metaTop.setValue("I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI XVII XVIII XIX XX XXI XXII");
claml.getMeta().add(metaTop);
ClassKinds clsKinds = factory.createClassKinds();
ClassKind cKind1 = factory.createClassKind();
cKind1.setName("chapter");
clsKinds.getClassKind().add(cKind1);
ClassKind cKind2 = factory.createClassKind();
cKind2.setName("block");
clsKinds.getClassKind().add(cKind2);
ClassKind cKind3 = factory.createClassKind();
cKind3.setName("category");
clsKinds.getClassKind().add(cKind3);
//ClassKind cKind4 = factory.createClassKind();
//cKind4.setName("modifiedcategory");
//clsKinds.getClassKind().add(cKind4);
claml.setClassKinds(clsKinds);
/*
UsageKinds useKinds = factory.createUsageKinds();
UsageKind useKind = factory.createUsageKind();
useKind.setMark("!");
useKind.setName("optional");
useKinds.getUsageKind().add(useKind);
claml.setUsageKinds(useKinds);
*/
RubricKinds rubKinds = factory.createRubricKinds();
//preferred
RubricKind rKind1 = factory.createRubricKind();
rKind1.setInherited("false");
rKind1.setName(icdContentModel.getPreferredProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind1);
//synonym property
/*
RubricKind rKind1_1 = factory.createRubricKind();
rKind1_1.setInherited("false");
rKind1_1.setName(icdContentModel.getSynonymProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind1_1);
*/
//definition property
RubricKind rKind1_2 = factory.createRubricKind();
rKind1_2.setInherited("false");
rKind1_2.setName(icdContentModel.getDefinitionProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind1_2);
//prefilled definition property
/*
RubricKind rKind1_3 = factory.createRubricKind();
rKind1_3.setInherited("false");
rKind1_3.setName(icdContentModel.getPrefilledDefinitionProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind1_3);
*/
//inclusion
RubricKind rKind2 = factory.createRubricKind();
rKind2.setInherited("false");
rKind2.setName(icdContentModel.getInclusionProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind2);
//exclusion
RubricKind rKind3 = factory.createRubricKind();
rKind3.setInherited("false");
rKind3.setName(icdContentModel.getExclusionProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind3);
//note property
RubricKind rKind5 = factory.createRubricKind();
rKind5.setInherited("false");
rKind5.setName(icdContentModel.getNoteProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind5);
//MorbidityParent property
/*
RubricKind rKind6 = factory.createRubricKind();
rKind6.setInherited("false");
rKind6.setName(icdContentModel.getMorbidityParentProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind6);
*/
//coding hint property
RubricKind rKind7 = factory.createRubricKind();
rKind7.setInherited("false");
rKind7.setName(icdContentModel.getCodingHintProperty().getBrowserText());
rubKinds.getRubricKind().add(rKind7);
//icd Reference property
//RubricKind rKind9 = factory.createRubricKind();
//rKind9.setInherited("false");
//rKind9.setName(icdContentModel.getIcdRefProperty().getBrowserText());
//rubKinds.getRubricKind().add(rKind9);
//set rubric kinds
claml.setRubricKinds(rubKinds);
//iterating icd categories
int index = 1;
for(Iterator it = icdCategories.iterator(); it.hasNext();){
RDFSNamedClass icdCategory = (RDFSNamedClass) it.next();
if(this.mapGeneratedCodes.containsKey(icdCategory)){ //only those categories with codes
//is included?
