Merge branch 'develop' of https://github.com/vivo-project/Vitro into develop

I haven't a clue what git is trying to do. I kind of miss svn at this point.

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

@@ -49,15 +49,6 @@ public class ApplicationBean {
     private String    copyrightAnchor;
     private String    themeDir;
        
-    public static ApplicationBean getAppBean(ServletContext sc){
-        if( sc != null ){
-            Object obj = sc.getAttribute("applicationBean");
-            if( obj != null )
-                return (ApplicationBean)obj;
-        }
-        return new ApplicationBean();
-    }
-
     public String toString() {
         String output = "Application Bean Contents:\n";
         output += "  initialized from DB:    [" + initialized             + "]\n";

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

@@ -33,9 +33,6 @@ import edu.cornell.mannlib.vitro.webapp.web.ContentType;
 public class OntologyController extends VitroHttpServlet{
     private static final Log log = LogFactory.getLog(OntologyController.class.getName());
     
-    private String default_jsp      = Controllers.BASIC_JSP;
-    private ApplicationBean appBean;
-    
 	public void doPost(HttpServletRequest request, HttpServletResponse response)
 	throws ServletException,IOException{
 		doGet(request, response);
@@ -242,7 +239,7 @@ public class OntologyController extends VitroHttpServlet{
     throws IOException, ServletException {
         VitroRequest vreq = new VitroRequest(req);
         
-        ApplicationBean appBean = ApplicationBean.getAppBean(getServletContext());
+        ApplicationBean appBean = vreq.getAppBean();
 
         //set title before we do the highlighting so we don't get markup in it.
         req.setAttribute("title","not found");

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

@@ -283,12 +283,8 @@ public class VitroRequest extends HttpServletRequestWrapper {
     }
     
     public ApplicationBean getAppBean(){
-        //return (ApplicationBean) getAttribute("appBean");
     	return getWebappDaoFactory().getApplicationDao().getApplicationBean();
     }
-    public void setAppBean(ApplicationBean ab){
-        setAttribute("appBean",ab);
-    }
 
     @SuppressWarnings("unchecked")
 	@Override

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/admin/StartupStatusController.java

@@ -7,7 +7,6 @@ import java.util.Map;
 
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.auth.requestedAction.Actions;
-import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.FreemarkerHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.freemarker.responsevalues.ResponseValues;
@@ -31,7 +30,7 @@ public class StartupStatusController extends FreemarkerHttpServlet {
 		body.put("title", "Startup Status");
 		body.put("status", StartupStatus.getBean(getServletContext()));
 		body.put("contextPath", getContextPath());
-		body.put("applicationName", getApplicationName());
+		body.put("applicationName", getApplicationName(vreq));
 
 		return new TemplateResponseValues("startupStatus-display.ftl", body);
 	}
@@ -45,11 +44,10 @@ public class StartupStatusController extends FreemarkerHttpServlet {
 		}
 	}
 
-	private Object getApplicationName() {
+	private Object getApplicationName(VitroRequest vreq) {
 		String name = "";
 		try {
-			ApplicationBean app = ApplicationBean.getAppBean(getServletContext());
+			name = vreq.getAppBean().getApplicationName();
-			name = app.getApplicationName();
 		} catch (Exception e) {
 			// deal with problems below
 		}

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalysisContext.java

@@ -15,12 +15,6 @@ public interface IndividualRequestAnalysisContext {
 	 */
 	String getDefaultNamespace();
 
-	/**
-	 * Is there a namespace for this prefix? If not, return an empty string, but
-	 * never null.
-	 */
-	String getNamespaceForPrefix(String prefix);
-
 	/**
 	 * Use the IndividualDao to get this individual.
 	 * 

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalysisContextImpl.java

@@ -15,8 +15,6 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.filestorage.model.FileInfo;
-import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
-import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapperFactory;
 
 /**
  * Implement all of the fiddly-bits that we need for analyzing the request for
@@ -45,25 +43,6 @@ public class IndividualRequestAnalysisContextImpl implements
 		return wadf.getDefaultNamespace();
 	}
 
