Merge r5933:5935 and r5937 from nihvivo-rel-1.1-maint
This commit is contained in:
rjy7
parent
715fad38f4
commit
503652796c
1 changed files with 312 additions and 147 deletions
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@ -63,15 +63,15 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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private static final int MAX_GROUP_DISPLAY_RANK = 99;
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/** Don't include these properties in the list. */
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private static final Collection<String> SUPPRESSED_OBJECT_PROPERTIES = Collections
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.unmodifiableCollection(Arrays
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.asList(new String[] { VitroVocabulary.IND_MAIN_IMAGE }));
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private static final Collection<String> SUPPRESSED_OBJECT_PROPERTIES = Collections
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.unmodifiableCollection(Arrays
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.asList(new String[] { VitroVocabulary.IND_MAIN_IMAGE }));
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public void doGet( HttpServletRequest request, HttpServletResponse res )
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throws IOException, ServletException {
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VitroRequest req = new VitroRequest(request);
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VitroRequest req = new VitroRequest(request);
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try {
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super.doGet(req, res);
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Object obj = req.getAttribute("entity");
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@ -118,12 +118,12 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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List<ObjectProperty> objectPropertyList = subject.getObjectPropertyList();
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for (ObjectProperty op : objectPropertyList) {
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if (!SUPPRESSED_OBJECT_PROPERTIES.contains(op)) {
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if (!SUPPRESSED_OBJECT_PROPERTIES.contains(op)) {
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op.setEditLabel(op.getDomainPublic());
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mergedPropertyList.add(op);
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}else{
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log.debug("suppressed " + op.getURI());
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}
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}else{
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log.debug("suppressed " + op.getURI());
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}
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}
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if (editMode) {
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@ -215,10 +215,16 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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if (g.getPropertyList()!=null && g.getPropertyList().size()>0) {
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for (Property p : g.getPropertyList()) {
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if (p instanceof ObjectProperty) {
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ObjectProperty op = (ObjectProperty)p;
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if (op.getObjectPropertyStatements()!=null && op.getObjectPropertyStatements().size()>0) {
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statementCount += op.getObjectPropertyStatements().size();
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}
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ObjectProperty op = (ObjectProperty)p;
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List<ObjectPropertyStatement> opStmts = op.getObjectPropertyStatements();
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if (op.getObjectPropertyStatements()!=null && opStmts.size()>0) {
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statementCount += opStmts.size();
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// If not collated, we need to apply custom sorting now.
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applyCustomSortToUncollatedProperty(op, opStmts);
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}
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}
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}
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}
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@ -228,18 +234,26 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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} catch (Exception ex) {
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log.error("Exception on trying to prune groups list with properties: "+ex.getMessage());
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}
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mergedPropertyList.clear();
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mergedPropertyList.clear();
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} else { // ungrouped mode
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for (Property p : mergedPropertyList) {
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if (p instanceof ObjectProperty) {
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ObjectProperty op = (ObjectProperty)p;
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applyCustomSortToUncollatedProperty(op, op.getObjectPropertyStatements());
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}
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}
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}
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}
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if (groupedMode) {
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req.setAttribute("groupsList",groupsList);
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} else {
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UnaryFunctor<List<Property>,List<Property>> entityPropertyListFilter = PropertyMaskingSetup.getEntityPropertyListFilter(getServletContext());
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if (entityPropertyListFilter != null) {
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mergedPropertyList = entityPropertyListFilter.fn(mergedPropertyList);
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}
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UnaryFunctor<List<Property>,List<Property>> entityPropertyListFilter = PropertyMaskingSetup.getEntityPropertyListFilter(getServletContext());
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if (entityPropertyListFilter != null) {
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mergedPropertyList = entityPropertyListFilter.fn(mergedPropertyList);
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}
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req.setAttribute("mergedList",mergedPropertyList);
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}
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@ -260,7 +274,7 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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public void doPost(HttpServletRequest request, HttpServletResponse response)
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public void doPost(HttpServletRequest request, HttpServletResponse response)
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throws ServletException,IOException {
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doGet(request, response);
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}
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@ -299,7 +313,7 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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}
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switch (count) {
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case 0: log.warn("groupsList has no groups on entering populateGroupsListWithProperties(); will create a new group \"other\"");
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break;
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break;
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case 1: break;
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default: try {
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Collections.sort(groupsList);
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@ -439,13 +453,20 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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private List<Property> collateBySubclass(List<Property> mergedPropertyList) {
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for( Property prop : mergedPropertyList){
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if( prop instanceof ObjectProperty && ((ObjectProperty)prop).getCollateBySubclass() ){
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collateBySubclass((ObjectProperty)prop);
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}
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}
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return mergedPropertyList;
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}
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for( Property prop : mergedPropertyList){
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if( prop instanceof ObjectProperty ) {
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ObjectProperty op = (ObjectProperty) prop;
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if (op.getCollateBySubclass() ){
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log.debug("Collating property " + prop.getURI() + " by subclass");
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collateBySubclass(op);
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} else {
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}
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}
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}
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return mergedPropertyList;
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}
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/**
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* Sort the object property statements for each property so that they
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@ -454,128 +475,272 @@ public class EntityMergedPropertyListController extends VitroHttpServlet {
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* This will be tricky since "subclass" is vaguely defined. Here directly
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* asserted classes are used.