//if(this.isIncludedInLinearizationForType(icdCategory, linearizationType)){
//RDFSNamedClass icdCategory = icdContentModel.getICDCategory("http://who.int/icd#I82.0");
//System.out.println("Displayed as in the tree: " + icdCategory.getBrowserText());
//System.out.println(index++ + "|" + icdCategory.getBrowserText());
edu.mayo.bmi.guoqian.claml.Class cls = factory.createClass();
/*
//get original code, if not availabel it is "TBD"
String classCode = getClassCode(icdCategory);
//if the code is "TBD", then find it from generated codes
if(classCode.equals("TBD")){
String generatedCode = (String)this.mapGeneratedCodes.get(icdCategory);
if(generatedCode != null){
classCode = generatedCode;
}else{// in case, no code generated
System.out.println("Code not generated for:" + icdCategory.getBrowserText());
}
}
*/
String classCode = (String) this.mapGeneratedCodes.get(icdCategory);
cls.setCode(classCode);
String cKindName = getClassKind(icdCategory);
ClassKind cKind = factory.createClassKind();
cKind.setName(cKindName);
cls.setKind(cKind);
//meta icat id
Meta metaICatId = factory.createMeta();
metaICatId.setName("iCatID");
metaICatId.setValue(icdCategory.getName());
cls.getMeta().add(metaICatId);
/*
//superclass codes
if(!cKindName.equals("chapter")){// chapter is the root
Collection superclassCodes = getSuperclassCodes(icdCategory);
if(superclassCodes != null){
for(Iterator it1 = superclassCodes.iterator(); it1.hasNext();){
String superclassCode = (String) it1.next();
SuperClass superclass = factory.createSuperClass();
superclass.setCode(superclassCode);
cls.getSuperClass().add(superclass);
}
}
}
*/
//linearization parent code
if(!cKindName.equals("chapter")){// chapter is the root
//String linearizationParent = this.getLinearizationParentForType(icdCategory, linearizationType);
String linearizationParent = model.getLinearParentCode(icdCategory); //20100613
//RDFSNamedClass realLinearParent = this.getRealLinearizationParent(icdCategory, linearizationParent);
//String superclassCode = (String)this.mapGeneratedCodes.get(realLinearParent);
//System.out.println(icdCategory.getBrowserText() + "|linear parent: " + linearizationParent);
SuperClass superclass = factory.createSuperClass();
superclass.setCode(linearizationParent);
cls.getSuperClass().add(superclass);
}
//subclass codes sorted with sortingLabel
//Object[] arrayCodes = getSubclassCodesSortingLabels(icdCategory);
Object[] arrayCodes = model.getLinearSubclassCodes(icdCategory); //20100613
if(arrayCodes != null){
for(int it2 = 0; it2 < arrayCodes.length; it2 ++){
//for(Iterator it2 = subclassCodes.iterator(); it2.hasNext();){
String subclassCode = (String) arrayCodes[it2];
//System.out.println(code + "|" + subclassCode);
SubClass subclass = factory.createSubClass();
subclass.setCode(subclassCode);
cls.getSubClass().add(subclass);
}
}
/*
//subclass codes
Collection subclassCodes = getSubclassCodes(icdCategory);
if(subclassCodes != null){
Object[] arrayCodes = subclassCodes.toArray();
Arrays.sort(arrayCodes);
for(int it2 = 0; it2 < arrayCodes.length; it2 ++){
//for(Iterator it2 = subclassCodes.iterator(); it2.hasNext();){
String subclassCode = (String) arrayCodes[it2];
if(subclassCode.equals("TBD"))
System.out.println(icdCategory.getBrowserText() + "|" + subclassCode);
SubClass subclass = factory.createSubClass();
subclass.setCode(subclassCode);
cls.getSubClass().add(subclass);
}
}
*/
//set preferred label and language
String sortingLabel = this.getSortingLabel(icdCategory);
String label = this.getClassPreferredLabel(icdCategory);
label = label.replaceAll("'", "");
String clsCode = getClassCode(icdCategory);
if(clsCode.equals("TBD")){
//label = this.getUserAssignedLabel(icdCategory);
label += "[" + sortingLabel + "]";
Rubric rubricLabel = factory.createRubric();
//rubricLabel.setId("id-to-be-added-later");
ClassKind cKindPreferred = factory.createClassKind();
cKindPreferred.setName("preferred");
rubricLabel.setKind(cKindPreferred);
Label clsLabel = factory.createLabel();
clsLabel.setLang("en");
clsLabel.setSpace("default");
