NIHVIVO-2317 NIHVIVO-2318 removing vitro namespace properties from editing and various Java classes and interfaces

webapp/src/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelper.java

@@ -52,24 +52,15 @@ public class PropertyRestrictionPolicyHelper {
 	private static final Collection<String> PERMITTED_EXCEPTIONS = Arrays
 			.asList(new String[] {
 					VitroVocabulary.MONIKER,
-					VitroVocabulary.BLURB,
-					VitroVocabulary.DESCRIPTION,
 					VitroVocabulary.MODTIME,
-					VitroVocabulary.TIMEKEY,
 
-					VitroVocabulary.CITATION,
 					VitroVocabulary.IND_MAIN_IMAGE,
 
 					VitroVocabulary.LINK,
 					VitroVocabulary.PRIMARY_LINK,
 					VitroVocabulary.ADDITIONAL_LINK,
 					VitroVocabulary.LINK_ANCHOR,
-					VitroVocabulary.LINK_URL,
+					VitroVocabulary.LINK_URL });
-
-					VitroVocabulary.KEYWORD_INDIVIDUALRELATION,
-					VitroVocabulary.KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD,
-					VitroVocabulary.KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL,
-					VitroVocabulary.KEYWORD_INDIVIDUALRELATION_MODE });
 
 	/**
 	 * The bean is attached to the ServletContext using this attribute name.

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/DataPropertyStatement.java

@@ -36,17 +36,5 @@ public interface DataPropertyStatement {
 
     public void setLanguage(String language);
 
-    public Date getSunrise();
-
-    public void setSunrise(Date sunrise);
-
-    public Date getSunset();
-
-    public void setSunset(Date sunset);
-    /*
-    public String getQualifier();
-
-    public void setQualifier(String qualifier);
-    */
     public String getString();
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/DataPropertyStatementImpl.java

@@ -8,7 +8,7 @@ import java.util.Date;
  * a class representing an particular instance of a data property
  *
  */
-public class DataPropertyStatementImpl implements VitroTimeWindowedResource, DataPropertyStatement
+public class DataPropertyStatementImpl implements DataPropertyStatement
 {
     private Individual individual = null;
     private String individualURI = null;
@@ -17,10 +17,6 @@ public class DataPropertyStatementImpl implements VitroTimeWindowedResource, Dat
     private String datatypeURI = null;
     private String language = null;
     
-    private Date sunrise = null;
-    private Date sunset = null;
-    //private String qualifier = null;
-
     public DataPropertyStatementImpl(){
     }
 
@@ -84,30 +80,6 @@ public class DataPropertyStatementImpl implements VitroTimeWindowedResource, Dat
         this.language = language;
     }
 
-    public Date getSunrise() {
-        return sunrise;
-    }
-
-    public void setSunrise(Date sunrise) {
-        this.sunrise = sunrise;
-    }
-
-    public Date getSunset() {
-        return sunset;
-    }
-
-    public void setSunset(Date sunset) {
-        this.sunset = sunset;
-    }
-    /*
-    public String getQualifier() {
-        return qualifier;
-    }
-
-    public void setQualifier(String qualifier) {
-        this.qualifier = qualifier;
-    }
-    */
     public String getString(){
         String out = "instance of dataprop: " + datapropURI;
 

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/Individual.java

@@ -17,7 +17,7 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
  * Date: Oct 18, 2007
  * Time: 3:08:33 PM
  */
-public interface Individual extends ResourceBean, VitroTimeWindowedResource, Comparable<Individual> {
+public interface Individual extends ResourceBean, Comparable<Individual> {
     String getName();
     void setName(String in);
 
@@ -31,15 +31,6 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     String getVClassURI();
     void setVClassURI(String in);
 
-    //Date getSunrise();
-    void setSunrise(Date in);
-
-    //Date getSunset();
-    void setSunset(Date in);
-
-    Date getTimekey();
-    void setTimekey(Date in);
-
     Timestamp getModTime();
     void setModTime(Timestamp in);
 
@@ -92,24 +83,6 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     List<DataPropertyStatement> getExternalIds();
     void setExternalIds(List<DataPropertyStatement> externalIds);
 
-    String getMoniker();
-    void setMoniker(String in);
-
-    String getDescription();
-    void setDescription(String in);
-
-    String getAnchor();
-    void setAnchor(String in);
-
-    String getBlurb();
-    void setBlurb(String in);
-
-    int getStatusId();
-    void setStatusId(int in);
-
-    String getStatus();
-    void setStatus(String s);
-
     void setMainImageUri(String mainImageUri);
     String getMainImageUri();
     
@@ -117,22 +90,6 @@ public interface Individual extends ResourceBean, VitroTimeWindowedResource, Com
     String getThumbUrl();
     boolean hasThumb();
 
-    String getUrl();
-    void setUrl(String url);
-
-    List<Link> getLinksList();
-    void setLinksList(List<Link> linksList);
-    
-    Link getPrimaryLink();
-    void setPrimaryLink(Link link);
-
-    List<String> getKeywords();
-    void setKeywords(List<String> keywords);
-    String getKeywordString();
-    
-    List<Keyword> getKeywordObjects();
-    void setKeywordObjects(List<Keyword> keywords);
-
     void sortForDisplay();
 
     JSONObject toJSON() throws JSONException;

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/IndividualImpl.java

@@ -2,17 +2,25 @@
 
 package edu.cornell.mannlib.vitro.webapp.beans;
 
+import java.lang.reflect.Method;
+import java.sql.Timestamp;
+import java.text.Collator;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeSet;
+
 import org.json.JSONException;
 import org.json.JSONObject;
 
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.ImageInfo;
 import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 
-import java.lang.reflect.Method;
-import java.sql.Timestamp;
-import java.text.Collator;
-import java.util.*;
-
 /**
  * Represents a single entity record.
 */
@@ -31,9 +39,6 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     protected VClass vClass = null;
     protected List<VClass> directVClasses = null;
     protected List<VClass> allVClasses = null;
-    protected Date sunrise = null;
-    protected Date sunset = null;
-    protected Date timekey = null;
     protected Timestamp modTime = null;
     protected List <ObjectProperty>propertyList = null;
     protected List<ObjectProperty> populatedObjectPropertyList = null;
@@ -46,19 +51,8 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     protected List <ObjectPropertyStatement>rangeEnts2Ents = null;
     protected List <DataPropertyStatement>externalIds = null;
 
-    protected String moniker = null;
-    protected String url = null;
-    protected String description = null;
-    protected String anchor = null;
-    protected String blurb = null;
     protected String mainImageUri = NOT_INITIALIZED;
     protected ImageInfo imageInfo = null;
-    protected int statusId = 0;
-    protected String status = null;
-    protected List <Link>linksList = null;
-    protected Link primaryLink = null;
-    protected List<String> keywords=null;
-    protected List<Keyword> keywordObjects=null;
     protected Float searchBoost;
     
     /** indicates if sortForDisplay has been called  */
@@ -87,22 +81,9 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
     public String getRdfsLabel(){ return rdfsLabel; }
     public void setRdfsLabel(String s){ rdfsLabel = s; }    	
 
-//     private String modTime = null;
-//     public String getModtime(){return modTime;}
-//     public void setModtime(String in){modTime=in;}
-
     public String getVClassURI(){return vClassURI;}
     public void setVClassURI(String in){vClassURI=in;}
 
-    public Date getSunrise(){return sunrise;}
-    public void setSunrise(Date in){sunrise=in;}
-
-    public Date getSunset(){return sunset;}
-    public void setSunset(Date in){sunset=in;}
-
-    public Date getTimekey(){return timekey;}
-    public void setTimekey(Date in){timekey=in;}
-
     /**
      * Returns the last time this object was changed in the model.
      * Notice Java API craziness: Timestamp is a subclass of Date
@@ -272,26 +253,6 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
         this.externalIds = externalIds;
     }
     
-
-    public String getMoniker(){return moniker;}
-    public void setMoniker(String in){moniker=in;}
-
-    public String getDescription(){return description;}
-    public void setDescription(String in){description=in;}
-
-    public String getAnchor(){return anchor;}
-    public void setAnchor(String in){anchor=in;}
-
-    public String getBlurb(){return blurb;}
-    public void setBlurb(String in){blurb=in;}
-    
-    public int getStatusId(){return statusId;}
-    public void setStatusId(int in){statusId=in;}
-
-    public String getStatus()         {return status;}
-    public void   setStatus(String s) {status=s;     }
-
-    
 	@Override
 	public String getMainImageUri() {
 		return (mainImageUri == NOT_INITIALIZED) ? null : mainImageUri;
@@ -313,61 +274,6 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
 		return "thumbUrl";
 	}
 
-	public String getUrl() {
-        return url;
-    }
-    public void setUrl(String url) {
-        this.url = url;
-    }
-    public List<Link> getLinksList() {
-        return linksList;
-    }
-    public void setLinksList(List <Link>linksList) {
-        this.linksList = linksList;
-    }
-    
-    public Link getPrimaryLink() {
-        return primaryLink;
-    }
-    
-    public void setPrimaryLink(Link link) {
-        primaryLink = link;
-    }
-    
-    public List<String> getKeywords() {     return keywords;    }
-    public void setKeywords(List<String> keywords) {this.keywords = keywords;}
-    public String getKeywordString(){
-        String rv = "";
-        List keywords=getKeywords();
-        if (getKeywords()!=null){
-            Iterator<String> it1 = getKeywords().iterator();
-            TreeSet<String> keywordSet = new TreeSet<String>(new Comparator<String>() {
-                public int compare( String first, String second ) {
-                    if (first==null) {
-                        return 1;
-                    }
-                    if (second==null) {
-                        return -1;
-                    }
-                    Collator collator = Collator.getInstance();
-                    return collator.compare(first,second);
-                }
-            });
-            while( it1.hasNext() ){
-                keywordSet.add(it1.next());
-            }
-            Iterator<String> it2 = keywordSet.iterator();
-            while (it2.hasNext()) {
-                rv+= it2.next();
-                if( it2.hasNext())
-                    rv+=", ";
-            }
-        }
-        return rv;
-    }
-    public List<Keyword> getKeywordObjects() { return keywordObjects; }
-    public void setKeywordObjects(List<Keyword> keywords) {this.keywordObjects = keywords;}
-
     public Float getSearchBoost() { return searchBoost;  }    
     public void setSearchBoost(Float boost) { searchBoost = boost; }
     
@@ -421,8 +327,6 @@ public class IndividualImpl extends BaseResourceBean implements Individual, Comp
 
        if( "name".equalsIgnoreCase(fieldName) )
            return getName();
-       if( "timekey".equalsIgnoreCase(fieldName) )
-           return getTimekey();
 
        //not one of the more common ones, try reflection
 

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatement.java

@@ -7,10 +7,6 @@ public interface ObjectPropertyStatement {
 
     public String toString();
 
-    public String getDescription();
-
-    public void setDescription(String description);
-
     public boolean isSubjectOriented();
 
     public void setSubjectOriented(boolean subjectOriented);
@@ -19,10 +15,6 @@ public interface ObjectPropertyStatement {
 
     public void setSubjectURI(String subjectURI);
 
-    public String getQualifier();
-
-    public void setQualifier(String qualifier);
-
     public String getObjectURI();
 
     public void setObjectURI(String objectURI);
@@ -43,14 +35,6 @@ public interface ObjectPropertyStatement {
 
     public void setPropertyURI(String URI);
 
-    public void setSunrise(Date date);
-
-    public Date getSunrise();
-
-    public void setSunset(Date date);
-
-    public Date getSunset();
-
     public PropertyInstance toPropertyInstance();
 
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/ObjectPropertyStatementImpl.java

@@ -9,7 +9,7 @@ import java.util.Date;
  * a class representing a particular instance of an object property
  *
  */
-public class ObjectPropertyStatementImpl implements VitroTimeWindowedResource, ObjectPropertyStatement
+public class ObjectPropertyStatementImpl implements ObjectPropertyStatement
 {
     private String subjectURI = null;
     private Individual subject = null;
@@ -41,22 +41,6 @@ public class ObjectPropertyStatementImpl implements VitroTimeWindowedResource, O
            return "Object Property Statements: "+dom+" "+prop+" to "+ran+" "+orent;
     }
 
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#getDescription()
-     */
-    public String getDescription() {
-        return description;
-    }
-
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setDescription(java.lang.String)
-     */
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#isSubjectOriented()
      */
@@ -87,22 +71,6 @@ public class ObjectPropertyStatementImpl implements VitroTimeWindowedResource, O
         this.subjectURI = subjectURI;
     }
 
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#getQualifier()
-     */
-    public String getQualifier() {
-        return qualifier;
-    }
-
-
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setQualifier(java.lang.String)
-     */
-    public void setQualifier(String qualifier) {
-        this.qualifier = qualifier;
-    }
-
-
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#getObjectURI()
      */
@@ -196,32 +164,6 @@ public class ObjectPropertyStatementImpl implements VitroTimeWindowedResource, O
         }
     }
 
-    private Date sunrise = null;
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setSunrise(java.util.Date)
-     */
-    public void setSunrise(Date date) {
-        sunrise = date;
-    }
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#getSunrise()
-     */
-    public Date getSunrise(){
-        return sunrise;
-    }
-
-    private Date sunset = null;
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#setSunset(java.util.Date)
-     */
-    public void setSunset(Date date) {
-        sunset = date;
-    }
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#getSunset()
-     */
-    public Date getSunset(){ return sunset; }
-
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement#toPropertyInstance()
      */
@@ -231,7 +173,6 @@ public class ObjectPropertyStatementImpl implements VitroTimeWindowedResource, O
         pi.setPropertyURI(propertyURI);
         pi.setSubjectEntURI(subjectURI);
         pi.setObjectEntURI(objectURI);
-        pi.setQualifier(qualifier);
         pi.setSubjectSide(subjectOriented);
         return pi;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/PropertyInstance.java

@@ -14,9 +14,6 @@ public class PropertyInstance implements PropertyInstanceIface, Comparable<Prope
     private String propertyURI = null;
     private String objectEntURI = null;
     private String subjectEntURI = null;
-    private String qualifier = null;
-    private Date sunrise = null;
-    private Date sunset = null;
 
     private String subjectName = null;
     private String objectName = null;
@@ -86,18 +83,6 @@ public class PropertyInstance implements PropertyInstanceIface, Comparable<Prope
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#getQualifier()
      */
-    public String getQualifier(){return qualifier;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#getSunrise()
-     */
-    public Date getSunrise(){return sunrise;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#getSunset()
-     */
-    public Date getSunset(){return sunset;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#getDomainSide()
-     */
     public boolean getSubjectSide(){return subjectSide;}
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#getDomainQuickEditJsp()
@@ -156,18 +141,6 @@ public class PropertyInstance implements PropertyInstanceIface, Comparable<Prope
      * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#setRangePublic(java.lang.String)
      */
     public void setRangePublic(String in){rangePublic=in;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#setQualifier(java.lang.String)
-     */
-    public void setQualifier(String in){qualifier=in;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#setSunrise(java.util.Date)
-     */
-    public void setSunrise(Date in){sunrise=in;}
-    /* (non-Javadoc)
-     * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#setSunset(java.util.Date)
-     */
-    public void setSunset(Date in){sunset=in;}
     /* (non-Javadoc)
      * @see edu.cornell.mannlib.vitro.beans.PropertyInstanceIface#setDomainSide(boolean)
      */

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/PropertyInstanceIface.java

@@ -10,9 +10,6 @@ public interface PropertyInstanceIface {
     public abstract String getPropertyURI();
     public abstract String getObjectEntURI();
     public abstract String getSubjectEntURI();
-    public abstract String getQualifier();
-    public abstract Date getSunrise();
-    public abstract Date getSunset();
 
 //  entities
     public abstract String getSubjectName();
@@ -56,12 +53,6 @@ public interface PropertyInstanceIface {
 
     public abstract void setRangePublic(String in);
 
-    public abstract void setQualifier(String in);
-
-    public abstract void setSunrise(Date in);
-
-    public abstract void setSunset(Date in);
-
     public abstract void setSubjectSide(boolean in);
 
     public abstract void setDomainQuickEditJsp(String in);

webapp/src/edu/cornell/mannlib/vitro/webapp/beans/VitroTimeWindowedResource.java

@@ -1,10 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.beans;
-
-import java.util.Date;
-
-public interface VitroTimeWindowedResource {
-    public Date getSunrise() ;
-    public Date getSunset() ;
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/CloneEntityServlet.java

@@ -91,19 +91,6 @@ public class CloneEntityServlet extends BaseEditController {
             ind.setName("CLONE OF "+ind.getName());
         }      
  
-        String timeKeyStr = request.getParameter("timekey");
-        if (timeKeyStr!=null && !timeKeyStr.equals("")) {
-            Date timekey = parseStringToDate(timeKeyStr);
-            if (timekey!=null) {
-                ind.setTimekey(timekey);
-            }
-        }
-        // specify other values that do NOT want to be carried over from the existing Individual
-        ind.setSunrise(new DateTime().toDate());
-        // cannot set these values to null because they will still be copies
-        ind.setBlurb("");
-        ind.setDescription("");        
- 
         String cloneURI=individualDao.insertNewIndividual(ind);
         if (cloneURI == null){ log.error("Error inserting cloned individual"); return; }
 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/EntityEditController.java

@@ -30,15 +30,11 @@ import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
 import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.beans.VClassGroup;
 import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.PropertyInstanceDao;
 
 public class EntityEditController extends BaseEditController {
@@ -77,11 +73,9 @@ public class EntityEditController extends BaseEditController {
         request.setAttribute("entity",ent);
 
         ArrayList<String> results = new ArrayList<String>();
-        int colCount = 6;
+        int colCount = 4;
         results.add("Name");
-        results.add("moniker");
         results.add("class");
-        results.add("blurb");
         results.add("display level");
         results.add("edit level");
         results.add("last updated");
@@ -100,8 +94,6 @@ public class EntityEditController extends BaseEditController {
         	rName = "[resource]";
         }
         results.add(rName);
-        String rMoniker = (ent.getMoniker()==null) ? "unspecified" : ent.getMoniker();
-        results.add(rMoniker);
         
         String classStr = "";
         List<VClass> classList = inferredEnt.getVClasses(false);
@@ -124,9 +116,6 @@ public class EntityEditController extends BaseEditController {
         }
         results.add(classStr);
                 
-        String rBlurb = (ent.getBlurb()==null) ? "" : ent.getBlurb();
-        results.add(rBlurb);
-        
         results.add(ent.getHiddenFromDisplayBelowRoleLevel()  == null ? "unspecified" : ent.getHiddenFromDisplayBelowRoleLevel().getLabel());
         results.add(ent.getProhibitedFromUpdateBelowRoleLevel() == null ? "unspecified" : ent.getProhibitedFromUpdateBelowRoleLevel().getLabel());
 
@@ -158,10 +147,6 @@ public class EntityEditController extends BaseEditController {
             OptionMap.put("externalIds", externalIdOptionList);
         } catch (Exception e) {e.printStackTrace();}
                 
-        try {
-            OptionMap.put("ExtraURL", FormUtils.makeOptionListFromBeans(ent.getLinksList(), "URI", "Anchor", null, null, false));
-        } catch (Exception e) {e.printStackTrace();}
-        
         List classGroups = vreq.getFullWebappDaoFactory().getVClassGroupDao().getPublicGroupsWithVClasses(true,true,false); // order by displayRank, include uninstantiated classes, don't count the individuals
         Iterator classGroupIt = classGroups.iterator();
         ListOrderedMap optGroupMap = new ListOrderedMap();
@@ -202,28 +187,6 @@ public class EntityEditController extends BaseEditController {
 
         foo.setOptionLists(OptionMap);
 
-        List<Option> existingKeywordRelations = new LinkedList();
-        KeywordIndividualRelationDao kirDao = vreq.getFullWebappDaoFactory().getKeys2EntsDao();
-        KeywordDao kDao = vreq.getFullWebappDaoFactory().getKeywordDao();
-        List kirs = kirDao.getKeywordIndividualRelationsByIndividualURI(ent.getURI());
-        if (kirs != null) {
-            Iterator kirIt = kirs.iterator();
-            while (kirIt.hasNext()) {
-                KeywordIndividualRelation kir = (KeywordIndividualRelation) kirIt.next();
-                if (kir.getKeyId() > 0) {
-                    Keyword k = kDao.getKeywordById(kir.getKeyId());
-                    if (k != null) {
-                        Option kOpt = new Option();
-                        kOpt.setValue(kir.getURI());
-                        kOpt.setBody(k.getTerm()+" ("+kir.getMode()+")");
-                        existingKeywordRelations.add(kOpt);
-                    }
-                }
-
-            }
-        }
-        foo.getOptionLists().put("existingKeywordRelations",existingKeywordRelations);
-
         epo.setFormObject(foo);
 
         RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/EntityRetryController.java

@@ -172,8 +172,6 @@ public class EntityRetryController extends BaseEditController {
 			hash.put("VClassURI", optList);
         }
         
-        hash.put("Moniker", getMonikerOptionsList(individualForEditing, ewDao));
-        
         hash.put("HiddenFromDisplayBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getDisplayOptionsList(individualForEditing));    
         hash.put("ProhibitedFromUpdateBelowRoleLevelUsingRoleUri",RoleLevelOptionsSetup.getUpdateOptionsList(individualForEditing));
 
@@ -279,20 +277,6 @@ public class EntityRetryController extends BaseEditController {
         DateFormat dateOnlyFormat = new SimpleDateFormat("yyyy-MM-dd");
 
         String html = FormUtils.htmlFormFromBean(individualForEditing,action,epo,foo,epo.getBadValueMap());
-        if (individualForEditing.getSunrise() != null)
-            foo.getValues().put("Sunrise", dateOnlyFormat.format(individualForEditing.getSunrise()));
-        if (individualForEditing.getSunset() != null)
-            foo.getValues().put("Sunset", minutesOnlyDateFormat.format(individualForEditing.getSunset()));
-        if (individualForEditing.getTimekey() != null)
-            foo.getValues().put("Timekey", minutesOnlyDateFormat.format(individualForEditing.getTimekey()));
-
-        HashMap defaultsHash = new HashMap();
-        if (action.equals("insert")) {
-            Calendar cal = Calendar.getInstance(TimeZone.getDefault());
-            defaultsHash.put("Sunrise", minutesOnlyDateFormat.format(cal.getTime()));
-            defaultsHash.put("Sunset", "9999-12-31");
-        }
-        epo.setDefaultValueMap(defaultsHash);
 
         List cList = new ArrayList();
         cList.add(new IndividualDataPropertyStatementProcessor());
@@ -328,24 +312,6 @@ public class EntityRetryController extends BaseEditController {
 
     }
 
-    private List<Option> getMonikerOptionsList(Individual entity,
-                                               IndividualDao indDao) {
-        ArrayList<Option> monikerOpts = new ArrayList<Option>();
-        monikerOpts.add(new Option("", "none", (entity.getMoniker() == null)));
-        if (entity.getVClassURI() != null) {
-            List<String> monikers = indDao.monikers(entity.getVClassURI());
-            if (monikers != null) {
-                for (String moniker : monikers) {
-                    monikerOpts.add(new Option(
-                            moniker, moniker, 
-                                    moniker.equals(entity.getMoniker())));
-                }
-            }
-        }
-        monikerOpts.add(new Option("", "[new moniker]"));
-        return monikerOpts;
-    }
-
     public void doGet (HttpServletRequest request, HttpServletResponse response) {
         doPost(request, response);
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/Keys2EntsRetryController.java

