documentation at
http://github.com/alphaville/ToxOtis/tree/master/doc/ . Here is an
example of how one can download a dataset and parse it in a Java object,
modify some value, create a weka.core.Instances object and post it back
again:

    VRI vri = new VRI(Services.IDEACONSULT.augment("dataset",
"54").addUrlParameter("max", "5"));
    Dataset ds = new Dataset(vri).loadFromRemote();
   ds.getDataEntries().get(0).getFeatureValue(2).setValue(new
TypedValue(4.32));

    Task t =
ds.publishOnline(Services.AMBIT_UNI_PLOVDIV.augment("dataset"), null);
        System.out.println(t.getHasStatus());
        while (t.getHasStatus().equals(Task.Status.RUNNING)) {
            t.loadFromRemote();
            Thread.sleep(100);
     }
     System.out.println(t.getResultUri());

    weka.core.Instances data = ds.getInstances();
    System.out.println(data);

ToxOtis paves the way towards its use in third party source codes and
applications. Let me mention, that ToxOtis not being a graphical tool
might be an advantage; for example most users of Weka use it as a Java
library and not as a GUI.

Best regards,
Pantelis


On Thu, 2010-09-16 at 21:00 +0530, surajit ray wrote:

> Hi Nina,
> 
> Managed to get the upload working ... the upload tasks are completed
> and the uploaded datasets can be viewed online as well.
> 
> Just to outline once finally - To make this a part of any other workflow :
> 
> a) post a dataset uri to the respective model (1,2 &3 ) -
> 
> ex.
> 
> curl -X POST "dataset_uri=http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/6?max=5"
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1
> 
> b) The resulting task will finally give the URI of the remote task on
> the ambit server
> 
> c) the result_URI of the remote task (on the ambit server) contains
> the uploaded dataset (although at this time the server at
> "http://apps.ideaconsult.net:8080/ambit2/dataset" seems to be down)
> 
> (I tried polling the server to provide the dataset uri directly - but
> since the server went down could not complete the necessary mods and
> test.)
> 
> Could you please check if the process is fully complaint ...
> 
> Thanks in advance
> Surajit
> 
> 
> 
> On 13 September 2010 15:00, Nina Jeliazkova <jeliazkova.nina at gmail.com> wrote:
> > Hi,
> >
> > This one should be sufficiently small (3 compounds, 2 features - 1 name, one
> > TUM fragment descriptor ).
> >
> > http://apps.ideaconsult.net:8080/ambit2/dataset/2675?max=3&feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/27962&feature_uris[]=http://apps.ideaconsult.net:8080/ambit2/feature/31185&media=application%2Frdf%2Bxml&rdfwriter=jena
> >
> > <rdf:RDF
> >     xmlns:ac="http://apps.ideaconsult.net:8080/ambit2/compound/"
> >     xmlns:ot="http://www.opentox.org/api/1.1#"
> >     xmlns:bx="http://purl.org/net/nknouf/ns/bibtex#"
> >     xmlns:otee="http://www.opentox.org/echaEndpoints.owl#"
> >     xmlns:dc="http://purl.org/dc/elements/1.1/"
> >     xmlns:ar="http://apps.ideaconsult.net:8080/ambit2/reference/"
> >     xmlns="http://apps.ideaconsult.net:8080/ambit2/"
> >     xmlns:am="http://apps.ideaconsult.net:8080/ambit2/model/"
> >     xmlns:af="http://apps.ideaconsult.net:8080/ambit2/feature/"
> >     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
> >     xmlns:ad="http://apps.ideaconsult.net:8080/ambit2/dataset/"
> >     xmlns:ag="http://apps.ideaconsult.net:8080/ambit2/algorithm/"
> >     xmlns:owl="http://www.w3.org/2002/07/owl#"
> >     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
> >     xmlns:ota="http://www.opentox.org/algorithmTypes.owl#"
> >     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
> >   xml:base="http://apps.ideaconsult.net:8080/ambit2/">
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#Dataset"/>
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#Compound"/>
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#Feature"/>
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#FeatureValue"/>
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#NumericFeature">
> >     <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
> >   </owl:Class>
