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.terminology.util.TerminologyException

  /**
   * remove existing concept
   * @param c
   */
  public boolean removeConcept(Concept c) throws TerminologyException{
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

  /**
   * get all available concept objects in terminology. Only sensible for small terminologies
   * @return
   */
  public Collection<Concept> getConcepts()  throws TerminologyException{
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

  /**
   * convert Template to XML DOM object representation
   * @return
   */
  public void fromElement(Element element) throws TerminologyException{
    throw new TerminologyException("Not implemented");
  }

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Examples of edu.pitt.terminology.util.TerminologyException

    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(infoMap.containsKey(RRFile)){
      offset = Integer.parseInt(infoMap.get(RRFile));
    }
    // if offset is smaller then total, read file

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Examples of edu.pitt.terminology.util.TerminologyException

    if(conceptMap instanceof JDBMMap && ((JDBMMap)conceptMap).isReadOnly()){
      dispose();
      try {
        load(name,false);
      } catch (IOException e) {
        throw new TerminologyException("Unable to gain write access to data tables",e);
      }
    }
    
    
    // get list of terms

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Examples of edu.pitt.terminology.util.TerminologyException

          File f = new File(name);
          if(f.getParentFile() != null)
            IndexFinderTerminology.setPersistenceDirectory(f.getParentFile());
          term = new IndexFinderTerminology(f.getName());
        } catch (IOException e) {
          throw new TerminologyException("Could not load IndexFinder terminology "+name,e);
        }
      }
    }catch(TerminologyException ex){
      ex.printStackTrace();
    }

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Examples of edu.pitt.terminology.util.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.terminology.util.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.terminology.util.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.terminology.util.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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