Thanks Nina,

that worked ...


On Sat, Feb 20, 2010 at 4:27 PM, Nina Jeliazkova <nina at acad.bg> wrote:

> Hi,
>
> This should work in Restlet 1.x :
>
>            Request request = new Request();
>            Client client = new Client(Protocol.HTTP);
>            request.setResourceRef(uri);
>            request.setMethod(Method.GET);
>            request.getClientInfo().getAcceptedMediaTypes().add(new
>    Preference<MediaType>(media));
>            Response response = client.handle(request);
>            if (expectedStatus.equals(Status.SUCCESS_OK)) {
>
>                InputStream in = response.getEntity().getStream();
>    //do something
>                in.close();
>            }
>
>      Regards,
> Nina
>
> surajit ray wrote:
> > Hi Nina,
> >
> > How do i set the mediatype of a request ...
> >
> > according to the restlet 1.0 tutorial :
> >
> > Note that the example above uses a simplified way to issue calls via
> > the generic Client class. A more flexible way is to create a new
> > Request object and to ask the Client to handle it. The example below
> > illustrate how to set some preferences in your call, like a referrer
> > URI. It could also be the languages and media types you prefer to
> > receive as a response:
> >
> >
> > But the tutorial does not show how to set the mediatype of the
> > request. Tried using
> >
> >             Request request = new Request(Method.GET, URIofCompound );
> >
> >  request.setReferrerRef(MaxtoxApplicationSettings.getServerRootPath());
> >
> >  request.getEntity().setMediaType(ChemicalMediaType.CHEMICAL_SMILES);
> >
> > but I got null pointer exceptions. also
> >
> >             request.getEntity().setMediaType(MediaType.TEXT_PLAIN);
> >
> > did not work either ... so its not the ChemicalMediaType which is the
> > problem
> > Could you tell me how the mediatype is et for a request ?
> >
> > Thanks
> > Surajit
> >
> >
> > On Sat, Feb 20, 2010 at 11:58 AM, Nina Jeliazkova <nina at acad.bg
> > <mailto:nina at acad.bg>> wrote:
> >
> >     surajit ray wrote:
> >     > Hi Nina,
> >     >
> >     > In the restlet media types there is no option for a chemical
> >     mime type
> >     > ... how do I assign this media type to a request ?
> >     This is what I do
> >
> >     public class ChemicalMediaType  {
> >
> >        public static final MediaType CHEMICAL_MDLSDF = new
> >     MediaType("chemical/x-mdl-sdfile");
> >        public static final MediaType CHEMICAL_MDLMOL= new
> >     MediaType("chemical/x-mdl-molfile");
> >        public static final MediaType CHEMICAL_CML = new
> >     MediaType("chemical/x-cml");
> >        public static final MediaType CHEMICAL_SMILES = new
> >     MediaType("chemical/x-daylight-smiles");
> >        public static final MediaType CHEMICAL_INCHI = new
> >     MediaType("chemical/x-inchi");
> >
> >
> >        protected ChemicalMediaType() {
> >
> >        }
> >     }
> >     >
> >     > Also it seems to return the smile as a file ... how can I get a
> >     string
> >     > response (and not a file ) ....?
> >     It returns a Representation - whether you treat it as a file or
> string
> >     is up to you.
> >
> >     Regards,
> >     Nina
> >     >
> >     > Thanks
> >     > Surajit
> >     >
> >     >
> >     > On Sat, Feb 20, 2010 at 11:03 AM, Nina Jeliazkova <nina at acad.bg
> >     <mailto:nina at acad.bg>
> >     > <mailto:nina at acad.bg <mailto:nina at acad.bg>>> wrote:
> >     >
> >     >     surajit ray wrote:
> >     >>     Hi Nina,
> >     >>
> >     >>     tried a few ... for example
> >     >>      (with mime type application/rdf+xml)
> >     >>
> >     >>
> >
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/3287/conformer/262287
> >     >>
> >
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/17611/conformer/262288
> >     >>
> >