> >   <owl:Class rdf:about="http://www.opentox.org/api/1.1#DataEntry"/>
> >   <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#dataEntry"/>
> >   <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#hasSource"/>
> >   <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#values"/>
> >   <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#compound"/>
> >   <owl:ObjectProperty rdf:about="http://www.opentox.org/api/1.1#feature"/>
> >   <owl:DatatypeProperty rdf:about="http://www.opentox.org/api/1.1#units"/>
> >   <owl:DatatypeProperty rdf:about="http://www.opentox.org/api/1.1#value"/>
> >   <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/type"/>
> >   <owl:AnnotationProperty
> > rdf:about="http://purl.org/dc/elements/1.1/title"/>
> >   <owl:AnnotationProperty
> > rdf:about="http://purl.org/dc/elements/1.1/description"/>
> >   <ot:Dataset rdf:about="dataset/2675">
> >     <ot:dataEntry>
> >       <ot:DataEntry>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
> >             >1.0</ot:value>
> >             <ot:feature>
> >               <ot:NumericFeature rdf:about="feature/31185">
> >                 <dc:creator>Default</dc:creator>
> >                 <ot:hasSource
> > rdf:resource="http://localhost:8080/OpenTox-dev/algorithm/FTM5/c%28%3Ac%28%3Ac%28-C%29%29%29%28%3Ac%28%3Ac%28%3Ac%29%29%29"/>
> >                 <owl:sameAs
> > rdf:resource="http://www.opentox.org/api/1.1#TUM_FTM_c%28%3Ac%28%3Ac%28-C%29%29%29%28%3Ac%28%3Ac%28%3Ac%29%29%29"/>
> >                 <ot:units>count</ot:units>
> >                 <dc:title>TUM_FTM_c(:c(:c(-C)))(:c(:c(:c)))</dc:title>
> >                 <rdf:type
> > rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
> >               </ot:NumericFeature>
> >             </ot:feature>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >             >zolpidem tartrate</ot:value>
> >             <ot:feature>
> >               <ot:Feature rdf:about="feature/27962">
> >                 <dc:creator>195.178.207.240</dc:creator>
> >                 <ot:hasSource>290.sdf</ot:hasSource>
> >                 <owl:sameAs
> > rdf:resource="http://www.opentox.org/api/1.1#ChemicalName"/>
> >                 <ot:units></ot:units>
> >                 <dc:title>Name</dc:title>
> >               </ot:Feature>
> >             </ot:feature>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:compound>
> >           <ot:Compound rdf:about="compound/153272/conformer/505875"/>
> >         </ot:compound>
> >       </ot:DataEntry>
> >     </ot:dataEntry>
> >     <ot:dataEntry>
> >       <ot:DataEntry>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
> >             >1.0</ot:value>
> >             <ot:feature rdf:resource="feature/31185"/>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >             >amoxicillin</ot:value>
> >             <ot:feature rdf:resource="feature/27962"/>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:compound>
> >           <ot:Compound rdf:about="compound/150568/conformer/505874"/>
> >         </ot:compound>
> >       </ot:DataEntry>
> >     </ot:dataEntry>
> >     <ot:dataEntry>
> >       <ot:DataEntry>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
> >             >1.0</ot:value>
> >             <ot:feature rdf:resource="feature/31185"/>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:values>
> >           <ot:FeatureValue>
> >             <ot:value rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
> >             >pioglitazone hydrochloride</ot:value>
> >             <ot:feature rdf:resource="feature/27962"/>
> >           </ot:FeatureValue>
> >         </ot:values>
> >         <ot:compound>
> >           <ot:Compound rdf:about="compound/150563/conformer/505873"/>
> >         </ot:compound>
> >       </ot:DataEntry>
> >     </ot:dataEntry>
> >   </ot:Dataset>
> > </rdf:RDF>
> >
> > Hope this helps,
> > Nina
> >
> > On Mon, Sep 13, 2010 at 12:19 PM, surajit ray <mr.surajit.ray at gmail.com>
> > wrote:
> >>
> >> Hi,
> >>
> >> It would be helpful to have a working sample of a short dataset in
> >> RDF. That way I can compare this to my dataset representation to check
> >> why the upload task is failing on the ambit server.
