hand-merging revision 6005 into trunk to get around PROPFIND error

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/EntityController.java

@@ -41,7 +41,10 @@ import edu.cornell.mannlib.vitro.webapp.beans.Portal;
 import edu.cornell.mannlib.vitro.webapp.beans.VClass;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.ObjectPropertyDao;
-import edu.cornell.mannlib.vitro.webapp.filestorage.model.FileInfo;
+import edu.cornell.mannlib.vitro.webapp.filestorage.FileModelHelper;
+import edu.cornell.mannlib.vitro.webapp.filestorage.FileServingHelper;
+import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorage;
+import edu.cornell.mannlib.vitro.webapp.filestorage.backend.FileStorageSetup;
 import edu.cornell.mannlib.vitro.webapp.search.beans.VitroQuery;
 import edu.cornell.mannlib.vitro.webapp.search.beans.VitroQueryWrapper;
 import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
@@ -99,7 +102,7 @@ public class EntityController extends VitroHttpServlet {
             }
 
             // If this is an uploaded file, redirect to its "alias URL".
-            String aliasUrl = getAliasUrlForBytestreamIndividual(req, indiv);
+            String aliasUrl = getAliasUrlForBytestreamIndividual(indiv);
             if (aliasUrl != null) {
             	res.sendRedirect(req.getContextPath() + aliasUrl);
             	return;
@@ -175,9 +178,9 @@ public class EntityController extends VitroHttpServlet {
                     }
                 }
             }
-        } else {
+        } else if (indiv.getVClassURI() != null) {
-            log.error("Entity " + indiv.getURI() + " with vclass URI " +
+            log.debug("Individual " + indiv.getURI() + " with class URI " +
-                    indiv.getVClassURI() + ", no vclass with that URI exists");
+                    indiv.getVClassURI() + ": no class found with that URI");
         }
         if (customView!=null) {
             // insert test for whether a css files of the same name exists, and populate the customCss string for use when construction the header
@@ -225,16 +228,10 @@ public class EntityController extends VitroHttpServlet {
         }
 
         if(  indiv.getURI().startsWith( vreq.getWebappDaoFactory().getDefaultNamespace() )){
-        	vreq.setAttribute("entityLinkedDataURL", indiv.getURI() + "/" + indiv.getLocalName() + ".rdf");	
+        	String entityLinkedDataURL = indiv.getURI() + "/" + indiv.getLocalName() + ".rdf";
+        	vreq.setAttribute("entityLinkedDataURL", entityLinkedDataURL);
         }   
 
-        
-		// generate link to RDF representation for semantic web clients like Piggy Bank
-		// BJL 2008-07-16: I'm temporarily commenting this out because I forgot we need to make sure it filters out the hidden properties
-        // generate url for this entity
-        // String individualToRDF = "http://"+vreq.getServerName()+":"+vreq.getServerPort()+vreq.getContextPath()+"/entity?home=1&uri="+forURL(entity.getURI())+"&view=rdf.rdf"; 
-        //css += "<link rel='alternate' type='application/rdf+xml' title='"+entity.getName()+"' href='"+individualToRDF+"' />";
-
         vreq.setAttribute("css",css);
         vreq.setAttribute("scripts", "/templates/entity/entity_inject_head.jsp");
 
@@ -273,14 +270,21 @@ public class EntityController extends VitroHttpServlet {
 		newModel.write( res.getOutputStream(), format );		
 	}
 
-	private void doRedirect(HttpServletRequest req, HttpServletResponse res,
+    private void doRedirect(HttpServletRequest req, HttpServletResponse res,
-			String redirectURL) {	
+            String redirectURL) {
-		// It seems like there must be a better way to do this
+        //It seems like there must be a more standard way to do a redirect in tomcat.
-		String hn = req.getHeader("Host");		
+        String hn = req.getHeader("Host");
-    	res.setHeader("Location", res.encodeURL( "http://" + hn + req.getContextPath() + redirectURL ));
+        if (req.isSecure()) {
-    	res.setStatus(res.SC_SEE_OTHER);		
+            res.setHeader("Location", res.encodeURL("https://" + hn
-	}
+                    + req.getContextPath() + redirectURL));
-
+            log.info("doRedirect by using HTTPS");
+        } else {
+            res.setHeader("Location", res.encodeURL("http://" + hn
+                    + req.getContextPath() + redirectURL));
+            log.info("doRedirect by using HTTP");
+        }
+        res.setStatus(res.SC_SEE_OTHER);
+    }
 
