Package edu.pitt.dbmi.nlp.noble.terminology

Examples of edu.pitt.dbmi.nlp.noble.terminology.TerminologyException


    storage.useTempWordFolder = true;
    String prefNameSource = null;
    offset = 0;
    RRFile = "MRCONSO.RRF";
    if(!new File(dir,RRFile).exists())
      throw new TerminologyException("RRF file "+(new File(dir,RRFile).getAbsolutePath()+" does not exist!"));
   
    if(storage.getInfoMap().containsKey(RRFile)){
      offset = Integer.parseInt(storage.getInfoMap().get(RRFile));
    }
    // if offset is smaller then total, read file
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              "org.LexGrid.concepts.Concept[@_entityCode="+filter(cui)+
              "]&codingSchemeName="+filter(scheme));
      List<Concept> list = processResponse(parseXML(u.openStream()));
      return list.isEmpty()?null:list.get(0);
    }catch(Exception ex){
      throw new TerminologyException("Problem w/ lookup",ex);
    }
  }
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      for(Concept c: list){
        c.setSearchString(text);
      }
      return list.toArray(new Concept [0]);
    }catch(Exception ex){
      throw new TerminologyException("Problem w/ lookup",ex);
    }
  }
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      c.setInitialized(true);
     
      return c;
     
    }catch(Exception ex){
      throw new TerminologyException("Error: Problem with lookup of "+cui,ex);
    }
  }
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        st.close();
       
       
        return conceptList.toArray(new Concept [0]);
      }catch(Exception ex){
        throw new TerminologyException("Error: UMLS search failed on "+text,ex);
      }
    }
    //return new Concept [0];
  }
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