> >>
> >> Regards
> >> Surajit
> >>
> >> On 10 September 2010 00:24, surajit ray <mr.surajit.ray at gmail.com> wrote:
> >> > Hi,
> >> >
> >> > Tried changing the order of the statements, putting this
> >> >
> >> > dataset.addProperty(OT.dataEntry, dataEntry);
> >> >
> >> > right after all the feature and feature value creation steps. I am
> >> > still getting the error on upload. Could you suggest the reason - so I
> >> > can troubleshoot it at our end
> >> >
> >> > Thanks
> >> > Surajit
> >> >
> >> > On 6 September 2010 12:27, Nina Jeliazkova <jeliazkova.nina at gmail.com>
> >> > wrote:
> >> >> Hi,
> >> >>
> >> >> On Fri, Sep 3, 2010 at 8:58 PM, surajit ray <mr.surajit.ray at gmail.com>
> >> >> wrote:
> >> >>>
> >> >>> Hi,
> >> >>>
> >> >>> Lemme take a look into that ....
> >> >>>
> >> >>> heres my code creating the dataset ... can you tell me whats wrong
> >> >>> with it
> >> >>> ?
> >> >>
> >> >>
> >> >>>
> >> >>> *****************************************
> >> >>>             this.resultDataset = createModel();
> >> >>>             Individual dataset =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(resultDataset.getOntClass(OT.OTClass.Dataset.getNS()));
> >> >>>             OT.OTClass.Dataset.createOntClass(resultDataset);
> >> >>
> >> >> Have to check if it indeed makes different to Jena, but may be worth
> >> >> changing the order of the two statements above (first creating the
> >> >> dataset
> >> >> class and then using it)
> >> >>
> >> >>>
> >> >>>             OT.OTClass.DataEntry.createOntClass(resultDataset);
> >> >>>             OT.OTClass.Feature.createOntClass(resultDataset);
> >> >>>             OT.OTClass.FeatureValue.createOntClass(resultDataset);
> >> >>>             OT.OTClass.Compound.createOntClass(resultDataset);
> >> >>>
> >> >>>
> >> >>>             for (int i=0 ; i<this.compoundURIs.length ; i++) {
> >> >>>                 //create data entry
> >> >>>                 Individual dataEntry =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(OT.OTClass.DataEntry.getOntClass(resultDataset));
> >> >>>                 dataset.addProperty(OT.dataEntry, dataEntry);
> >> >>>                 //add compound to data entry
> >> >>>                 Individual newcompound =
> >> >>> resultDataset.createIndividual(this.compoundURIs[i],
> >> >>> OT.OTClass.Compound.getOntClass(resultDataset));
> >> >>>                 dataEntry.addProperty(OT.compound, newcompound);
> >> >>>                 //First value
> >> >>>                 Individual feature1 =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(MaxtoxApplicationSettings.getServerRootPath()
> >> >>> + "/feature/" + modelNumber + "_prediction",
> >> >>> OT.OTClass.Feature.getOntClass(resultDataset));
> >> >>>                 Individual featureValue1 =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(OT.OTClass.FeatureValue.getOntClass(resultDataset));
> >> >>>                 featureValue1.addProperty(OT.feature, feature1);
> >> >>>                 featureValue1.addLiteral(OT.value,
> >> >>> resultDataset.createTypedLiteral(this.predictions[i],
> >> >>> XSDDatatype.XSDstring));
> >> >>>
> >> >>>                 //Second value
> >> >>>                 Individual feature2 =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(MaxtoxApplicationSettings.getServerRootPath()
> >> >>> + "/feature/" + modelNumber + "_fingerprint",
> >> >>> OT.OTClass.Feature.getOntClass(resultDataset));
> >> >>>                 Individual featureValue2 =
> >> >>>
> >> >>>
> >> >>> resultDataset.createIndividual(OT.OTClass.FeatureValue.getOntClass(resultDataset));
> >> >>>                 featureValue2.addProperty(OT.feature, feature2);
> >> >>>                 featureValue2.addLiteral(OT.value,
> >> >>> resultDataset.createTypedLiteral(this.fingerprints[i],
> >> >>> XSDDatatype.XSDdouble));
> >> >>>
> >> >>>                 //and finally add values to the data entry
> >> >>>                 dataEntry.addProperty(OT.values, featureValue1);
> >> >>>                 dataEntry.addProperty(OT.values, featureValue2);
> >> >>>             }
> >> >>> *******************************************************
> >> >>>
> >> >>>
> >> >>
> >> >> Can't really spot what's wrong, will try to run it.
> >> >>>
> >> >>> On 3 September 2010 22:34, Nina Jeliazkova <jeliazkova.nina at gmail.com>
> >> >>> wrote:
> >> >>> > Hi Surajit,
> >> >>> >
> >> >>> > I assume resultDataset variable is a Jena Model?