 	private static Pattern LINKED_DATA_URL = Pattern.compile("^/individual/([^/]*)$");		
 	private static Pattern NS_PREFIX_URL = Pattern.compile("^/individual/([^/]*)/([^/]*)$");
@@ -488,16 +492,39 @@ public class EntityController extends VitroHttpServlet {
 	 * If this entity represents a File Bytestream, get its alias URL so we can
 	 * properly serve the file contents.
 	 */
-	private String getAliasUrlForBytestreamIndividual(HttpServletRequest req, Individual entity)
+	private String getAliasUrlForBytestreamIndividual(Individual entity)
 			throws IOException {
-		FileInfo fileInfo = FileInfo.instanceFromBytestreamUri(new VitroRequest(
+		if (!FileModelHelper.isFileBytestream(entity)) {
-				req).getWebappDaoFactory(), entity.getURI());
+			log.debug("Entity at '" + entity.getURI()
-		if (fileInfo == null) {
+					+ "' is not recognized as a FileByteStream.");
-			log.trace("Entity '" + entity.getURI() + "' is not a bytestream.");
+			return null;
+		}
+
+		FileStorage fs = (FileStorage) getServletContext().getAttribute(
+				FileStorageSetup.ATTRIBUTE_NAME);
+		if (fs == null) {
+			log.error("Servlet context does not contain file storage at '"
+					+ FileStorageSetup.ATTRIBUTE_NAME + "'");
+			return null;
+		}
+
+		String filename = fs.getFilename(entity.getURI());
+		if (filename == null) {
+			log.error("Entity at '" + entity.getURI()
+					+ "' is recognized as a FileByteStream, "
+					+ "but the file system does not recognize it.");
+			return null;
+		}
+
+		String url = FileServingHelper.getBytestreamAliasUrl(entity.getURI(),
+				filename);
+		if (url.equals(entity.getURI())) {
+			log.error("Entity at '" + entity.getURI()
+					+ "' is recognized as a FileByteStream, "
+					+ "but can't be translated to an alias URL.");
 			return null;
 		}
 
-		String url = fileInfo.getBytestreamAliasUrl();
 		log.debug("Alias URL for '" + entity.getURI() + "' is '" + url + "'");
 		return url;
 	}

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

@@ -79,6 +79,7 @@ import edu.cornell.mannlib.vitro.webapp.utils.Csv2Rdf;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.JenaIngestWorkflowProcessor;
 import edu.cornell.mannlib.vitro.webapp.utils.jena.WorkflowOntology;
+
 import edu.cornell.mannlib.vitro.webapp.beans.Ontology;
 import edu.cornell.mannlib.vitro.webapp.dao.OntologyDao;
 
@@ -420,10 +421,10 @@ public class JenaIngestController extends BaseEditController {
 			  if(modelName!=null){
 			  Model m = maker.getModel(modelName);
 			  ArrayList namespaceList = new ArrayList();
-			  ResIterator resItr = m.listResourcesWithProperty((Property)null);
+              ResIterator resItr = m.listResourcesWithProperty((Property)null);
 			  
 			  if(resItr!=null){
-          	while(resItr.hasNext()){
+          	    while(resItr.hasNext()){
           		String namespace = resItr.nextResource().getNameSpace();
                 if(!namespaceList.contains(namespace)){
                 	namespaceList.add(namespace);
@@ -442,7 +443,6 @@ public class JenaIngestController extends BaseEditController {
 			  }
 			  else if(oldModel!=null){
 				  doPermanentURI(oldModel,newModel,oldNamespace,newNamespace,dNamespace,maker,vreq);
-		
 				  request.setAttribute("title","Ingest Menu");
 				  request.setAttribute("bodyJsp",INGEST_MENU_JSP);
 			  }
@@ -736,10 +736,8 @@ public class JenaIngestController extends BaseEditController {
         	VitroJenaSDBModelMaker vjmm = new VitroJenaSDBModelMaker(store);
         	vreq.getSession().setAttribute("vitroJenaModelMaker",vjmm);
 		} else {
-			DBConnection dbConn = new DBConnection(jdbcUrl,username,password,dbType);
 			System.out.println("Connecting to DB at "+jdbcUrl);
-	        ModelMaker mMaker = ModelFactory.createModelRDBMaker(dbConn);
+	        VitroJenaModelMaker vjmm = new VitroJenaModelMaker(jdbcUrl, username, password, dbType);
-	        VitroJenaModelMaker vjmm = new VitroJenaModelMaker(mMaker);
 	        vreq.getSession().setAttribute("vitroJenaModelMaker",vjmm);
 		}
 	}
@@ -1052,8 +1050,6 @@ public class JenaIngestController extends BaseEditController {
 				
 			}
 			}	
-		
-	
 	private String getUnusedURI(String newNamespace,WebappDaoFactory wdf){
 		String uri = null;
 		String errMsg = null;

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

@@ -2,21 +2,32 @@
 
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
+import java.sql.SQLException;
 import java.util.HashMap;
+import java.util.List;
 
 import javax.servlet.http.HttpServletRequest;
 