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*/
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private void collateBySubclass(ObjectProperty prop) {
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List<ObjectPropertyStatement> orgStmtList = prop.getObjectPropertyStatements();
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if( orgStmtList == null )
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return;
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Map<String,VClass> directClasses = getDirectClasses( getObjectsFromStmts( orgStmtList ) );
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//don't do collateBySubclass if there is only one class
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if( directClasses.size() < 2 )
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prop.setCollateBySubclass(false); //this overrides the value from the model
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else{
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System.out.println("statements for object property: " + orgStmtList.size());
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//get list of direct classes and sort them
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List<VClass> vclasses = new LinkedList<VClass>(directClasses.values());
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Collections.sort(
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vclasses,
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new Comparator<VClass>(){
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public int compare(VClass o1, VClass o2) {
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return o1.getName().compareTo(o2.getName());
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}
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});
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//order object property statements by sorted direct class list
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List<ObjectPropertyStatement> sortedStmtList = new LinkedList<ObjectPropertyStatement>();
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for (VClass clazz : vclasses) {
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// get all obj prop stmts with objects of this class
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List<ObjectPropertyStatement> stmtsForClass = new ArrayList<ObjectPropertyStatement>();
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System.out.println("statements for object property: " + orgStmtList.size());
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Iterator<ObjectPropertyStatement> it = orgStmtList.iterator();
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while( it.hasNext()){
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ObjectPropertyStatement stmt = it.next();
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//if (stmt.getObject().getVClasses(true).contains(clazz)) {
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Individual obj = stmt.getObject();
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List<VClass> vclassesForObj = obj.getVClasses(true);
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if (vclassesForObj != null && vclassesForObj.contains(clazz)) {
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System.out.println("adding " + stmt + " to class "
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+ clazz.getURI());
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System.out.println("subjectURI " + stmt.getSubjectURI()
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+ " objectURI" + stmt.getObject().getURI());
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System.out.println("stmtsForclass size: "
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+ stmtsForClass.size());
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System.out.println("stmtsForclass size: "
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+ stmtsForClass.size());
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stmtsForClass.add(stmt);
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}
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}
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//bdc34: What do we do if a object individual is directly asserted to two different
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//types? For now we just show them in whichever type shows up first. related to NIHVIVO-876
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orgStmtList.removeAll(stmtsForClass);
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Collections.sort(stmtsForClass,
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new Comparator<ObjectPropertyStatement>() {
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public int compare(ObjectPropertyStatement o1,
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ObjectPropertyStatement o2) {
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return o1.getObject().getName().compareTo(
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o2.getObject().getName());
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}
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});
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System.out.println("stmtsForclass size after sort: "
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+ stmtsForClass.size());
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System.out.println("sortedStmtList size before add: "
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+ sortedStmtList.size());
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sortedStmtList.addAll(stmtsForClass);
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System.out.println("sortedStmtList size after add: "
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+ sortedStmtList.size());
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}
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prop.setObjectPropertyStatements(sortedStmtList);
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}
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}
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private void collateBySubclass(ObjectProperty prop) {
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List<ObjectPropertyStatement> orgStmtList = prop.getObjectPropertyStatements();
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if( orgStmtList == null )
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return;
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Map<String,VClass> directClasses = getDirectClasses( getObjectsFromStmts( orgStmtList ) );
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//don't do collateBySubclass if there is only one class
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if( directClasses.size() < 2 ) {
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prop.setCollateBySubclass(false); //this overrides the value from the model
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}
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else{
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log.debug("statements for object property: " + orgStmtList.size());
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//get list of direct classes and sort them
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List<VClass> vclasses = new LinkedList<VClass>(directClasses.values());
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Collections.sort(
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vclasses,
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new Comparator<VClass>(){
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public int compare(VClass o1, VClass o2) {
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return o1.getName().compareTo(o2.getName());
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}
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});
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//order object property statements by sorted direct class list