@@ -1,199 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.edit;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.beans.FormObject;
-import edu.cornell.mannlib.vedit.beans.Option;
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
-import edu.cornell.mannlib.vedit.util.FormUtils;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.EditIndividuals;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
-import edu.cornell.mannlib.vitro.webapp.edit.listener.impl.KeywordSearchReindexer;
-
-public class Keys2EntsRetryController extends BaseEditController {
-
-    private static final Log log = LogFactory.getLog(Keys2EntsRetryController.class.getName());
-
-    public void doPost (HttpServletRequest req, HttpServletResponse response) {
-        if (!isAuthorizedToDisplayPage(req, response, new Actions(new EditIndividuals()))) {
-        	return;
-        }
-
-    	VitroRequest request = new VitroRequest(req);
-
-        //create an EditProcessObject for this and put it in the session
-        EditProcessObject epo = super.createEpo(request);
-
-        boolean isDashboardForm=false;
-        String action = "insert";
-        if ("dashboardDelete".equals(request.getParameter("action"))){
-            action = "delete"; // will change -- ignore for now
-            isDashboardForm=true;
-        } else if ("dashboardInsert".equals(request.getParameter("action"))){
-            isDashboardForm=true;
-        }
-
-        KeywordIndividualRelationDao k2eDao = request.getFullWebappDaoFactory().getKeys2EntsDao();
-        epo.setDataAccessObject(k2eDao);
-        KeywordDao kDao = request.getFullWebappDaoFactory().getKeywordDao();
-        IndividualDao eDao = request.getFullWebappDaoFactory().getIndividualDao();
-
-        KeywordIndividualRelation objectForEditing = new KeywordIndividualRelation();
-
-        String uri = request.getParameter("uri");
-        if (uri != null) {
-            try {
-                objectForEditing = k2eDao.getKeywordIndividualRelationByURI(uri);
-                action = "update";
-            } catch (NullPointerException e) {
-                log.error("Could not find KeywordIndividualRelation "+uri);
-            }
-        }
-        
-        String individualURI = request.getParameter("individualURI");
-        Individual ent = null;
-        
-        HashMap<String,List<Option>> optionMap = new HashMap<String,List<Option>>();
-        List<Option> entList = new LinkedList<Option>();
-        Option entOpt = null;
-        if (individualURI != null) {
-            objectForEditing.setEntURI(individualURI);
-            ent = eDao.getIndividualByURI(objectForEditing.getEntURI());
-            if (ent==null) {
-                log.error("cannot find entity via URI '"+individualURI+"'");
-                throw new Error("cannot find entity via URI '"+individualURI+"' in Keys2EntsRetryController");
-            }
-            entOpt = new Option(ent.getURI(),ent.getName(),true);
-        } else {
-            entOpt = new Option("-1", "Error: the entity must be specified", false);
-        }
-        entList.add(entOpt);
-        optionMap.put("EntId",entList);
-        
-        /*
-        List<KeywordIndividualRelation> k2iList = null;
-        if (action.equals("remove")){
-            k2iList = k2eDao.getKeywordIndividualRelationsByIndividualURI(individualURI);
-        } */
-        
-        epo.setOriginalBean(objectForEditing);
-
-        populateBeanFromParams(objectForEditing, request);
-
-        //set up any listeners
-        List changeListenerList = new LinkedList();
-        changeListenerList.add(new KeywordSearchReindexer());
-        epo.setChangeListenerList(changeListenerList);
-
-
-        //set the getMethod so we can retrieve a new bean after we've inserted it
-        try {
-            Class[] args = new Class[1];
-            args[0] = String.class;
-            epo.setGetMethod(k2eDao.getClass().getDeclaredMethod("getKeywordIndividualRelationByURI",args));
-        } catch (NoSuchMethodException e) {
-            log.error("Keys2EntsRetryController could not find the getKeywordIndividualRelationByURI method");
-        }
-
-        FormObject foo = new FormObject();
-
-        if (isDashboardForm && action.equals("delete")) {
-            List<Option> existingKeywordRelations = new LinkedList();
-            KeywordIndividualRelationDao kirDao = request.getFullWebappDaoFactory().getKeys2EntsDao();
-            List kirs = kirDao.getKeywordIndividualRelationsByIndividualURI(ent.getURI());
-            if (kirs != null) {
-                Iterator kirIt = kirs.iterator();
-                while (kirIt.hasNext()) {
-                    KeywordIndividualRelation kir = (KeywordIndividualRelation) kirIt.next();
-                    if (kir.getKeyId() > 0) {
-                        Keyword k = kDao.getKeywordById(kir.getKeyId());
-                        if (k != null) {
-                            Option kOpt = new Option();
-                            kOpt.setValue(kir.getURI());
-                            kOpt.setBody(k.getTerm()+" ("+kir.getMode()+")");
-                            existingKeywordRelations.add(kOpt);
-                        }
-                    }
-                }
-            }
-            //foo.getOptionLists().put("existingKeywordRelations",existingKeywordRelations);
-            optionMap.put("KeyId",existingKeywordRelations);
-            //optionMap.put("KeyId",FormUtils.makeOptionListFromBeans((List)ent.getKeywordObjects(), "Id", "Term", Integer.toString(objectForEditing.getKeyId()), null));
-            action = "update"; //reset for processing
-        } else {
-            optionMap.put("KeyId",FormUtils.makeOptionListFromBeans((List)kDao.getAllKeywords(), "Id", "Term", Integer.toString(objectForEditing.getKeyId()), null));
-        }
-
-        List modeOptionList = new LinkedList();
-        String VISIBLE = "visible";
-        Option visibleOption = new Option(VISIBLE);
-        if (isDashboardForm){
-            visibleOption.setSelected(true);
-        } else {
-            String HIDDEN = "hidden";
-            Option hiddenOption = new Option(HIDDEN);
-            if (objectForEditing.getMode().equalsIgnoreCase(HIDDEN)) {
-                hiddenOption.setSelected(true);
-            } else /*if (objectForEditing.getMode().equalsIgnoreCase(VISIBLE))*/ { //make this the default
-                visibleOption.setSelected(true);
-            }
-            modeOptionList.add(hiddenOption);
-        }
-        modeOptionList.add(visibleOption);
-        optionMap.put("Mode", modeOptionList);
-
-        foo.setOptionLists(optionMap);
-        epo.setFormObject(foo);
-
-        String html = FormUtils.htmlFormFromBean(objectForEditing,action,foo);
-
-        RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
-        request.setAttribute("formHtml",html);
-        request.setAttribute("bodyJsp","/templates/edit/formBasic.jsp");
-        if (isDashboardForm) {
-            request.setAttribute("formJsp","/templates/edit/specific/keys2ents_dashboard_retry.jsp");
-        } else {
-            request.setAttribute("formJsp","/templates/edit/specific/keys2ents_retry.jsp");
-        }
-        request.setAttribute("scripts","/templates/edit/formBasic.js");
-        request.setAttribute("title","Individual-Keyword Link Editing Form");
-        request.setAttribute("_action",action);
-        request.setAttribute("unqualifiedClassName","Keys2Ents");
-        setRequestAttributes(request,epo);
-
-        try {
-            rd.forward(request, response);
-        } catch (Exception e) {
-            log.error("Keys2EntsRetryController could not forward to view.");
-            log.error(e.getMessage());
-            log.error(e.getStackTrace());
-        }
-
-    }
-
-    public void doGet (HttpServletRequest request, HttpServletResponse response) {
-        doPost(request, response);
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/KeywordEditController.java

@@ -1,67 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.edit;
-
-import java.util.HashMap;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.beans.FormObject;
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.EditIndividuals;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-
-public class KeywordEditController extends BaseEditController {
-	
-	private static final Log log = LogFactory.getLog(KeywordEditController.class.getName());
-
-    public void doPost (HttpServletRequest request, HttpServletResponse response) {
-        if (!isAuthorizedToDisplayPage(request, response, new Actions(new EditIndividuals()))) {
-        	return;
-        }
-
-        VitroRequest vreq = new VitroRequest(request);
-        // we need to extract the keyword id from a Fetch parameter
-        String linkwhereId = request.getParameter("linkwhere");
-        String theKeywordId = linkwhereId.substring(15,linkwhereId.length()-1);
-        int kwId = Integer.decode(theKeywordId);
-
-        Keyword k = vreq.getFullWebappDaoFactory().getKeywordDao().getKeywordById(kwId);
-
-        EditProcessObject epo = super.createEpo(request);
-        FormObject foo = new FormObject();
-        HashMap OptionMap = new HashMap();
-        foo.setOptionLists(OptionMap);
-        epo.setFormObject(foo);
-
-        RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
-        request.setAttribute("epoKey",epo.getKey());
-        request.setAttribute("keyword", k);
-        request.setAttribute("bodyJsp","/templates/edit/specific/keyterms_edit.jsp");
-        request.setAttribute("title","Keyword Control Panel");
-        request.setAttribute("css", "<link rel=\"stylesheet\" type=\"text/css\" href=\""+vreq.getAppBean().getThemeDir()+"css/edit.css\"/>");
-
-        try {
-            rd.forward(request, response);
-        } catch (Exception e) {
-            log.error("KeywordEditController could not forward to view.");
-            log.error(e.getMessage());
-            log.error(e.getStackTrace());
-        }
-
-    }
-
-    public void doGet (HttpServletRequest request, HttpServletResponse response) {
-        doPost(request,response);
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/KeywordRetryController.java

@@ -1,204 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.edit;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.beans.FormObject;
-import edu.cornell.mannlib.vedit.beans.Option;
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
-import edu.cornell.mannlib.vedit.listener.ChangeListener;
-import edu.cornell.mannlib.vedit.util.FormUtils;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.EditIndividuals;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
-import edu.cornell.mannlib.vitro.webapp.edit.listener.impl.KeywordSearchReindexer;
-import edu.cornell.mannlib.vitro.webapp.edit.validator.impl.KeywordStemmerAndValidator;
-
-public class KeywordRetryController extends BaseEditController {
-	
-	private static final Log log = LogFactory.getLog(KeywordRetryController.class.getName());
-
-    public void doPost (HttpServletRequest req, HttpServletResponse response) {
-        if (!isAuthorizedToDisplayPage(req, response, new Actions(new EditIndividuals()))) {
-        	return;
-        }
-
-    	VitroRequest request = new VitroRequest(req);
-
-        //create an EditProcessObject for this and put it in the session
-        EditProcessObject epo = super.createEpo(request);
-
-        /*for testing*/
-        Keyword testMask = new Keyword();
-        epo.setBeanClass(Keyword.class);
-        epo.setBeanMask(testMask);
-
-        KeywordDao kDao = request.getFullWebappDaoFactory().getKeywordDao();
-        epo.setDataAccessObject(kDao);
-        epo.getAdditionalDaoMap().put("KeywordIndividualRelationDao", request.getFullWebappDaoFactory().getKeys2EntsDao());
-
-        String action="insert";
-        
-        Keyword keywordForEditing = null;
-        if (!epo.getUseRecycledBean()){
-            if (request.getParameter("id") != null) {
-                int id = Integer.parseInt(request.getParameter("id"));
-                if (id > 0) {
-                    try {
-                        keywordForEditing = kDao.getKeywordById(id);
-                        action = "update";
-                    } catch (NullPointerException e) {
-                        log.error("Need to implement 'record not found' error message.");
-                    }
-                }
-            } else {
-                keywordForEditing = new Keyword();
-                keywordForEditing.setType("keyword");
-                keywordForEditing.setOrigin("unspecified"); // may be reset below
-                keywordForEditing.setSource("unspecified"); // may be reset below
-            }
-            epo.setOriginalBean(keywordForEditing);
-        } else {
-            keywordForEditing = (Keyword) epo.getNewBean();
-            keywordForEditing.setType("keyword");
-            keywordForEditing.setOrigin("unspecified"); // may be reset below
-            keywordForEditing.setSource("unspecified"); // may be reset below
-        }
-
-        //make a simple mask for the class's id
-        Object[] simpleMaskPair = new Object[2];
-        simpleMaskPair[0]="Id";
-        simpleMaskPair[1]=Integer.valueOf(keywordForEditing.getId());
-        epo.getSimpleMask().add(simpleMaskPair);
-
-        //set up any validators
-        LinkedList lnList = new LinkedList();
-        lnList.add(new KeywordStemmerAndValidator(epo,kDao));
-        epo.getValidatorMap().put("Term",lnList);
-
-        //set up any listeners
-        String entityURI = request.getParameter("individualURI");
-        if (entityURI != null && request.getParameter("mode") != null) {
-            List listenerList = new LinkedList();
-            listenerList.add(new newKeywordToEntityLinker(entityURI, request.getParameter("mode")));
-            listenerList.add(new KeywordSearchReindexer());
-            epo.setChangeListenerList(listenerList);
-        }
-
-        //set the getMethod so we can retrieve a new bean after we've inserted it
-        try {
-            Class[] args = new Class[1];
-            args[0] = int.class;
-            epo.setGetMethod(kDao.getClass().getDeclaredMethod("getKeywordById",args));
-        } catch (NoSuchMethodException e) {
-            log.error("KeywordRetryController could not find the getKeywordById method");
-        }
-
-
-        FormObject foo = new FormObject();
-        
-        boolean useShortForm=false;
-        if ("dashboardCreate".equals(request.getParameter("action"))) {
-            keywordForEditing.setOrigin("user-added");
-            keywordForEditing.setSource("user-added");
-            useShortForm=true;
-        } else if ("editorCreate".equals(request.getParameter("action"))) {
-            keywordForEditing.setOrigin("curator-added");
-            keywordForEditing.setSource("curator-added");
-            useShortForm=true;
-        } else {
-            HashMap OptionMap = new HashMap();
-            List originsList = kDao.getAllOrigins();
-            List originsOptList = new LinkedList();
-            originsOptList.add(new Option("","[new origin]",false));
-            Iterator originsIt = originsList.iterator();
-            while (originsIt.hasNext()) {
-                String optStr = (String)originsIt.next();
-                boolean selected = (keywordForEditing.getOrigin()==null) ? false : keywordForEditing.getOrigin().equals(optStr);
-                Option opt = new Option(optStr, optStr, selected);
-                originsOptList.add(opt);
-            }
-            OptionMap.put("Origin", originsOptList);
-            foo.setOptionLists(OptionMap);
-        }
-        
-        foo.setErrorMap(epo.getErrMsgMap());
-
-        epo.setFormObject(foo);
-
-        String html = FormUtils.htmlFormFromBean(keywordForEditing,action,foo,epo.getBadValueMap());
-
-        RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
-        request.setAttribute("formHtml",html);
-        request.setAttribute("bodyJsp","/templates/edit/formBasic.jsp");
-        if (useShortForm) {
-            request.setAttribute("formJsp","/templates/edit/specific/keyterms_dashboard_retry.jsp");
-        } else {
-            request.setAttribute("formJsp","/templates/edit/specific/keyterms_retry.jsp");
-        }
-        request.setAttribute("scripts","/templates/edit/formBasic.js");
-        request.setAttribute("title","Keyword Editing Form");
-        request.setAttribute("_action",action);
-        request.setAttribute("unqualifiedClassName","Keyword");
-        setRequestAttributes(request,epo);
-
-        try {
-            rd.forward(request, response);
-        } catch (Exception e) {
-            log.error("KeywordRetryController could not forward to view.");
-            log.error(e.getMessage());
-            log.error(e.getStackTrace());
-        }
-
-    }
-
-    public void doGet (HttpServletRequest request, HttpServletResponse response) {
-        doPost(request, response);
-    }
-
-    public class newKeywordToEntityLinker implements ChangeListener {
-    // should be a better way to do this
-    // cascading deletes should be implemented differently
-        String entityURI = null;
-        String mode = "hidden";
-        private newKeywordToEntityLinker(String entityURI, String mode) {
-            this.entityURI = entityURI;
-            this.mode = mode;
-        }
-
-        public void doInserted(Object newObj, EditProcessObject epo) {
-            Keyword k = (Keyword) newObj;
-            KeywordIndividualRelation k2e = new KeywordIndividualRelation();
-            k2e.setKeyId(k.getId());
-            k2e.setEntURI(entityURI);
-            k2e.setMode(mode);
-            ((KeywordIndividualRelationDao)epo.getAdditionalDaoMap().get("KeywordIndividualRelationDao")).insertNewKeywordIndividualRelation(k2e);
-        }
-        public void doUpdated(Object oldObj, Object newObj, EditProcessObject epo) {
-            // nothing required
-        }
-        public void doDeleted(Object oldObj, EditProcessObject epo) {
-            // nothing required
-        }
-
-
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/LinkRetryController.java

@@ -1,146 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.controller.edit;
-
-import java.util.HashMap;
-import java.util.LinkedList;
-import java.util.List;
-
-import javax.servlet.RequestDispatcher;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.beans.FormObject;
-import edu.cornell.mannlib.vedit.beans.Option;
-import edu.cornell.mannlib.vedit.controller.BaseEditController;
-import edu.cornell.mannlib.vedit.util.FormUtils;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.usepages.EditIndividuals;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Link;
-import edu.cornell.mannlib.vitro.webapp.controller.Controllers;
-import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
-import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-
-public class LinkRetryController extends BaseEditController {
-	
-	private static final Log log = LogFactory.getLog(LinkRetryController.class.getName());
-
-    public void doPost (HttpServletRequest req, HttpServletResponse response) {
-        if (!isAuthorizedToDisplayPage(req, response, new Actions(new EditIndividuals()))) {
-        	return;
-        }
-
-    	VitroRequest request = new VitroRequest(req);
-
-        //create an EditProcessObject for this and put it in the session
-        EditProcessObject epo = super.createEpo(request);
-        request.setAttribute("epo",epo);
-
-        /*for testing*/
-        Link testMask = new Link();
-        epo.setBeanClass(Link.class);
-        epo.setBeanMask(testMask);
-
-        String action = "insert";
-
-        WebappDaoFactory wadf = (request.getAssertionsWebappDaoFactory() != null) 
-        		? request.getAssertionsWebappDaoFactory() 
-        		: request.getFullWebappDaoFactory();
-        
-        LinksDao lDao = wadf.getLinksDao();
-        epo.setDataAccessObject(lDao);
-        LinktypeDao ltDao = wadf.getLinktypeDao();
-        IndividualDao eDao = wadf.getIndividualDao();
-
-        Link linkForEditing = null;
-        if (!epo.getUseRecycledBean()){
-            String linkUri = request.getParameter("uri");
-            if (linkUri != null) {
-                try {
-                    linkForEditing = lDao.getLinkByURI(linkUri);
-                    action = "update";
-                } catch (NullPointerException e) {
-                    log.error("Need to implement 'record not found' error message.");
-                }
-            } else {
-                linkForEditing = new Link();
-                if (request.getParameter("entityUri") != null) {
-                    try {
-                        linkForEditing.setEntityURI(request.getParameter("entityUri"));
-                    } catch (NumberFormatException e) {
-                        // oh well; it was worth a shot
-                    }
-                }
-            }
-            epo.setOriginalBean(linkForEditing);
-        } else {
-            linkForEditing = (Link) epo.getNewBean();
-            action = "update";
-            log.error("using newBean");
-        }
-
-        //set up any listeners
-
-        //set the getMethod so we can retrieve a new bean after we've inserted it
-        try {
-            Class[] args = new Class[1];
-            args[0] = int.class;
-            epo.setGetMethod(lDao.getClass().getDeclaredMethod("getLinkById",args));
-        } catch (NoSuchMethodException e) {
-            log.error("LinkRetryController could not find the namespaceById method in the facade");
-        }
-
-
-        FormObject foo = new FormObject();
-        HashMap OptionMap = new HashMap();
-        List entityList = new LinkedList();
-        if (linkForEditing.getEntityURI() != null) {
-            Individual theEnt = eDao.getIndividualByURI(linkForEditing.getEntityURI());
-            entityList.add(new Option(theEnt.getURI(),theEnt.getName(),true));
-        } else {
-            entityList.add(new Option ("", "Error: the entity must be specified", true));
-        }
-        OptionMap.put("EntityId",entityList);
-        List linkTypeOptList = FormUtils.makeOptionListFromBeans(ltDao.getAllLinktypes(), "URI", "Type", linkForEditing.getTypeURI(),"");
-        linkTypeOptList.add(0,new Option("","unspecified"));
-        OptionMap.put("TypeURI", linkTypeOptList);
-        foo.setOptionLists(OptionMap);
-        foo.setErrorMap(epo.getErrMsgMap());
-
-        epo.setFormObject(foo);
-
-        String html = FormUtils.htmlFormFromBean(linkForEditing,action,foo,epo.getBadValueMap());
-
-        RequestDispatcher rd = request.getRequestDispatcher(Controllers.BASIC_JSP);
-        request.setAttribute("formHtml",html);
-        request.setAttribute("bodyJsp","/templates/edit/formBasic.jsp");
-        request.setAttribute("formJsp","/templates/edit/specific/links_retry.jsp");
-        request.setAttribute("scripts","/templates/edit/formBasic.js");
-        request.setAttribute("title","Hyperlink Editing Form");
-        request.setAttribute("_action",action);
-        request.setAttribute("unqualifiedClassName","Link");
-        setRequestAttributes(request,epo);
-
-        try {
-            rd.forward(request, response);
-        } catch (Exception e) {
-            log.error("NamespaceRetryController could not forward to view.");
-            log.error(e.getMessage());
-            log.error(e.getStackTrace());
-        }
-
-    }
-
-    public void doGet (HttpServletRequest request, HttpServletResponse response) {
-        doPost(request, response);
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/ObjectPropertyStatementRetryController.java

@@ -54,10 +54,21 @@ public class ObjectPropertyStatementRetryController extends BaseEditController {
         Class[] classarray = {PropertyInstanceIface.class};
         try {
         	epo.setInsertMethod(PropertyInstanceDao.class.getMethod("insertProp", classarray));
+        	epo.setUpdateMethod(epo.getInsertMethod());
         } catch (NoSuchMethodException nsme) {
         	log.error("Unable to find "+PropertyInstanceDao.class.getName()+".insertProp("+PropertyInstanceIface.class.getName()+")");
         }
         
+        try {
+        	epo.setDeleteMethod(
+        			PropertyInstanceDao.class.getMethod(
+        					"deletePropertyInstance", classarray));
+        } catch(NoSuchMethodException nsme) {
+        	log.error("Unable to find "+PropertyInstanceDao.class.getName()+
+        			".deletePropertyInstance("+
+        					PropertyInstanceIface.class.getName()+")");
+        }
+                
         String action = "insert";
 
         PropertyInstanceDao piDao = vreq.getFullWebappDaoFactory().getPropertyInstanceDao();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/edit/listing/IndividualsListingController.java

@@ -61,7 +61,6 @@ public class IndividualsListingController extends BaseEditController {
         results.add("XX");
         results.add("Individual");
         results.add("class");
-        results.add("moniker");
 
         if (inds != null && inds.size()>0) {
             Iterator indsIt = inds.iterator();
@@ -93,9 +92,6 @@ public class IndividualsListingController extends BaseEditController {
                     results.add(vclassURI);
                 }
 
-                String monikerStr = (ind.getMoniker() != null) ? ind.getMoniker() : "unspecified";
-                results.add(monikerStr);
-
             }
         } else {
             results.add("XX");
@@ -104,13 +100,10 @@ public class IndividualsListingController extends BaseEditController {
 
         request.setAttribute("results",results);
 
-        request.setAttribute("columncount",new Integer(4));
+        request.setAttribute("columncount",new Integer(3));
         request.setAttribute("suppressquery","true");
         request.setAttribute("title", "Individuals in Class "+ ( (vc != null) ? vc.getName() : vclassURI ) );
         request.setAttribute("bodyJsp", Controllers.HORIZONTAL_JSP);
-//        request.setAttribute("horizontalJspAddButtonUrl", Controllers.RETRY_URL);
-//        request.setAttribute("horizontalJspAddButtonText", "Add new individual");
-//        request.setAttribute("horizontalJspAddButtonControllerParam", "Individual");
 
         // new individual button
         List <ButtonForm> buttons = new ArrayList<ButtonForm>();

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/freemarker/IndividualController.java

@@ -111,7 +111,7 @@ public class IndividualController extends FreemarkerHttpServlet {
 	            return doHelp();
 	        }
 	        
-	        if( individual == null || checkForHidden(vreq, individual) || checkForSunset(vreq, individual)){
+	        if( individual == null ){
 	        	return doNotFound(vreq);
 	        }
 
@@ -255,7 +255,6 @@ public class IndividualController extends FreemarkerHttpServlet {
 		
     	IndividualDao iwDao = vreq.getWebappDaoFactory().getIndividualDao();
         
-        individual.setKeywords(iwDao.getKeywordsForIndividualByMode(individual.getURI(),"visible"));
         individual.sortForDisplay();
 
         return new IndividualTemplateModel(individual, vreq);
@@ -583,18 +582,6 @@ public class IndividualController extends FreemarkerHttpServlet {
 		return null;
 	}  
     
-	@SuppressWarnings("unused")
-	private boolean checkForSunset(VitroRequest vreq, Individual entity) {
-        // TODO Auto-generated method stub
-        return false;
-    }
-
-    @SuppressWarnings("unused")
-	private boolean checkForHidden(VitroRequest vreq, Individual entity){ 
-        // TODO Auto-generated method stub
-        return false;
-    }
-    
 	/**
 	 * If this entity represents a File Bytestream, get its alias URL so we can
 	 * properly serve the file contents.