+import org.apache.commons.dbcp.BasicDataSource;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.db.DBConnection;
+import com.hp.hpl.jena.graph.Graph;
 import com.hp.hpl.jena.graph.GraphMaker;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.ModelMaker;
 import com.hp.hpl.jena.rdf.model.ModelReader;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
+import com.hp.hpl.jena.util.iterator.NiceIterator;
+import com.hp.hpl.jena.util.iterator.WrappedIterator;
+
+import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
+import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
 
 /**
  * This is a bit of a nutty idea but we'll see if it works.  This can wrap an RDBModelMaker and return a memory model 
@@ -30,43 +41,54 @@ import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 public class VitroJenaModelMaker implements ModelMaker {
 	
 	private static final Log log = LogFactory.getLog(VitroJenaModelMaker.class);
+	private static final String DEFAULT_DRIVER = "com.mysql.jdbc.Driver";
 	
-	private ModelMaker innerModelMaker = null;
+	private String jdbcUrl;
-	private HashMap<String,Model> modelCache = null;
+	private String username;
+	private String password;
+	private String dbTypeStr;
+	private BasicDataSource dataSource;
+	private HashMap<String,Model> modelCache;
 	private HttpServletRequest request = null;
 	
-	public VitroJenaModelMaker(ModelMaker mm) {
+	public VitroJenaModelMaker(String jdbcUrl, String username, String password, String dbTypeStr) {
-		this.innerModelMaker = mm;
+		this.jdbcUrl = jdbcUrl;
+		this.username = username;
+		this.password = password;
+		this.dbTypeStr = dbTypeStr;
+		String driverName = ConfigurationProperties
+			.getProperty("VitroConnection.DataSource.driver");
+		// This property is no longer used?
+		// We'll change it all around in 1.2 anyway.
+		if(driverName == null) {
+			driverName = DEFAULT_DRIVER;
+		}
+		this.dataSource = JenaDataSourceSetupBase.makeBasicDataSource(
+				driverName,
+					jdbcUrl, username, password);
 		modelCache = new HashMap<String,Model>();
 	}
 	
-	public VitroJenaModelMaker(ModelMaker mm,  HttpServletRequest request) {
+//	public VitroJenaModelMaker(ModelMaker mm,  HttpServletRequest request) {
-		this.innerModelMaker = mm;
+//		this.innerModelMaker = mm;
-		if (mm instanceof VitroJenaModelMaker) { 
+//		if (mm instanceof VitroJenaModelMaker) { 
-			log.debug("Using cache from inner model maker ");
+//			log.debug("Using cache from inner model maker ");
-			this.modelCache = ((VitroJenaModelMaker)mm).getCache();
+//			this.modelCache = ((VitroJenaModelMaker)mm).getCache();
-		} else {
+//		} else {
-			log.debug("Creating new cache");
+//			log.debug("Creating new cache");
-			this.modelCache = new HashMap<String,Model>();
+//			this.modelCache = new HashMap<String,Model>();
-		}
+//		}
-		this.request = request;
+//		this.request = request;
-	}
+//	}
-	
+//	
-	public ModelMaker getInnerModelMaker() {
+//	public ModelMaker getInnerModelMaker() {
-		return this.innerModelMaker;
+//		return this.innerModelMaker;
-	}
+//	}
 	
 	protected HashMap<String,Model> getCache() {
 		return this.modelCache;
 	}
 	
-	private Model copyModelIntoMem(Model underlyingModel) {
-		Model memModel = ModelFactory.createDefaultModel();
-		memModel.add(underlyingModel);
-		memModel.register(new ModelSynchronizer(underlyingModel));
-		return memModel;
-	}
-	
 	public void close() {
 		// TODO Auto-generated method stub
 		// So, in theory, this should close database connections and drop references
@@ -81,7 +103,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 			log.debug("Returning "+arg0+" ("+cachedModel.hashCode()+") from cache");
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.createModel(arg0));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 log.debug("Returning "+arg0+" ("+newModel.hashCode()+") from cache");
 			 return newModel;
@@ -95,22 +117,42 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.createModel(arg0,arg1));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
 	}
 	
 	public GraphMaker getGraphMaker() {
-		return innerModelMaker.getGraphMaker();
+		throw new UnsupportedOperationException(this.getClass().getName() +
+				" does not support getGraphMaker()"); 
 	}
 
 	public boolean hasModel(String arg0) {
-		return innerModelMaker.hasModel(arg0);
+		DBConnection conn = new DBConnection(jdbcUrl, username, password, dbTypeStr);
+		try {
+			return ModelFactory.createModelRDBMaker(conn).hasModel(arg0);
+		} finally {
+			try {
+				conn.close();
+			} catch (SQLException sqle) {
+				throw new RuntimeException(sqle);
+			}
+		}
 	}
 