clsLabel.getContent().add(label);
rubricLabel.getLabel().add(clsLabel);
cls.getRubric().add(rubricLabel);
}else{
label += "{" + clsCode + "}"; //add ICD10 code in label
label += "[" + sortingLabel + "]";
Rubric rubricLabel = factory.createRubric();
String rubricId = this.getClassPreferredLabelRubricID(icdCategory);
rubricLabel.setId(rubricId);
ClassKind cKindPreferred = factory.createClassKind();
cKindPreferred.setName("preferred");
rubricLabel.setKind(cKindPreferred);
Label clsLabel = factory.createLabel();
clsLabel.setLang("en");
clsLabel.setSpace("default");
clsLabel.getContent().add(label);
/*
try{
Collection<RDFResource> clamlRefCodes = this.getTermClaMLReferences(icdContentModel.getTerm(icdCategory, icdContentModel.getIcdTitleProperty()));
if(clamlRefCodes != null){
for (RDFResource clamlRefCode : clamlRefCodes) {
Reference refCode = factory.createReference();
refCode.setClazz("in brackets");
refCode.setContent((String)clamlRefCode.getPropertyValue(icdContentModel.getTextProperty()));
//String refCodeText = ((RDFResource)clamlRefCode.getPropertyValue(icdContentModel.getIcdRefProperty())).getBrowserText();
String thisCode = (String)clamlRefCode.getPropertyValue(icdContentModel.getTextProperty());
if(thisCode.indexOf("-") >= 0){
thisCode = this.getCodeFromLabel(thisCode);
}
refCode.setCode(thisCode);
clsLabel.getContent().add(refCode);
}
}
}catch(Exception e){
e.printStackTrace();
System.out.println("preferred" + "|" + icdCategory.getBrowserText());
Collection clamlRefCodes = this.getTermClaMLReferences(icdContentModel.getTerm(icdCategory, icdContentModel.getIcdTitleProperty()));
if(clamlRefCodes != null){
for (Iterator itref = clamlRefCodes.iterator(); itref.hasNext();){
String clamlRefCode = (String) itref.next();
Reference refCode = factory.createReference();
refCode.setClazz("in brackets");
refCode.setContent(clamlRefCode);
//String refCodeText = ((RDFResource)clamlRefCode.getPropertyValue(icdContentModel.getIcdRefProperty())).getBrowserText();
String thisCode = clamlRefCode;
if(thisCode.indexOf("-") >= 0){
thisCode = this.getCodeFromLabel(thisCode);
}
refCode.setCode(thisCode);
clsLabel.getContent().add(refCode);
}
}
continue;
}
*/
rubricLabel.getLabel().add(clsLabel);
cls.getRubric().add(rubricLabel);
}
//synonyms
/*
Collection colSynonyms = this.getSynonyms(icdCategory);
if(colSynonyms != null){
for(Iterator itpd = colSynonyms.iterator(); itpd.hasNext();){
String synonym = (String) itpd.next();
if(synonym != null && synonym.length() > 0){
Rubric rubricSynonym = factory.createRubric();
rubricSynonym.setId("id-to-be-added-later-" + rubricIndex++);
ClassKind cKindSynonym = factory.createClassKind();
cKindSynonym.setName(icdContentModel.getSynonymProperty().getBrowserText());
rubricSynonym.setKind(cKindSynonym);
Label labelSynonym = factory.createLabel();
labelSynonym.setLang("en");
labelSynonym.setSpace("default");
labelSynonym.getContent().add(synonym);
rubricSynonym.getLabel().add(labelSynonym);
cls.getRubric().add(rubricSynonym);
}
}
}
*/
//definition
Collection definitions = this.getClassDefinitions(icdCategory);
if(definitions != null){
for(Iterator itdef = definitions.iterator(); itdef.hasNext();){
RDFResource defTerm = (RDFResource) itdef.next();
String defText = this.getDefinitionTermText(defTerm);
String defRubricID = this.getTermRubricID(defTerm);
if(definitions.size() > 1){
//System.out.println(classCode + "|" + defRubricID + "|" + defText);
}
//if(defText != null){
Rubric rubricDefinition = factory.createRubric();
rubricDefinition.setId(defRubricID);
ClassKind cKindDefinition = factory.createClassKind();
cKindDefinition.setName(icdContentModel.getDefinitionProperty().getBrowserText());
rubricDefinition.setKind(cKindDefinition);
Label labelDefinition = factory.createLabel();
labelDefinition.setLang("en");
labelDefinition.setSpace("default");
labelDefinition.getContent().add(defText);
rubricDefinition.getLabel().add(labelDefinition);
cls.getRubric().add(rubricDefinition);
//}// not null
}
}
//prefilled definitions
/*
