Package edu.mayo.bmi.guoqian.claml

Examples of edu.mayo.bmi.guoqian.claml.Reference


    /**
     * Create an instance of {@link Reference }
     *
     */
    public Reference createReference() {
        return new Reference();
    }
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                     try{
                  if(clamlRefCodes != null){
                    for (RDFResource clamlRefCode : clamlRefCodes) {

                      Reference refCode = factory.createReference();
                          refCode.setClazz("in brackets");
                      String thisCode = (String)clamlRefCode.getPropertyValue(icdContentModel.getTextProperty());
                      if(thisCode.indexOf("-") >= 0){
                        thisCode = this.getCodeFromLabel(thisCode);
                      }
                     
                      String thisGeneratedCode = this.getGeneratedCodeForICDCategoryCode(thisCode);
                        if(thisGeneratedCode == null){
                          thisGeneratedCode = thisCode;
                        }
                         
                         
                         
                      refCode.setContent(thisGeneratedCode);
                      //String refCodeText = ((RDFResource)clamlRefCode.getPropertyValue(icdContentModel.getIcdRefProperty())).getBrowserText();
                     
                      refCode.setCode(thisGeneratedCode);
                      labelInclusion.getContent().add(refCode);                   
                   
                      }
                  }
                  }catch(Exception e){
                    e.printStackTrace();
                          System.out.println("inclusion" + "|" + icdCategory.getBrowserText());
                            continue;
                  }
                 
                 
                  rubricInclusion.getLabel().add(labelInclusion);
                  cls.getRubric().add(rubricInclusion);
               

                }
              }             

              //exclusion terms
              Collection colExclusions = this.getExclusionTerms(icdCategory);

              Collection<String> colSortedExclusions = new ArrayList();
              Map<String, RDFResource> mapSortedExclusions = new HashMap();
             
             
             
              if(colExclusions != null){
                for(Iterator it4 = colExclusions.iterator(); it4.hasNext();){
                  RDFResource exclusion = (RDFResource) it4.next();
                        String exclusionLabel = this.getExclusionTermText(exclusion);
                        String exclusionId = this.getTermRubricID(exclusion);
                        //Collection<RDFResource> clamlRefCodes = this.getTermClaMLReferences(exclusion);
                       
                        String exclusionLabelId = exclusionLabel + "|" + exclusionId;
                        colSortedExclusions.add(exclusionLabelId);
                        mapSortedExclusions.put(exclusionLabelId, exclusion);
                       

                }
                        //alphabetically sort the rubrics
                        Object[] arraySortedExclusions = colSortedExclusions.toArray();
                        List listSortedExclusions = Arrays.asList(arraySortedExclusions);
                        Collections.sort(listSortedExclusions, String.CASE_INSENSITIVE_ORDER);
                        for(ListIterator li1 = listSortedExclusions.listIterator(); li1.hasNext();){
                        //for(int jj = 0; jj < arraySortedExclusions.length; jj++){
                          String sortedExclusionLabelId = (String)li1.next();
                       
                         
                          String[] labelId = sortedExclusionLabelId.split("\\|");
                          RDFResource sortedExclusion = (RDFResource)mapSortedExclusions.get(sortedExclusionLabelId);
                 
                  //System.out.println(icdCategory.getBrowserText() + "|" + sortedExclusionLabelId);
                         
                  Rubric rubricInclusion = factory.createRubric();
                  if(!labelId[1].equals("null")) //if null, do nothing
                    rubricInclusion.setId(labelId[1]);
                  ClassKind cKindInclusion = factory.createClassKind();
                  cKindInclusion.setName("exclusion");
                  rubricInclusion.setKind(cKindInclusion);
                  Label labelInclusion = factory.createLabel();
                  labelInclusion.setLang("en");
                  labelInclusion.setSpace("default");
                  labelInclusion.getContent().add(labelId[0]);
                 
                  Collection<RDFResource> clamlRefCodes = this.getTermClaMLReferences(sortedExclusion);
                 
                 
                  //if(sortedExclusion.getPropertyValues(icdContentModel.getClamlReferencesProperty()) != null){
                  //Collection<RDFResource> clamlRefCodes = sortedExclusion.getPropertyValues(icdContentModel.getClamlReferencesProperty());
                 
                  try{
                  if(clamlRefCodes != null){
                   
                   
                    for (RDFResource clamlRefCode : clamlRefCodes) {
                   
                          Reference refCode = factory.createReference();
                          refCode.setClazz("in brackets");
                         
                      String thisCode = (String)clamlRefCode.getPropertyValue(icdContentModel.getTextProperty());
                      if(thisCode.indexOf("-") >= 0){
                        thisCode = this.getCodeFromLabel(thisCode);
                      }
                     
                      String thisGeneratedCode = this.getGeneratedCodeForICDCategoryCode(thisCode);
                        if(thisGeneratedCode == null){
                          thisGeneratedCode = thisCode;
                        }
                         
                         
                      refCode.setContent(thisGeneratedCode);
                      //String refCodeText = ((RDFResource)clamlRefCode.getPropertyValue(icdContentModel.getIcdRefProperty())).getBrowserText();

                     
                      refCode.setCode(thisGeneratedCode);
                      labelInclusion.getContent().add(refCode);                   
                   
                      }
                  }
                  }catch(Exception e){
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