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java

@@ -146,7 +146,9 @@ public class RDFUploadController extends BaseEditController {
 		    OntModel tboxChangeModel=null;
 		    Model aboxChangeModel=null;
 		    if (tboxModel != null) {
-		    	tboxChangeModel = xutil.extractTBox(uploadModel);
+		    	boolean AGGRESSIVE = true;
+		    	tboxChangeModel = xutil.extractTBox(uploadModel, AGGRESSIVE);
+		    	// aggressively seek all statements that are part of the TBox  
 		        tboxstmtCount = operateOnModel(
 		        		request.getFullWebappDaoFactory(),
 		                tboxModel,tboxChangeModel,

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/IndividualDao.java

@@ -107,19 +107,6 @@ public interface IndividualDao extends ObjectSourceIface {
     
 	void fillVClassForIndividual(Individual individual);
 
-	List<String> monikers(String vclassURI);
-
-	List<String> getKeywordsForIndividual(String individualURI);
-
-	List<String> getKeywordsForIndividualByMode(String individualURI,
-			String modeStr);
-
-	List<Keyword> getKeywordObjectsForIndividual(String individualURI);
-
-	String getNetId(String entityURI);
-
-	String getStatus(String entityURI);
-
 	/**
 	 * Standard way to get a new URI that is not yet used.
 	 * @param individual, may be null
@@ -130,12 +117,4 @@ public interface IndividualDao extends ObjectSourceIface {
 	
 	EditLiteral getLabelEditLiteral(String individualUri);
 	
-    @Deprecated
-    public abstract Individual getIndividualByExternalId(int externalIdType,
-                                                         String externalIdValue);
-
-    @Deprecated
-    Individual getIndividualByExternalId(int externalIdType,
-                                         String externalIdValue,
-                                         String vClassURI);
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/KeywordDao.java

@@ -1,30 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: bdc34
- * Date: Apr 18, 2007
- * Time: 3:18:29 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface KeywordDao {
-    Keyword getKeywordById(int id);
-
-    List<Keyword> getAllKeywords();
-
-    List<Keyword> getKeywordsByStem(String stem);
-
-    int insertNewKeyword(Keyword k);
-
-    void updateKeyword(Keyword k);
-
-    void deleteKeyword(Keyword keyword);
-
-    List /*String*/ getAllOrigins();
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/KeywordIndividualRelationDao.java

@@ -1,26 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao;
-
-import java.util.List;
-
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
-
-/**
- * Created by IntelliJ IDEA.
- * User: bdc34
- * Date: Apr 18, 2007
- * Time: 3:17:51 PM
- * To change this template use File | Settings | File Templates.
- */
-public interface KeywordIndividualRelationDao {
-    KeywordIndividualRelation getKeywordIndividualRelationByURI(String URI);
-
-    List<KeywordIndividualRelation> getKeywordIndividualRelationsByIndividualURI(String individualURI);
-
-    String insertNewKeywordIndividualRelation(KeywordIndividualRelation k);
-
-    void updateKeywordIndividualRelation(KeywordIndividualRelation k);
-
-    void deleteKeywordIndividualRelation(KeywordIndividualRelation k);
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/VitroVocabulary.java

@@ -42,7 +42,6 @@ public class VitroVocabulary {
 
     // properties found on the beans
     
-    public static final String DESCRIPTION = vitroURI+"description";
     public static final String DESCRIPTION_ANNOT = vitroURI + "descriptionAnnot";
     public static final String PUBLIC_DESCRIPTION_ANNOT = vitroURI + "publicDescriptionAnnot";
     public static final String SHORTDEF = vitroURI+"shortDef";
@@ -69,32 +68,21 @@ public class VitroVocabulary {
     
     public static final String SEARCH_BOOST_ANNOT = vitroURI + "searchBoostAnnot";
 
-    public static final String SUNRISE = vitroURI+"sunrise";
-    public static final String SUNSET = vitroURI+"sunset";
-
     public static final String DEPENDENT_RESORUCE = "http://vivoweb.org/ontology/core#DependentResource";
     
     //////////////////////////////////////////
 
-
-    public static final String CURATOR_NOTE = vitroURI+"curatorNote";
-
     public static final String MONIKER = vitroURI+"moniker";
 
-    public static final String BLURB = vitroURI+"blurb";
-
     public static final String CLASSGROUP = vitroURI+"ClassGroup";
     public static final String IN_CLASSGROUP = vitroURI+"inClassGroup";
 
     public static final String MODTIME = vitroURI+"modTime";
-    public static final String TIMEKEY = vitroURI+"timekey";
 
     public static final String DISPLAY_RANK = vitroURI+"displayRank";
     public static final String DISPLAY_RANK_ANNOT = vitroURI+"displayRankAnnot";
     public static final String DISPLAY_LIMIT = vitroURI+"displayLimitAnnot";
     
-    public static final String CITATION = vitroURI+"citation";
-    
     // ================== property related =================================
 
     public static final String PROPERTY_ENTITYSORTDIRECTION = vitroURI+"individualSortDirectionAnnot";
@@ -102,8 +90,6 @@ public class VitroVocabulary {
     public static final String PROPERTY_OBJECTINDIVIDUALSORTPROPERTY = vitroURI+"objectIndividualSortProperty";
     public static final String PROPERTY_FULLPROPERTYNAMEANNOT = vitroURI+"fullPropertyNameAnnot";
     public static final String PROPERTY_CUSTOMSEARCHVIEWANNOT = vitroURI+"customSearchViewAnnot";
-    //public static final String PROPERTY_SELFEDITPROHIBITEDANNOT = vitroURI+"selfEditProhibitedAnnot";
-    //public static final String PROPERTY_CURATOREDITPROHIBITEDANNOT = vitroURI+"curatorEditProhibitedAnnot";
     public static final String PROPERTY_CUSTOMENTRYFORMANNOT = vitroURI+"customEntryFormAnnot";
     public static final String PROPERTY_CUSTOMDISPLAYVIEWANNOT = vitroURI+"customDisplayViewAnnot";
     public static final String PROPERTY_CUSTOMSHORTVIEWANNOT = vitroURI+"customShortViewAnnot";
@@ -117,19 +103,6 @@ public class VitroVocabulary {
     public static final String PROPERTY_STUBOBJECTPROPERTYANNOT = vitroURI + "stubObjectPropertyAnnot";
 	public static final String PROPERTY_COLLATEBYSUBCLASSANNOT = vitroURI + "collateBySubclassAnnot";
 
-    // ================== keyword related ==================================
-
-    public static final String KEYWORD = vitroURI+"Keyword";
-    public static final String KEYWORD_STEM = vitroURI+"keywordStem";
-    public static final String KEYWORD_TYPE = vitroURI+"keywordType";
-    public static final String KEYWORD_SOURCE = vitroURI+"keywordSource";
-    public static final String KEYWORD_ORIGIN = vitroURI+"keywordOrigin";
-    public static final String KEYWORD_COMMENTS = vitroURI+"keywordComment";
-    public static final String KEYWORD_INDIVIDUALRELATION = vitroURI+"KeywordRelation";
-    public static final String KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD = vitroURI+"involvesKeyword";
-    public static final String KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL = vitroURI+"involvesIndividual";
-    public static final String KEYWORD_INDIVIDUALRELATION_MODE = vitroURI+"keywordMode";
-
     // ================== link related =====================================
 
     public static final String LINK = vitroURI+"Link";

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactory.java

@@ -111,12 +111,6 @@ public interface WebappDaoFactory {
 
     public ApplicationDao getApplicationDao();
 
-    public KeywordIndividualRelationDao getKeys2EntsDao();
-    public KeywordDao getKeywordDao();
-
-    public LinksDao getLinksDao();
-    public LinktypeDao getLinktypeDao();
-
     public UserAccountsDao getUserAccountsDao();
 
     public VClassGroupDao getVClassGroupDao();

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/DataPropertyStatementFiltering.java

@@ -54,14 +54,6 @@ public class DataPropertyStatementFiltering implements DataPropertyStatement {
         return innerStmt.getDatapropURI();
     }
     
-    public Date getSunrise() {
-        return innerStmt.getSunrise();
-    }
-
-    public Date getSunset() {
-        return innerStmt.getSunset();
-    }
-    
     public String getString() {
         return innerStmt.getString();
     }
@@ -90,12 +82,4 @@ public class DataPropertyStatementFiltering implements DataPropertyStatement {
         innerStmt.setDatapropURI(datapropURI);
     }
     
-    public void setSunrise(Date date) {
-        innerStmt.setSunrise(date);
-    }
-
-    public void setSunset(Date date) {
-        innerStmt.setSunset(date);
-    }
-    
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/IndividualDaoFiltering.java

@@ -63,25 +63,6 @@ class IndividualDaoFiltering extends BaseFiltering implements IndividualDao{
             return null;        
     }
     
-    @Deprecated
-    public Individual getIndividualByExternalId(int externalIdType,
-            String externalIdValue, String classURI) {
-        Individual ind = innerIndividualDao.getIndividualByExternalId(externalIdType,externalIdValue,classURI);
-        if( ind != null &&  filters.getIndividualFilter().fn(ind) )
-            return new IndividualFiltering(ind, filters );
-        else
-            return null;
-    }
-
-    @Deprecated
-    public Individual getIndividualByExternalId(int externalIdType,
-            String externalIdValue) {
-        Individual ind = innerIndividualDao.getIndividualByExternalId(externalIdType,externalIdValue);
-        if( ind != null && filters.getIndividualFilter().fn(ind))
-            return new IndividualFiltering(ind,filters);
-        else
-            return null;
-    }
     public void fillVClassForIndividual(Individual individual) {
         innerIndividualDao.fillVClassForIndividual(individual);
     }
@@ -192,31 +173,6 @@ class IndividualDaoFiltering extends BaseFiltering implements IndividualDao{
         innerIndividualDao.markModified(individual);
     }
 
-    public List<String> getKeywordsForIndividual(String individualURI) {
-        return innerIndividualDao.getKeywordsForIndividual(individualURI);
-    }
-
-    public List<String> getKeywordsForIndividualByMode(String individualURI,
-            String modeStr) {
-        return innerIndividualDao.getKeywordsForIndividualByMode(individualURI,modeStr);
-    }
-
-    public List<Keyword> getKeywordObjectsForIndividual(String individualURI) {
-        return innerIndividualDao.getKeywordObjectsForIndividual(individualURI);
-    }
-
-    public String getNetId(String entityURI) {
-        return innerIndividualDao.getNetId(entityURI);
-    }
-
-    public String getStatus(String entityURI) {
-        return innerIndividualDao.getStatus(entityURI);
-    }
-
-    public List monikers(String vclassURI) {
-        return innerIndividualDao.monikers(vclassURI);
-    }
-
     public String toString(){
         return "IndividualDaoFiltering filter: " + filters.getIndividualFilter().toString() + "\n" +
                 "InnerDao: " + innerIndividualDao.toString();
@@ -230,7 +186,6 @@ class IndividualDaoFiltering extends BaseFiltering implements IndividualDao{
 		return innerIndividualDao.getUnusedURI(individual);
 	}
 
-
     @Override
     public EditLiteral getLabelEditLiteral(String individualUri) {
         return innerIndividualDao.getLabelEditLiteral(individualUri);

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/IndividualFiltering.java

@@ -210,21 +210,6 @@ public class IndividualFiltering implements Individual {
         return _innerIndividual.equals(obj);
     }
 
-    @Override
-    public String getAnchor() {
-        return _innerIndividual.getAnchor();
-    }
-
-    @Override
-    public String getBlurb() {
-        return _innerIndividual.getBlurb();
-    }  
-    
-    @Override
-    public String getDescription() {
-        return _innerIndividual.getDescription();
-    }
-
     @Override
     public List<DataPropertyStatement> getExternalIds() {
         return _innerIndividual.getExternalIds();
@@ -251,26 +236,6 @@ public class IndividualFiltering implements Individual {
 		return _innerIndividual.getThumbUrl();
 	}
 
-    @Override
-	public List<String> getKeywords() {
-        return _innerIndividual.getKeywords();
-    }
-
-    @Override
-    public String getKeywordString() {
-        return _innerIndividual.getKeywordString();
-    }
-
-    @Override
-    public List<Link> getLinksList() {
-        return _innerIndividual.getLinksList();
-    }
-
-    @Override
-    public Link getPrimaryLink() {
-        return _innerIndividual.getPrimaryLink();
-    }
-
     @Override
     public String getLocalName() {
         return _innerIndividual.getLocalName();
@@ -281,11 +246,6 @@ public class IndividualFiltering implements Individual {
         return _innerIndividual.getModTime();
     }
 
-    @Override
-    public String getMoniker() {
-        return _innerIndividual.getMoniker();
-    }
-
     @Override
     public String getName() {
         return _innerIndividual.getName();
@@ -301,43 +261,11 @@ public class IndividualFiltering implements Individual {
         return _innerIndividual.getNamespace();
     }
 
-    @Override
-    public String getStatus() {
-        return _innerIndividual.getStatus();
-    }
-
-
-    @Override
-    public int getStatusId() {
-        return _innerIndividual.getStatusId();
-    }
-
-
-    @Override
-    public Date getSunrise() {
-        return _innerIndividual.getSunrise();
-    }
-
-    @Override
-    public Date getSunset() {
-        return _innerIndividual.getSunset();
-    }
-
-    @Override
-    public Date getTimekey() {
-        return _innerIndividual.getTimekey();
-    }
-
     @Override
     public String getURI() {
         return _innerIndividual.getURI();
     }
 
-    @Override
-    public String getUrl() {
-        return _innerIndividual.getUrl();
-    }
-
     @Override
     public VClass getVClass() {
         return _innerIndividual.getVClass();
@@ -353,16 +281,6 @@ public class IndividualFiltering implements Individual {
         return _innerIndividual.hashCode();
     }
 
-    @Override
-    public void setAnchor(String in) {
-        _innerIndividual.setAnchor(in);
-    }
-
-    @Override
-    public void setBlurb(String in) {
-        _innerIndividual.setBlurb(in);
-    }
-
     @Override
     public void setDatatypePropertyList(List<DataProperty> datatypePropertyList) {
         _innerIndividual.setDatatypePropertyList(datatypePropertyList);
@@ -373,11 +291,6 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setPopulatedDataPropertyList(dataPropertyList);
     }
 
-    @Override
-    public void setDescription(String in) {
-        _innerIndividual.setDescription(in);
-    }
-
     @Override
     public void setObjectPropertyStatements(List<ObjectPropertyStatement> list) {
         _innerIndividual.setObjectPropertyStatements(list);
@@ -398,21 +311,6 @@ public class IndividualFiltering implements Individual {
     	_innerIndividual.setMainImageUri(mainImageUri);
 	}
     
-    @Override
-    public void setKeywords(List<String> keywords) {
-        _innerIndividual.setKeywords(keywords);
-    }
-
-    @Override
-    public void setLinksList(List<Link> linksList) {
-        _innerIndividual.setLinksList(linksList);
-    }
-
-    @Override
-    public void setPrimaryLink(Link link) {
-        _innerIndividual.setPrimaryLink(link);
-    }
-
     @Override
     public void setLocalName(String localName) {
         _innerIndividual.setLocalName(localName);
@@ -423,11 +321,6 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setModTime(in);
     }
 
-    @Override
-    public void setMoniker(String in) {
-        _innerIndividual.setMoniker(in);
-    }
-
     @Override
     public void setName(String in) {
         _innerIndividual.setName(in);
@@ -448,41 +341,11 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setPopulatedObjectPropertyList(propertyList);
     }
 
-    @Override
-    public void setStatus(String s) {
-        _innerIndividual.setStatus(s);
-    }
-
-    @Override
-    public void setStatusId(int in) {
-        _innerIndividual.setStatusId(in);
-    }
-
-    @Override
-    public void setSunrise(Date in) {
-        _innerIndividual.setSunrise(in);
-    }
-
-    @Override
-    public void setSunset(Date in) {
-        _innerIndividual.setSunset(in);
-    }
-
-    @Override
-    public void setTimekey(Date in) {
-        _innerIndividual.setTimekey(in);
-    }
-
     @Override
     public void setURI(String URI) {
         _innerIndividual.setURI(URI);
     }
 
-    @Override
-    public void setUrl(String url) {
-        _innerIndividual.setUrl(url);
-    }
-
     @Override
     public void setVClass(VClass class1) {
         _innerIndividual.setVClass(class1);
@@ -493,20 +356,11 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setVClassURI(in);
     }
 
-//    public void shallowCopy(Individual target) {
-//        _innerIndividual.shallowCopy(target);
-//    }
-
     @Override
     public void sortForDisplay() {
         _innerIndividual.sortForDisplay();
     }
 
-    @Override
-    public List<Keyword> getKeywordObjects() {
-        return _innerIndividual.getKeywordObjects();
-    }
-
     @Override
     public List<VClass> getVClasses() {
         return _innerIndividual.getVClasses();
@@ -532,11 +386,6 @@ public class IndividualFiltering implements Individual {
         _innerIndividual.setDataPropertyMap(propertyMap);
     }
 
-    @Override
-    public void setKeywordObjects(List<Keyword> keywords) {
-        _innerIndividual.setKeywordObjects(keywords);
-    }
-
     @Override
     public void setObjectPropertyMap(Map<String, ObjectProperty> propertyMap) {
         _innerIndividual.setObjectPropertyMap(propertyMap);

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/ObjectPropertyStatementFiltering.java

@@ -44,10 +44,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         return innerStmt.toString();
     }
 
-    public String getDescription() {
-        return innerStmt.getDescription();
-    }
-
     public String getObjectURI() {
         return innerStmt.getObjectURI();
     }
@@ -56,30 +52,14 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         return innerStmt.getPropertyURI();
     }
 
-    public String getQualifier() {
-        return innerStmt.getQualifier();
-    }
-
     public String getSubjectURI() {
         return innerStmt.getSubjectURI();
     }
 
-    public Date getSunrise() {
-        return innerStmt.getSunrise();
-    }
-
-    public Date getSunset() {
-        return innerStmt.getSunset();
-    }
-
     public boolean isSubjectOriented() {
         return innerStmt.isSubjectOriented();
     }
 
-    public void setDescription(String description) {
-        innerStmt.setDescription(description);
-    }
-
     public void setObject(Individual object) {
         innerStmt.setObject(object);
     }
@@ -96,10 +76,6 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         innerStmt.setPropertyURI(URI);
     }
 
-    public void setQualifier(String qualifier) {
-        innerStmt.setQualifier(qualifier);
-    }
-
     public void setSubject(Individual subject) {
         innerStmt.setSubject(subject);
     }
@@ -112,12 +88,4 @@ public class ObjectPropertyStatementFiltering implements ObjectPropertyStatement
         innerStmt.setSubjectURI(subjectURI);
     }
 
-    public void setSunrise(Date date) {
-        innerStmt.setSunrise(date);
-    }
-
-    public void setSunset(Date date) {
-        innerStmt.setSunset(date);
-    }
-
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/WebappDaoFactoryFiltering.java

@@ -13,10 +13,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.MenuDao;
 import edu.cornell.mannlib.vitro.webapp.dao.NamespaceDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
@@ -168,22 +164,6 @@ public class WebappDaoFactoryFiltering implements WebappDaoFactory {
         return innerWebappDaoFactory.getUserURI();
     }
 
-    public KeywordIndividualRelationDao getKeys2EntsDao() {
-        return innerWebappDaoFactory.getKeys2EntsDao();
-    }
-
-    public KeywordDao getKeywordDao() {
-        return innerWebappDaoFactory.getKeywordDao();
-    }
-
-    public LinksDao getLinksDao() {
-        return innerWebappDaoFactory.getLinksDao();
-    }
-
-    public LinktypeDao getLinktypeDao() {
-        return innerWebappDaoFactory.getLinktypeDao();
-    }
-
     public ApplicationDao getApplicationDao() {
     	return innerWebappDaoFactory.getApplicationDao();
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/filters/VitroFilterUtils.java

@@ -60,30 +60,11 @@ public class VitroFilterUtils {
         private final Comparator<? super Individual> comparator;
 
         public EntitySortTransform( String fieldName, boolean ascending){
-            if ( "timekey".equalsIgnoreCase( fieldName )){
-                if( ascending )
-                    comparator = timekeyComp;
-                else
-                    comparator = timekeyCompDesc;
-
-            } else if ( "sunset".equalsIgnoreCase(  fieldName )){
-                if( ascending )
-                    comparator = sunsetComp;
-                else
-                    comparator = sunsetCompDesc;
-
-            } else if ( "sunrise".equalsIgnoreCase( fieldName )){
-                if( ascending )
-                    comparator = sunriseComp;
-                else
-                    comparator = sunriseCompDesc;
-            } else {
                 if( ascending )
                     comparator = nameComp;
                 else
                     comparator = nameCompDesc;
         }
-        }
 
         @Override
 		public List<Individual> fn(List<Individual> individuals) {
@@ -91,57 +72,6 @@ public class VitroFilterUtils {
             return individuals;
         }
 
-        private static Comparator<? super Individual> timekeyComp =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getTimekey();
-                        Date time2 = o2.getTimekey();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return 1;
-                        if( time2 == null)
-                            return -1;
-                        return time1.compareTo(time2);
-                    }
-                    @Override
-					public String toString(){ return "timekeyComp"; }
-                };
-        private static Comparator<? super Individual> sunsetComp =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getSunset();
-                        Date time2 = o2.getSunset();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return 1;
-                        if( time2 == null)
-                            return -1;
-                        return time1.compareTo(time2);
-                    }
-                    @Override
-					public String toString(){ return "sunsetComp"; }
-                };
-        private static Comparator<? super Individual> sunriseComp =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getSunrise();
-                        Date time2 = o2.getSunrise();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return 1;
-                        if( time2 == null)
-                            return -1;
-                        return time1.compareTo(time2);
-                    }
-                    @Override
-					public String toString(){ return "sunriseComp"; }
-                };
         private static Comparator<? super Individual> nameComp =
                 new Comparator<Individual>(){
             // return ((Individual)o1).getName().compareTo(((Individual)o2).getName());
@@ -164,57 +94,6 @@ public class VitroFilterUtils {
 					public String toString(){ return "nameComp"; }
                 };
 
-               private static Comparator<? super Individual> timekeyCompDesc =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getTimekey();
-                        Date time2 = o2.getTimekey();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return -1;
-                        if( time2 == null)
-                            return 1;
-                        return time2.compareTo(time1);
-                    }
-                    @Override
-					public String toString(){ return "timkeyCompDesc"; }
-                };
-        private static Comparator<? super Individual> sunsetCompDesc =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getSunset();
-                        Date time2 = o2.getSunset();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return -1;
-                        if( time2 == null)
-                            return 1;
-                        return time2.compareTo(time1);
-                    }
-                    @Override
-					public String toString(){ return "sunsetCompDesc"; }
-                };
-        private static Comparator<? super Individual> sunriseCompDesc =
-                new Comparator<Individual>(){
-                    @Override
-					public int compare(Individual o1, Individual o2) {
-                        Date time1 = o1.getSunrise();
-                        Date time2 = o2.getSunrise();
-                        if( time1 == null && time2 == null )
-                            return 0;
-                        if( time1 == null )
-                            return -1;
-                        if( time2 == null)
-                            return 1;
-                        return time2.compareTo(time1);
-                    }
-                    @Override
-					public String toString(){ return "sunriseCompDesc"; }
-                };
         private static Comparator<? super Individual> nameCompDesc =
                 new Comparator<Individual>(){
                     @Override

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/DataPropertyStatementDaoSDB.java

@@ -89,6 +89,7 @@ public class DataPropertyStatementDaoSDB extends DataPropertyStatementDaoJena
                     boolean addToList = /*allowAnyNameSpace ? st.getObject().canAs(Literal.class) :*/ st.getObject().isLiteral() && 
                           (
                               (RDF.value.equals(st.getPredicate()) || VitroVocabulary.value.equals(st.getPredicate().getURI())) 
+                              || this.MONIKER.equals(st.getPredicate())
                               || !(NONUSER_NAMESPACES.contains(st.getPredicate().getNameSpace()))
                           );
                     if( addToList )