> >> >>> >
> >> >>> > Here is one of the RDF files you've tried to upload
> >> >>> >
> >> >>> > http://www.ideaconsult.net/downloads/maxtox/ambit2_22761.rdf
> >> >>> >
> >> >>> > First observation there is no any ot:Dataset instance. There are
> >> >>> > multile
> >> >>> > ot:DataEntry, but no dataset to where they belong.  This is
> >> >>> > definitely a
> >> >>> > reason the dataset could not be imported - the parser simply doesn't
> >> >>> > find a
> >> >>> > dataset to work with and does nothing.
> >> >>> >
> >> >>> > Second observation - you have defined value of type double, but the
> >> >>> > value
> >> >>> > itself is a string of 0 and 1s (the fingerprint).  This is at least
> >> >>> > not
> >> >>> > correct and will most probably result in errors when parsing values.
> >> >>> >
> >> >>> >        <ot:FeatureValue>
> >> >>> >             <ot:value
> >> >>> > rdf:datatype="http://www.w3.org/2001/XMLSchema#double"
> >> >>> >
> >> >>>
> >> >>> >>
> >> >>> >> >> >>0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0</ot:value>
> >> >>> >             <ot:feature
> >> >>> >
> >> >>> > rdf:resource="http://localhost:8080/MaxtoxTest/feature/1_fingerprint"/>
> >> >>> >           </ot:FeatureValue>
> >> >>> >
> >> >>> Corrected that ... I had interchanged the types between prediction and
> >> >>> fingerprint
> >> >>>
> >> >>> > Ah, and (relatively minor)  issue - the feature URI
> >> >>> > http://localhost:8080/MaxtoxTest/feature/1_fingerprint will not be
> >> >>> > dereferencable, even if you are running feature service at your
> >> >>> > machine
> >> >>> > -
> >> >>> > just because "localhost" means your machine for you, but my machine
> >> >>> > to
> >> >>> > me.
> >> >>> >
> >> >>>
> >> >>> Yeah ... that was during testing from my machine ...I have loaded the
> >> >>> same on the freiburg server which has the correct (absolute) server
> >> >>> path.
> >> >>>
> >> >>> > If you are not running feature service elsewehere it would be better
> >> >>> > to
> >> >>> > either have anonymous node for it, or create it beforehand  (POST to
> >> >>> > http://{host}/ambit2/feature) and provide the URI in the dataset
> >> >>> > RDF.
> >> >>> > TUM
> >> >>> > and NTUA developers can share their experience/code as well.
> >> >>> >
> >> >>>
> >> >>> Will try that in a future iteration ... however I have a thought
> >> >>> regarding this. Remoting is good as long as the information load to be
> >> >>> maintained is high and the connection is good. I believe localizing
> >> >>> the smaller stuff is better - as it leads to fewer steps that can fail
> >> >>> (in the course of a bad connection)
> >> >>
> >> >> Both approaches above a valid, the point is to have the information
> >> >> about
> >> >> the feature stored somewhere and linked to the rest.
> >> >> Low quality connection is what stateless protocols are good for.
> >> >>
> >> >>>
> >> >>> > Third,  this  code will not work as you might expect:
> >> >>> >
> >> >>> > this.uploaded_URI = output.getText(); ,
> >> >>> >
> >> >>> > because task RDF will be returned, not a single URI (you have
> >> >>> > specified
> >> >>> > request.getClientInfo().getAcceptedMediaTypes().add(new
> >> >>> > Preference<MediaType>(MediaType.APPLICATION_RDF_XML));
> >> >>> >
> >> >>>
> >> >>> Do I have to drill through the RDF representation to reach the URI ?
> >> >>
> >> >> If requesting RDF, yes.  But you might also set accepted media type to
> >> >> text/uri-list , this will return URI only.
> >> >>
> >> >>>
> >> >>> Also if its taking a long time what is your polling strategy ?
> >> >>>
> >> >>
> >> >> The polling strategy is decided by the client side.
> >> >>
> >> >>>
> >> >>> Are there any ready pieces of code for polling ?
> >> >>>
> >> >>>
> >> >> Look at RemoteTask class at the opentox-client SVN link
> >> >> Nina
> >> >>
> >> >>>
> >> >>> > Hope this helps,
> >> >>> > Nina
> >> >>> >
> >> >>>
> >> >>> Lastly some links I had left out (for reference)
> >> >>>
> >> >>> models at :
> >> >>> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model
> >> >>> particular (for ex model no 1) :
> >> >>> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1
> >> >>>
> >> >>> models take a dataset as the input and generate the fingerprints and
> >> >>> the predictions.