-	@Override
-	public String getNamespaceForPrefix(String prefix) {
-		if (prefix == null) {
-			return "";
-		}
-
-		NamespaceMapper namespaceMapper = NamespaceMapperFactory
-				.getNamespaceMapper(ctx);
-		if (namespaceMapper == null) {
-			log.warn("No NamespaceMapper in ServletContext. Request URL was '"
-					+ vreq.getRequestURL() + "'");
-			return "";
-		}
-
-		String ns = namespaceMapper.getNamespaceForPrefix(prefix);
-
-		return (ns == null) ? "" : ns;
-	}
-
 	@Override
 	public Individual getIndividualByURI(String individualUri) {
 		if (individualUri == null) {

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzer.java

@@ -30,7 +30,6 @@ public class IndividualRequestAnalyzer {
 	private static Pattern RDF_REQUEST = Pattern.compile("^/individual/([^/]+)/\\1\\.(rdf|n3|ttl)$");
     private static Pattern HTML_REQUEST = Pattern.compile("^/display/([^/]+)$");
 	private static Pattern LINKED_DATA_URL = Pattern.compile("^/individual/([^/]+)$");		
-	private static Pattern NS_PREFIX_URL = Pattern.compile("^/individual/([^/]*)/([^/]+)$");
 	
 	private final VitroRequest vreq;
 	private final IndividualRequestAnalysisContext analysisContext;
@@ -164,7 +163,6 @@ public class IndividualRequestAnalyzer {
 	 *     /individual/localname/localname.rdf
 	 *     /individual/localname/localname.n3
 	 *     /individual/localname/localname.ttl
-	 *     /individual/nsprefix/localname
 	 * </pre>
 	 * 
 	 * @return null on failure.
@@ -202,14 +200,6 @@ public class IndividualRequestAnalyzer {
 				return getIndividualByLocalname(rdfMatch.group(1));
 			}
 	
-			// Does the URL look like a namespace prefix followed by a local
-			// name?
-			Matcher prefix_match = NS_PREFIX_URL.matcher(url);
-			if (prefix_match.matches() && prefix_match.groupCount() == 2) {
-				return getIndividualByPrefixAndLocalname(prefix_match.group(1),
-						prefix_match.group(2));
-			}
-	
 			// Couldn't match it to anything.
 			return null;
 		} catch (Throwable e) {
@@ -299,12 +289,6 @@ public class IndividualRequestAnalyzer {
 		return getIndividualByUri(uri);
 	}
 
-	private Individual getIndividualByPrefixAndLocalname(String prefix,
-			String localName) {
-		String ns = analysisContext.getNamespaceForPrefix(prefix);
-		return getIndividualByUri(ns + localName);
-	}
-
 	private Individual getIndividualByNetId(String netId) {
 		return analysisContext.getIndividualByNetId(netId);
 	}

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/serving/FileServingServlet.java

@@ -94,6 +94,10 @@ public class FileServingServlet extends VitroHttpServlet {
 			String actualFilename = findAndValidateFilename(fileInfo, path);
 
 			in = openImageInputStream(fileInfo, actualFilename);
+		} catch (FileServingException e) {
+			log.info("Failed to serve the file at '" + path + "' -- " + e.getMessage());
+			in = openMissingLinkImage(request);
+			mimeType = "image/png";
 		} catch (Exception e) {
 			log.warn("Failed to serve the file at '" + path + "' -- " + e.getMessage());
 			in = openMissingLinkImage(request);

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/StartupStatusDisplayFilter.java

@@ -21,6 +21,8 @@ import javax.servlet.http.HttpServletResponse;
 import org.apache.commons.lang.StringUtils;
 
 import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
+import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
+import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 import freemarker.cache.WebappTemplateLoader;
 import freemarker.template.Configuration;
@@ -67,9 +69,10 @@ public class StartupStatusDisplayFilter implements Filter {
 		statusAlreadyDisplayed = true;
 	}
 
-	private void displayStartupStatus(ServletRequest req, ServletResponse resp) throws IOException,
+	private void displayStartupStatus(ServletRequest req, ServletResponse resp)
-			ServletException {
+			throws IOException, ServletException {
-		HttpServletResponse hResp = (HttpServletResponse) resp;
+		HttpServletResponse hresp = (HttpServletResponse) resp;
+		HttpServletRequest hreq = (HttpServletRequest) req;
 
 		try {
 			Map<String, Object> bodyMap = new HashMap<String, Object>();
@@ -78,25 +81,24 @@ public class StartupStatusDisplayFilter implements Filter {
 			bodyMap.put("contextPath", getContextPath());
 			bodyMap.put("applicationName", getApplicationName());
 