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoJena.java

@@ -2,12 +2,10 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import java.text.Collator;
 import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.Comparator;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -50,11 +48,9 @@ import com.hp.hpl.jena.vocabulary.RDFS;
 import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualCreationEvent;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.IndividualDeletionEvent;
@@ -260,49 +256,13 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
                         ind.addRDFType(ResourceFactory.createResource(vc.getURI()));
                     }
                 }
-                addPropertyStringValue(ind,MONIKER,ent.getMoniker(),ontModel);
-                addPropertyStringValue(ind,BLURB,ent.getBlurb(),ontModel);
-                addPropertyStringValue(ind,DESCRIPTION,ent.getDescription(),ontModel);
-                addPropertyDateTimeValue(ind,SUNRISE,ent.getSunrise(), ontModel);
-                addPropertyDateTimeValue(ind,SUNSET,ent.getSunset(), ontModel);
-                addPropertyDateTimeValue(ind,TIMEKEY,ent.getTimekey(), ontModel);
                 addPropertyDateTimeValue(ind,MODTIME,Calendar.getInstance().getTime(),ontModel);
                 if (ent.getMainImageUri() != null) {
                 	addPropertyResourceURIValue(ind, IND_MAIN_IMAGE, ent.getMainImageUri());
                 }                
-                
-                if (ent.getAnchor()!= null && ent.getAnchor().length()>0 && LINK != null) {
-                    com.hp.hpl.jena.ontology.Individual primaryLink = ontModel.createIndividual(entURI+"_primaryLink", LINK);
-                    primaryLink.addProperty(RDF.type, LINK);
-                    if (log.isTraceEnabled()) {
-                    	log.trace("added RDF type Link to primary link in insertNewIndividual() for new individual "+ent.getName());
-                    }
-                    addPropertyStringValue(primaryLink, LINK_ANCHOR, ent.getAnchor(),ontModel);
-                    addPropertyStringValue(primaryLink, LINK_URL,ent.getUrl(),ontModel);
-                    ind.addProperty(PRIMARY_LINK,primaryLink);
-                }
                 if( ent.getSearchBoost() != null ) {
                     addPropertyFloatValue(ind,SEARCH_BOOST_ANNOT, ent.getSearchBoost(), ontModel);
                 }
-                /* 2009-01-27 hold off on individual-level filtering for now
-                ind.removeAll(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
-                if (HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT != null && ent.getHiddenFromDisplayBelowRoleLevel() != null) { // only need to add if present
-                    try {
-                        ind.addProperty(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(ent.getHiddenFromDisplayBelowRoleLevel().getURI()));
-                    } catch (Exception e) {
-                        log.error("error adding HiddenFromDisplayBelowRoleLevel annotation to individual "+ent.getURI());
-                    }
-                }
-
-                ind.removeAll(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
-                if (PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT != null && ent.getProhibitedFromUpdateBelowRoleLevel() != null) { // only need to add if present
-                    try {
-                        ind.addProperty(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(ent.getProhibitedFromUpdateBelowRoleLevel().getURI()));
-                    } catch (Exception e) {
-                        log.error("error adding ProhibitedFromUpdateBelowRoleLevel annotation to individual "+ent.getURI());
-                    }
-                }
-                */
             } catch (Exception e) {
                 log.error("Exception inserting individual: ",e);
             }
@@ -323,37 +283,19 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
     }
 
     private void initInd(Individual ent) {
-        ent.getAnchor();
-        ent.getBlurb();
         ent.getClass();
         ent.getVClasses(false);
         ent.getDataPropertyList();
         ent.getDataPropertyStatements();
-        ent.getDescription();
         ent.getExternalIds();
         ent.getMainImageUri();
-        ent.getImageUrl();
-        ent.getThumbUrl();
-        ent.getKeywords();
-        ent.getKeywordString();
-        ent.getLinksList();
-        ent.getPrimaryLink();
         ent.getModTime();
-        ent.getMoniker();
         ent.getName();
         ent.getNamespace();
         ent.getObjectPropertyList();
-        ent.getStatus();
-        ent.getStatusId();
-        ent.getSunrise();
-        ent.getSunset();
-        ent.getTimekey();
-        ent.getUrl();
         ent.getVClassURI();
         ent.getVClass();
         ent.getVClassURI();
-        //ent.getHiddenFromDisplayBelowRoleLevel();
-        //ent.getProhibitedFromUpdateBelowRoleLevel();
     }
 
     public int updateIndividual(Individual ent, OntModel ontModel) {
@@ -402,83 +344,11 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
                         ind.addRDFType(ResourceFactory.createResource(uri));
                     }
                 }
-                updatePropertyStringValue(ind,MONIKER,ent.getMoniker(),ontModel);
-                updatePropertyStringValue(ind,BLURB,ent.getBlurb(),ontModel);
-                updatePropertyStringValue(ind,DESCRIPTION,ent.getDescription(),ontModel);                
-                updatePropertyDateTimeValue(ind,SUNRISE,ent.getSunrise(), ontModel);
-                updatePropertyDateTimeValue(ind,SUNSET,ent.getSunset(), ontModel);
-                updatePropertyDateTimeValue(ind,TIMEKEY,ent.getTimekey(), ontModel);
                 updatePropertyDateTimeValue(ind,MODTIME,Calendar.getInstance().getTime(),ontModel);
                 updatePropertyResourceURIValue(ind, IND_MAIN_IMAGE, ent.getMainImageUri(), ontModel);
-                if (ent.getAnchor()!= null && ent.getAnchor().length()>0) {
-                    if (LINK != null && PRIMARY_LINK != null) {
-                        boolean updatedExisting = false;
-                        try {
-                            Resource primaryLink = (Resource) ind.getPropertyValue(PRIMARY_LINK);
-                            if (primaryLink != null) {
-                            	if (log.isTraceEnabled()) {
-                            		log.trace("Modifying the primary link to entity "+ent.getName());
-                            	}
-                                updatePropertyStringValue(primaryLink, LINK_ANCHOR, ent.getAnchor(), ontModel);
-                                updatePropertyStringValue(primaryLink, LINK_URL, ent.getUrl(), ontModel);
-                                updatedExisting = true;
-                            }
-                        } catch (Exception e) {}
-                        if (!updatedExisting) {
-                        	if (log.isTraceEnabled()) {
-                        		log.trace("Adding a primary link to entity "+ent.getName());
-                        	}
-                            ind.removeAll(PRIMARY_LINK);
-                            com.hp.hpl.jena.ontology.Individual primaryLink = LINK.createIndividual(ent.getURI()+"_primaryLink");
-                            primaryLink.addProperty(RDF.type, LINK);
-                            addPropertyStringValue(primaryLink, LINK_ANCHOR, ent.getAnchor(), ontModel);
-                            addPropertyStringValue(primaryLink, LINK_URL,ent.getUrl(), ontModel);
-                            ind.addProperty(PRIMARY_LINK,primaryLink);
-                        }
-                    }
-                } else {
-                    ind.removeAll(PRIMARY_LINK);
-                }
                 if( ent.getSearchBoost() != null ) {
                     updatePropertyFloatValue(ind, SEARCH_BOOST_ANNOT, ent.getSearchBoost(), ontModel);
                 }
-                /*
-                if (HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT != null) {
-                    try {
-                        ind.removeAll(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);
-                        if (ent.getHiddenFromDisplayBelowRoleLevel()!=null) {
-                            String badURIErrorStr = checkURI(ent.getHiddenFromDisplayBelowRoleLevel().getURI());
-                            if (badURIErrorStr == null) {
-                                ind.addProperty(HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(ent.getHiddenFromDisplayBelowRoleLevel().getURI()));
-                            } else {
-                                log.error(badURIErrorStr);
-                            }
-                        }
-                    } catch (Exception e) {
-                        log.error("error linking individual "+ent.getURI()+" to HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL edit role");
-                    }
-                } else {
-                    log.error("vitro:hiddenFromDisplayBelowRoleLevelAnnot property not found in RBox");
-                }
-
-                if (PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT != null) {
-                    try {
-                        ind.removeAll(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);
-                        if (ent.getProhibitedFromUpdateBelowRoleLevel()!=null) {
-                            String badURIErrorStr = checkURI(ent.getProhibitedFromUpdateBelowRoleLevel().getURI());
-                            if (badURIErrorStr == null) {
-                                ind.addProperty(PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT, ResourceFactory.createResource(ent.getProhibitedFromUpdateBelowRoleLevel().getURI()));
-                            } else {
-                                log.error(badURIErrorStr);
-                            }
-                        }
-                    } catch (Exception e) {
-                        log.error("error linking individual "+ent.getURI()+" to PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL edit role");
-                    }
-                } else {
-                    log.error("vitro:prohibitedFromUpdateBelowRoleLevelAnnot property not found in RBox");
-                }
-                */
             return 0;
             } else {
                 return 1;
@@ -569,89 +439,6 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
         entity.setVClass(getWebappDaoFactory().getVClassDao().getVClassByURI(entity.getVClassURI()));
     }
 
-    public List<String> monikers( String typeURI ) {
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            HashSet<String> monikers = new HashSet<String>();
-            OntClass cls = getOntModel().getOntClass(typeURI);
-            ResIterator inds = getOntModel().listSubjectsWithProperty(
-            		RDF.type, ResourceFactory.createResource(typeURI));
-            while (inds.hasNext()) {
-            	Resource ind = inds.nextResource();
-                if (MONIKER != null) {
-                Iterator<Statement> monikerIt = ind.listProperties(MONIKER);
-                    while (monikerIt.hasNext()) {
-                        Statement monikerStmt = monikerIt.next();
-                        monikers.add(((Literal)monikerStmt.getObject()).getString());
-                    }
-                }
-            }
-            List<String> monikerList = new ArrayList<String>();
-            if (monikers.size()>0) {
-                Iterator<String> monikerIt = monikers.iterator();
-                while (monikerIt.hasNext()) {
-                    monikerList.add(monikerIt.next());
-                }
-                Collections.sort(monikerList,new Comparator<String>() {
-                    public int compare( String first, String second ) {
-                        if (first==null) {
-                            return 1;
-                        }
-                        if (second==null) {
-                            return -1;
-                        }
-                        Collator collator = Collator.getInstance();
-                        return collator.compare(first,second);
-                    }
-                });
-                return monikerList;
-            }
-            else
-                return null;
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-    }
-
-    public List<String> getKeywordsForIndividual(String entityURI) {
-        KeywordDao kDao = getWebappDaoFactory().getKeywordDao();
-        List<String> keywords = new LinkedList<String>();
-        List<KeywordIndividualRelation> kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI);
-        Iterator<KeywordIndividualRelation> kirsIt = kirs.iterator();
-        while (kirsIt.hasNext()) {
-            Keyword keyword = kDao.getKeywordById(kirsIt.next().getKeyId());
-            keywords.add(keyword.getTerm());
-        }
-        return keywords;
-    }
-
-    public List<String> getKeywordsForIndividualByMode(String entityURI, String modeStr) {
-        KeywordDao kDao = getWebappDaoFactory().getKeywordDao();
-        List<String> keywords = new LinkedList<String>();
-        List<KeywordIndividualRelation> kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI);
-        Iterator<KeywordIndividualRelation> kirsIt = kirs.iterator();
-        while (kirsIt.hasNext()) {
-            KeywordIndividualRelation kir = kirsIt.next();
-            if (kir.getMode().equalsIgnoreCase(modeStr)) {
-                Keyword keyword = kDao.getKeywordById(kir.getKeyId());
-                keywords.add(keyword.getTerm());
-            }
-        }
-        return keywords;
-    }
-
-    public List<Keyword> getKeywordObjectsForIndividual(String entityURI) {
-        KeywordDao kDao = getWebappDaoFactory().getKeywordDao();
-        List<Keyword> keywords = new LinkedList<Keyword>();
-        List<KeywordIndividualRelation> kirs = getWebappDaoFactory().getKeys2EntsDao().getKeywordIndividualRelationsByIndividualURI(entityURI);
-        Iterator<KeywordIndividualRelation> kirsIt = kirs.iterator();
-        while (kirsIt.hasNext()) {
-            Keyword keyword = kDao.getKeywordById(kirsIt.next().getKeyId());
-            keywords.add(keyword);
-        }
-        return keywords;
-    }
-
     /**
      * In Jena it can be difficult to get an object with a given dataproperty if
      * you do not care about the datatype or lang of the literal.  Use this
@@ -822,24 +609,6 @@ public class IndividualDaoJena extends JenaBaseDao implements IndividualDao {
         return inds;
     }    
 
-    @Deprecated
-    public Individual getIndividualByExternalId(int externalIdType, String externalIdValue ) {
-        return null;
-    }
-
-    @Deprecated
-    public Individual getIndividualByExternalId(int externalIdType, String externalIdValue, String vClassURI) {
-        return null;
-    }
-
-    public String getNetId(String entityURI) {
-        return null;
-    }
-
-    public String getStatus(String entityURI) {
-        return null;
-    }
-
     public Iterator<String> getAllOfThisTypeIterator() {
         //this is implemented in IndivdiualSDB
         throw new NotImplementedException();

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualDaoSDB.java

@@ -34,7 +34,6 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
@@ -50,7 +49,6 @@ public class IndividualDaoSDB extends IndividualDaoJena {
 
 	private DatasetWrapperFactory dwf;
     private SDBDatasetMode datasetMode;
-	private WebappDaoFactoryJena wadf;
 	
     public IndividualDaoSDB(DatasetWrapperFactory dwf, 
                             SDBDatasetMode datasetMode, 
@@ -176,10 +174,6 @@ public class IndividualDaoSDB extends IndividualDaoJena {
                     "    ?ind a <" + theClass.getURI() + "> . \n" +
 	    		 	"    ?ind  <" + RDFS.label.getURI() + "> ?label \n" +
 	    		 	"} \n" +
-	    		 	"UNION { \n" +
-                    "    ?ind a <" + theClass.getURI() + "> . \n" +
-	    		 	"    ?ind  <" + VitroVocabulary.MONIKER + "> ?moniker \n" +
-	    		 	"} \n" +
 	    		 "} ORDER BY ?ind ?label";
     		ResultSet rs =QueryExecutionFactory.create(
     		        QueryFactory.create(query), dataset)
@@ -194,13 +188,12 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		        continue;
     		    }
     		    if (uri != null && !uri.equals(currRes.getURI())) {
-    		        Individual ent = makeIndividual(uri, label, moniker);
+    		        Individual ent = makeIndividual(uri, label);
     		        if (ent != null) {
     		            ents.add(ent);
     		        }
     	            uri = currRes.getURI();
     	            label = null;
-    	            moniker = null;
     		    } else if (uri == null) {
     		        uri = currRes.getURI();
     		    }
@@ -208,12 +201,8 @@ public class IndividualDaoSDB extends IndividualDaoJena {
                 if (labelLit != null) {
                     label = labelLit.getLexicalForm();
                 }
-                Literal monikerLit = sol.getLiteral("moniker");
-                if (monikerLit != null) {
-                    moniker = monikerLit.getLexicalForm();
-                }
                 if (!rs.hasNext()) {
-                    Individual ent = makeIndividual(uri, label, moniker);
+                    Individual ent = makeIndividual(uri, label);
                     if (ent != null) {
                         ents.add(ent);
                     }
@@ -250,7 +239,7 @@ public class IndividualDaoSDB extends IndividualDaoJena {
     		        continue;
     		    }
     		    filteredIndividualList.add(
-    		    		makeIndividual(currRes.getURI(), null, null));
+    		    		makeIndividual(currRes.getURI(), null));
     		}
        	} finally {
     		dataset.getLock().leaveCriticalSection();
@@ -259,14 +248,11 @@ public class IndividualDaoSDB extends IndividualDaoJena {
        	return filteredIndividualList;
     }
     
-    private Individual makeIndividual(String uri, 
+    private Individual makeIndividual(String uri, String label) {
-    		                          String label, 
-    		                          String moniker) {
         Individual ent = new IndividualSDB(uri, 
                 this.dwf, datasetMode, getWebappDaoFactory(), 
                 SKIP_INITIALIZATION);
         ent.setName(label);
-        ent.setMoniker(moniker);
         return ent;
     }
 	

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualJena.java

@@ -2,8 +2,6 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
 import java.sql.Timestamp;
 import java.text.Collator;
 import java.util.ArrayList;
@@ -153,41 +151,6 @@ public class IndividualJena extends IndividualImpl implements Individual {
         }
     }
 
-    @Deprecated
-    public int getFlag1Numeric() {
-    	return 1;
-    }
-
-    @Deprecated
-    public String getFlag1Set() {
-    	return "1";
-    }
-
-    @Deprecated
-    public String getFlag2Set() {
-    	return "";
-    }
-
-    @Deprecated
-    public boolean doesFlag1Match(int flagBitMask) {
-    	return true;
-    }
-
-    @Deprecated
-    public Date getSunrise() {
-    	return null;
-    }
-
-    @Deprecated
-    public Date getSunset() {
-    	return null;
-    }
-
-    @Deprecated
-    public Date getTimekey() {
-    	return null;
-    }
-
     public Timestamp getModTime() {
         if (modTime != null) {
             return modTime;
@@ -205,118 +168,6 @@ public class IndividualJena extends IndividualImpl implements Individual {
         }
     }
 
-    public String getMoniker() {
-        if (moniker != null) {
-            return moniker;
-        } else {
-            ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                moniker = webappDaoFactory.getJenaBaseDao().getPropertyStringValue(ind,webappDaoFactory.getJenaBaseDao().MONIKER);
-                if (moniker == null) {
-                  //Changing behavior to moniker because it is taking extra time to get the vclass
-                  //alternative if the moniker isn't filled out.  That time is wasted if the vclass alternative isn't desired.
-                  //see NIHVIVO-2001
-                    moniker = "";
-                }
-                return moniker;
-            } finally {
-                ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
-    /* 2009-01-27 hold off on individual-level filtering for now
-    @Override
-    public RoleLevel getHiddenFromDisplayBelowRoleLevel(){
-        if( this.hiddenFromDisplayBelowRoleLevel != null )
-            return this.hiddenFromDisplayBelowRoleLevel;
-        
-        OntModel model = ind.getOntModel(); 
-        model.enterCriticalSection(Lock.READ);
-        try {
-            NodeIterator it = model.listObjectsOfProperty(ind, model.getAnnotationProperty(VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT));
-            if( it == null )
-                return BaseResourceBean.RoleLevel.values()[0];
-            BaseResourceBean.RoleLevel role = BaseResourceBean.RoleLevel.values()[0];            
-            while( it.hasNext() ) {
-                RDFNode node = it.nextNode();
-                if( node != null && node.isURIResource() ) {
-                    BaseResourceBean.RoleLevel foundRole = BaseResourceBean.RoleLevel.getRoleByUri( node.asNode().getURI() );
-                    if( role.compareTo(foundRole ) < 0 ) { // find the lowest of all levels
-                        role = foundRole;
-                    }
-                }
-            }
-            return this.hiddenFromDisplayBelowRoleLevel = role;
-        } finally {
-            model.leaveCriticalSection();
-        }
-    }
-
-    /**
-     * this seems like a mismatch with the RDF storage model.
-     * We could have multiple statements in the model that associated
-     * the individual with multiple or redundant edit display levels.
-     */
-    
-    /*
-    @Override
-    public RoleLevel getProhibitedFromUpdateBelowRoleLevel() {
-        if( this.prohibitedFromUpdateBelowRoleLevel != null )
-            return this.prohibitedFromUpdateBelowRoleLevel;
-        
-        OntModel model = ind.getOntModel(); 
-        model.enterCriticalSection(Lock.READ);
-        try {
-            NodeIterator it = model.listObjectsOfProperty(ind, model.getAnnotationProperty(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT));
-            if( it == null )
-                return BaseResourceBean.RoleLevel.values()[0];
-            BaseResourceBean.RoleLevel role = BaseResourceBean.RoleLevel.values()[0];
-            while( it.hasNext() ){
-                RDFNode node = it.nextNode();
-                if( node != null && node.isURIResource() ) {
-                    BaseResourceBean.RoleLevel foundRole = BaseResourceBean.RoleLevel.getRoleByUri( node.asNode().getURI() );
-                    if( role.compareTo(foundRole ) < 0 ) // find the lowest of all roles
-                        role = foundRole;                    
-                }
-            } 
-            return this.prohibitedFromUpdateBelowRoleLevel = role;            
-        } finally {
-            model.leaveCriticalSection();
-        }                
-    }
-    */
-  
-
-    public String getBlurb() {
-        if (this.blurb != null) {
-            return blurb;
-        } else {
-            ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                blurb = webappDaoFactory.getJenaBaseDao().getPropertyStringValue(ind,webappDaoFactory.getJenaBaseDao().BLURB);
-                return blurb;
-            } finally {
-                ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
-    public String getDescription() {
-        if (this.description != null) {
-            return description;
-        } else {
-            ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                description = webappDaoFactory.getJenaBaseDao().getPropertyStringValue(ind,webappDaoFactory.getJenaBaseDao().DESCRIPTION);
-                return description;
-            } finally {
-                ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
-
     public Float getSearchBoost(){
         if( this._searchBoostJena != null ){
             return this._searchBoostJena;
@@ -380,122 +231,12 @@ public class IndividualJena extends IndividualImpl implements Individual {
 		return this.imageInfo.getThumbnail().getBytestreamAliasUrl();
 	}
 
-	public String getAnchor() {
-        if (this.anchor != null) {
-            return anchor;
-        } else {
-            doUrlAndAnchor();
-            return anchor;
-        }
-    }
-
-    public String getUrl() {
-        if (this.url != null) {
-            return url;
-        } else {
-            doUrlAndAnchor();
-            return url;
-        }
-    }
-
-    private void doUrlAndAnchor() {
-        ind.getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            if (webappDaoFactory.getJenaBaseDao().PRIMARY_LINK != null) {
-                Iterator links = ind.listPropertyValues(webappDaoFactory.getJenaBaseDao().PRIMARY_LINK);
-                if (links.hasNext()) {
-                    try {
-                        com.hp.hpl.jena.ontology.Individual linkInd = ((com.hp.hpl.jena.ontology.Individual)((Resource) links.next()).as(com.hp.hpl.jena.ontology.Individual.class));
-                        if (webappDaoFactory.getJenaBaseDao().LINK_ANCHOR != null) {
-                            try {
-                                Literal l = (Literal) linkInd.getPropertyValue(webappDaoFactory.getJenaBaseDao().LINK_ANCHOR);
-                                if (l != null) {
-                                    anchor = l.getString();
-                                }
-                            } catch (ClassCastException e) {}
-                        }
-                        if (webappDaoFactory.getJenaBaseDao().LINK_URL != null) {
-                            try {
-                                Literal l = (Literal) linkInd.getPropertyValue(webappDaoFactory.getJenaBaseDao().LINK_URL);
-                                if (l != null) {
-                                    try {
-                                        url = URLDecoder.decode(l.getString(), "UTF-8");
-                                    } catch (UnsupportedEncodingException use) {}
-                                }
-                            } catch (ClassCastException e) {}
-                        }
-                    } catch (ClassCastException cce) {}
-                }
-            }
-        } finally {
-            ind.getOntModel().leaveCriticalSection();
-        }
-    }
-
-    public List <Link> getLinksList() {
-        if (this.linksList != null) {
-            return this.linksList;
-        } else {
-            try {
-                webappDaoFactory.getLinksDao().addLinksToIndividual( this );
-            } catch (Exception e) {
-                log.debug(this.getClass().getName()+" could not addLinksToIndividual for "+this.getURI());
-            }
-            return this.linksList;
-        }
-    }
-
-    public Link getPrimaryLink() {
-        if (this.primaryLink != null) {
-            return this.primaryLink;
-        } else {
-            try {
-                webappDaoFactory.getLinksDao().addPrimaryLinkToIndividual( this );
-            } catch (Exception e) {
-                log.debug(this.getClass().getName()+" could not addPrimaryLinkToIndividual for "+this.getURI());
-            }
-            return this.primaryLink;
-        }
-    }
-
-
-    public List<String> getKeywords() {
-        if (this.keywords != null) {
-            return this.keywords;
-        } else {
-            try {
-                this.setKeywords(webappDaoFactory.getIndividualDao().getKeywordsForIndividual(this.getURI()));
-            } catch (Exception e) {
-                log.debug(this.getClass().getName()+" could not getKeywords for "+this.getURI());
-            }
-            return this.keywords;
-        }
-    }
-    
-    public List<Keyword> getKeywordObjects() {
-        if (this.keywordObjects != null) {
-            return this.keywordObjects;
-        } else {
-            try {
-                this.setKeywordObjects(webappDaoFactory.getIndividualDao().getKeywordObjectsForIndividual(this.getURI()));
-            } catch (Exception e) {
-                log.error(this.getClass().getName()+" could not get Keyword Objects for "+this.getURI());
-            }
-        }
-        return this.keywordObjects;
-    }
-
     public List<ObjectPropertyStatement> getObjectPropertyStatements() {
         if (this.objectPropertyStatements != null) {
             return this.objectPropertyStatements;
         } else {
             try {
                 webappDaoFactory.getObjectPropertyStatementDao().fillExistingObjectPropertyStatements(this);
-                //Iterator stmtIt = this.getObjectPropertyStatements().iterator();
-                //while (stmtIt.hasNext()) {
-                //    ObjectPropertyStatement stmt = (ObjectPropertyStatement) stmtIt.next();
-                //    stmt.setObject(webappDaoFactory.getIndividualDao().getIndividualByURI(stmt.getObject().getURI()));
-                //}
             } catch (Exception e) {
                 log.error(this.getClass().getName()+" could not fill existing ObjectPropertyStatements for "+this.getURI(), e);
             }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/IndividualSDB.java

@@ -88,15 +88,11 @@ public class IndividualSDB extends IndividualImpl implements Individual {
 	    		"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
 	    		        "> ?ooo. \n" +
 	    		   "<"+individualURI+">  a ?type . \n" +
-	    		   "<"+individualURI+"> <" + VitroVocabulary.MONIKER + 
-	    		           "> ?moniker \n" +
 	    		 "} \n" +
 	    		 "WHERE { \n" +
 	    		 	"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
 	    		 	        "> ?ooo }  \n" +
 	    		 	" UNION { <"+individualURI+"> a ?type } \n" +
-	    		 	" UNION { <"+individualURI+"> <" + VitroVocabulary.MONIKER +
-	    		 	        "> ?moniker } \n" +
 	    		 "} "; 
     		this.model = QueryExecutionFactory.create(
     		        QueryFactory.create(getStatements), initModel)
@@ -134,18 +130,11 @@ public class IndividualSDB extends IndividualImpl implements Individual {
     	    		"CONSTRUCT " +
     	    		"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
     	    		        "> ?ooo. \n" +
-//    	    		   "<"+individualURI+">  a ?type . \n" +
     	    		   "<"+individualURI+">  <" + VitroVocabulary.MONIKER + 
     	    		           "> ?moniker \n" +
     	    		 "} WHERE {" +
     	    		 	"{ <"+individualURI+">  <" + RDFS.label.getURI() + 
     	    		 	        "> ?ooo } \n" +
-    	    		 	"UNION { <" +
-    	    		 	    individualURI+">  <" + VitroVocabulary.MONIKER + 
-    	    		 	        "> ?moniker \n" +
-    	    		 	"}  \n" +
-//    	    		 	"UNION { <"
-//    	    		 	    + individualURI + "> a ?type } \n" +
     	    		 "}";
         		model = QueryExecutionFactory.create(
         		        QueryFactory.create(getStatements), dataset)
@@ -278,39 +267,6 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         } 
     }
 
-    @Deprecated
-    public int getFlag1Numeric() { 
-    	return 1;
-    }
- 
-    @Deprecated
-    public String getFlag1Set() { 
-        return null;
-    }
-
-    @Deprecated
-    public String getFlag2Set() { 
-        return null;
-    }
-
-    @Deprecated
-    public boolean doesFlag1Match(int flagBitMask) { 
-    	return true;
-    }
-
-    @Deprecated
-    public Date getSunrise() {
-        return null;
-    }
-
-    public Date getSunset() {        
-        return null;   
-    }
-
-    public Date getTimekey() { 
-    	return null;
-    }
-
     public Timestamp getModTime() {
         if (modTime != null) {
             return modTime;
@@ -332,62 +288,6 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         }
     }
 
