Examples of TerminologyException

edu.pitt.dbmi.nlp.noble.terminology.TerminologyException
generic exception that wraps other ones @author tseytlin
edu.pitt.terminology.util.TerminologyException
generic exception that wraps other ones @author tseytlin

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

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

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

      c.setInitialized(true);
      
      return c;
      
    }catch(Exception ex){
      throw new TerminologyException("Error: Problem with lookup of "+cui,ex);
    }
  }

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

        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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Examples of edu.pitt.terminology.util.TerminologyException

  
  /**
   * Get all supported relations between concepts
   */
  public Relation[] getRelations() throws TerminologyException {
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

  /**
   * Get all relations for specific concept, one actually needs to explore
   * a concept graph (if available) to determine those
   */
  public Relation[] getRelations(Concept c) throws TerminologyException {
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

   * get all root concepts. This makes sence if Terminology is in fact ontology
   * that has heirchichal structure
   * @return
   */
  public Concept[] getRootConcepts() throws TerminologyException {
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

  /**
   * add new concept to the terminology
   * @param c
   */
  public boolean addConcept(Concept c) throws TerminologyException{
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

  /**
   * update concept information
   * @param c
   */
  public boolean updateConcept(Concept c) throws TerminologyException{
    throw new TerminologyException("Not implemented");
  }

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