Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology

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

Examples of edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology

edu.pitt.dbmi.nlp.noble.terminology.impl.NobleCoderTerminology
Implementation of Terminology using IndexFinder algorithm @author Eugene Tseytlin (University of Pittsburgh)

          .getResourceFilePath(PARAM_NOBLE_CODER_TERMINOLOGY_URL);
      File f = new File(terminologyPath);
      f = f.getParentFile().getParentFile();
      terminologyPath = f.getAbsolutePath() + File.separator + "META";
      System.out.println("terminologyPath is " + terminologyPath);
      terminology = new NobleCoderTerminology(terminologyPath);
    } catch (Exception e) {
      throw new ResourceInitializationException(e);
    }
  }

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        String name = terminologyParams.get(type).trim();
        try {
          File f = new File(name);
          if(f.getParentFile() != null)
            NobleCoderTerminology.setPersistenceDirectory(f.getParentFile());
          term = new NobleCoderTerminology(f.getName());
        } catch (IOException e) {
          throw new TerminologyException("Could not load IndexFinder terminology "+name,e);
        }
      }
    }catch(TerminologyException ex){

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      for(File f: dir.listFiles()){
        String sf = NobleCoderTerminology.TERM_SUFFIX;
        if(f.getName().endsWith(sf)){
          Terminology t;
          try {
            t = new NobleCoderTerminology(f.getName().substring(0,f.getName().length()-sf.length()));
            terminologies.put(t.getName(),t);
          } catch (UnsupportedOperationException e){
            System.err.println("Corrupted termonology detected at "+f.getAbsolutePath()+". skipping ...");
          //} catch (Error e){
          //  System.err.println("Corrupted termonology detected at "+f.getAbsolutePath()+". skipping ...");

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    }
    
    //load terminology
    List<Terminology> terms = new ArrayList<Terminology>();
    for(Element t: XMLUtils.getElementsByTagName(element,"Terminology")){
      NobleCoderTerminology term = new NobleCoderTerminology();
      term.fromElement(t);
      terms.add(term);
    }
    //term.setCachingEnabled(false);
    if(terms.size() == 1){
      setTerminology(terms.get(0));

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  /**
   * create a template from terminology where each root is a template item
   * @param url
   */
  private void addTerminologyTemplate(String url) throws Exception {
    Terminology terminology = new NobleCoderTerminology(url);
    
    // setup template
    Template template = new Template();
    template.setName(terminology.getName()+" Template");
    template.setDescription(terminology.getDescription());
    template.setTerminology(terminology);
    template.getFilters().add(new DocumentFilter("(?s)^BACKGROUND:$.*^$",true));
    
    for(Concept c: terminology.getRootConcepts()){
      TemplateItem item = new TemplateItem();
      /*      
      {
        //TODO: this is a hack for BRAF, let it stay for now?
        public List<ItemInstance> process(TemplateDocument doc) throws TerminologyException {

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  private void addSlideTutorTemplates(String url) throws Exception {
    IOntology ont = OOntology.loadOntology(url);
    ConceptRegistry.REGISTRY.put(url,SlideTutorConcept.class.getName());
    
    // create in-memory terminology from this ontology
    NobleCoderTerminology term = new NobleCoderTerminology();
    term.loadOntology(ont,null,true,true);
    term.setScoreConcepts(false);
    term.setSelectBestCandidate(false);
    term.setCachingEnabled(false);
    
    NobleCoderTerminology aterm = new NobleCoderTerminology();
    aterm.loadOntology(OOntology.loadOntology(""+ANATOMY_ONTOLOGY_URI),null,true,true);
    aterm.setCachingEnabled(false);
    
    // add a terminology to it
    CompositTerminology terminology = new CompositTerminology();
    terminology.addTerminology(term);
    terminology.addTerminology(aterm);

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  /**
   * @param args
   */
  public static void main(String[] args) throws Exception {
    NobleCoderTerminology.setPersistenceDirectory(new File("/home/tseytlin/Data/Terminologies/IndexFinder"));
    Terminology terminology = new NobleCoderTerminology("TIES_Pathology");
    //Terminology terminology = new NobleCoderTerminology("NCI_Thesaurus");
    PathHelper ph = new PathHelper(terminology);
    //ph.createAncestryCache();
    for(String text: Arrays.asList("melanoma","nevus","skin","margin")){
      for(Concept c: terminology.search(text)){
        long t = System.currentTimeMillis();
        // lookup paths
        
        List<ConceptPath> path = ph.getPaths(c);
        t = System.currentTimeMillis()-t;

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    return ont;
  }


  
  public Terminology createTerminology() throws TerminologyException {
    return new NobleCoderTerminology();
  }

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    if("done".equals(storage.getInfoMap().get("status")))
      return;
    
    
    // handle memory nightmare (save when you reach 90%)
    final NobleCoderTerminology t = term;
    MemoryManager.setMemoryThreshold(new Runnable(){
      public void run() {
        t.crash();
      }
    },0.95);
    
    // load classes for the very first time
    pcs.firePropertyChange(LOADING_MESSAGE,null,"Loading Ontology "+ontology.getName()+" from "+ontology.getLocation()+" ...");

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    // check if already loaded
    if("done".equals(storage.getInfoMap().get("status")))
      return;      
        
    // handle memory nightmare (save when you reach 90%)
    final NobleCoderTerminology t = term;
    MemoryManager.setMemoryThreshold(new Runnable(){
      public void run() {
        t.crash();
      }
    },0.95);
    
    // load classes for the very first time
    pcs.firePropertyChange(LOADING_MESSAGE,null,"Loading Text from "+file.getAbsolutePath()+" ...");

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