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[bioontology-support] Repeated w correct email addressesFW: java.io.FileNotFoundException: http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C90069

Mona Salem monasalem123 at gmail.com
Fri Feb 28 13:19:44 PST 2014


 

Hi All

I am getting the following error:

 

java.io.FileNotFoundException:
http://data.bioontology.org/ontologies/NCIT/classes/http%3A%2F%2Fncicb.nci.n
ih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C90069

            at
sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)

            at TextAnnotation.get(TextAnnotation.java:102)

            at TextAnnotation.stringToAnnotate(TextAnnotation.java:51)

            at sitemapParser.getAllUrlNames(sitemapParser.java:163)

            at sitemapParser.main(sitemapParser.java:682)

com.fasterxml.jackson.databind.JsonMappingException: No content to map due
to end-of-input

 at [Source: java.io.StringReader at 1ff2b382; line: 1, column: 1]

 

 

I am calling stringToAnnotate  method from my code, (no hierarchies req'd):

public class TextAnnotation {

 

    static final String REST_URL = "http://data.bioontology.org";

    static final String API_KEY = "";

    static final ObjectMapper mapper = new ObjectMapper();

 

    public void stringToAnnotate(String abstractInfo, Model model2, String
URLaddress) throws UnsupportedEncodingException {    

                        

        String textToAnnotate = URLEncoder.encode(abstractInfo, "UTF-8");
//1-31 UTF-8 changed

                        

        Resource SoftwareProduct = model2.createResource(URLaddress);  

                        

       JsonNode annotations = jsonToNode(get(REST_URL +
"/annotator?ontologies=NCIT&text=" + textToAnnotate)); 

 

      for (JsonNode annotation : annotations) {

            

            JsonNode classDetails =
jsonToNode(get(annotation.get("annotatedClass").get("links").get("self").asT
ext()));

 

           SoftwareProduct.addProperty(AnnotationLabel,
classDetails.get("prefLabel").asText());

            //System.out.println("\tontology: " +
classDetails.get("links").get("ontology").asText());

           // System.out.println("\n");

 

        }

    }

 

}

 

Thanks for any help

Mona Nafoosi

G6G Consulting Group

Santa Monica CA

 

 

 

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