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List<ObjectPropertyStatement> sortedStmtList = new LinkedList<ObjectPropertyStatement>();
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for (VClass clazz : vclasses) {
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// get all obj prop stmts with objects of this class
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List<ObjectPropertyStatement> stmtsForClass = new ArrayList<ObjectPropertyStatement>();
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log.debug("statements for object property: " + orgStmtList.size());
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Iterator<ObjectPropertyStatement> it = orgStmtList.iterator();
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while( it.hasNext()){
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ObjectPropertyStatement stmt = it.next();
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//if (stmt.getObject().getVClasses(true).contains(clazz)) {
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Individual obj = stmt.getObject();
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List<VClass> vclassesForObj = obj.getVClasses(true);
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if (vclassesForObj != null && vclassesForObj.contains(clazz)) {
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log.debug("adding " + stmt + " to class "
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+ clazz.getURI());
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log.debug("subjectURI " + stmt.getSubjectURI()
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+ " objectURI" + stmt.getObject().getURI());
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log.debug("stmtsForclass size: "
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+ stmtsForClass.size());
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log.debug("stmtsForclass size: "
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+ stmtsForClass.size());
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stmtsForClass.add(stmt);
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}
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}
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//bdc34: What do we do if a object individual is directly asserted to two different
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//types? For now we just show them in whichever type shows up first. related to NIHVIVO-876
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orgStmtList.removeAll(stmtsForClass);
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sortStatements(prop, stmtsForClass);
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log.debug("stmtsForclass size after sort: "
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+ stmtsForClass.size());
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log.debug("sortedStmtList size before add: "
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+ sortedStmtList.size());
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sortedStmtList.addAll(stmtsForClass);
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log.debug("sortedStmtList size after add: "
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+ sortedStmtList.size());
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}
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prop.setObjectPropertyStatements(sortedStmtList);
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}
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}
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private void sortStatements(ObjectProperty prop, List<ObjectPropertyStatement> statements) {
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if (!applyCustomSort(prop, statements)) {
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Collections.sort(statements,
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new Comparator<ObjectPropertyStatement>() {
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public int compare(ObjectPropertyStatement o1,
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ObjectPropertyStatement o2) {
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return o1.getObject().getName().compareTo(
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o2.getObject().getName());
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}
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});
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}
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}
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// rjy7 Quick and dirty fix to achieve custom sorting for specific properties in the VIVO ontology.
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// See NIHVIVO-426, NIHVIVO-1158, NIHVIVO-1160. Some of these involve sorting on data properties of an
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// individual two graph edges away from the individual being displayed, for which there is currently
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// no provision. A better strategy will be designed and implemented in a later version, in particular
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// one that does not involve hard-coded references to the VIVO ontology in the Vitro core.
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private boolean applyCustomSort(ObjectProperty prop, List<ObjectPropertyStatement> statements) {
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String vivoCoreOntology = "http://vivoweb.org/ontology/core#";
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String propertyUri = prop.getURI();
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// Positions in an organization
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if (propertyUri.equals(vivoCoreOntology + "organizationForPosition")) {
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sortByRelatedIndividualNames(statements, vivoCoreOntology + "positionForPerson");
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return true;
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}
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// Person's positions
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if (propertyUri.equals(vivoCoreOntology + "personInPosition")) {
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sortReverseChron(statements, vivoCoreOntology + "endYear", vivoCoreOntology + "startYear");
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return true;
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}
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// // Person's publications
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// if (propertyUri.equals(vivoCoreOntology + "authorInAuthorship")) {
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// sortByReverseChronAndRelatedIndividualName(statements, vivoCoreOntology + " ", vivoCoreOntology + " ");
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// return true;
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// }
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return false;
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}
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private List<Individual> getObjectsFromStmts(List<ObjectPropertyStatement> orgStmtList) {
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List<Individual> individuals = new LinkedList<Individual>();
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for( ObjectPropertyStatement stmt : orgStmtList ){
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individuals.add( stmt.getObject() );
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}
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return individuals;
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}
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// Apply custom sorting to an uncollated property. If the property is collated, the custom sorting has already
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// been applied to each subclass listing individually.