-    public String getMoniker() { 
-        if (moniker != null) {
-            return moniker;
-        } else {         
-        	ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                moniker = webappDaoFactory.getJenaBaseDao()
-                        .getPropertyStringValue(
-                                ind,webappDaoFactory.getJenaBaseDao().MONIKER);
-                if (moniker == null) {
-                    //Changing behavior to moniker because it is taking extra time to get the vclass
-                    //alternative if the moniker isn't filled out.  That time is wasted if the vclass alternative isn't desired.
-                    //see NIHVIVO-2001
-                      moniker = "";
-                  }                
-                return moniker;
-            } finally {
-            	ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
-    public String getBlurb() { 
-        if (this.blurb != null) {
-            return blurb;
-        } else {
-            constructProperty(ind, VitroVocabulary.BLURB);
-        	ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                blurb = webappDaoFactory.getJenaBaseDao().getPropertyStringValue(ind,webappDaoFactory.getJenaBaseDao().BLURB);
-                return blurb;
-            } finally {
-               
-            	ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
-    public String getDescription() { 
-        if (this.description != null) {
-            return description;
-        } else {
-            constructProperty(ind, VitroVocabulary.DESCRIPTION);
-        	ind.getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                description = webappDaoFactory.getJenaBaseDao()
-                        .getPropertyStringValue(
-                             ind,webappDaoFactory.getJenaBaseDao().DESCRIPTION);
-                return description;
-            } finally {
-                
-            	ind.getOntModel().leaveCriticalSection();
-            }
-        }
-    }
-
     private synchronized void constructProperty(OntResource ind, String propertyURI) {
         DatasetWrapper w = getDatasetWrapper();
         Dataset dataset = w.getDataset();
@@ -526,125 +426,6 @@ public class IndividualSDB extends IndividualImpl implements Individual {
         }
 	}
 	
-	
-	public String getAnchor() { 
-        if (this.anchor != null) {
-            return anchor;
-        } else {
-            doUrlAndAnchor();
-            return anchor;
-        }
-    }
-
-    public String getUrl() { 
-        if (this.url != null) {
-            return url;
-        } else {
-            doUrlAndAnchor();
-            return url;
-        }
-    }
-
-    private void doUrlAndAnchor() { 
-        Model tempModel = ModelFactory.createDefaultModel();
-        OntModel ontModel = ModelFactory.createOntologyModel(
-                OntModelSpec.OWL_MEM);
-        DatasetWrapper w = getDatasetWrapper();
-        Dataset dataset = w.getDataset();
-    	dataset.getLock().enterCriticalSection(Lock.READ);
-        try {
-        	StringBuffer selectPrimaryLinkQueryBuff = new StringBuffer().append(
-        		"SELECT ?url ?anchor \n" ).append(" WHERE { \n").append(
-        		"    <" + this.individualURI + "> ").append(
-        		             "<" + VitroVocabulary.PRIMARY_LINK + "> " ).append(
-        		                     "?link . \n").append(
-        		"    ?link <" + VitroVocabulary.LINK_URL + "> ?url . \n" 
-        		        ).append(
-        		"    ?link <" + VitroVocabulary.LINK_ANCHOR + "> ?anchor . \n" 
-        		        ).append(
-        		"} \n");
-        	QueryExecution qexec = QueryExecutionFactory.create(
-                    QueryFactory.create(selectPrimaryLinkQueryBuff.toString())
-                            , dataset);
-        	try {
-        	    ResultSet linkResults = qexec.execSelect();
-        	    if (linkResults.hasNext()) {
-        	        QuerySolution solution = linkResults.next();
-        	        this.setUrl(solution.getLiteral("url").getLexicalForm());
-        	        this.setAnchor(solution.getLiteral("anchor")
-        	                .getLexicalForm());
-        	    }
-        	} finally {
-        	    qexec.close();
-        	}            
-        } finally {
-        	tempModel.close();
-        	ontModel.close();
-        	dataset.getLock().leaveCriticalSection();
-        	w.close();
-        }
-    }
-
-    public List <Link> getLinksList() { 
-        if (this.linksList != null) {
-            return this.linksList;
-        } else {
-            try {
-                webappDaoFactory.getLinksDao().addLinksToIndividual(this);
-            } catch (Exception e) {
-                log.debug(this.getClass().getName() + 
-                        " could not addLinksToIndividual for " + this.getURI());
-            }
-            return this.linksList;
-        }
-    }
-
-    public Link getPrimaryLink() { 
-        if (this.primaryLink != null) {
-            return this.primaryLink;
-        } else {
-            try {
-                webappDaoFactory.getLinksDao().addPrimaryLinkToIndividual(this);
-            } catch (Exception e) {
-                log.debug(this.getClass().getName() + 
-                        " could not addPrimaryLinkToIndividual for " + 
-                                this.getURI());
-            }
-            return this.primaryLink;
-        }
-    }
-
-
-    public List<String> getKeywords() { 
-        if (this.keywords != null) {
-            return this.keywords;
-        } else {
-            try {
-                this.setKeywords(webappDaoFactory.getIndividualDao()
-                        .getKeywordsForIndividual(this.getURI()));
-            } catch (Exception e) {
-                log.debug(this.getClass().getName() + 
-                        " could not getKeywords for " + this.getURI());
-            }
-            return this.keywords;
-        }
-    }
-    
-    public List<Keyword> getKeywordObjects() {
-        if (this.keywordObjects != null) { 
-            return this.keywordObjects;
-        } else {
-            try {
-                this.setKeywordObjects(webappDaoFactory.getIndividualDao()
-                        .getKeywordObjectsForIndividual(this.getURI()));
-            } catch (Exception e) {
-                log.error(this.getClass().getName() + 
-                        " could not get Keyword Objects for " + this.getURI());
-            }
-        }
-        return this.keywordObjects;
-    }
-
     public List<ObjectPropertyStatement> getObjectPropertyStatements() { 
         if (this.objectPropertyStatements != null) {
             return this.objectPropertyStatements;

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaBaseDaoCon.java

@@ -36,14 +36,10 @@ public class JenaBaseDaoCon {
     
     /* ***************** Vitro ontology constants ***************** */
 
-    public    DatatypeProperty   SUNRISE = _constModel.createDatatypeProperty(VitroVocabulary.SUNRISE);
-    public    DatatypeProperty   SUNSET = _constModel.createDatatypeProperty(VitroVocabulary.SUNSET);
     protected AnnotationProperty DATAPROPERTY_ISEXTERNALID = _constModel.createAnnotationProperty(VitroVocabulary.DATAPROPERTY_ISEXTERNALID);
         
     protected AnnotationProperty HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.HIDDEN_FROM_DISPLAY_BELOW_ROLE_LEVEL_ANNOT);    
-    //protected AnnotationProperty PROHIBITED_FROM_CREATE_BELOW_ROLE_LEVEL_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROHIBITED_FROM_CREATE_BELOW_ROLE_LEVEL_ANNOT);
     protected AnnotationProperty PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROHIBITED_FROM_UPDATE_BELOW_ROLE_LEVEL_ANNOT);    
-    //protected AnnotationProperty PROHIBITED_FROM_DELETE_BELOW_ROLE_LEVEL_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROHIBITED_FROM_DELETE_BELOW_ROLE_LEVEL_ANNOT);
     
     protected AnnotationProperty SEARCH_BOOST_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.SEARCH_BOOST_ANNOT);
     
@@ -52,15 +48,10 @@ public class JenaBaseDaoCon {
     protected AnnotationProperty PUBLIC_DESCRIPTION_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PUBLIC_DESCRIPTION_ANNOT);
     protected AnnotationProperty SHORTDEF = _constModel.createAnnotationProperty(VitroVocabulary.SHORTDEF);
 
-    protected DatatypeProperty   CURATOR_NOTE = _constModel.createDatatypeProperty(VitroVocabulary.CURATOR_NOTE);
     protected DatatypeProperty   MONIKER = _constModel.createDatatypeProperty(VitroVocabulary.MONIKER);
-    protected DatatypeProperty   DESCRIPTION = _constModel.createDatatypeProperty(VitroVocabulary.DESCRIPTION);
-    protected DatatypeProperty   BLURB = _constModel.createDatatypeProperty(VitroVocabulary.BLURB);
     protected OntClass           CLASSGROUP = _constModel.createClass(VitroVocabulary.CLASSGROUP);
     protected AnnotationProperty IN_CLASSGROUP = _constModel.createAnnotationProperty(VitroVocabulary.IN_CLASSGROUP);
     protected DatatypeProperty   MODTIME = _constModel.createDatatypeProperty(VitroVocabulary.MODTIME);
-    protected DatatypeProperty   TIMEKEY = _constModel.createDatatypeProperty(VitroVocabulary.TIMEKEY);
-    protected DatatypeProperty   CITATION = _constModel.createDatatypeProperty(VitroVocabulary.CITATION);
 
     protected DatatypeProperty   DISPLAY_RANK = _constModel.createDatatypeProperty(VitroVocabulary.DISPLAY_RANK);
     protected AnnotationProperty DISPLAY_RANK_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.DISPLAY_RANK_ANNOT);
@@ -76,7 +67,6 @@ public class JenaBaseDaoCon {
     protected AnnotationProperty PROPERTY_CUSTOMSHORTVIEWANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_CUSTOMSHORTVIEWANNOT);
     protected AnnotationProperty PROPERTY_CUSTOM_LIST_VIEW_ANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_CUSTOM_LIST_VIEW_ANNOT);
     protected AnnotationProperty PROPERTY_CUSTOMSEARCHVIEWANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_CUSTOMSEARCHVIEWANNOT);
-    //protected AnnotationProperty PROPERTY_FORCESTUBDELETIONANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_FORCESTUBDELETIONANNOT);
     protected AnnotationProperty PROPERTY_SELECTFROMEXISTINGANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_SELECTFROMEXISTINGANNOT);
     protected AnnotationProperty PROPERTY_OFFERCREATENEWOPTIONANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_OFFERCREATENEWOPTIONANNOT);
     protected AnnotationProperty PROPERTY_INPROPERTYGROUPANNOT = _constModel.createAnnotationProperty(VitroVocabulary.PROPERTY_INPROPERTYGROUPANNOT);
@@ -85,17 +75,6 @@ public class JenaBaseDaoCon {
     
     protected OntClass 		     PROPERTYGROUP = _constModel.createClass(VitroVocabulary.PROPERTYGROUP);
 
-    protected OntClass           KEYWORD = _constModel.createClass(VitroVocabulary.KEYWORD);
-    protected DatatypeProperty   KEYWORD_STEM = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_STEM);
-    protected DatatypeProperty   KEYWORD_TYPE = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_TYPE);
-    protected DatatypeProperty   KEYWORD_SOURCE = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_SOURCE);
-    protected DatatypeProperty   KEYWORD_ORIGIN = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_ORIGIN);
-    protected DatatypeProperty   KEYWORD_COMMENTS = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_COMMENTS);
-    protected OntClass           KEYWORD_INDIVIDUALRELATION = _constModel.createClass(VitroVocabulary.KEYWORD_INDIVIDUALRELATION);
-    protected ObjectProperty     KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD = _constModel.createObjectProperty(VitroVocabulary.KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD);
-    protected ObjectProperty     KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL = _constModel.createObjectProperty(VitroVocabulary.KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL);
-    protected DatatypeProperty   KEYWORD_INDIVIDUALRELATION_MODE = _constModel.createDatatypeProperty(VitroVocabulary.KEYWORD_INDIVIDUALRELATION_MODE);
-
     protected OntClass           LINK = _constModel.createClass(VitroVocabulary.LINK);
     protected ObjectProperty     PRIMARY_LINK = _constModel.createObjectProperty(VitroVocabulary.PRIMARY_LINK);
     protected ObjectProperty     ADDITIONAL_LINK = _constModel.createObjectProperty(VitroVocabulary.ADDITIONAL_LINK);
@@ -104,22 +83,9 @@ public class JenaBaseDaoCon {
     protected DatatypeProperty   LINK_TYPE = _constModel.createDatatypeProperty(VitroVocabulary.LINK_TYPE);
     protected DatatypeProperty   LINK_DISPLAYRANK = _constModel.createDatatypeProperty(VitroVocabulary.LINK_DISPLAYRANK_URL);
 
-//    protected  OntClass           APPLICATION = null;
-//    protected  DatatypeProperty   APPLICATION_FLAG1NAME = null;
-//    protected  DatatypeProperty   APPLICATION_FLAG2NAME = null;
-//    protected  DatatypeProperty   APPLICATION_FLAG3NAME = null;
-//    protected  DatatypeProperty   APPLICATION_MINSHAREDPORTALID = null;
-//    protected  DatatypeProperty   APPLICATION_MAXSHAREDPORTALID = null;
-//    protected  DatatypeProperty   APPLICATION_KEYWORDHEADING = null;
-//    protected  DatatypeProperty   APPLICATION_ROOTLOGOTYPEIMAGE = null;
-//    protected  DatatypeProperty   APPLICATION_ONLYCURRENT = null;
-//    protected  DatatypeProperty   APPLICATION_MAXPORTALID = null;
-
     protected  OntClass           PORTAL = _constModel.createClass(VitroVocabulary.PORTAL);
     protected  DatatypeProperty   APPLICATION_THEMEDIR = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_THEMEDIR);
     protected  DatatypeProperty   PORTAL_BANNERIMAGE = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_BANNERIMAGE);
-    //protected  DatatypeProperty   PORTAL_FLAG2VALUES = null;
-    //protected  DatatypeProperty   PORTAL_FLAG1VALUES = null;
     protected  DatatypeProperty   APPLICATION_CONTACTMAIL = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_CONTACTMAIL);
     protected  DatatypeProperty   APPLICATION_CORRECTIONMAIL = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_CORRECTIONMAIL);
     protected  DatatypeProperty   PORTAL_SHORTHAND = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_SHORTHAND);
@@ -127,7 +93,6 @@ public class JenaBaseDaoCon {
     protected  DatatypeProperty   APPLICATION_ACKNOWLEGETEXT = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_ACKNOWLEGETEXT);
     protected  DatatypeProperty   PORTAL_BANNERWIDTH = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_BANNERWIDTH);
     protected  DatatypeProperty   PORTAL_BANNERHEIGHT = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_BANNERHEIGHT);
-    //protected  DatatypeProperty   PORTAL_FLAG3VALUES = null;
     protected  DatatypeProperty   APPLICATION_COPYRIGHTURL = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_COPYRIGHTURL);
     protected  DatatypeProperty   APPLICATION_COPYRIGHTANCHOR = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_COPYRIGHTANCHOR);
     protected  DatatypeProperty   PORTAL_ROOTBREADCRUMBURL = _constModel.createDatatypeProperty(VitroVocabulary.PORTAL_ROOTBREADCRUMBURL);

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java

@@ -103,17 +103,29 @@ public class JenaModelUtils {
 	}
 	
 	private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
+	private final boolean NORMAL = false;
+	private final boolean AGGRESSIVE = true;
+
 
 	public OntModel extractTBox( Model inputModel ) {
 	    return extractTBox(inputModel, null);	
 	}
 	
+	public OntModel extractTBox( Model inputModel, boolean MODE ) {
+	    Dataset dataset = DatasetFactory.create(inputModel);
+        return extractTBox(dataset, null, null, MODE);   
+    }
+	
 	public OntModel extractTBox( Model inputModel, String namespace ) {
 	    Dataset dataset = DatasetFactory.create(inputModel);
-        return extractTBox( dataset, namespace, null );
+        return extractTBox( dataset, namespace, null, NORMAL );
 	}
 	
 	public OntModel extractTBox( Dataset dataset, String namespace, String graphURI) {
+	    return extractTBox( dataset, namespace, graphURI, NORMAL);
+	}
+	
+	public OntModel extractTBox( Dataset dataset, String namespace, String graphURI, boolean mode ) {
 		OntModel tboxModel = ModelFactory.createOntologyModel(DEFAULT_ONT_MODEL_SPEC);
 		
 		List<String> queryStrList = new LinkedList<String>();
@@ -121,6 +133,7 @@ private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
 		// Use SPARQL DESCRIBE queries to extract the RDF for named ontology entities
 		
 		queryStrList.add( makeDescribeQueryStr( OWL.Class.getURI(), namespace, graphURI ) );
+		queryStrList.add( makeDescribeQueryStr( OWL.Restriction.getURI(), namespace, graphURI ) );
 		queryStrList.add( makeDescribeQueryStr( OWL.ObjectProperty.getURI(), namespace, graphURI ) );
 		queryStrList.add( makeDescribeQueryStr( OWL.DatatypeProperty.getURI(), namespace, graphURI ) );
 		queryStrList.add( makeDescribeQueryStr( OWL.AnnotationProperty.getURI(), namespace, graphURI ) );
@@ -144,8 +157,56 @@ private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
 			}
 		}
 		
+		// Perform possibly-redundant extraction to try ensure we don't miss 
+		// individual axioms floating around.  We still might miss things;
+		// this approach isn't perfect.
+		if (mode = AGGRESSIVE) {
+			tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subClassOf));
+			tboxModel.add(construct(dataset, namespace, graphURI, RDFS.subPropertyOf));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.equivalentClass));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.unionOf));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.intersectionOf));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.complementOf));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.onProperty));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.allValuesFrom));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.someValuesFrom));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.hasValue));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.minCardinality));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.maxCardinality));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.cardinality));
+			tboxModel.add(construct(dataset, namespace, graphURI, OWL.disjointWith));	
+		}
 		return tboxModel;
+	}
 	
+	private Model construct(Dataset dataset, 
+	                        String namespace, 
+	                        String graphURI, 
+	                        Resource property) {
+	    dataset.getLock().enterCriticalSection(Lock.READ);
+	    try {
+	        StringBuffer buff = new StringBuffer();
+	        buff.append("PREFIX afn: <http://jena.hpl.hp.com/ARQ/function#> \n")
+	        .append("CONSTRUCT { \n")
+	        .append("  ?res <" + property.getURI() + "> ?o WHERE { \n");
+	        if (graphURI != null) {
+	            buff.append("    GRAPH " + graphURI + " { \n");
+	        }
+	        buff.append("      ?res <" + property.getURI() + "> ?o \n");
+	        buff.append(getNamespaceFilter(namespace));
+	        if (graphURI != null) {
+	            buff.append("    } \n");
+	        }
+	        Query constructProp = QueryFactory.create(buff.toString());
+	        QueryExecution qe = QueryExecutionFactory.create(constructProp, dataset);
+	        try {
+	            return qe.execConstruct();
+	        } finally {
+	            qe.close();
+	        }
+	    } finally {
+	        dataset.getLock().leaveCriticalSection();
+	    }
 	}
 	
 	private String makeDescribeQueryStr( String typeURI, String namespace ) {
@@ -166,31 +227,10 @@ private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
 			.append("    ?res rdf:type <").append(typeURI).append("> . \n");
 			
 			describeQueryStrBuff
-			.append("    FILTER (!isBlank(?res)) \n");
+			.append("    FILTER (!isBlank(?res)) \n")
+	
+			.append(getNamespaceFilter(namespace));
 	
-		if (namespace == null) {
-			// exclude resources in the Vitro internal namespace or in the 
-			// OWL namespace, but allow all others
-			describeQueryStrBuff
-			//.append("    FILTER (afn:namespace(?res) != \"")
-			//.append("http://vitro.mannlib.cornell.edu/ns/vitro/0.7#")
-			//.append("\") \n")
-			.append("    FILTER (afn:namespace(?res) != \"")
-			.append("http://www.w3.org/2002/07/owl#")
-			.append("\") \n")
-			//.append("    FILTER (?res != <")
-			//.append("http://vitro.mannlib.cornell.edu/ns/vitro/0.7")
-			//.append(">) \n")
-			.append("    FILTER (?res != <")
-			.append("http://www.w3.org/2002/07/owl")
-			.append(">) \n");
-		} else {
-			// limit resources to those in the supplied namespace
-			describeQueryStrBuff
-			.append("    FILTER (afn:namespace(?res) = \"")
-			.append(namespace)
-			.append("\") \n");	
-		}
 		if (graphURI != null) {
 			describeQueryStrBuff
 			.append("} \n");
@@ -202,6 +242,28 @@ private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
 		
 	}
 	
+	private String getNamespaceFilter(String namespace) {
+	    StringBuffer buff = new StringBuffer();
+	    if (namespace == null) {
+            // exclude resources in the Vitro internal namespace or in the 
+            // OWL namespace, but allow all others
+            buff
+            .append("    FILTER (afn:namespace(?res) != \"")
+            .append("http://www.w3.org/2002/07/owl#")
+            .append("\") \n")
+            .append("    FILTER (?res != <")
+            .append("http://www.w3.org/2002/07/owl")
+            .append(">) \n");
+        } else {
+            // limit resources to those in the supplied namespace
+            buff
+            .append("    FILTER (afn:namespace(?res) = \"")
+            .append(namespace)
+            .append("\") \n");  
+        }
+	    return buff.toString();
+	}
+	
 	public Model extractABox(Model inputModel){
 		Dataset dataset = DatasetFactory.create(inputModel);
 	    return extractABox(dataset, null, null);
@@ -221,7 +283,6 @@ private final OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
 		//: ModelFactory.createOntologyModel( DEFAULT_ONT_MODEL_SPEC, inputModel );
 		OntModel ontModel = extractTBox(unionDataset, null, graphURI);	
 	
-	
 		try {
 			ontModel.enterCriticalSection(Lock.READ);
 			Iterator classIt = ontModel.listNamedClasses();

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/KeywordDaoJena.java

@@ -1,212 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
-
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatement;
-import edu.cornell.mannlib.vitro.webapp.beans.DataPropertyStatementImpl;
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.IndividualImpl;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.beans.VClass;
-import edu.cornell.mannlib.vitro.webapp.dao.InsertException;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-
-public class KeywordDaoJena extends JenaBaseDao implements KeywordDao {
-    private static final Log log = LogFactory.getLog(KeywordDaoJena.class.getName());
-    
-    private String KEYWORD_URI_PREFIX = DEFAULT_NAMESPACE + "keyword";
-
-    private WebappDaoFactory webappDaoFactory = null;
-
-    public KeywordDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-        this.webappDaoFactory = getWebappDaoFactory();
-    }
-
-    public void deleteKeyword(Keyword keyword) {
-        webappDaoFactory.getIndividualDao().deleteIndividual(KEYWORD_URI_PREFIX+keyword.getId());
-    }
-
-    public List<Keyword> getAllKeywords() {
-        VClass keywordClass = webappDaoFactory.getVClassDao().getVClassByURI(KEYWORD.getURI());
-        List keywordInds = webappDaoFactory.getIndividualDao().getIndividualsByVClass(keywordClass);
-        List keywords = new ArrayList();
-        Iterator keywordIndIt = keywordInds.iterator();
-        while (keywordIndIt.hasNext()) {
-            keywords.add(keywordFromKeywordIndividual((Individual)keywordIndIt.next()));
-        }
-        return keywords;
-    }
-
-    public List<Keyword> getKeywordsByStem(String stem) {
-        List<Keyword> matchingKeywords = new ArrayList<Keyword>();
-        List<Keyword> all = getAllKeywords();
-        Iterator<Keyword> allIt = all.iterator();
-        while (allIt.hasNext()) {
-            Keyword k = allIt.next();
-            if (k.getStem()!= null && k.getStem().equalsIgnoreCase(stem)) {
-                matchingKeywords.add(k);
-            }
-        }
-        return matchingKeywords;
-    }
-
-    public List getAllOrigins() {
-        List origins = new ArrayList();
-        HashSet originSet = new HashSet();
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            ClosableIterator stmtIt = getOntModel().listStatements(null, KEYWORD_ORIGIN, (Literal)null);
-            try {
-                while (stmtIt.hasNext()) {
-                    Statement stmt = (Statement) stmtIt.next();
-                    Literal lit = (Literal) stmt.getObject();
-                    String originStr = (String)lit.getString();
-                    if (!originSet.contains(originStr)) {
-                        originSet.add(originStr);
-                    }
-                }
-            } finally {
-                stmtIt.close();
-            }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-        origins.addAll(originSet);
-        return origins;
-    }
-
-    public Keyword getKeywordById(int id) {
-        Individual keywordIndividual = webappDaoFactory.getIndividualDao().getIndividualByURI(KEYWORD_URI_PREFIX+id);
-        Keyword k = keywordFromKeywordIndividual(keywordIndividual);
-        k.setId(id);
-        return k;
-    }
-
-    private Keyword keywordFromKeywordIndividual(Individual keywordIndividual) {
-           Keyword keyword = new Keyword();
-           if (keywordIndividual != null) {
-                keyword.setTerm(keywordIndividual.getName());
-                keyword.setId(Integer.decode(keywordIndividual.getLocalName().substring(7,keywordIndividual.getLocalName().length())));
-                try {
-                    keyword.setStem( ((DataPropertyStatement)(webappDaoFactory.getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(keywordIndividual, KEYWORD_STEM.getURI()).toArray())[0]).getData() );
-                } catch (Exception e) {
-                    // e.printStackTrace();
-                }
-                try {
-                    keyword.setOrigin( ((DataPropertyStatement)(webappDaoFactory.getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(keywordIndividual, KEYWORD_ORIGIN.getURI()).toArray())[0]).getData() );
-                } catch (Exception e) {
-                    // e.printStackTrace();
-                }
-                try {
-                    keyword.setType( ((DataPropertyStatement)(webappDaoFactory.getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(keywordIndividual, KEYWORD_TYPE.getURI()).toArray())[0]).getData() );
-                } catch (Exception e) {
-                    // e.printStackTrace();
-                }
-                try {
-                    keyword.setSource( ((DataPropertyStatement)(webappDaoFactory.getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(keywordIndividual, KEYWORD_SOURCE.getURI()).toArray())[0]).getData() );
-                } catch (Exception e) {
-                    // e.printStackTrace();
-                }
-                try {
-                    keyword.setComments( ((DataPropertyStatement)(webappDaoFactory.getDataPropertyStatementDao().getDataPropertyStatementsForIndividualByDataPropertyURI(keywordIndividual, KEYWORD_COMMENTS.getURI()).toArray())[0]).getData() );
-                } catch (Exception e) {
-                    // e.printStackTrace();
-                }
-           }
-            return keyword;
-    }
-
-    public synchronized int insertNewKeyword(Keyword k) {
-        int kId = -1;
-        if (k.getId()>0) {
-            kId = k.getId();
-        } else {
-            String term = k.getTerm();
-            int count = 0;
-            while ((webappDaoFactory.getIndividualDao().getIndividualByURI(KEYWORD_URI_PREFIX+Math.abs(term.hashCode())) != null) && count < 32) {
-                term+="a";
-                log.debug(term);
-                log.debug(KEYWORD_URI_PREFIX+Math.abs(term.hashCode()));
-                count++;
-            }
-
-            kId = Math.abs(term.hashCode());
-        }
-        Individual keywordIndividual = new IndividualImpl();
-        keywordIndividual.setURI(KEYWORD_URI_PREFIX+kId);
-        keywordIndividual.setVClassURI(KEYWORD.getURI());
-        keywordIndividual.setName(k.getTerm());
-        String keywordURI = null;
-        try {
-        	keywordURI = webappDaoFactory.getIndividualDao().insertNewIndividual(keywordIndividual);
-        } catch (InsertException e) {
-        	log.error(e, e);
-        }
-      log.debug("KeywordDaoJena.insertNewKeyword() : "+keywordURI);
-        
-        DataPropertyStatement stem = new DataPropertyStatementImpl();
-      log.debug("KeywordDaoJena.insertNewKeyword() stem : "+k.getStem());
-        stem.setData(k.getStem());
-        stem.setDatapropURI(KEYWORD_STEM.getURI());
-        stem.setIndividualURI(keywordURI);
-        webappDaoFactory.getDataPropertyStatementDao().insertNewDataPropertyStatement(stem);
-        
-      log.debug("KeywordDaoJena.insertNewKeyword() type : "+k.getType());
-        DataPropertyStatement type = new DataPropertyStatementImpl();
-        type.setData(k.getType());
-        type.setDatapropURI(KEYWORD_TYPE.getURI());
-        type.setIndividualURI(keywordURI);
-        webappDaoFactory.getDataPropertyStatementDao().insertNewDataPropertyStatement(type);
-        
-      log.debug("KeywordDaoJena.insertNewKeyword() source : "+k.getSource());
-        if (k.getSource()==null || k.getSource().equals("")) {
-            k.setSource("unspecified");
-        }
-        DataPropertyStatement source = new DataPropertyStatementImpl();
-        source.setData(k.getSource());
-        source.setDatapropURI(KEYWORD_SOURCE.getURI());
-        source.setIndividualURI(keywordURI);
-        webappDaoFactory.getDataPropertyStatementDao().insertNewDataPropertyStatement(source);
-        
-      log.debug("KeywordDaoJena.insertNewKeyword() origin : "+k.getOrigin());
-        if (k.getOrigin()==null || k.getOrigin().equals("")) {
-            k.setOrigin("unspecified");
-        }
-        DataPropertyStatement origin = new DataPropertyStatementImpl();
-        origin.setData(k.getOrigin());
-        origin.setDatapropURI(KEYWORD_ORIGIN.getURI());
-        origin.setIndividualURI(keywordURI);
-        webappDaoFactory.getDataPropertyStatementDao().insertNewDataPropertyStatement(origin);
-        
-        if (k.getComments()!=null && !k.getComments().equals("")) {
-          log.debug("KeywordDaoJena.insertNewKeyword() comments : "+k.getComments());
-            DataPropertyStatement comments = new DataPropertyStatementImpl();
-            comments.setData(k.getComments());
-            comments.setDatapropURI(KEYWORD_COMMENTS.getURI());
-            comments.setIndividualURI(keywordURI);
-            webappDaoFactory.getDataPropertyStatementDao().insertNewDataPropertyStatement(comments);
-        }
-        return kId;
-    }
-
-    public void updateKeyword(Keyword k) {
-        deleteKeyword(k);
-        insertNewKeyword(k);
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/KeywordIndividualRelationDaoJena.java

@@ -1,184 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.RDF;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.KeywordIndividualRelation;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-
-public class KeywordIndividualRelationDaoJena extends JenaBaseDao implements KeywordIndividualRelationDao {
-
-    public KeywordIndividualRelationDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-
-    @Override
-    protected OntModel getOntModel() {
-    	return getOntModelSelector().getABoxModel();
-    }
-    
-    public void deleteKeywordIndividualRelation(KeywordIndividualRelation k) {
-    	deleteKeywordIndividualRelation(k,getOntModel());
-    }
-
-    public void deleteKeywordIndividualRelation(KeywordIndividualRelation k, OntModel ontModel) {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        try {
-            com.hp.hpl.jena.ontology.Individual kirInd = ontModel.getIndividual(k.getURI());
-            if (kirInd != null) {
-                kirInd.remove();
-            }
-        } finally {
-            ontModel.leaveCriticalSection();
-        }
-        if (k.getEntURI() != null) {
-            Individual ind = getWebappDaoFactory().getIndividualDao().getIndividualByURI(k.getEntURI());
-            getWebappDaoFactory().getIndividualDao().markModified(ind);
-        }
-    }
-
-    public KeywordIndividualRelation getKeywordIndividualRelationByURI(String URI) {
-        com.hp.hpl.jena.ontology.Individual kirInd = getOntModel().getIndividual(URI);
-        if (kirInd != null) {
-            return keywordIndividualRelationFromIndividual(kirInd);
-        } else {
-            return null;
-        }
-    }
-
-       public List<KeywordIndividualRelation> getKeywordIndividualRelationsByIndividualURI(String individualURI) {
-            List kirList = new ArrayList();
-            if (individualURI == null) {
-            	return kirList;
-            }
-            getOntModel().enterCriticalSection(Lock.READ);
-            try {
-                Resource individual = ResourceFactory.createResource(individualURI);
-                if (individual != null) {
-                    ClosableIterator stmtIt = getOntModel().listStatements(null, KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL, individual);
-                    try {
-                        while (stmtIt.hasNext()) {
-                            Statement stmt = (Statement) stmtIt.next();
-                            Resource kirRes = stmt.getSubject();
-                            if (kirRes != null) {
-                                boolean checked = false;
-                                ClosableIterator checkIt = kirRes.listProperties(RDF.type);
-                                try {
-                                    while (checkIt.hasNext()) {
-                                        Statement chk = (Statement) checkIt.next();
-                                        if (((Resource)chk.getObject()).getURI().equals(KEYWORD_INDIVIDUALRELATION.getURI())) {
-                                            checked = true;
-                                            break;
-                                        }
-                                    }
-                                } finally {
-                                    checkIt.close();
-                                }
-                                if (checked) {
-                                    com.hp.hpl.jena.ontology.Individual kirInd = getOntModel().getIndividual(kirRes.getURI());
-                                    kirList.add(keywordIndividualRelationFromIndividual(kirInd));
-                                }
-                            }
-                        }
-                    } finally {
-                        stmtIt.close();
-                    }
-                }
-            } finally {
-                getOntModel().leaveCriticalSection();
-            }
-            return kirList;
-        }
-
-    public String insertNewKeywordIndividualRelation(KeywordIndividualRelation k) {
-    	return insertNewKeywordIndividualRelation(k,getOntModel());
-    }
-
-    public String insertNewKeywordIndividualRelation(KeywordIndividualRelation k, OntModel ontModel) {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        String uriToUse = null;
-        try {
-            Resource individual = ontModel.getResource(k.getEntURI());
-            Resource keyword = ontModel.getResource(DEFAULT_NAMESPACE+"keyword"+k.getKeyId());
-            if (k.getURI() != null) {
-                uriToUse = k.getURI();
-            } else {
-                String dedup = DEFAULT_NAMESPACE+"keywordIndividualRelation_"+k.getKeyId()+"_"+individual.getLocalName();
-                //while (ontModel.getResource(dedup) != null) {
-                //  dedup += "a";
-                //}
-                uriToUse = dedup;
-            }
-            OntClass KeywordIndividualRelationOntClass = ontModel.getOntClass(VitroVocabulary.KEYWORD_INDIVIDUALRELATION);
-            if (KeywordIndividualRelationOntClass != null) {
-                com.hp.hpl.jena.ontology.Individual tirInd = KeywordIndividualRelationOntClass.createIndividual(uriToUse);
-                addPropertyResourceValue(tirInd, KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD, keyword);
-                addPropertyResourceValue(tirInd, KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL, individual);
-                addPropertyStringValue(tirInd, KEYWORD_INDIVIDUALRELATION_MODE, k.getMode(), ontModel);
-            } else {
-                log.error(VitroVocabulary.KEYWORD_INDIVIDUALRELATION+" class not found");
-            }
-        } finally {
-            ontModel.leaveCriticalSection();
-        }
-        if (k.getEntURI() != null) {
-            Individual ind = getWebappDaoFactory().getIndividualDao().getIndividualByURI(k.getEntURI());
-            getWebappDaoFactory().getIndividualDao().markModified(ind);
-        }
-        return uriToUse;
-    }
-
-    public void updateKeywordIndividualRelation(KeywordIndividualRelation k) {
-    	updateKeywordIndividualRelation(k,getOntModel());
-    }
-
-    public void updateKeywordIndividualRelation(KeywordIndividualRelation k, OntModel ontModel) {
-           ontModel.enterCriticalSection(Lock.WRITE);
-            try {
-                com.hp.hpl.jena.ontology.Individual kirInd = ontModel.getIndividual(k.getURI());
-                Resource individual = ontModel.getResource(k.getEntURI());
-                Resource keyword = ontModel.getResource(DEFAULT_NAMESPACE+"keyword"+k.getKeyId());
-                updatePropertyResourceValue(kirInd, KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD, keyword);
-                updatePropertyResourceValue(kirInd, KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL, individual);
-                updatePropertyStringValue(kirInd, KEYWORD_INDIVIDUALRELATION_MODE, k.getMode(), ontModel);
-            } finally {
-                ontModel.leaveCriticalSection();
-            }
-            if (k.getEntURI() != null) {
-                Individual ind = getWebappDaoFactory().getIndividualDao().getIndividualByURI(k.getEntURI());
-                getWebappDaoFactory().getIndividualDao().markModified(ind);
-            }
-    }
-
-       private KeywordIndividualRelation keywordIndividualRelationFromIndividual(com.hp.hpl.jena.ontology.Individual ind) {
-            KeywordIndividualRelation kir = new KeywordIndividualRelation();
-            kir.setURI(ind.getURI());
-            try {
-                kir.setEntURI(((Resource)ind.getPropertyValue(KEYWORD_INDIVIDUALRELATION_INVOLVESINDIVIDUAL)).getURI());
-            } catch (Exception e) {/* TODO log */}
-            try {
-                String keywordLocalName = ((Resource)ind.getPropertyValue(KEYWORD_INDIVIDUALRELATION_INVOLVESKEYWORD)).getLocalName();
-                kir.setKeyId(Integer.decode(keywordLocalName.substring(7,keywordLocalName.length())));
-
-            } catch (Exception e) {/* TODO log */}
-            kir.setMode(getPropertyStringValue(ind,KEYWORD_INDIVIDUALRELATION_MODE));
-            return kir;
-        }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/LinksDaoJena.java

@@ -1,385 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
-import java.net.URLEncoder;
-import java.text.Collator;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.Literal;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.RDF;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Individual;
-import edu.cornell.mannlib.vitro.webapp.beans.Link;
-import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
-import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatementImpl;
-import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
-
-public class LinksDaoJena extends JenaBaseDao implements LinksDao {
-
-    protected static final Log log = LogFactory.getLog(LinksDaoJena.class.getName());
-    
-    public LinksDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-    
-    @Override
-    protected OntModel getOntModel() {
-    	return getOntModelSelector().getABoxModel();
-    }
-
-    public void addLinksToIndividual(Individual individual) {
-        List<Link> linksList = new ArrayList<Link>();
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            Resource entInd = ResourceFactory.createResource(individual.getURI());
-            if (ADDITIONAL_LINK != null) {
-                ClosableIterator<Statement> links = getOntModel().listStatements(entInd,ADDITIONAL_LINK,(Resource)null);
-                try {
-                    while (links.hasNext()) {
-                        try {
-                            Resource linkRes = (Resource) links.next().getObject();
-                            linksList.add(linkFromLinkResource(linkRes, ADDITIONAL_LINK));
-                        } catch (ClassCastException cce) {/*no thanks; we don't want any*/}
-                    }
-                } finally {
-                    links.close();
-                }
-                
-                if (linksList.size()>1) { // sort
-                    Collections.sort(linksList,new Comparator<Link>() {
-                        public int compare( Link first, Link second ) {
-                            if (first==null) {
-                                return 1;
-                            }
-                            if (second==null) {
-                                return -1;
-                            }
-                            Collator collator = Collator.getInstance();
-                            int compval = collator.compare(first.getDisplayRank(),second.getDisplayRank());
-                            if (compval == 0) {
-                                String firstAnchor = first.getAnchor();
-                                String secondAnchor = second.getAnchor();
-                                if (firstAnchor == null) {
-                                    if (secondAnchor == null) {
-                                        return 0;
-                                    }
-                                    return 1;
-                                } 
-                                if (secondAnchor == null) {
-                                    return -1;
-                                }
-                                compval = collator.compare(firstAnchor, secondAnchor);
-                            }
-                            return compval;
-                        }
-                    });
-                }
-                individual.setLinksList(linksList);
-            }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-    }
-    
-    public void addPrimaryLinkToIndividual(Individual individual) {
-        List<Link> linksList = new ArrayList<Link>();
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            com.hp.hpl.jena.ontology.Individual entInd = getOntModel().getIndividual(individual.getURI());
-            if (PRIMARY_LINK != null) {
-                ClosableIterator<Statement> links = getOntModel().listStatements(entInd,PRIMARY_LINK,(Resource)null);
-                try {
-                    while (links.hasNext()) {
-                        try {
-                            Resource linkRes = (Resource) links.next().getObject();
-                            linksList.add(linkFromLinkResource(linkRes,PRIMARY_LINK));
-                        } catch (ClassCastException cce) {/*no thanks; we don't want any*/}
-                    }
-                } finally {
-                    links.close();
-                }
-                
-                if (linksList.size()>1) { // sort
-                    Collections.sort(linksList,new Comparator<Link>() {
-                        public int compare( Link first, Link second ) {
-                            if (first==null) {
-                                return 1;
-                            }
-                            if (second==null) {
-                                return -1;
-                            }
-                            Collator collator = Collator.getInstance();
-                            int compval = collator.compare(first.getDisplayRank(),second.getDisplayRank());
-                            if (compval == 0) {
-                                String firstAnchor = first.getAnchor();
-                                String secondAnchor = second.getAnchor();
-                                if (firstAnchor == null) {
-                                    if (secondAnchor == null) {
-                                        return 0;
-                                    }
-                                    return 1;
-                                } 
-                                if (secondAnchor == null) {
-                                    return -1;
-                                }                                
-                                compval = collator.compare(firstAnchor, secondAnchor);
-                            }
-                            return compval;
-                        }
-                    });
-                }
-                
-                if (linksList.size()>0) {
-                    Iterator<Link> iter = linksList.iterator();
-                    if (iter.hasNext()) { // take the first only
-                        individual.setPrimaryLink(iter.next());
-                    }
-                }
-            }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-    }
-
-
-    public void addLinksToIndividualsInObjectPropertyStatement(List<ObjectPropertyStatement> objectPropertyStatements) {
-        if (objectPropertyStatements != null) {
-            Iterator<ObjectPropertyStatement> objectPropertyStatementsIt = objectPropertyStatements.iterator();
-            while (objectPropertyStatementsIt.hasNext()) {
-                ObjectPropertyStatement ops = objectPropertyStatementsIt.next();
-                if (ops.getSubject() != null && ops.getSubject() instanceof Individual)
-                    addLinksToIndividual((Individual)ops.getSubject());
-                if (ops.getObject() != null && ops.getObject() instanceof Individual)
-                    addLinksToIndividual((Individual)ops.getObject());
-            }
-        }
-    }
-
-    public void deleteLink(Link link) {
-    	deleteLink(link,getOntModel());
-    }
-
-    public void deleteLink(Link link, OntModel ontModel) {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        try {
-            Resource linkRes = ontModel.getResource(link.getURI());
-            if (linkRes != null) {
-                ontModel.removeAll(linkRes, null, null);
-                ontModel.removeAll(null, null, linkRes);
-            }
-        } finally {
-            ontModel.leaveCriticalSection();
-        }
-    }
-
-    public Link getLinkByURI(String URI) {
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-            Resource linkRes = getOntModel().getResource(URI);
-            if (linkRes != null) {
-                return linkFromLinkResource(linkRes,ADDITIONAL_LINK);
-            } else {
-                return null;
-            }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-    }
-
-    public String insertNewLink(Link link) {
-    	return insertNewLink(link,getOntModel());
-    }
-
-    public String insertNewLink(Link link, OntModel ontModel) {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        try {
-            Resource indRes = ontModel.getResource(link.getEntityURI());
-            if (indRes == null) {
-                return null;
-            }
-            String linkUri = null;
-            if (link.getURI() != null && link.getURI().length()>0) {
-                linkUri = link.getURI();
-            } else {
-                linkUri = DEFAULT_NAMESPACE+"link_"+indRes.getLocalName()+link.getAnchor().replaceAll("\\W","");
-            }
-            Resource test = ontModel.getResource(linkUri);
-            int count = 0;
-            while (test != null) {
-                ++count;
-                linkUri+="_"+count;
-                test = ontModel.getIndividual(linkUri);
-            }
-            Resource linkRes = ontModel.createResource(linkUri);
-            linkRes.addProperty(RDF.type, LINK);
-            if (link.getTypeURI() != null && link.getTypeURI().length()>0) {
-                try {
-                    linkRes.addProperty(RDF.type, ontModel.getResource(link.getTypeURI()));
-                } catch (Exception e) {}
-            }
-            String urlString = link.getUrl();
-            try {
-                urlString = URLEncoder.encode(urlString, "UTF-8");
-            } catch (UnsupportedEncodingException e) {}
-
-            linkRes.addProperty(LINK_URL, urlString, XSDDatatype.XSDanyURI);
-            linkRes.addProperty(LINK_ANCHOR, link.getAnchor(), XSDDatatype.XSDstring);
-            linkRes.addProperty(LINK_DISPLAYRANK, ontModel.createTypedLiteral(link.getDisplayRank())); // String for now
-            
-            ontModel.add(indRes, ADDITIONAL_LINK, linkRes);
-            return linkUri;
-        } finally {
-            ontModel.leaveCriticalSection();
-        }
-    }
-
-    public void updateLink(Link link) {
-    	updateLink(link,getOntModel());
-    }
-
-    public void updateLink(Link link, OntModel ontModel) {
-        ontModel.enterCriticalSection(Lock.WRITE);
-        try {
-            Resource linkRes = ontModel.getResource(link.getURI());
-            Resource indRes = ontModel.getResource(link.getEntityURI());
-            if (linkRes != null) {
-                linkRes.removeAll(RDF.type);  // BJL note: a transactionless DL reasoner might choke on this approach
-                linkRes.addProperty(RDF.type, LINK);
-                if (link.getTypeURI() != null && link.getTypeURI().length()>0) {
-                    try {
-                        linkRes.addProperty(RDF.type, ontModel.getResource(link.getTypeURI()));
-                    } catch (Exception e) {e.printStackTrace();}
-                }
-                linkRes.removeAll(LINK_URL);
-                String urlString = link.getUrl();
-                try {
-                    urlString = URLEncoder.encode(urlString, "UTF-8");
-                } catch (UnsupportedEncodingException e) {}
-                linkRes.addProperty(LINK_URL, urlString, XSDDatatype.XSDanyURI);
-                linkRes.removeAll(LINK_ANCHOR);
-                linkRes.addProperty(LINK_ANCHOR, link.getAnchor(), XSDDatatype.XSDstring);
-                if (indRes != null) {
-                    ontModel.removeAll(null, ADDITIONAL_LINK, linkRes);
-                    ontModel.add(indRes, ADDITIONAL_LINK, linkRes);
-                }
-                linkRes.removeAll(LINK_DISPLAYRANK);
-                linkRes.addProperty(LINK_DISPLAYRANK, ontModel.createTypedLiteral(link.getDisplayRank())); // String for now
-            }
-        } finally {
-            ontModel.leaveCriticalSection();
-        }
-    }
-
-    private Link linkFromLinkResource(Resource linkRes, com.hp.hpl.jena.ontology.ObjectProperty whichLinkProp) {
-        Link link = new Link();
-        link.setURI(linkRes.getURI());
-        ClosableIterator<Statement> typesIt = linkRes.listProperties(RDF.type);
-        try {
-            while (typesIt.hasNext()) {
-                Statement st = typesIt.next();
-                try {
-                    Resource typeRes = (Resource) st.getObject();
-                    if (!typeRes.getURI().equalsIgnoreCase(LINK.getURI())) {  // TODO: remove IgnoreCase ; there because some serializations use "link" instead of "Link"
-                        link.setTypeURI(typeRes.getURI());
-                    }
-                } catch (ClassCastException e) {}
-            }
-        } finally {
-            typesIt.close();
-        }
-        if (LINK_ANCHOR != null) {
-            try {
-                ClosableIterator<Statement> anchorStatements = getOntModel().listStatements(linkRes, LINK_ANCHOR, (Literal)null);
-                try {
-                    if (anchorStatements.hasNext()) {
-                        Literal l = (Literal) anchorStatements.next().getObject();
-                        if (l != null) {
-                            link.setAnchor(l.getString());
-                        }
-                    }
-                } finally {
-                    anchorStatements.close();
-                }
-            } catch (ClassCastException e) {}
-        }
-        if (LINK_URL != null) {
-            try {
-                ClosableIterator<Statement> UrlStatements = getOntModel().listStatements(linkRes, LINK_URL, (Literal)null);
-                try {
-                    if (UrlStatements.hasNext()) {
-                        Literal l = (Literal) UrlStatements.next().getObject();
-                        if (l != null) {
-							if( (l.getDatatype() != null) && XSDDatatype.XSDanyURI.equals(l.getDatatype()) ) {
-								try {
-	                                link.setUrl(URLDecoder.decode(l.getLexicalForm(),"UTF-8"));
-	                            } catch (UnsupportedEncodingException use) {}
-							} else {
-								link.setUrl(l.getLexicalForm());
-							}
-                            
-                        }
-                    }
-                } finally {
-                    UrlStatements.close();
-                }
-            } catch (ClassCastException e) {}
-        }
-        if (LINK_DISPLAYRANK != null) {
-            try {
-                ClosableIterator<Statement> rankStatements = getOntModel().listStatements(linkRes, LINK_DISPLAYRANK, (Literal)null);
-                try {
-                    if (rankStatements.hasNext()) {
-                        Literal l = (Literal) rankStatements.next().getObject();
-                        if (l != null) {
-                            if (l.getDatatype()==XSDDatatype.XSDinteger) {
-                                link.setDisplayRank(String.valueOf(l.getInt()));
-                            } else if (l.getDatatype()==XSDDatatype.XSDstring) {
-                                link.setDisplayRank(l.getString());
-                            } else {
-                                log.debug("unexpected literal datatype; saved as displayRank 10");
-                                link.setDisplayRank("10");
-                            }
-                        }
-                    }
-                } finally {
-                    rankStatements.close();
-                }
-            } catch (ClassCastException e) {}
-        }
-
-        ClosableIterator<Statement> stmtIt = getOntModel().listStatements(null, (com.hp.hpl.jena.rdf.model.Property)whichLinkProp, linkRes); // jena Property, not vitro Property
-        try {
-            if (stmtIt.hasNext()) {
-                Statement stmt = stmtIt.next();
-                Resource indRes = stmt.getSubject();
-                link.setEntityURI(indRes.getURI());
-                ObjectPropertyStatement op = new ObjectPropertyStatementImpl();
-                op.setPropertyURI(whichLinkProp.getURI()); // "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#additionalLink");
-                op.setSubjectURI(indRes.getURI());
-                op.setObjectURI(linkRes.getURI());
-                link.setObjectPropertyStatement(op);
-            }
-        } finally {
-            stmtIt.close();
-        }
-        return link;
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/LinktypeDaoJena.java

@@ -1,53 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.dao.jena;
-
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.shared.Lock;
-import com.hp.hpl.jena.util.iterator.ClosableIterator;
-
-import edu.cornell.mannlib.vitro.webapp.beans.Linktype;
-import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
-import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
-
-public class LinktypeDaoJena extends JenaBaseDao implements LinktypeDao {
-
-    public LinktypeDaoJena(WebappDaoFactoryJena wadf) {
-        super(wadf);
-    }
-
-    @Override
-    protected OntModel getOntModel() {
-    	return getOntModelSelector().getABoxModel();
-    }
-    
-    public List<Linktype> getAllLinktypes() {
-        List<Linktype> linkTypes = new LinkedList<Linktype>();
-        getOntModel().enterCriticalSection(Lock.READ);
-        try {
-           OntClass linkClass = getOntModel().getOntClass(LINK.getURI());
-           ClosableIterator cIt = linkClass.listSubClasses();
-           try {
-               while (cIt.hasNext()) {
-                   OntClass lCls = (OntClass) cIt.next();
-                   Linktype lt = new Linktype();
-                   lt.setURI(lCls.getURI());
-                   lt.setType(getLabelOrId(lCls));
-                   linkTypes.add(lt);
-               }
-           } finally {
-               cIt.close();
-           }
-        } finally {
-            getOntModel().leaveCriticalSection();
-        }
-        return linkTypes;
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/PropertyInstanceDaoJena.java