> http://ambit.uni-plovdiv.bg:8080/ambit2/compound/3287/conformer/262287
> >     >>
> >     >>     I tried the same with Chemical mime type and got an sdf
> >     file ...
> >     >>
> >     >>     However I could not get a SMILE string anywhere in the
> response
> >     >>     .... do I have to do something else to get a smile string in a
> >     >>     response ?
> >     >
> >     >     Have you tried mime type "chemical/x-daylight-smiles"  ?  This
> >     >     will you give you SMILES string.
> >     >
> >     >>
> >     >>     Also is there an easy way to get a set of molecules and their
> >     >>     smiles. This currently looks like I have to first get and
> >     iterate
> >     >>     over the rdf model and then send individual get requests (with
> >     >>     chemical mime type) to get the SDF file (how to get SMILE - i
> >     >>     still dont know ...)
> >     >     The SDF/MOL itself contains structures, no need of SMILES;
> >     if only
> >     >     SMILES is what you are looking for, use mime type
> >     >     "chemical/x-daylight-smiles" . I think Christoph is using
> SMILES
> >     >     as well.
> >     >
> >     >     Regards,
> >     >     Nina
> >     >
> >     >>
> >     >>     Thanks
> >     >>     Surajit
> >     >>
> >     >>     On Sat, Feb 20, 2010 at 1:01 AM, Nina Jeliazkova
> >     <nina at acad.bg <mailto:nina at acad.bg>
> >     >>     <mailto:nina at acad.bg <mailto:nina at acad.bg>>> wrote:
> >     >>
> >     >>
> >     >>         >
> >     >>         > b) how do I retrieve the value contained in the Feature
> >     >>         node in the
> >     >>         > statement :
> >     >>         >
> >     >>         >                 RDFNode value =
> >     >>         fv.getProperty(OT.value).getObject();
> >     >>         >                 out.write(String.format("%s=%s\n",
> >     >>         >                         //Feature
> >     >>         >
> >     >>         fv.getProperty(OT.feature).getObject().toString(),
> >     >>         >                         //Value
> >     >>         >                         value));
> >     >>         >
> >     >>         > Value is a string representation of the node like so
> >     >>         > : Cc1ccc(N=Nc2c(O)ccc3ccccc23)c(c1)N(=O)O^^
> >     >>         > http://www.w3.org/2001/XMLSchema#string
> >     >>         >
> >     >>         > I would like to retrieve the just the value (the smile
> >     >>         string ...)
> >     >>         >
> >     >>         >
> >     >>
> >     >>            if (value.isLiteral() )
> >     >>               ((Literal) value).getString();
> >     >>
> >     >>
> >     >>         will return the string value; there are similar
> >     functions for
> >     >>         other data
> >     >>         types.   But again, use it for data values, not chemical
> >     >>         structures.
> >     >>
> >     >>         Regards,
> >     >>         Nina
> >     >>
> >     >>
> >     >>         _______________________________________________
> >     >>         Development mailing list
> >     >>         Development at opentox.org
> >     <mailto:Development at opentox.org> <mailto:Development at opentox.org
> >     <mailto:Development at opentox.org>>
> >     >>         http://www.opentox.org/mailman/listinfo/development
> >     >>
> >     >>
> >     >>
> >     >>
> >     >>     --
> >     >>     Surajit Ray
> >     >>     Partner
> >     >>     www.rareindianart.com <http://www.rareindianart.com>
> >     <http://www.rareindianart.com>
> >     >
> >     >
> >     >
> >     >
> >     > --
> >     > Surajit Ray
> >     > Partner
> >     > www.rareindianart.com <http://www.rareindianart.com>
> >     <http://www.rareindianart.com>
> >
> >
> >
> >
> > --
> > Surajit Ray
> > Partner
> > www.rareindianart.com <http://www.rareindianart.com>
>
>


-- 
Surajit Ray
Partner
www.rareindianart.com