-	        HttpServletRequest httpreq = (HttpServletRequest) req;
+			String url = "";
-	        String url = "";
 
-	        String path = httpreq.getRequestURI();
+			String path = hreq.getRequestURI();
-	        if( path != null ){
+			if (path != null) {
-	        	url = path;
+				url = path;
-	        }
+			}
 
-	        String query = httpreq.getQueryString();
+			String query = hreq.getQueryString();
-	        if( !StringUtils.isEmpty( query )){
+			if (!StringUtils.isEmpty(query)) {
-	        	url = url + "?" + query;
+				url = url + "?" + query;
-	        }	
+			}
 
-			bodyMap.put("url", url );
+			bodyMap.put("url", url);
 
-			hResp.setContentType("text/html;charset=UTF-8");
+			hresp.setContentType("text/html;charset=UTF-8");
-			hResp.setStatus(SC_INTERNAL_SERVER_ERROR);
+			hresp.setStatus(SC_INTERNAL_SERVER_ERROR);
 			Template tpl = loadFreemarkerTemplate();
-			tpl.process(bodyMap, hResp.getWriter());
+			tpl.process(bodyMap, hresp.getWriter());
 		} catch (TemplateException e) {
 			throw new ServletException("Problem with Freemarker Template", e);
 		}
@@ -114,7 +116,9 @@ public class StartupStatusDisplayFilter implements Filter {
 	private Object getApplicationName() {
 		String name = "";
 		try {
-			ApplicationBean app = ApplicationBean.getAppBean(ctx);
+			WebappDaoFactory wadf = (WebappDaoFactory) ctx
+					.getAttribute("webappDaoFactory");
+			ApplicationBean app = wadf.getApplicationDao().getApplicationBean();
 			name = app.getApplicationName();
 		} catch (Exception e) {
 			// deal with problems below

webapp/src/edu/cornell/mannlib/vitro/webapp/filters/VitroRequestPrep.java

@@ -38,7 +38,6 @@ import edu.cornell.mannlib.vitro.webapp.auth.identifier.RequestIdentifiers;
 import edu.cornell.mannlib.vitro.webapp.auth.permissions.SimplePermission;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.PolicyHelper;
 import edu.cornell.mannlib.vitro.webapp.auth.policy.ServletPolicyList;
-import edu.cornell.mannlib.vitro.webapp.beans.ApplicationBean;
 import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
 import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
@@ -82,19 +81,10 @@ public class VitroRequestPrep implements Filter {
     };
 
     private ServletContext _context;
-    private ApplicationBean _appbean;    
     
     @Override
 	public void init(FilterConfig filterConfig) throws ServletException {
         _context = filterConfig.getServletContext();
-        
-        Object o =  _context.getAttribute("applicationBean");
-        if (o instanceof ApplicationBean) {
-            _appbean = (ApplicationBean) o; 
-        } else {
-            _appbean = new ApplicationBean();
-        }
-        log.debug("VitroRequestPrep: AppBean theme " + _appbean.getThemeDir());
     }    
     
     @Override
@@ -132,9 +122,6 @@ public class VitroRequestPrep implements Filter {
         
         VitroRequest vreq = new VitroRequest(req);
         
-        //-- setup appBean --//
-        vreq.setAppBean(_appbean);
-        
         //-- setup DAO factory --//
         WebappDaoFactory wdf = getWebappDaoFactory(vreq);
         //TODO: get accept-language from request and set as preferred languages

webapp/test/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalyzerTest.java

@@ -52,15 +52,6 @@ public class IndividualRequestAnalyzerTest extends AbstractTestClass {
 	private static final String URL_BYTESTREAM_ALIAS = URL_HOME_PAGE + "/file/"
 			+ ID_FILE_BYTESTREAM + "/" + BYTESTREAM_FILENAME;
 
