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[bioontology-support] Java/Jena example 500 error

Paul R Alexander palexander at stanford.edu
Fri Nov 1 20:06:56 PDT 2013


Michael,

The link you provided works for me using curl, Firefox, and other HTTP tools. What exactly is the failure you are seeing?

I’m testing this URL:
http://data.bioontology.org/ontologies/NDDF/submissions/1/download?apikey=81ac8eba-12ca-4b94-a80f-82e4cfd2291a

Paul


On Nov 1, 2013, at 7:53 PM, Celeste, Michael <michael.celeste at pfizer.com> wrote:

> Yes, the link below works. I gave you the wrong key. When I try to query using java with the key below I get the 500 error but if I use this key 4ea81d74-8960-4525-810b-fa1baab576ff then the program works.
>  
> So basically my question is why does this key not work: 81ac8eba-12ca-4b94-a80f-82e4cfd2291a
>  
> Michael
>  
> From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
> Sent: Friday, November 01, 2013 9:10 PM
> To: Celeste, Michael; support at bioontology.org
> Cc: Manuel Salvadores
> Subject: RE: [bioontology-support] Java/Jena example 500 error
>  
> 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) throwsException {
>                  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#> " +
>                                            "SELECT ?ont ?name ?acr " +
>                                            "WHERE { ?ont a omv:Ontology; " +
>                                            "omv:acronym ?acr; " +
>                                            "omv:name ?name . " +
>                                            "}";
>                 try {
>                 JenaARQTest test = newJenaARQTest(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);
>                 }
>         }
> }
>  
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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