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private void applyCustomSortToUncollatedProperty(ObjectProperty op, List<ObjectPropertyStatement> opStmts) {
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// This includes the case where the ontology doesn't specify collating, as well as the case
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// where we don't collate because only one subclass is populated, since then we've set
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// the collation value to false.
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if (!op.getCollateBySubclass()) {
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if (applyCustomSort(op, opStmts)) {
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op.setObjectPropertyStatements(opStmts);
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}
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}
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}
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private void sortReverseChron(List<ObjectPropertyStatement> statements, String endYearPredicate, String startYearPredicate) {
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// 1. Sort by end date descending, null dates first
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// 2. Then by start date descending, null dates last
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// 3. No sorting for entries with no start or end date - just put at the bottom in random order
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final String endYearProperty = endYearPredicate;
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final String startYearProperty = startYearPredicate;
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Collections.sort(statements, new Comparator<ObjectPropertyStatement>() {
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public int compare(ObjectPropertyStatement left, ObjectPropertyStatement right) {
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String endLeftValue = left.getObject().getDataValue(endYearProperty);
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Integer endLeft = endLeftValue == null ? null : Integer.valueOf(endLeftValue);
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private Map<String,VClass> getDirectClasses(List<Individual> objectsFromStmts) {
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Map<String,VClass> directClasses = new HashMap<String,VClass>();
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String startLeftValue = left.getObject().getDataValue(startYearProperty);
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Integer startLeft = startLeftValue == null ? null : Integer.valueOf(startLeftValue);
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String endRightValue = right.getObject().getDataValue(endYearProperty);
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Integer endRight = endRightValue == null ? null : Integer.valueOf(endRightValue);
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for (Individual ind : objectsFromStmts) {
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for (VClass clazz : ind.getVClasses(true)) {
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directClasses.put(clazz.getURI(),clazz);
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}
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}
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return directClasses;
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}
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String startRightValue = right.getObject().getDataValue(startYearProperty);
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Integer startRight = startRightValue == null ? null : Integer.valueOf(startRightValue);
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// No sorting for entries with no start or end date - just put at the bottom in random order
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if (endLeft == null && startLeft == null) {
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return 1;
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}
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if (endRight == null && startRight == null) {
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return -1;
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}
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// First sort by end date
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// A null end date precedes
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// But if both end dates are null, compare start dates
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if ( ! (endLeft == null && endRight == null) ) {
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if (endLeft == null) {
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return -1;
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}
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if (endRight == null) {
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return 1;
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}
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int endComp = endLeft.compareTo(endRight);
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if (endComp != 0) {
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return 0 - endComp;
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}
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}
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// If end dates are equal, sort by start date
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// A null start date follows
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if (startLeft == null) {
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return 1;
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}
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if (startRight == null) {
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return -1;
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}
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return 0 - startLeft.compareTo(startRight);
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}
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});
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}
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// private void sortByReverseChronAndRelatedIndividualName(List<ObjectPropertyStatement> statements,
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// String datePredicate, String relatedIndividualPredicate) {
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//
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// }
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// Sort statements by the name of the individual on the other side of the context node.
