Working on new navigation controllers and model. NIHVIVO-633

webapp/config/web.xml

@@ -82,7 +82,7 @@
     <listener-class>
         edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup
     </listener-class>
-  </listener>
+  </listener> 
   
   <!-- Invokes a process to move any uploaded files into the new file storage system. -->
   <!-- Needs to run after FileStorageSetup and JenaDataSourceSetup. -->
@@ -91,7 +91,7 @@
     <listener-class>
         edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateUploadedFiles
     </listener-class>
-  </listener>
+  </listener> 
   
   <!-- Attaching submodels permits extra RDF files to be made visible without storing the data in the DB. -->
   <listener>
@@ -99,7 +99,7 @@
   </listener>
 
   <!-- Pellet setup enables reasoning.  Inferences are cached in a separate DB graph. -->
-  <!-- Changing the class name sets the kindss of inferences that are materialized. -->
+  <!-- Changing the class name sets the kinds of inferences that are materialized. -->
   <!-- See documentation for details. -->
   <!-- If used, must be run after JenaDataSourceSetup -->
 
@@ -295,6 +295,15 @@
     <url-pattern>/SearchIndex</url-pattern>
   </servlet-mapping>
 
+  <servlet>
+  	<servlet-name>NavigationController</servlet-name>
+  	<servlet-class>edu.cornell.mannlib.vitro.webapp.controller.freemarker.NavigationController</servlet-class>
+  </servlet>
+  <servlet-mapping>
+  	<servlet-name>NavigationController</servlet-name>
+  	<url-pattern>/nav/*</url-pattern>
+  </servlet-mapping>
+  
   <servlet>
     <servlet-name>TestController</servlet-name>
     <servlet-class>edu.cornell.mannlib.vitro.webapp.controller.TestController</servlet-class>

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

@@ -0,0 +1,215 @@
+package edu.cornell.mannlib.vitro.webapp.controller.freemarker;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.servlet.ServletConfig;
+import javax.servlet.ServletException;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.ontology.Individual;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.rdf.listeners.StatementListener;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.NodeIterator;
+import com.hp.hpl.jena.rdf.model.RDFNode;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
+
+import edu.cornell.mannlib.vitro.webapp.web.DisplayVocabulary;
+
+public class NavigationController extends FreeMarkerHttpServlet {
+	private static final long serialVersionUID = 1L;
+	private static final Log log = LogFactory.getLog(NavigationController.class.getName());
+	
+	//private Map<Pattern,String> urlPatternToURI;
+	private NavigationURLPatternListener urlPatterns;
+	
+	@Override
+	public void init(ServletConfig config) throws ServletException {
+		super.init(config);
+		OntModel displayOntModel = (OntModel)config.getServletContext().getAttribute("displayOntModel");
+		this.urlPatterns = new NavigationURLPatternListener( );
+		displayOntModel.getBaseModel().register( urlPatterns );
+	}
+	
+	@Override
+	protected String getBody() {		
+		OntModel displayOntModel = (OntModel)getServletContext().getAttribute("displayOntModel");
+		OntModel jenaOntModel = (OntModel)getServletContext().getAttribute("jenaOntModel");
+				
+		//figure out what is being requested
+		Individual ind = urlPatterns.getDisplayIndividual(vreq.getPathInfo(),displayOntModel);		
+		Map<String,Object> values = getValues(ind, displayOntModel,jenaOntModel, getValuesFromRequest(/*?*/) );		
+		String template = getTemplate(ind, displayOntModel);		
+		
+		return mergeBodyToTemplate(template, values);
+	}
+	
+	private Map<String,Object>getValuesFromRequest(){
+		// TODO: figure out how to get request for FreeMarkerHttpServlet. 
+		return Collections.emptyMap();
+	}
+	
+	private String getTemplate(Individual ind, OntModel displayOntModel) {
+		if( ind == null ) return "defaultBody";
+		
+		// check vitroDisplay:requiresBodyTemplate
+		displayOntModel.enterCriticalSection(Model.READ);
+		StmtIterator it = displayOntModel.listStatements(ind, DisplayVocabulary.REQUIRES_BODY_TEMPLATE, (RDFNode) null);
+		//NodeIterator it = ind.listPropertyValues(DisplayVocabulary.REQUIRES_BODY_TEMPLATE);
+		try{										
+			while(it.hasNext()){
+				Statement stmt = it.nextStatement();
+				if(  stmt.getObject().isLiteral() ){
+					String template = ((Literal)stmt.getObject().as(Literal.class)).getLexicalForm();
+					if( template != null && template.length() > 0 ){
+						return template;							
+					}
+				}
+			}
+		}finally{
+			it.close();
+			displayOntModel.leaveCriticalSection();
+		}
+		return "defaultBody";
+	}
+
+	Map<String,Object> getValues(Individual ind, OntModel displayOntModel, OntModel assertionModel, Map<String,Object> baseValues){
+		if( ind == null ) return Collections.emptyMap();
+								
+		/* Figure out what ValueFactories are specified in the display ontology for this individual. */
+		Set<ValueFactory> valueFactories = new HashSet<ValueFactory>();
+		displayOntModel.enterCriticalSection(Model.READ);
+		StmtIterator stmts = ind.listProperties(DisplayVocabulary.REQUIRES_VALUES);		
+		try{										
+			while(stmts.hasNext()){
+				Statement stmt = stmts.nextStatement();
+				RDFNode obj =  stmt.getObject();
+				valueFactories.addAll(getValueFactory(obj,displayOntModel));
+			}
+		}finally{
+			stmts.close();
+			displayOntModel.leaveCriticalSection();
+		}
+		
+		/* Get values from the ValueFactories. */
+		HashMap<String,Object> values = new HashMap<String,Object>();
+		values.putAll(baseValues);
+		for(ValueFactory vf : valueFactories){
+			values.putAll( vf.getValues(assertionModel, values));
+		}
+		return values;
+	}
+	
+	protected Set<ValueFactory> getValueFactory( RDFNode valueNode, OntModel displayOntModel) {
+		//maybe use jenabean or owl2java for this?
+		if(  valueNode.isResource() ){
+			Resource res = (Resource)valueNode.as(Resource.class);
+			Statement stmt = res.getProperty(DisplayVocabulary.JAVA_CLASS_NAME);
+			if( stmt == null || !stmt.getObject().isLiteral() ){
+				log.debug("Cannot build value factory: java class was " + stmt.getObject());
+				return Collections.emptySet();
+			}
+			String javaClassName = ((Literal)stmt.getObject().as(Literal.class)).getLexicalForm();
+			if( javaClassName == null || javaClassName.length() == 0 ){
+				log.debug("Cannot build value factory: no java class was set.");
+				return Collections.emptySet();
+			}
+			Class<?> clazz;
+			Object newObj;
+			try {
+				clazz = Class.forName(javaClassName);
+			} catch (ClassNotFoundException e) {
+				log.debug("Cannot build value factory: no class found for " + javaClassName);
+				return Collections.emptySet();
+			}
+			try {
+				newObj = clazz.newInstance();
+			} catch (Exception e) {
+				log.debug("Cannot build value factory: exception while creating object of java class " + javaClassName + " " + e.getMessage());
+				return Collections.emptySet();
+			}
+			if( newObj instanceof ValueFactory){
+				ValueFactory valueFactory = (ValueFactory)newObj;
+				return Collections.singleton( valueFactory );
+			}else{
+				log.debug("Cannot build value factory: " + javaClassName + " does not implement " + ValueFactory.class.getName() );
+				return Collections.emptySet();
+			}			
+		}else{
+			log.debug("Cannot build value factory for " + valueNode);
+			return Collections.emptySet();
+		}		
+	}
+	
+	 interface ValueFactory {
+		void configure( Map<String,String> config);
+		Map<String,Object> getValues(OntModel model, Map<String,Object> values);		
+	}
+	
+	@Override
+	protected String getTitle() {
+		// TODO Auto-generated method stub
+		return super.getTitle();
+	}
+		
+	private class NavigationURLPatternListener extends StatementListener {		
+		private Map<Pattern,String> urlPatternToURI;
+		
+		public synchronized Map<Pattern,String> getUrlPatternToURIMap(){
+			if( urlPatternToURI == null || urlPatternToURI.isEmpty() ){
+				this.urlPatternToURI = buildUrlPatternToURI();
+			}
+			return urlPatternToURI;
+		}
+		
+		protected synchronized void invalidateURLPatternMap(){
+			this.urlPatternToURI = null;
+		}
+		
+		public Individual getDisplayIndividual( String pathInfo , OntModel displayModel){
+			Map<Pattern,String> map = getUrlPatternToURIMap();
+			for( Pattern regex : map.keySet()){
+				Matcher m = regex.matcher(pathInfo);
+				if(m.matches() ){
+					return displayModel.getIndividual(map.get(regex));
+				}
+			}
+			return null;
+		}
+		
+		protected synchronized Map<Pattern,String> buildUrlPatternToURI(){
+			OntModel displayModel = (OntModel)getServletContext().getAttribute("displayOntModel");
+			Map<Pattern,String> map = new HashMap<Pattern,String>();
+			StmtIterator stmts = displayModel.listStatements(null, DisplayVocabulary.URL_MAPPING,(Literal)null);		
+			while(stmts.hasNext()){			
+				Statement stmt = stmts.nextStatement();
+				if( stmt.getSubject().isURIResource() && stmt.getObject().isLiteral()){
+					Resource r = (Resource)stmt.getSubject().as( Resource.class);				
+					Pattern regex = Pattern.compile(stmt.getLiteral().getLexicalForm());
+					map.put(regex,r.getURI());
+				}
+			}
+			return map;
+		}			
+		
+		@Override
+		public void addedStatement(Statement s) {
+			invalidateURLPatternMap();
+		}
+		@Override
+		public void removedStatement(Statement s) {
+			invalidateURLPatternMap();
+		}	
+	}	
+}

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

@@ -21,6 +21,7 @@ public class SimpleOntModelSelector implements OntModelSelector {
 	private OntModel userAccountsModel;
 	
 	private OntModelSpec DEFAULT_ONT_MODEL_SPEC = OntModelSpec.OWL_MEM;
+	private OntModel displayModel;
 	
 	/**
 	 * Construct an OntModelSelector with a bunch of empty models
@@ -116,4 +117,10 @@ public class SimpleOntModelSelector implements OntModelSelector {
 		this.userAccountsModel = userAccountsModel;
 	}
 
+	public void setDisplayModel(OntModel displayModel) {
+		this.displayModel = displayModel;		
+	}
+	public OntModel getDisplayModel(){
+		return this.displayModel;
+	}
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetup.java

@@ -8,7 +8,6 @@ import javax.servlet.ServletContextEvent;
 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.Individual;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.rdf.model.Literal;
@@ -17,7 +16,6 @@ import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.util.iterator.ClosableIterator;
-import com.hp.hpl.jena.vocabulary.OWL;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
@@ -61,6 +59,13 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
         	inferenceOms.setUserAccountsModel(userAccountsModel);
         	unionOms.setUserAccountsModel(userAccountsModel);       
             
+        	OntModel displayModel = ontModelFromContextAttribute(sce.getServletContext(),"displayOntModel");
+        	OntModel displayUnionModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC,ModelFactory.createUnion(displayModel, unionModel));
+        	sce.getServletContext().setAttribute("displayOntModel", displayUnionModel);
+        	baseOms.setDisplayModel(displayModel);
+        	inferenceOms.setDisplayModel(displayModel);
+        	unionOms.setDisplayModel(displayModel);
+        			
             sce.getServletContext().setAttribute("baseOntModel", memModel);
             WebappDaoFactory baseWadf = new WebappDaoFactoryJena(baseOms, defaultNamespace, null, null);
             sce.getServletContext().setAttribute("assertionsWebappDaoFactory",baseWadf);
@@ -87,7 +92,7 @@ public class JenaDataSourceSetup extends JenaDataSourceSetupBase implements java
 	            if (userAccountsModel.size() == 0) {
 	            	createInitialAdminUser(userAccountsModel);
 	            }
-            }
+            }                        
             
             ensureEssentialInterfaceData(memModel, sce, wadf);
         

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaDataSourceSetupBase.java

@@ -39,6 +39,7 @@ public class JenaDataSourceSetupBase {
    protected static String USERPATH = BASE+"user/";
    protected static String SYSTEMPATH = BASE+"system/";
    protected static String AUTHPATH = BASE+"auth/";
+   protected static String APPPATH = BASE+"app/";
 
    String DB_USER =   "jenatest";                          // database user id
    String DB_PASSWD = "jenatest";                          // database password
@@ -49,6 +50,7 @@ public class JenaDataSourceSetupBase {
    static final String JENA_INF_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-inf";
    static final String JENA_USER_ACCOUNTS_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts";
    static final String JENA_APPLICATION_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadata";
+   static final String JENA_DISPLAY_METADATA_MODEL = "http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata";
 
    static final String DEFAULT_DEFAULT_NAMESPACE = "http://vitro.mannlib.cornell.edu/ns/default#";
    

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/JenaPersistentDataSourceSetup.java

@@ -104,6 +104,19 @@ public class JenaPersistentDataSourceSetup extends JenaDataSourceSetupBase imple
         	log.error("Unable to load user accounts model from DB", t);
         }
              
+        // display, editing and navigation Model 
+	    try {
+	    	Model appDbModel = makeDBModelFromConfigurationProperties(JENA_DISPLAY_METADATA_MODEL, DB_ONT_MODEL_SPEC);
+			if (appDbModel.size() == 0) 
+				readOntologyFilesInPathSet(APPPATH, sce.getServletContext(),appDbModel);			
+	    	OntModel appModel = ModelFactory.createOntologyModel(MEM_ONT_MODEL_SPEC);
+	    	appModel.add(appDbModel);
+	    	appModel.getBaseModel().register(new ModelSynchronizer(appDbModel));
+	    	sce.getServletContext().setAttribute("displayOntModel", appModel);
+	    } catch (Throwable t) {
+	    	log.error("Unable to load user application configuration model from DB", t);
+	    }
+	    
         sce.getServletContext().setAttribute("jenaOntModel", memModel);
        
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/web/DisplayVocabulary.java

@@ -0,0 +1,74 @@
+package edu.cornell.mannlib.vitro.webapp.web;
+ 
+import com.hp.hpl.jena.ontology.DatatypeProperty;
+import com.hp.hpl.jena.ontology.Individual;
+import com.hp.hpl.jena.ontology.ObjectProperty;
+import com.hp.hpl.jena.ontology.OntClass;
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Resource;
+ 
+/**
+ * Vocabulary definitions from /home/bdc34/swoop/display.rdf 
+ * @author Auto-generated by schemagen on 18 Jun 2010 16:57 
+ */
+public class DisplayVocabulary {
+    /** <p>The ontology model that holds the vocabulary terms</p> */
+    private static OntModel m_model = ModelFactory.createOntologyModel( OntModelSpec.OWL_MEM, null );
+    
+    /** <p>The namespace of the vocabulary as a string</p> */
+    public static final String NS = "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#";
+    
+    /** <p>The namespace of the vocabulary as a string</p>
+     *  @see #NS */
+    public static String getURI() {return NS;}
+    
+    /** <p>The namespace of the vocabulary as a resource</p> */
+    public static final Resource NAMESPACE = m_model.createResource( NS );
+    
+    public static final ObjectProperty REQUIRES_VALUES = m_model.createObjectProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#requiresValues" );
+    
+    public static final ObjectProperty TO_PAGE = m_model.createObjectProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#toPage" );
+    
+    /** <p>Java package and class name. ex edu.cornell.mannlib.vitro.webapps.functions.ExampleFunction</p> */
+    public static final DatatypeProperty JAVA_CLASS_NAME = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#javaClassName" );
+    
+    public static final DatatypeProperty MENU_POSITION = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#menuPosition" );
+    
+    public static final DatatypeProperty PARAMETER_NAME = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#parameterName" );
+    
+    public static final DatatypeProperty PARAMETER_VALUE = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#parameterValue" );
+    
+    public static final DatatypeProperty REQUIRES_BODY_TEMPLATE = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#requiresBodyTemplate" );
+    
+    /** <p>Values from HttpRequest.getPathInfo() will be mapped to values from urlMapping.</p> */
+    public static final DatatypeProperty URL_MAPPING = m_model.createDatatypeProperty( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#urlMapping" );
+    
+    /** <p>This represents a menu item or other general navigation item.</p> */
+    public static final OntClass NAVIGATION_ELEMENT = m_model.createClass( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#NavigationElement" );
+    
+    /** <p>Class of pages.</p> */
+    public static final OntClass PAGE = m_model.createClass( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Page" );
+    
+    //public static final Individual EVENTS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Events", PAGE );
+    
+    //public static final Individual EVENTS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#EventsMenuItem", NAVIGATION_ELEMENT );
+    
+    //public static final Individual HOME = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Home", PAGE );
+    
+    //public static final Individual HOME_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#HomeMenuItem", NAVIGATION_ELEMENT );
+    
+    //public static final Individual ORGANIZATIONS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Organizations", PAGE );
+    
+    //public static final Individual ORGANIZATIONS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#OrganizationsMenuItem", NAVIGATION_ELEMENT );
+    
+    //public static final Individual PEOPLE = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#People", PAGE );
+    
+    //public static final Individual PEOPLE_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PeopleMenuItem", NAVIGATION_ELEMENT );
+    
+    //public static final Individual PUBLICATIONS = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#Publications", PAGE );
+    
+    //public static final Individual PUBLICATIONS_MENU_ITEM = m_model.createIndividual( "http://vitro.mannlib.cornell.edu/ontologies/display/1.1#PublicationsMenuItem", NAVIGATION_ELEMENT );
+    
+}

webapp/web/templates/freemarker/body/home.ftl

@@ -0,0 +1 @@
+<h1>Welcome to VIVO</h1>