@@ -48,7 +48,7 @@ public class PropertyInstanceDaoJena extends JenaBaseDao implements
     }
 
     public void deleteObjectPropertyStatement(String subjectURI, String propertyURI, String objectURI) {
-    	deleteObjectPropertyStatement(subjectURI, propertyURI, objectURI, getOntModelSelector().getFullModel());
+    	deleteObjectPropertyStatement(subjectURI, propertyURI, objectURI, getOntModelSelector().getABoxModel());
     }
 
     public void deleteObjectPropertyStatement(String subjectURI, String propertyURI, String objectURI, OntModel ontModel) {

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/WebappDaoFactoryJena.java

@@ -42,8 +42,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao;
 import edu.cornell.mannlib.vitro.webapp.dao.FlagDao;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
 import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.MenuDao;
@@ -61,14 +59,11 @@ import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.pellet.PelletListener;
 import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
-import edu.cornell.mannlib.vitro.webapp.dao.jena.PropertyGroupDaoJena;
 
 public class WebappDaoFactoryJena implements WebappDaoFactory {
 
     protected IndividualDao entityWebappDao;
     protected FlagDao flagDao;
-    protected KeywordIndividualRelationDao keys2EntsDao;
-    protected KeywordDao keywordDao;
     protected LinksDao linksDao;
     protected LinktypeDao linktypeDao;
     protected ApplicationDaoJena applicationDao;
@@ -444,34 +439,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
             return entityWebappDao = new IndividualDaoJena(this);
     }
     
-    public KeywordIndividualRelationDao getKeys2EntsDao() {
-        if (keys2EntsDao != null)
-            return keys2EntsDao;
-        else
-            return keys2EntsDao = new KeywordIndividualRelationDaoJena(this);
-    }
-
-    public KeywordDao getKeywordDao() {
-        if (keywordDao != null)
-            return keywordDao;
-        else
-            return keywordDao = new KeywordDaoJena(this);
-    }
-
-    public LinksDao getLinksDao() {
-        if (linksDao != null)
-            return linksDao;
-        else
-            return linksDao = new LinksDaoJena(this);
-    }
-
-    public LinktypeDao getLinktypeDao() {
-        if (linktypeDao != null)
-            return linktypeDao;
-        else
-            return linktypeDao = new LinktypeDaoJena(this);
-    }
-    
     public ApplicationDao getApplicationDao() {
     	if (applicationDao != null) {
     		return applicationDao;
@@ -697,10 +664,6 @@ public class WebappDaoFactoryJena implements WebappDaoFactory {
     	//and tbox model
     	WebappDaoFactoryJena specialWadfj = new WebappDaoFactoryJena(specialSelector);
     	entityWebappDao = specialWadfj.getIndividualDao();
-    	keys2EntsDao = specialWadfj.getKeys2EntsDao();
-    	keywordDao = specialWadfj.getKeywordDao();
-    	linksDao = specialWadfj.getLinksDao();
-    	linktypeDao = specialWadfj.getLinktypeDao();
     	vClassGroupDao = specialWadfj.getVClassGroupDao();
     	//To allow for testing, add a property group, this will allow
     	//the unassigned group method section to be executed and main Image to be assigned to that group

webapp/src/edu/cornell/mannlib/vitro/webapp/dwr/EntityDWR.java

@@ -62,47 +62,6 @@ public class EntityDWR {
         return ind;
     }
 
-    /**
-       Gets entities that can be in a propertyId relation with classId but
-       excludes entity with id of ignoredEntId.  If classId < 0 then it the
-       query is not limited by vclass.
-       @param propertyId - which relation to get entities for column properties.id
-       @param ignoredEntId - the entity with this id is excluded from the
-       result collection.  Set to < 0 if you don't want to ignore any entities.
-       @param classId - if > 0 then only ents with this vClassId or which are subclasses
-       of this are included in results.
-       @param domainSide - if true, return RANGE entities of relation, if false return
-        DOMAIN entities of relation.
-       @return - Entities that can satisify the property.  Only the name and id of the
-        object will be filled out.
-    */
-    @Deprecated
-    public Collection getEntitiesByProperties(String propertyURI,
-                                              String ignoredEntURI,
-                                              String classURI,
-                                              boolean domainSide ){
-    	return new LinkedList();
-//        WebContext ctx = WebContextFactory.get();
-//        HttpServletRequest req = ctx.getHttpServletRequest();
-//        VitroRequest vreq = new VitroRequest(req);
-//        IndividualDao entityWADao = vreq.getWebappDaoFactory().getIndividualDao();
-//        
-//        return entityWADao.getIndividualsByProperty(
-//                propertyURI,ignoredEntURI,classURI,domainSide);
-    }
-
-    /**
-     *  Gets the monikers for a vclass.
-     */
-    public List monikers( String vClassURI ){
-        WebContext ctx = WebContextFactory.get();
-        HttpServletRequest req = ctx.getHttpServletRequest();
-        VitroRequest vreq = new VitroRequest(req);
-        IndividualDao entityWADao = vreq.getWebappDaoFactory().getIndividualDao();
-                
-        return entityWADao.monikers( vClassURI );
-    }
-
     /**
      * Gets all of the entities given the vclass.
      * This returns a collection of EntityWebapp objects.

webapp/src/edu/cornell/mannlib/vitro/webapp/dwr/PropertyDWR.java

@@ -82,31 +82,6 @@ public class PropertyDWR {
        return wdf.getPropertyInstanceDao().getProperty(subjectURI, predicateURI, objectURI);
     }
 
-    /**
-       The following fields are used by this method to write this property
-       to the object property statement table:
-
-         domainEntId
-         rangeEntId
-         PropertyId
-         sunrise - optional
-         sunset - optional
-         qualifier - optional
-
-       Initially this tries an insert, if that fails then an update is attempted.
-       @return -1 for error, 0 for no write due to duplicate, > 0 is auto-gen 
-       objectPropertyStatement.id
-    */
-    @Deprecated
-    public int writeProp(PropertyInstance prop ){
-//        WebContext ctx = WebContextFactory.get();
-//        HttpServletRequest req = ctx.getHttpServletRequest();
-//        VitroRequest vreq = new VitroRequest(req);
-//
-//        return getUnfilteredWebappDaoFactory(vreq).getPropertyInstanceDao().writeProp(prop);
-        return -1;
-    }
-
     public int insertProp( PropertyInstance prop) {
         WebContext ctx = WebContextFactory.get();
         HttpServletRequest req = ctx.getHttpServletRequest();

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/listener/impl/IndividualDataPropertyStatementProcessor.java

@@ -34,7 +34,7 @@ public class IndividualDataPropertyStatementProcessor implements ChangeListener
     }
 
     public void doDeleted(Object oldObj, EditProcessObject epo) {
-        // sunset all data property statements associated with entity
+        // do nothing
     }
 
     private void processDataprops (EditProcessObject epo) {

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/SelectListGenerator.java

@@ -304,14 +304,6 @@ public class SelectListGenerator {
                         if (individuals.size()==0){ 
                             log.error("No individuals of type "+vclass.getName()+" to add to pick list in SelectListGenerator.getOptions(); check portal visibility");
                             optionsMap.put("", "No " + vclass.getName() + " found");
-                        }else{                
-                            for( Individual ind : individuals ) {
-                                // note that don't want the individual URI -- the option should hold 2 copies of the moniker //
-                                if (ind.getMoniker()!=null && ind.getMoniker().trim().length()>0) {
-                                    optionsMap.put(ind.getMoniker(),ind.getMoniker().trim());                        
-                                    ++optionsCount;
-                                }
-                            }
                         }
                     }
                 }

webapp/src/edu/cornell/mannlib/vitro/webapp/edit/validator/impl/KeywordStemmerAndValidator.java

@@ -1,69 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package edu.cornell.mannlib.vitro.webapp.edit.validator.impl;
-
-import java.util.Iterator;
-import java.util.List;
-
-import edu.cornell.mannlib.vedit.beans.EditProcessObject;
-import edu.cornell.mannlib.vedit.validator.ValidationObject;
-import edu.cornell.mannlib.vedit.validator.Validator;
-import edu.cornell.mannlib.vitro.webapp.beans.Keyword;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.edit.listener.impl.KeywordPreProcessor;
-import edu.cornell.mannlib.vitro.webapp.utils.Stemmer;
-
-public class KeywordStemmerAndValidator implements Validator {
-
-    private int MAX_LENGTH = 32;
-
-    private EditProcessObject epo = null;
-    private KeywordDao kDao = null;
-
-    public KeywordStemmerAndValidator(EditProcessObject in, KeywordDao keywordDao) {
-        this.epo = in;
-        this.kDao = keywordDao;
-    }
-
-    public ValidationObject validate (Object obj) throws IllegalArgumentException {
-
-        ValidationObject vo = new ValidationObject();
-
-        if (obj==null || (obj instanceof String && ((String)obj).length()>0)) {
-            String keywordString = (String) obj;
-            String stemmedString = Stemmer.StemString(keywordString, MAX_LENGTH);
-            epo.getPreProcessorList().add(new KeywordPreProcessor(stemmedString));
-            List<Keyword> matches = kDao.getKeywordsByStem(stemmedString);
-            if (matches.size() > 0) {
-                vo.setValid(false);
-                String suggestionsStr = new String();
-                Iterator<Keyword> matchesIt = matches.iterator();
-                boolean first = true;
-                while (matchesIt.hasNext()) {
-                    Keyword k = matchesIt.next();
-                    if (!matchesIt.hasNext() && !first) {
-                        suggestionsStr += "or ";
-                    }
-                    suggestionsStr += "'"+k.getTerm();
-                    if (matchesIt.hasNext()) {
-                        suggestionsStr += ",' ";
-                    } else {
-                        suggestionsStr += "'";
-                    }
-                    first = false;
-                }
-                vo.setMessage("Keyword identified as redundant.  Please modify term or consider canceling and instead linking individual to existing keyword "+suggestionsStr);
-            } else {
-                vo.setValid(true);
-            }
-        } else {
-            vo.setValid(false);
-            vo.setMessage("Please enter a keyword.");
-        }
-        vo.setValidatedObject(obj);
-
-        return vo;
-
-    }
-
-}

webapp/src/edu/cornell/mannlib/vitro/webapp/search/VitroSearchTermNames.java

@@ -18,21 +18,11 @@ public class VitroSearchTermNames {
 
     /** time of index in msec since epoc */
     public static String INDEXEDTIME= "indexedTime";
-    /** timekey of entity in yyyymmddhhmm  */
-    public static String TIMEKEY="TIMEKEY";
-    /** time of sunset/end of entity in yyyymmddhhmm  */
-    public static String SUNSET="SUNSET";
-    /** time of sunrise/start of entity in yyyymmddhhmm  */
-    public static String SUNRISE="SUNRISE";
-    /** entity's moniker */
-    public static String MONIKER="moniker";
     /** text for 'full text' search, this is stemmed */
     public static String ALLTEXT    = "ALLTEXT";
     /** text for 'full text' search, this is unstemmed for
      * use with wildcards and prefix queries */
     public static String ALLTEXTUNSTEMMED = "ALLTEXTUNSTEMMED";
-    /** keywords */
-    public static final String KEYWORDS = "KEYWORDS";
     /** Does the individual have a thumbnail image? 1=yes 0=no */
     public static final String THUMBNAIL = "THUMBNAIL";        
     /** Should individual be included in full text search results? 1=yes 0=no */

webapp/src/edu/cornell/mannlib/vitro/webapp/search/beans/VitroHighlighter.java

@@ -51,10 +51,7 @@ public abstract class VitroHighlighter extends UnaryFunctor<String,String> {
         if( ent == null)
             return;
 
-        ent.setBlurb( this.highlight(ent.getBlurb()));
         ent.setName( this.highlight(ent.getName()));
-        ent.setMoniker( this.highlight(ent.getMoniker()));
-        ent.setDescription( this.highlight(ent.getDescription()));
         Iterator edIt = ent.getDataPropertyStatements().iterator();
         while (edIt.hasNext()) {
             DataPropertyStatement dataPropertyStmt = (DataPropertyStatement)edIt.next();
@@ -68,7 +65,6 @@ public abstract class VitroHighlighter extends UnaryFunctor<String,String> {
             object.setName(this.highlight(object.getName()));
         }
         */
-        highlightKeywords(ent);
     }
 
     /**
@@ -83,21 +79,9 @@ public abstract class VitroHighlighter extends UnaryFunctor<String,String> {
         //highlight the name, anchor and moniker and place back in entity object
         if( ent.getName() != null )
             ent.setName(  highlight( stripHtml(ent.getName() )));
-        if( ent.getAnchor() != null )
-            ent.setAnchor(  highlight( stripHtml(ent.getAnchor() )));
-        if( ent.getMoniker() != null )
-            ent.setMoniker( highlight( stripHtml(ent.getMoniker() )));
 
         //make a buffer of text to use the fragmenting hightlighter on
         StringBuffer sb = new StringBuffer("");
-        if(ent.getBlurb() != null){
-            sb.append(ent.getBlurb());
-            sb.append(' ');
-        }
-        if(ent.getDescription() != null ){
-            sb.append(ent.getDescription());
-            sb.append(' ');
-        }
         if(ent.getDataPropertyStatements() != null) {
             Iterator edIt = ent.getDataPropertyStatements().iterator();
             while (edIt.hasNext()) {
@@ -120,22 +104,6 @@ public abstract class VitroHighlighter extends UnaryFunctor<String,String> {
             	}
             }
         }
-        String keywords = ent.getKeywordString();
-        if( keywords != null )
-            sb.append(keywords);
-
-        ent.setDescription(getHighlightFragments(  stripHtml( sb.toString() )));
-    }
-
-    private void highlightKeywords(Individual ent){
-        List<String> terms = ent.getKeywords();
-        if( terms == null || terms.size() == 0) return;
-
-        List<String> replacement = new ArrayList<String>(terms.size());
-        for(String term : ent.getKeywords()){
-            replacement.add( highlight(term ) );
-        }
-        ent.setKeywords(replacement);
     }
 
     private final String stripHtml(String in){

webapp/src/edu/cornell/mannlib/vitro/webapp/search/controller/PagedSearchController.java

@@ -685,7 +685,6 @@ public class PagedSearchController extends FreemarkerHttpServlet implements Sear
     	        VitroLuceneTermNames.NAME_STEMMED,
     	        VitroLuceneTermNames.NAME_UNSTEMMED,
     	        VitroLuceneTermNames.RDFTYPE,
-    	        VitroLuceneTermNames.MONIKER,
     	        VitroLuceneTermNames.ALLTEXT,
     	        VitroLuceneTermNames.ALLTEXTUNSTEMMED,
     	        VitroLuceneTermNames.NAME_LOWERCASE,

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/Entity2LuceneDoc.java

@@ -52,14 +52,6 @@ public class Entity2LuceneDoc  implements Obj2DocIface{
 
         /** time of index in msec since epoc */
         public static String INDEXEDTIME= "indexedTime";
-        /** timekey of entity in yyyymmddhhmm  */
-        public static String TIMEKEY="TIMEKEY";
-        /** time of sunset/end of entity in yyyymmddhhmm  */
-        public static String SUNSET="SUNSET";
-        /** time of sunrise/start of entity in yyyymmddhhmm  */
-        public static String SUNRISE="SUNRISE";
-        /** entity's moniker */
-        public static String MONIKER="moniker";
         /** text for 'full text' search, this is stemmed */
         public static String ALLTEXT    = "ALLTEXT";
         /** text for 'full text' search, this is unstemmed for
@@ -67,8 +59,6 @@ public class Entity2LuceneDoc  implements Obj2DocIface{
         public static String ALLTEXTUNSTEMMED = "ALLTEXTUNSTEMMED";
         /** class name for storing context nodes **/
         public static final String CONTEXTNODE = "contextNode";
-        /** keywords */
-        public static final String KEYWORDS = "KEYWORDS";
         /** Does the individual have a thumbnail image? 1=yes 0=no */
         public static final String THUMBNAIL = "THUMBNAIL";        
         /** Should individual be included in full text search results? 1=yes 0=no */
@@ -255,13 +245,6 @@ public class Entity2LuceneDoc  implements Obj2DocIface{
        /* Field contextNodeInformation = new Field(term.CONTEXTNODE, contextNodePropertyValues, Field.Store.YES, Field.Index.ANALYZED );
         doc.add(contextNodeInformation);*/
         
-        //Moniker
-        
-        if(ent.getMoniker() != null){
-        	Field moniker = new Field(term.MONIKER, ent.getMoniker(), Field.Store.YES, Field.Index.NOT_ANALYZED_NO_NORMS);
-        	doc.add(moniker);
-        }
-        
         //boost for entity
         if( ent.getSearchBoost() != null && ent.getSearchBoost() != 0 )
             doc.setBoost(ent.getSearchBoost());
@@ -275,17 +258,6 @@ public class Entity2LuceneDoc  implements Obj2DocIface{
 //        }
 //        doc.add(  new Field(term.MODTIME, value , Field.Store.YES, Field.Index.NOT_ANALYZED_NO_NORMS));      
         
-        /* timekey */
-//        try{
-//            value = null;
-//            if( ent.getTimekey() != null ){
-//                value = (new DateTime(ent.getTimekey().getTime())).toString(LuceneIndexer.DATE_FORMAT);
-//                doc.add(new Field(term.TIMEKEY, value, Field.Store.YES, Field.Index.NOT_ANALYZED_NO_NORMS));
-//            }
-//        }catch(Exception ex){            
-//            log.error("could not save timekey " + ex);            
-//        }        
-        
         /* thumbnail */
         try{
             value = null;
@@ -309,10 +281,6 @@ public class Entity2LuceneDoc  implements Obj2DocIface{
             String t=null;
             value =""; 
             value+= " "+( ((t=ent.getName()) == null)?"":t );  
-            value+= " "+( ((t=ent.getAnchor()) == null)?"":t); 
-            value+= " "+ ( ((t=ent.getMoniker()) == null)?"":t ); 
-            value+= " "+ ( ((t=ent.getDescription()) == null)?"":t ); 
-            value+= " "+ ( ((t=ent.getBlurb()) == null)?"":t ); 
             value+= " "+ getKeyterms(ent); 
     
             value+= " " + classPublicNames; 

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSearcher.java

@@ -254,53 +254,6 @@ public class LuceneSearcher implements Searcher {
         close();
     }
 
-    //bdc34 as of 2009-01-30, getting rid of time windows
-//    public synchronized Filter getTimeWindowCachingFilter(){
-//        if( timeWindowCachingFilter == null || timeWinCacheStale() ){
-//            Filter defaultFilter = new QueryFilter( makeDefaultTimeWindowQuery() );
-//            timeWindowCachingFilter = new CachingWrapperFilter( defaultFilter );
-//            timeWinFilterBorn = System.currentTimeMillis();
-//            log.debug("getTimeWindowCachingFilter() made new cache " + timeWinFilterBorn);
-//        }
-//        return timeWindowCachingFilter;
-//    }
-
-    //bdc34 as of 2009-01-30, getting rid of time windows
-//    private final long timeWinCacheShelfLife = ( 60 * 1000 ) * 1; //in msec
-//    private boolean  timeWinCacheStale(){
-//        long dt = (System.currentTimeMillis() - timeWinFilterBorn);
-//        return dt > timeWinCacheShelfLife;
-//    }
-
-
-    //bdc34 as of 2009-01-30, getting rid of time windows
-    /**
-     * Adds a Query that will get doc where the
-     * SUNSET is > NOW  and SUNRISE <= NOW. We'll do
-     * this by creating two RangeQueries, one to
-     * check that SUNRISE is between [BEGINNING_OF_TIME, NOW]
-     * and that SUNSET is between [NOW, END_OF_TIME]
-     * There don't seem to be any GraterThanQuery
-     * or LessThanQuery classes in lucene.
-     */
-//    private BooleanQuery makeDefaultTimeWindowQuery(){
-//        String nowStr = new DateTime().toString(LuceneIndexer.DATE_FORMAT);
-//
-//        Term BEGINNING_OF_TIME = null;
-//        Term now = new Term(Entity2LuceneDoc.term.SUNRISE,nowStr );
-//        RangeQuery sunriseBeforeNow = new RangeQuery(BEGINNING_OF_TIME,now, true);
-//
-//        Term END_OF_TIME = null;
-//        now = new Term(Entity2LuceneDoc.term.SUNSET,nowStr);
-//        RangeQuery sunsetAfterNow = new RangeQuery(now,END_OF_TIME, false);
-//
-//        BooleanQuery qRv = new BooleanQuery();
-//        qRv.add( sunriseBeforeNow, BooleanClause.Occur.MUST);
-//        qRv.add( sunsetAfterNow, BooleanClause.Occur.MUST);
-//
-//        return qRv;
-//    }
-
     /**
      * We need access to the index to make a highligher because
      * we need to 'rewrite' the query.  That takes any wild cards

webapp/src/edu/cornell/mannlib/vitro/webapp/search/lucene/LuceneSetup.java

@@ -7,7 +7,6 @@ import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.Vi
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.CLASSLOCALNAME;
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.CLASSLOCALNAMELOWERCASE;
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.CONTEXTNODE;
-import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.MONIKER;
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.NAME_STEMMED;
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.NAME_UNSTEMMED;
 import static edu.cornell.mannlib.vitro.webapp.search.lucene.Entity2LuceneDoc.VitroLuceneTermNames.RDFTYPE;
@@ -255,7 +254,6 @@ public class LuceneSetup implements javax.servlet.ServletContextListener {
         analyzer.addAnalyzer(ALLTEXTUNSTEMMED, new HtmlLowerStopAnalyzer());
         analyzer.addAnalyzer(NAME_UNSTEMMED, new HtmlLowerStopAnalyzer());      
         analyzer.addAnalyzer(NAME_STEMMED, new HtmlLowerStopStemAnalyzer());
-        analyzer.addAnalyzer(MONIKER, new StandardAnalyzer(Version.LUCENE_29));
         analyzer.addAnalyzer(RDFTYPE, new StandardAnalyzer(Version.LUCENE_29));
         analyzer.addAnalyzer(CONTEXTNODE, new StandardAnalyzer(Version.LUCENE_29));
         analyzer.addAnalyzer(CLASSLOCALNAME, new HtmlLowerStopAnalyzer());

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/IndividualToSolrDocument.java

@@ -153,8 +153,6 @@ public class IndividualToSolrDocument {
         allTextValue.append(" ");
         allTextValue.append(((t=ind.getName()) == null)?"":t);   
         allTextValue.append(" ");     
-        allTextValue.append(((t=ind.getAnchor()) == null)?"":t); 
-        allTextValue.append(" ");     
         allTextValue.append(classPublicNames);
 
         //collecting data property statements

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/SolrSetup.java

@@ -17,6 +17,7 @@ import org.apache.solr.client.solrj.impl.XMLResponseParser;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.DatasetFactory;
 
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
@@ -73,7 +74,7 @@ public class SolrSetup implements javax.servlet.ServletContextListener{
             
             OntModel abox = ModelContext.getBaseOntModelSelector(context).getABoxModel();            
             OntModel inferences = (OntModel)context.getAttribute( JenaBaseDao.INFERENCE_ONT_MODEL_ATTRIBUTE_NAME);
-            Dataset dataset = WebappDaoFactoryJena.makeInMemoryDataset(abox, inferences);
+            Dataset dataset = DatasetFactory.create(ModelContext.getJenaOntModel(context));
 
             OntModel jenaOntModel = ModelContext.getJenaOntModel(context);
             

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/ListedIndividualTemplateModel.java

@@ -65,20 +65,24 @@ public class ListedIndividualTemplateModel extends BaseTemplateModel {
         return thumbUrl == null ? null : getUrl(thumbUrl);
     } 
     
+    @Deprecated
     public Link getPrimaryLink() {
-        Link primaryLink = null;
+//        Link primaryLink = null;
-        String anchor = individual.getAnchor();
+//        String anchor = individual.getAnchor();
-        String url = individual.getUrl();
+//        String url = individual.getUrl();
-        if ( !(StringUtils.isEmpty(anchor)) && !(StringUtils.isEmpty(url)) ) {
+//        if ( !(StringUtils.isEmpty(anchor)) && !(StringUtils.isEmpty(url)) ) {
-            primaryLink = new Link();
+//            primaryLink = new Link();
-            primaryLink.setAnchor(anchor);
+//            primaryLink.setAnchor(anchor);
-            primaryLink.setUrl(url);           
+//            primaryLink.setUrl(url);           
-        } 
+//        } 
-        return primaryLink;
+//        return primaryLink;
+    	return null;
     }
   
+    @Deprecated
     public List<Link> getAdditionalLinks() {
-        return individual.getLinksList(); // returns an empty list, but not null
+//        return individual.getLinksList(); // returns an empty list, but not null
+    	return new ArrayList<Link>();
     }
     
     public List<Link> getLinks() {
@@ -101,8 +105,10 @@ public class ListedIndividualTemplateModel extends BaseTemplateModel {
         return individual.getName();
     }
 