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private void sortByRelatedIndividualNames(List<ObjectPropertyStatement> statements, String predicateUri) {
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log.debug("In sortByRelatedIndividualNames(), before sorting");
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if (log.isDebugEnabled()) {
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for (ObjectPropertyStatement ops : statements) {
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log.debug(ops.getObject().getRelatedIndividual(predicateUri).getName());
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}
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}
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final String propertyUri = predicateUri;
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Collections.sort(statements, new Comparator<ObjectPropertyStatement>() {
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public int compare(ObjectPropertyStatement left, ObjectPropertyStatement right) {
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Individual indLeft = left.getObject().getRelatedIndividual(propertyUri);
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Individual indRight = right.getObject().getRelatedIndividual(propertyUri);
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return indLeft.getName().compareTo(indRight.getName());
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}
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});
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log.debug("In sortByRelatedIndividualNames(), after sorting");
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if (log.isDebugEnabled()) {
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for (ObjectPropertyStatement ops : statements) {
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log.debug(ops.getObject().getRelatedIndividual(predicateUri).getName());
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}
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}
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}
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/**
|
||||
* Look for filter in servlet context and filter properties with it if there is one.
|
||||
*
|
||||
* This allows a vitro instance to have specialized filtering for display. It was originally
|
||||
* created to deal with problems caused by custom short views.
|
||||
* *
|
||||
* @param objectPropertyList
|
||||
* @param wdf
|
||||
* @return
|
||||
*/
|
||||
private Individual filterFromContext(Individual ind ) {
|
||||
try{
|
||||
UnaryFunctor<Individual,Individual> filter = getMergedPropertyListFilter(getServletContext());
|
||||
if( filter == null )
|
||||
return ind;
|
||||
else
|
||||
return filter.fn(ind);
|
||||
}catch(Throwable t){
|
||||
log.error(t,t);
|
||||
}
|
||||
return ind;
|
||||
}
|
||||
|
||||
public static void setMergedPropertyListFilter( UnaryFunctor<Individual,Individual>fn, ServletContext sc){
|
||||
sc.setAttribute("EntityMergedPropertyListController.toFilteringIndividual", fn);
|
||||
}
|
||||
|
||||
public static UnaryFunctor<Individual,Individual> getMergedPropertyListFilter( ServletContext sc){
|
||||
return(UnaryFunctor<Individual,Individual>)sc.getAttribute("EntityMergedPropertyListController.toFilteringIndividual");
|
||||
}
|
||||
private List<Individual> getObjectsFromStmts(List<ObjectPropertyStatement> orgStmtList) {
|
||||
List<Individual> individuals = new LinkedList<Individual>();
|
||||
for( ObjectPropertyStatement stmt : orgStmtList ){
|
||||
individuals.add( stmt.getObject() );
|
||||
}
|
||||
return individuals;
|
||||
}
|
||||
|
||||
private Map<String,VClass> getDirectClasses(List<Individual> objectsFromStmts) {
|
||||
Map<String,VClass> directClasses = new HashMap<String,VClass>();
|
||||
|
||||
for (Individual ind : objectsFromStmts) {
|
||||
for (VClass clazz : ind.getVClasses(true)) {
|
||||
directClasses.put(clazz.getURI(),clazz);
|
||||
}
|
||||
}
|
||||
return directClasses;
|
||||
}
|
||||
|
||||
/**
|
||||
* Look for filter in servlet context and filter properties with it if there is one.
|
||||
*
|
||||
* This allows a vitro instance to have specialized filtering for display. It was originally
|
||||
* created to deal with problems caused by custom short views.
|
||||
* *
|
||||
* @param objectPropertyList
|
||||
* @param wdf
|
||||
* @return
|
||||
*/
|
||||
private Individual filterFromContext(Individual ind ) {
|
||||
try{
|
||||
UnaryFunctor<Individual,Individual> filter = getMergedPropertyListFilter(getServletContext());
|
||||
if( filter == null )
|
||||
return ind;
|
||||
else
|
||||
return filter.fn(ind);
|
||||
}catch(Throwable t){
|
||||
log.error(t,t);
|
||||
}
|
||||
return ind;
|
||||
}
|
||||
|
||||
public static void setMergedPropertyListFilter( UnaryFunctor<Individual,Individual>fn, ServletContext sc){
|
||||
sc.setAttribute("EntityMergedPropertyListController.toFilteringIndividual", fn);
|
||||
}
|
||||
|
||||
public static UnaryFunctor<Individual,Individual> getMergedPropertyListFilter( ServletContext sc){
|
||||
return(UnaryFunctor<Individual,Individual>)sc.getAttribute("EntityMergedPropertyListController.toFilteringIndividual");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue