Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Java/Jena example 500 error

Ray Fergerson ray.fergerson at stanford.edu
Fri Nov 1 18:10:04 PDT 2013


The link below appears to work now and downloads a file (NDDF.ttl). Can
you confirm? Have I misunderstood what you want?

 

Ray

 

From: Celeste, Michael [mailto:michael.celeste at pfizer.com] 
Sent: Thursday, October 24, 2013 3:10 PM
To: Ray Fergerson; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Here's an example of one from this url:
http://bioportal.bioontology.org/ontologies/NDDF

 

Here's the link with the API key:
http://data.bioontology.org/ontologies/NDDF/submissions/1/download?apikey=
81ac8eba-12ca-4b94-a80f-82e4cfd2291a

 

Michael

 

From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
Sent: Thursday, October 24, 2013 6:09 PM
To: Celeste, Michael; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Sorry but I am still a bit lost. What keys are you referring to that are
associated with the ontology download links? Where do you see these links?
Are they in some sample code that we provide?

 

Ray

 

From: Celeste, Michael [mailto:michael.celeste at pfizer.com] 
Sent: Thursday, October 24, 2013 2:58 PM
To: Ray Fergerson; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Yes, there are keys associated to the ontology download links. If I use
one of those then I get data using the sample java programs.

 

Michael

 

From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
Sent: Thursday, October 24, 2013 5:56 PM
To: Celeste, Michael; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Why do you say this? If you use someone else's api key does it work?

 

Ray

 

From: Celeste, Michael [mailto:michael.celeste at pfizer.com] 
Sent: Thursday, October 24, 2013 2:51 PM
To: Ray Fergerson; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Ok, thank you for your reply.


I actually think it's my API key that is the problem:
81ac8eba-12ca-4b94-a80f-82e4cfd2291a

 

Michael

 

From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
Sent: Thursday, October 24, 2013 5:47 PM
To: Celeste, Michael; support at bioontology.org
Cc: Manuel Salvadores
Subject: RE: [bioontology-support] Java/Jena example 500 error

 

Our expert on this is half-way around the world this week. He should be
able to respond next week.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Celeste, Michael
Sent: Friday, October 18, 2013 3:22 AM
To: support at bioontology.org
Subject: [bioontology-support] Java/Jena example 500 error

 

Hello,

I am trying to run the java file using Jena below after supplying my
apikey but I keep getting an HTTP 500 error. I also tried adding a query
parameter but get the same error.

 

Thanks,
Michael

 

package businessdevelopment;

 

import com.hp.hpl.jena.query.Query;

import com.hp.hpl.jena.query.QueryExecutionFactory;

import com.hp.hpl.jena.query.QueryFactory;

import com.hp.hpl.jena.query.QuerySolution;

import com.hp.hpl.jena.query.ResultSet;

import com.hp.hpl.jena.rdf.model.Literal;

import com.hp.hpl.jena.rdf.model.RDFNode;

import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;

 

/**

* This is an example built on top of the Jena ARQ library.

* See: http://jena.sourceforge.net/ARQ/documentation.html

*/

public class JenaARQTest {

        

        private String service = null;

        private String apikey = null;

        

        public JenaARQTest(String service, String apikey) {

                this.service = service;

                this.apikey = apikey;

        }

        public ResultSet executeQuery(String queryString) throws Exception
{

                 Query query = QueryFactory.create(queryString) ;

 

                 QueryEngineHTTP qexec =
QueryExecutionFactory.createServiceRequest(this.service, query);

                 qexec.addParam("apikey", this.apikey);

                 //qexec.addParam("query", queryString);                 

                 ResultSet results = qexec.execSelect() ;

                 return results;

 

        }

        public static void main(String[] args) throws Exception {

                String sparqlService =
"http://sparql.bioontology.org/sparql";

                String apikey = "81ac8eba-12ca-4b94-a80f-82e4cfd2291a";

 

                /*

                 * More query examples here:

                 * http://sparql.bioontology.org/examples

                 */

                String query = "PREFIX omv:
<http://omv.ontoware.org/2005/05/ontology#
<http://omv.ontoware.org/2005/05/ontology> > " +

                                           "SELECT ?ont ?name ?acr " +

                                           "WHERE { ?ont a omv:Ontology; "
+

                                           "omv:acronym ?acr; " +

                                           "omv:name ?name . " +

                                           "}";

                try {

                JenaARQTest test = new JenaARQTest(sparqlService,apikey);

                ResultSet results = test.executeQuery(query);

                    for ( ; results.hasNext() ; ) {

                      QuerySolution soln = results.nextSolution() ;

                      RDFNode ontUri = soln.get("ont") ;

                      Literal name = soln.getLiteral("name") ;

                      Literal acr = soln.getLiteral("acr") ;

                      System.out.println(ontUri + " ---- " + name + " ----
" + acr);

                    }

                }

                catch(Exception e) {

                  System.out.println(e);

                }

        }

}

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131101/60a3d62f/attachment-0001.html>


More information about the bioontology-support mailing list