+    @Deprecated
     public String getMoniker() {
-        return individual.getMoniker();
+    	return "";
+//        return individual.getMoniker();
     }
 
     public String getUri() {

webapp/test/edu/cornell/mannlib/vitro/webapp/auth/policy/bean/PropertyRestrictionPolicyHelperTest.java

@@ -47,7 +47,7 @@ public class PropertyRestrictionPolicyHelperTest extends AbstractTestClass {
 			VitroVocabulary.vitroURI, "" };
 
 	private static final String[] PERMITTED_EXCEPTIONS = new String[] {
-			VitroVocabulary.MONIKER, VitroVocabulary.BLURB };
+			VitroVocabulary.MONIKER };
 
 	private OntModel ontModel;
 	private ModelWrapper wrapper;

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/filtering/filters/HiddenFromDisplayBelowRoleLevelFilterTest.java

@@ -170,7 +170,6 @@ public class HiddenFromDisplayBelowRoleLevelFilterTest extends
 	private static Individual individual(String moniker,
 			RoleLevel displayThreshhold) {
 		Individual i = new IndividualImpl();
-		i.setMoniker(moniker);
 		i.setURI("uri:" + moniker);
 		i.setHiddenFromDisplayBelowRoleLevel(displayThreshhold);
 		return i;
@@ -575,7 +574,7 @@ public class HiddenFromDisplayBelowRoleLevelFilterTest extends
 			if (individual == null) {
 				message += ", individual=null";
 			} else {
-				message += ", individual=" + individual.getMoniker();
+				message += ", individual=" + individual.getLocalName();
 			}
 			return message;
 		}
@@ -703,7 +702,7 @@ public class HiddenFromDisplayBelowRoleLevelFilterTest extends
 			if (subject == null) {
 				message += ", subject=null";
 			} else {
-				message += ", subject=" + subject.getMoniker();
+				message += ", subject=" + subject.getLocalName();
 			}
 
 			if (predicate == null) {
@@ -760,7 +759,7 @@ public class HiddenFromDisplayBelowRoleLevelFilterTest extends
 			if (subject == null) {
 				message += ", subject=null";
 			} else {
-				message += ", subject=" + subject.getMoniker();
+				message += ", subject=" + subject.getLocalName();
 			}
 
 			if (predicate == null) {
@@ -772,7 +771,7 @@ public class HiddenFromDisplayBelowRoleLevelFilterTest extends
 			if (object == null) {
 				message += ", object=null";
 			} else {
-				message += ", object=" + object.getMoniker();
+				message += ", object=" + object.getLocalName();
 			}
 
 			return message;

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/IndividualDaoStub.java

@@ -169,63 +169,12 @@ public class IndividualDaoStub implements IndividualDao {
 				"IndividualDaoStub.fillVClassForIndividual() not implemented.");
 	}
 
-	@Override
-	public List<String> monikers(String vclassURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.monikers() not implemented.");
-	}
-
-	@Override
-	public List<String> getKeywordsForIndividual(String individualURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getKeywordsForIndividual() not implemented.");
-	}
-
-	@Override
-	public List<String> getKeywordsForIndividualByMode(String individualURI,
-			String modeStr) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getKeywordsForIndividualByMode() not implemented.");
-	}
-
-	@Override
-	public List<Keyword> getKeywordObjectsForIndividual(String individualURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getKeywordObjectsForIndividual() not implemented.");
-	}
-
-	@Override
-	public String getNetId(String entityURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getNetId() not implemented.");
-	}
-
-	@Override
-	public String getStatus(String entityURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getStatus() not implemented.");
-	}
-
 	@Override
 	public String getUnusedURI(Individual individual) throws InsertException {
 		throw new RuntimeException(
 				"IndividualDaoStub.getUnusedURI() not implemented.");
 	}
 
-	@Override
-	public Individual getIndividualByExternalId(int externalIdType,
-			String externalIdValue) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getIndividualByExternalId() not implemented.");
-	}
-
-	@Override
-	public Individual getIndividualByExternalId(int externalIdType,
-			String externalIdValue, String vClassURI) {
-		throw new RuntimeException(
-				"IndividualDaoStub.getIndividualByExternalId() not implemented.");
-	}
-
     @Override
     public EditLiteral getLabelEditLiteral(String individualUri) {
         throw new RuntimeException(

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/dao/WebappDaoFactoryStub.java

@@ -13,10 +13,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.DataPropertyStatementDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DatatypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.DisplayModelDao;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordDao;
-import edu.cornell.mannlib.vitro.webapp.dao.KeywordIndividualRelationDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinksDao;
-import edu.cornell.mannlib.vitro.webapp.dao.LinktypeDao;
 import edu.cornell.mannlib.vitro.webapp.dao.MenuDao;
 import edu.cornell.mannlib.vitro.webapp.dao.NamespaceDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
@@ -198,30 +194,6 @@ public class WebappDaoFactoryStub implements WebappDaoFactory {
 				"WebappDaoFactory.getApplicationDao() not implemented.");
 	}
 
-	@Override
-	public KeywordIndividualRelationDao getKeys2EntsDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getKeys2EntsDao() not implemented.");
-	}
-
-	@Override
-	public KeywordDao getKeywordDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getKeywordDao() not implemented.");
-	}
-
-	@Override
-	public LinksDao getLinksDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getLinksDao() not implemented.");
-	}
-
-	@Override
-	public LinktypeDao getLinktypeDao() {
-		throw new RuntimeException(
-				"WebappDaoFactory.getLinktypeDao() not implemented.");
-	}
-
 	@Override
 	public VClassGroupDao getVClassGroupDao() {
 		throw new RuntimeException(

webapp/web/js/ents_edit.js

@@ -332,8 +332,6 @@ function fillForm(aprop)  {
   var vclass = gProperty.domainClass;
   
   DWRUtil.setValues(gProperty);
-  setDateValue("sunset", gProperty.sunset );
-  setDateValue("sunrise", gProperty.sunrise );
 
   toggleDisabled("newPropButton");
   
@@ -612,23 +610,7 @@ Check to see if property edit form is valid
 *****************************************************************/
 function validateForm(){
   var dateEx = "\nDates should be in the format YYYY-MM-DD";
-  var value = DWRUtil.getValue("sunrise");
+  /* used to check dates here */ 
-  try{   
-    var date = parseDateString(value);
-  }catch(e){ date = null; }  
-  if( value && value.length > 0 && ! isDate(date)) {
-    alert( "Surise date " + value + " is invalid: \n" + date + dateEx);
-    return false;
-  }
-  
-  value = DWRUtil.getValue("sunset");
-  try{  
-    date = parseDateString(value);
-  }catch(e){ date = null; }
-  if( value && value.length > 0 && ! isDate(date)) {
-    alert( "Sunset date " + value + " is invalid: \n" + date + dateEx);
-    return false;
-  }
   return true;
 }
 
@@ -650,15 +632,6 @@ function writeProp()  {
   newP.subjectEntURI= gEntity.URI;
   newP.objectEntURI = selected ;
   
-  try{
-    var date = parseDateString( DWRUtil.getValue("sunrise") );
-    newP.sunrise = ( isDate( date ) ? date : null );
-  }catch(e){ newP.sunrise = null; }    
-  try{
-    var date = parseDateString( DWRUtil.getValue("sunset") );
-    newP.sunset = ( isDate( date ) ? date : null );
-  }catch(e){ newP.sunset = null; }
-
   var callback = function(result){
     editingNewProp = false;
     justwritenProp = newP;

webapp/web/templates/edit/specific/entity_retry.jsp

@@ -5,34 +5,11 @@
     <tr class="editformcell" id="entityNameTr">
         <td valign="bottom" id="entityNameTd" colspan="2">
 			<b>Individual Name</b><br/>
-            <input style="width:80%;" type="text" name="Name" value="<form:value name="Name"/>" maxlength="255" />
+            <input style="width:80%;" type="text" name="Name" value="<form:value name="Name"/>" />
             <p class="error"><form:error name="Name"/></p>
         </td>
     </tr>
 
-    <tr class='editformcell' id='GenericTypeTr'>
-        <td valign="top" id="genericTypeTd" colspan="2">
-			<b>Generic Type<br/>
-			<select disabled="disabled" id="VClassURI" name="VClassURI" onChange="update();">
-					<form:option name="VClassURI"/>
-			</select>
-			<p class="error"><form:error name="VClassURI"/></p>
-        </td>
-    </tr>
-
-    <tr class="editformcell" id='urlTr'>
-        <td id="urlTd" valign="bottom" colspan="1">
-			<b>URL</b><br />
-				<input style="width:80%;" type="text" name="Url" value="<form:value name="Url"/>" maxlength="255" />
-                <p><form:error name="Url"/></p>
-        </td>
-        <td id="urlAnchorTd" valign="bottom" colspan="1">
-			<b>Anchor Text for URL</b> <em> Required if URL is to be visible</em><br />
-				<input style="width:65%;" type="text" name="Anchor" value="<form:value name="Anchor"/>" maxlength="255" />
-                <p class="error"><form:error name="Anchor"/></p>
-        </td>
-    </tr>
-
     <!-- begin datatype properties section -->
     
     <tr class="editformcell" style="border-collapse:collapse;">
@@ -46,20 +23,4 @@
     <!-- end datatype properties section -->    
 
 
-    <tr class="editformcell" id='blurbTr'>
-        <td id="blurbTd" valign="bottom" colspan="2">
-	        <b>Blurb</b> <em>Usually optional; shows up when this entity is included underneath a tab;</em> <b> max 255 chars</b><br />
-                <input style="width:80%;" type="text" name="Blurb" value="<form:value name="Blurb"/>" maxlength="255" />
-                <p class="error"><form:error name="Blurb"/></p>
-        </td>
-    </tr>
-    <tr class="editformcell" id='descriptionTr'>
-        <td id="descriptionTd" valign="bottom" colspan="2">
-        	<b>Description</b> <em>Optional.  Consider using more specific datatype properties where possible.</em><br/>
-                <textarea id="Description" name="Description" ROWS="15" COLS="115" wrap="physical"><form:value name="Description"/></textarea>
-                <p class="error"><form:error name="Description"/></p>
-        </td>
-    </tr>
-
-
 

webapp/web/templates/edit/specific/entity_retry_init.jsp

@@ -26,44 +26,5 @@
 			<br><font size="2" color="red"><form:error name="VClassId"/></font>
         </td>
     </tr>
-    <tr class='editformcell' id='specificTypeTr'>
-        <td valign="top" id="specificTypeTd" colspan="1">
-	        <b>Specific Type</b><br/>
-				<select name="Moniker" id="Moniker">
-					<form:option name="Moniker"/>
-				</select>
-				<br><font size="2" color="red"><form:error name="Moniker"/></font>
-		</td>
-		<td id="newMonikerTd" valign="top">If [new moniker] is selected, enter here:<br/>
-                <input name="Moniker" value="<form:value name="Moniker"/>"/>
-                <i>otherwise leave this field blank</i>
-        </td>
-    </tr>
-    <tr class="editformcell" id='urlTr'>
-        <td id="urlTd" valign="bottom" colspan="1">
-			<b>URL</b><br />
-				<input type="text" name="Url" value="<form:value name="Url"/>" size="80" maxlength="255" />
-                <font size="2" color="red"><form:error name="Url"/></font>
-        </td>
-        <td id="urlAnchorTd" valign="bottom" colspan="1">
-			<b>Anchor Text for URL</b> <em> Required if URL is to be visible</em><br />
-				<input type="text" name="Anchor" value="<form:value name="Anchor"/>" size="30" maxlength="255" />
-                <font size="2" color="red"><form:error name="Anchor"/></font>
-        </td>
-    </tr>
-    <tr class="editformcell" id='blurbTr'>
-        <td id="blurbTd" valign="bottom" colspan="2">
-	        <b>Blurb</b> <em>Usually optional; shows up when this entity is included underneath a tab;</em> <b> max 255 chars</b><br />
-                <input type="text" name="Blurb" value="<form:value name="Blurb"/>" size="153" maxlength="255" />
-                <font size="2" color="red"><form:error name="Blurb"/></font>
-        </td>
-    </tr>
-    <tr class="editformcell" id='descriptionTr'>
-        <td id="descriptionTd" valign="bottom" colspan="2">
-        	<b>Description</b> <em>Optional; may include valid HTML</em><br/>
-                <textarea name="Description" ROWS="5" COLS="115" wrap="physical"><form:value name="Description"/></textarea>
-                <font size="2" color="red"><form:error name="Description"/></font>
-        </td>
-    </tr>
     
 

webapp/web/templates/edit/specific/ents2ents_retry_rangeSide.jsp

@@ -20,19 +20,3 @@
 			</select>            <span class="warning"><form:error name="DomainId"/></span>
         </td>
     </tr>
-    <tr class="editformcell">
-        <td valign="top" colspan="2">
-            <b>Sunrise</b><br/>
-			<input name="Sunrise" value="<form:value name="Sunrise"/>" />
-        </td>
-        <td valign="top" colspan="1">
-            <b>Sunset</b><br/>
-			<input name="Sunset" value="<form:value name="Sunset"/>"/>
-        </td>
-    </tr>
-    <tr class="editformcell">
-        <td valign="top">
-            <b>Qualifier</b><br/>
-			<input name="Qualifier" value="<form:value name="Qualifier"/>"/>
-        </td>
-    </tr>    

webapp/web/templates/edit/specific/ents_edit.jsp

@@ -70,20 +70,9 @@
         	<form action="editForm" method="get">
             	<input name="uri" type = "hidden" value="${individual.URI}" />
             	<input name="controller" type = "hidden" value="Entity" />
-            	<input type="submit" class="form-button" value="Edit This Individual"/>
+            	<input type="submit" class="form-button" value="Edit This Individual's Datatype Properties"/>
         	</form><br/>
 	
-
-        	<c:if test="${!empty individual.linksList}"> 
-            	<form action="editForm" method="get">
-					<select name="uri" class="form-item">
-						<form:option name="ExtraURL"/>
-					</select><br />
-	                <input type="submit" class="form-button" value="Edit Extra URLs"/>
-        	        <input type="hidden" name="controller" value="Link"/>
-            	</form>
-			</c:if>
-	
         	<c:if test="${!empty individual.externalIds}"> 
 	        	<form action="editForm" method="get">
 	            	<select name="multiplexedParam" class="form-item">
@@ -104,11 +93,6 @@
             	<input type="hidden" name="controller" value="Entity"/>
         	</form>
         	<form action="editForm" method="get">
-            	<input type="submit" class="form-button" value="Add Another URL"/>
-            	<input type="hidden" name="entityUri" value="${individual.URI}"/>
-            	<input type="hidden" name="controller" value="Link"/>
-        	</form>
-        	<form action="editForm" method="get">
             	<input type="submit" class="form-button" value="Add an External Identifier"/>
             	<input type="hidden" name="IndividualURI" value="${individual.URI}"/>
             	<input type="hidden" name="controller" value="ExternalId"/>
@@ -119,10 +103,6 @@
             	<input type="hidden" name="mode" value="renameResource"/>
             	<input type="hidden" name="controller" value="Refactor"/>
         	</form>
-        	<form action="uploadImages" method="get">
-            	<input type="submit" class="form-button" value="Upload Image"/>
-            	<input type="hidden" name="entityUri" value="${individual.URI}"/>
-        	</form>
     	</td>
     </tr>
     <tr><td colspan="3"><hr/></td></tr>
@@ -216,11 +196,6 @@
                     	<td colspan="9"><select id="entitiesList" class="form-item"><option>select individual</option></select></td>
                 	</tr>
                 	
-                	<!-- no longer available in v.0.7 : something to reimplement in 0.8 or 0.9 -->
-                	<tr style="display:none;">
-                    	<td>Sunrise:</td><td><input id="sunrise" class="form-item" type="text"/></td>
-                    	<td>Sunset:</td><td><input id="sunset" class="form-item" type="text"/></td>
-                	</tr>
                 	
                 	<tr>
                     	<td><input type="button" id="saveButt" class="form-button"
@@ -236,51 +211,6 @@
 
 	</c:if> <!-- end dwr section -->
 
-<!-- __________ Relationships to object nodes (domain id is broader or parent side, range id is narrower or child side) _________________ -->
-
-	<table class="form-background" border="0" cellpadding="2" cellspacing="2" width="100%">
-		<tr><td colspan="3" align="center">
-        	<div style="color: black; cursor: pointer;" onclick="javascript:switchGroupDisplay('oldEditing','oldEditingSw0','${appBean.themeDir}site_icons')" title="old editing" class="navlinkblock" onmouseover="onMouseOverHeading(this)" onmouseout="onMouseOutHeading(this)">
-                <span class="entityRelationsSpan"><img src="${appBean.themeDir}site_icons/plus.gif" id="oldEditingSw0"/>
-                Click here for original-style object property statement editing (should work on any browser)</span>
-			</div>
-		</td></tr>
-	</table>
-
-	<div id="oldEditing" style="display:none;">
-		<table class="form-background" border="0" cellpadding="2" cellspacing="2" width="100%">
-			<tr valign="bottom" align="center">
-    			<td colspan="3"><i>This individual is the subject in the following relationships to other object individuals</i></td>
-			</tr>
-			<tr valign="bottom" align="center">
-    			<td/>
-    			<td valign="bottom" align="center">
-              		<c:if test="${!empty epo.formObject.optionLists['ExistingPropertyInstances']}">
-                    	<form action="editForm" method="edit">
-                        	<select name="multiplexedParam" class="form-item">
-                          		<form:option name="ExistingPropertyInstances"/>
-                        	</select><br/>
-                        	<input type="hidden" name="SubjectEntURI" value="${individual.URI}"/>
-                        	<input type="submit" class="form-button" value="Edit Statement"/>
-                        	<input type="hidden" name="controller" value="ObjectPropertyStatement"/>
-                    	</form>
-               		</c:if>
-    			</td>
-    			<td>
-                	<form action="editForm" method="get">
-                		<input type="hidden" name="SubjectEntURI" value="${individual.URI}"/>
-                		<select name="PropertyURI" class="form-item">
-                    		<form:option name="PropertyURI"/>
-                		</select><br/>
-                		<input type="hidden" name="controller" value="ObjectPropertyStatement"/>
-                		<input type="hidden" name="domainSide" value="true"/>
-                		<input type="submit" class="form-button" value="new link for this individual"/>
-                	</form>
-    			</td>
-			</tr>
-			<tr><td colspan="3"></td></tr>
-		</table>
-	</div><!-- END div  "oldEditing" -->
 	</div><!-- END div "authorized" -->
 </c:if><!-- end if (securityLevel less than MIN_EDIT_ROLE) -->
 </div><!-- END div "anybody" -->

webapp/web/templates/edit/specific/keys2ents_dashboard_retry.jsp

@@ -1,12 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ taglib prefix="form" uri="http://vitro.mannlib.cornell.edu/edit/tags" %>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="2">
-			<b>Keyword</b><br/>
-				<select name="KeyId">
-					<form:option name="KeyId"/>
-				</select>
-				<font size="2" color="red"><form:error name="KeyId"/></font>
-		</td>
-	</tr>

webapp/web/templates/edit/specific/keys2ents_retry.jsp

@@ -1,29 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ taglib prefix="form" uri="http://vitro.mannlib.cornell.edu/edit/tags" %>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="2">
-			<b>Keyword</b><br/>
-				<select name="KeyId">
-					<form:option name="KeyId"/>
-				</select>
-				<font size="2" color="red"><form:error name="KeyId"/></font>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="top" colspan="2">
-			<b>Individual</b><br>
-				<select name="EntId">
-					<form:option name="EntId"/>
-				</select>
-				<font size="2" color="red"><form:error name="EntId"/></font>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="2">
-				<select name="Mode">
-					<form:option name="Mode"/>
-				</select>
-				<font size="2" color="red"><form:error name="Mode"/></font>
-		</td>
-	</tr>

webapp/web/templates/edit/specific/keyterms_dashboard_retry.jsp

@@ -1,17 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ taglib prefix="form" uri="http://vitro.mannlib.cornell.edu/edit/tags" %>
-	<tr class="editformcell">
-		<td valign="top" colspan="2">
-			<b>Keyword</b><br />
-				<input type="text" name="Term" value="<form:value name="Term"/>" size="60" maxlength="255" />
-				<p><font size="2" color="red"><form:error name="Term"/></font></p>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="3">
-			<b>Comment</b> <i>limited to ~255 characters</i><br />
-				<textarea name="Comments" ROWS="3" COLS="80" wrap="physical"><form:value name="Comments"/></textarea>
-				<font size="2" color="red"><form:error name="Comments"/></font>
-		</td>
-	</tr>

webapp/web/templates/edit/specific/keyterms_retry.jsp

@@ -1,29 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ taglib prefix="form" uri="http://vitro.mannlib.cornell.edu/edit/tags" %>
-	<tr class="editformcell">
-		<td valign="top" colspan="2">
-			<b>Keyword</b><br />
-				<input type="text" name="Term" value="<form:value name="Term"/>" size="60" maxlength="255" />
-				<p><font size="2" color="red"><form:error name="Term"/></font></p>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="top" colspan="1">
-			<b>Origin</b> <i>(source of 1st use of this keyword)</i><br/>
-				<select name="Origin" >
-					<form:option name="Origin"/>
-				</select>
-				<font size="2" color="red"><form:error name="Origin"/></font>
-			</td>
-			<td valign="top"><sup>*</sup>If [new origin] is selected, optionally enter a <b>new origin</b> here:<br/>
-				<input type="text" name="Origin" size="30" maxlength="80" /><br>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="3">
-			<b>Comment</b> <i>limited to ~255 characters</i><br />
-				<textarea name="Comments" ROWS="3" COLS="80" wrap="physical"><form:value name="Comments"/></textarea>
-				<font size="2" color="red"><form:error name="Comments"/></font>
-		</td>
-	</tr>

webapp/web/templates/edit/specific/links_retry.jsp

@@ -1,40 +0,0 @@
-<%-- $This file is distributed under the terms of the license in /doc/license.txt$ --%>
-
-<%@ taglib prefix="form" uri="http://vitro.mannlib.cornell.edu/edit/tags" %>
-<%@ taglib prefix="c" uri="http://java.sun.com/jstl/core" %>
-
-	<tr class="editformcell">
-		<td valign="top" colspan="3">
-			<b>Individual Name</b><br/>
-				<select name="EntityId" >
-					<form:option name="EntityId"/></option>
- 				</select>
-				<font size="2" color="red"><form:error name="EntityId"/></font>
-		</td>
-	</tr>
-  <c:if test="${!empty epo.formObject.optionLists['TypeURI']}">
-	<tr class='editformcell'>
-		<td valign="top" colspan="3">
-			<b>Link Type</b><br>
-				<select name="TypeURI">
-					<form:option name="TypeURI"/>
-				</select>
-				<br><font size="2" color="red"><form:error name="TypeURI"/></font>
-		</td>
-	</tr>
-  </c:if>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="3">
-			<b>URL</b> itself (http://...)<br/>
-				<input type="text" name="Url" style="width:32em;" value="<form:value name="Url"/>"/>
-				<font size="2" color="red"><form:error name="Url"/></font>
-		</td>
-	</tr>
-	<tr class="editformcell">
-		<td valign="bottom" colspan="2">
-			<b>anchor text for above URL</b><br/>
-				<input type="text" name="Anchor" value="<form:value name="Anchor"/>" style="width:24em;" maxlength="255" />
-				<font size="2" color="red"><form:error name="Anchor"/></font>
-		</td>
-	</tr>
-

webapp/web/templates/edit/specific/property_retry.jsp

@@ -135,7 +135,7 @@
 <tr class="editformcell">
     <td valign="bottom" colspan="2">
         <em>Optional: <strong>sort related individuals</strong> by<br />
-	    (name,timekey,sunrise,or sunset; default is name)</em><br/>
+	    (default is sort by name)</em><br/>
         <input name="DomainEntitySortField" value="<form:value name="DomainEntitySortField"/>" />
         <font size="2" color="red"><form:error name="DomainEntitySortField"/></font><br />
     </td>
@@ -254,7 +254,7 @@
     <tr class="editformcell">
         <td valign="bottom" colspan="2">
             <em>Optional: <strong>sort related object individuals of inverse property</strong> by<br />
-	    (name,timekey,sunrise,or sunset; default is name)</em><br/>
+	    (default is sort by name)</em><br/>
             <input name="RangeEntitySortField" value="<form:value name="RangeEntitySortField"/>" />
                 <font size="2" color="red"><form:error name="RangeEntitySortField"/></font>
         </td>

webapp/web/templates/entity/entityListForTabs.jsp

@@ -77,10 +77,8 @@
     						<c:param name="uri" value="${ent.URI}"/>
     					</c:url>
                   <div class="tab-image"><a class="image" href="<c:out value="${imageHref}"/>"><img width="${IMG_WIDTH}" src="${pageContext.request.contextPath}${ent.thumbUrl}" title="${ent.name}" alt="" /></a></div>
-                  <c:if test="${not empty ent.blurb}"><div class='blurb'>${ent.blurb}</div></c:if>
             </c:when>
             <c:otherwise>
-                <c:if test="${not empty ent.blurb}"><div class='blurb'>${ent.blurb}</div></c:if>
             </c:otherwise>
             </c:choose>
         </li>