Collection colPrefilledDefinitions = this.getPrefilledDefinitions(icdCategory);
if(colPrefilledDefinitions != null){
for(Iterator itpd = colPrefilledDefinitions.iterator(); itpd.hasNext();){
String pdefinition = (String) itpd.next();
if(pdefinition != null){
Rubric rubricpDefinition = factory.createRubric();
rubricpDefinition.setId("id-to-be-added-later-" + rubricIndex++);
ClassKind cKindpDefinition = factory.createClassKind();
cKindpDefinition.setName(icdContentModel.getPrefilledDefinitionProperty().getBrowserText());
rubricpDefinition.setKind(cKindpDefinition);
Label labelpDefinition = factory.createLabel();
labelpDefinition.setLang("en");
labelpDefinition.setSpace("default");
labelpDefinition.getContent().add(definition);
rubricpDefinition.getLabel().add(labelpDefinition);
cls.getRubric().add(rubricpDefinition);
}
}
}
*/
//inclusion terms
Collection colInclusions = this.getInclusionTerms(icdCategory);
Collection colSortedInclusions = new ArrayList();
Map mapSortedInclusions = new HashMap();
if(colInclusions != null){
for(Iterator it3 = colInclusions.iterator(); it3.hasNext();){
RDFResource inclusion = (RDFResource) it3.next();
String inclusionLabel = this.getInclusionTermText(inclusion);
String inclusionId = this.getTermRubricID(inclusion);
String inclusionLabelId = inclusionLabel + "|" + inclusionId;
colSortedInclusions.add(inclusionLabelId);
mapSortedInclusions.put(inclusionLabelId, inclusion);
}
//alphabetically sort the rubrics
Object[] arraySortedInclusions = colSortedInclusions.toArray();
List listSortedInclusions = Arrays.asList(arraySortedInclusions);
Collections.sort(listSortedInclusions, String.CASE_INSENSITIVE_ORDER);
for(ListIterator li0 = listSortedInclusions.listIterator(); li0.hasNext();){
String sortedInclusionLabelId = (String)li0.next();
String[] labelId = sortedInclusionLabelId.split("\\|");
RDFResource sortedInclusion = (RDFResource)mapSortedInclusions.get(sortedInclusionLabelId);
Rubric rubricInclusion = factory.createRubric();
if(!labelId[1].equals("null")) //if null, do nothing
rubricInclusion.setId(labelId[1]);
ClassKind cKindInclusion = factory.createClassKind();
cKindInclusion.setName("inclusion");
rubricInclusion.setKind(cKindInclusion);
Label labelInclusion = factory.createLabel();
labelInclusion.setLang("en");
labelInclusion.setSpace("default");
labelInclusion.getContent().add(labelId[0]);
Collection<RDFResource> clamlRefCodes = this.getTermClaMLReferences(sortedInclusion);
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){
e.printStackTrace();
System.out.println("exclusion" + "|" + icdCategory.getBrowserText());
continue;
}
//}
rubricInclusion.getLabel().add(labelInclusion);
cls.getRubric().add(rubricInclusion);
}
}
//notes term
Collection colNotes = this.getNoteTerms(icdCategory);
if(colNotes != null){
for(Iterator it6 = colNotes.iterator(); it6.hasNext();){
RDFResource note = (RDFResource) it6.next();
String noteLabel = this.getNoteTermText(note);
String noteId = this.getTermRubricID(note);
Rubric rubricNote = factory.createRubric();
rubricNote.setId(noteId);
ClassKind cKindNote = factory.createClassKind();
cKindNote.setName("note");
rubricNote.setKind(cKindNote);
Label labelNote = factory.createLabel();
labelNote.setLang("en");
labelNote.setSpace("default");
labelNote.getContent().add(noteLabel);
rubricNote.getLabel().add(labelNote);
cls.getRubric().add(rubricNote);
}
}
//codinghint term
Collection colCodingHints = this.getCodingHintTerms(icdCategory);
if(colCodingHints != null){
for(Iterator it7 = colCodingHints.iterator(); it7.hasNext();){
RDFResource note = (RDFResource) it7.next();
String noteLabel = this.getCodingHintTermText(note);
String noteId = this.getTermRubricID(note);
Rubric rubricNote = factory.createRubric();
rubricNote.setId(noteId);
ClassKind cKindNote = factory.createClassKind();
cKindNote.setName(icdContentModel.getCodingHintProperty().getBrowserText());
rubricNote.setKind(cKindNote);
Label labelNote = factory.createLabel();
labelNote.setLang("en");
labelNote.setSpace("default");
labelNote.getContent().add(noteLabel);