 	public ExtendedIterator listModels() {
-		return innerModelMaker.listModels();
+		DBConnection conn = new DBConnection(jdbcUrl, username, password, dbTypeStr);
+		try {
+			List<String> modelList = ModelFactory.createModelRDBMaker(conn).listModels().toList();
+			return WrappedIterator.create(modelList.iterator());
+		} finally {
+			try {
+				conn.close();
+			} catch (SQLException sqle) {
+				throw new RuntimeException(sqle);
+			}
+		}
 	}
 
 	public Model openModel(String arg0, boolean arg1) {
@@ -120,7 +162,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.openModel(arg0,arg1));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
@@ -132,7 +174,16 @@ public class VitroJenaModelMaker implements ModelMaker {
 			m.close();
 			modelCache.remove(arg0);
 		}
-		innerModelMaker.removeModel(arg0);
+		DBConnection conn = new DBConnection(jdbcUrl, username, password, dbTypeStr);
+		try {
+			ModelFactory.createModelRDBMaker(conn).removeModel(arg0);
+		} finally {
+			try {
+				conn.close();
+			} catch (SQLException sqle) {
+				throw new RuntimeException(sqle);
+			}
+		}
 	}
 
 	
@@ -160,13 +211,14 @@ public class VitroJenaModelMaker implements ModelMaker {
 	}
 	
 	public Model createDefaultModel() {
-		return innerModelMaker.createDefaultModel();
+		throw new UnsupportedOperationException(this.getClass().getName() +
+				" does not support createDefaultModel()");
 	}
 
 	
 	public Model createFreshModel() {
-		return innerModelMaker.createFreshModel();
+		throw new UnsupportedOperationException(this.getClass().getName() +
-	}
+				" does not support createFreshModel()");	}
 
 	@Deprecated
 	public Model createModel() {
@@ -188,7 +240,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.openModel(arg0));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
@@ -202,7 +254,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.openModelIfPresent(arg0));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
@@ -216,7 +268,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.getModel(arg0));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
@@ -230,7 +282,7 @@ public class VitroJenaModelMaker implements ModelMaker {
 		if (cachedModel != null) {
 			return cachedModel;
 		} else {
-			 Model newModel = copyModelIntoMem(innerModelMaker.getModel(arg0));
+			 Model newModel = makeDBModel(arg0);
 			 modelCache.put(arg0,newModel);
 			 return newModel;
 		}
@@ -274,4 +326,21 @@ public class VitroJenaModelMaker implements ModelMaker {
 		return null;
 	}
 	
+	private OntModel makeDBModel(String jenaDbModelName) {
+    	OntModel memCache = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
+        RDBGraphGenerator gen = new RDBGraphGenerator(dataSource, dbTypeStr, jenaDbModelName);
+        Graph g = gen.generateGraph();
+        Model m = ModelFactory.createModelForGraph(g);	
+        memCache.add(m);
+        memCache.register(new MemToRDBModelSynchronizer(gen));
+        m.close();
+        try {
+            gen.getConnection().close();
+        } catch (SQLException e) {
+        	log.warn("Unable to close connection for graph", e);
+        }
+        // This next piece is so that we return a fresh model object each time so we don't get cross-contamination of extra listeners, etc.
+        return ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, ModelFactory.createUnion(memCache, ModelFactory.createDefaultModel()));
+    }
+
 }

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

@@ -19,10 +19,11 @@ import com.hp.hpl.jena.rdf.model.Resource;
 
 import edu.cornell.mannlib.vitro.webapp.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDaoCon;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RDBGraphGenerator;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.RegeneratingGraph;
 
-public class JenaDataSourceSetupBase {
+public class JenaDataSourceSetupBase extends JenaBaseDaoCon {
 	private static final Log log = LogFactory.getLog(JenaDataSourceSetupBase.class);
 
 	protected final static int DEFAULT_MAXWAIT = 10000, // ms

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

@@ -33,8 +33,8 @@ public class VitroJenaModelMakerSetup implements ServletContextListener {
 			String password = ConfigurationProperties.getProperty("VitroConnection.DataSource.password");
 				
 			DBConnection dbConn = new DBConnection(jdbcUrl, username, password, DB_TYPE);
-			ModelMaker mMaker = ModelFactory.createModelRDBMaker(dbConn);
+			;
-			VitroJenaModelMaker vjmm = new VitroJenaModelMaker(mMaker);
+			VitroJenaModelMaker vjmm = new VitroJenaModelMaker(jdbcUrl, username, password, DB_TYPE);
 			arg0.getServletContext().setAttribute("vitroJenaModelMaker", vjmm);
 			log.debug("VitroJenaModelMaker set up");
 		} catch (Throwable t) {