> >> >>>
> >> >>> Regards
> >> >>> Surajit
> >> >>>
> >> >>> >
> >> >>> > On Fri, Sep 3, 2010 at 6:33 PM, surajit ray
> >> >>> > <mr.surajit.ray at gmail.com>
> >> >>> > wrote:
> >> >>> >>
> >> >>> >> Hi,
> >> >>> >>
> >> >>> >> Tried uploading using this piece of code
> >> >>> >>
> >> >>> >> ************************************
> >> >>> >> System.out.println(result_dataset_URI);
> >> >>> >>            Representation representation = new
> >> >>> >> OutputRepresentation(MediaType.APPLICATION_RDF_XML) {
> >> >>> >>
> >> >>> >>                @Override
> >> >>> >>                public void write(OutputStream out) throws
> >> >>> >> IOException {
> >> >>> >>                    resultDataset.write(out, "RDF/XML-ABBREV");
> >> >>> >>                }
> >> >>> >>            };
> >> >>> >>
> >> >>> >>            Request request = new Request();
> >> >>> >>            Client client = new Client(Protocol.HTTP);
> >> >>> >>            request.setResourceRef(result_dataset_URI);
> >> >>> >>
> >> >>> >>
> >> >>> >>  request.setReferrerRef(MaxtoxApplicationSettings.getServerRootPath());
> >> >>> >>            request.setMethod(Method.POST);
> >> >>> >>            request.getClientInfo().getAcceptedMediaTypes().add(new
> >> >>> >> Preference<MediaType>(MediaType.APPLICATION_RDF_XML));
> >> >>> >>            request.setEntity(representation);
> >> >>> >>
> >> >>> >>
> >> >>> >>            Response response = client.handle(request);
> >> >>> >>            // Get the output from the response
> >> >>> >>            Representation output = response.getEntity();
> >> >>> >>            this.uploaded_URI = output.getText();
> >> >>> >> ************************************
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> I got this as the result
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> *************************************
> >> >>> >> 0.0 Error 1283527568408 File import application/rdf+xml [-1] The
> >> >>> >> server has fulfilled the request but does not need to return an
> >> >>> >> entity-body, and might want to return updated metainformation The
> >> >>> >> server has fulfilled the request but does not need to return an
> >> >>> >> entity-body, and might want to return updated metainformation 500
> >> >>> >> *************************************
> >> >>> >>
> >> >>> >> Could you clarify ?
> >> >>> >>
> >> >>> >> I am using the http://apps.ideaconsult.net:8080/ambit2/dataset for
> >> >>> >> testing as the other server was down - sorry for that.
> >> >>> >
> >> >>> >
> >> >>> >>
> >> >>> >> I just uploaded
> >> >>> >> twice so you can delete 2 vague looking databases ...
> >> >>> >
> >> >>> >
> >> >>> >
> >> >>> >>
> >> >>> >> Regards
> >> >>> >> Surajit
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> On 3 September 2010 11:46, Nina Jeliazkova
> >> >>> >> <jeliazkova.nina at gmail.com>
> >> >>> >> wrote:
> >> >>> >> > Hi Surajit,
> >> >>> >> >
> >> >>> >> > On Fri, Sep 3, 2010 at 1:50 AM, surajit ray
> >> >>> >> > <mr.surajit.ray at gmail.com>
> >> >>> >> > wrote:
> >> >>> >> >>
> >> >>> >> >> From your previous example I gathered this
> >> >>> >> >>
> >> >>> >> >> RDFRepresentation r = new RDFRepresentation();
> >> >>> >> >> Representation rep = r.createRepresentation(rdfDataset,
> >> >>> >> >> MediaType.APPLICATION_RDF_XML);
> >> >>> >> >>
> >> >>> >> >> The problem is this representation does not exist in the stable
> >> >>> >> >> version of Restlets !
> >> >>> >> >
> >> >>> >> > If you refer to opentox-client examples, then RDFRepresentation
> >> >>> >> > is
> >> >>> >> > not a
> >> >>> >> > Restlet class at all, but custom one, using Jena writers for
> >> >>> >> > serializing
> >> >>> >> > RDF.
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/main/java/org/opentox/rdf/representation/RDFRepresentation.java
> >> >>> >> >
> >> >>> >> > Restlet RDF support is rather minimalistic (graph representation,
> >> >>> >> > no
> >> >>> >> > querying, let alone reasoning), I am not sure if any of the
> >> >>> >> > partners
> >> >>> >> > actually uses it. If you are working with 1.x Restlet , there is
> >> >>> >> > indeed
> >> >>> >> > no
> >> >>> >> > RDF support there. But Restlet RDF support can be safely ignored
> >> >>> >> > if
> >> >>> >> > you
> >> >>> >> > are
> >> >>> >> > already using Jena (though I would be curious to see performance
> >> >>> >> > comparison
> >> >>> >> > between the two).
> >> >>> >> >
> >> >>> >> > Using StringRepresentation/ FileRepresentation with media type
> >> >>> >> > "application/rdf+xml" does the same job.  RDFRepresentation class
> >> >>> >> > discussed
> >> >>> >> > above actually creates OutputStreamRepresentation.
> >> >>> >> >
> >> >>> >> > Upload examples can be found here
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/test/java/org/opentox/dataset/test/DatasetTest.java
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/test/java/org/opentox/dataset/test/FeatureTest.java
> >> >>> >> >
> >> >>> >> > The examples above are cleaned up versions of ambit code. JUnit
> >> >>> >> > tests
> >> >>> >> > of
> >> >>> >> > ambit dataset services can be found here
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-www/src/test/java/ambit2/rest/test/dataset/DatasetsResourceTest.java
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >>
> >> >>> >> >> Also the example uses a RemoteTask to achieve the actual upload.
> >> >>> >> >> Therefore I could not exactly fathom how to do the upload.
> >> >>> >> >
> >> >>> >> > Here is a summary
> >> >>> >> >
> >> >>> >> > curl -X POST -d "@filecontent" -H
> >> >>> >> > "Content-type:application/rdf+xml"
> >> >>> >> > http://datasetservice/dataset
> >> >>> >> >
> >> >>> >> > This returns Task object (either URI, if -H
> >> >>> >> > "Accept:text/uri-list" is
> >> >>> >> > specified or Task RDF representation if -H
> >> >>> >> > "Accept:application/rdf+xml"
> >> >>> >> > is
> >> >>> >> > specified).  Task RDF representation is defined in
> >> >>> >> > http://opentox.org/api/1_1/opentox.owl
> >> >>> >> >
> >> >>> >> > If the task is still running you'll get result codes 201 or 202 ,
> >> >>> >> > this
> >> >>> >> > means
> >> >>> >> > you need to query again the returned task URI.  If code 200 is
> >> >>> >> > returned,
> >> >>> >> > the
> >> >>> >> > URI returned is where the result should be found.   In the
> >> >>> >> > examples
> >> >>> >> > there is
> >> >>> >> > a RemoteTask class that handles all this.
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/main/java/org/opentox/task/RemoteTask.java
> >> >>> >> >>
> >> >>> >> >> On 3 September 2010 03:47, surajit ray
> >> >>> >> >> <mr.surajit.ray at gmail.com>
> >> >>> >> >> wrote:
> >> >>> >> >> > Hi,
> >> >>> >> >> >
> >> >>> >> >> > I have managed to get a dataset (RDF) made using the results
> >> >>> >> >> > of a
> >> >>> >> >> > model prediction run. Could you please tell me a dataset
> >> >>> >> >> > service
> >> >>> >> >> > where
> >> >>> >> >> > I could upload the same ?
> >> >>> >> >
> >> >>> >> > For testing
> >> >>> >> >
> >> >>> >> > http://ambit-uni-plovdiv.bg:8080/ambit2/dataset
> >> >>> >> >
> >> >>> >> > For your final models/results , especially if you would like them
> >> >>> >> > appearing
> >> >>> >> > in ToxPredict.
> >> >>> >> >
> >> >>> >> > http://apps.ideaconsult.net:8080/ambit2/dataset
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >>
> >> >>> >> >> Also it would be very helpful if you could
> >> >>> >> >> > give an example of an upload request using restlets ...
> >> >>> >> >
> >> >>> >> > See above.
> >> >>> >> >
> >> >>> >> > Hope this helps,
> >> >>> >> > Nina
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >> >
> >> >>> >> >> > Thanx
> >> >>> >> >> > Surajit
> >> >>> >> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >> >
> >> >>> >
> >> >>>
> >> >>> >
> >> >>
> >> >>
> >> >>
> >> >
> >>
> >>
> >>
> >> --
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