-	/**
-	 * Info about an individual that appears in a different namespace.
-	 */
-	private static final String SOME_PREFIX = "somePrefix";
-	private static final String SOME_NAMESPACE = "http://some.namespace/";
-	private static final String ID_INDIVIDUAL_FOREIGN = "foreignId";
-	private static final String URI_INDIVIDUAL_FOREIGN = SOME_NAMESPACE
-			+ ID_INDIVIDUAL_FOREIGN;
-
 	private IndividualRequestAnalyzer analyzer;
 	private IndividualRequestAnalysisContextStub analysisContext;
 	private HttpServletRequestStub req;
@@ -69,7 +60,6 @@ public class IndividualRequestAnalyzerTest extends AbstractTestClass {
 
 	private IndividualStub testIndividual;
 	private IndividualStub bytestreamIndividual;
-	private IndividualStub foreignIndividual;
 
 	@Before
 	public void setup() {
@@ -83,10 +73,6 @@ public class IndividualRequestAnalyzerTest extends AbstractTestClass {
 		bytestreamIndividual = new IndividualStub(URI_FILE_BYTESTREAM);
 		analysisContext.addIndividual(bytestreamIndividual);
 		analysisContext.setAliasUrl(URI_FILE_BYTESTREAM, URL_BYTESTREAM_ALIAS);
-
-		foreignIndividual = new IndividualStub(URI_INDIVIDUAL_FOREIGN);
-		analysisContext.addIndividual(foreignIndividual);
-		analysisContext.setNamespacePrefix(SOME_PREFIX, SOME_NAMESPACE);
 	}
 
 	// ----------------------------------------------------------------------
@@ -132,16 +118,6 @@ public class IndividualRequestAnalyzerTest extends AbstractTestClass {
 		assertDefaultRequestInfo("find by display path", URI_INDIVIDUAL_TEST);
 	}
 
-	/** /individual/nsPrefix/localname */
-	@Test
-	public void findByPrefixAndLocalname() {
-		req.setRequestUrl(url(DEFAULT_NAMESPACE + SOME_PREFIX + "/"
-				+ ID_INDIVIDUAL_FOREIGN));
-		analyzeIt();
-		assertDefaultRequestInfo("find by prefix and localname",
-				URI_INDIVIDUAL_FOREIGN);
-	}
-
 	/** /individual/a/b/c fails. */
 	@Test
 	public void unrecognizedPath() {

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRequestAnalysisContextStub.java

@@ -21,7 +21,6 @@ public class IndividualRequestAnalysisContextStub implements
 	private final String defaultNamespace;
 	private final Map<String, Individual> individualsByUri = new HashMap<String, Individual>();
 	private final Map<String, Individual> profilePages = new HashMap<String, Individual>();
-	private final Map<String, String> namespacesByPrefix = new HashMap<String, String>();
 	private final Map<String, String> aliasUrlsByIndividual = new HashMap<String, String>();
 
 	public IndividualRequestAnalysisContextStub(String defaultNamespace) {
@@ -36,10 +35,6 @@ public class IndividualRequestAnalysisContextStub implements
 		profilePages.put(netId, individual);
 	}
 
-	public void setNamespacePrefix(String prefix, String namespace) {
-		namespacesByPrefix.put(prefix, namespace);
-	}
-
 	public void setAliasUrl(String individualUri, String aliasUrl) {
 		aliasUrlsByIndividual.put(individualUri, aliasUrl);
 	}
@@ -53,15 +48,6 @@ public class IndividualRequestAnalysisContextStub implements
 		return defaultNamespace;
 	}
 
-	@Override
-	public String getNamespaceForPrefix(String prefix) {
-		if (prefix == null) {
-			return "";
-		}
-		String namespace = namespacesByPrefix.get(prefix);
-		return (namespace == null) ? "" : namespace;
-	}
-
 	@Override
 	public Individual getIndividualByURI(String individualUri) {
 		if (individualUri == null) {

webapp/test/stubs/edu/cornell/mannlib/vitro/webapp/utils/NamespaceMapperStub.java

@@ -1,123 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-package stubs.edu.cornell.mannlib.vitro.webapp.utils;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-
-import edu.cornell.mannlib.vitro.webapp.utils.NamespaceMapper;
-
-/**
- * A minimal implementation of the NamespaceMapper.
- * 
- * I have only implemented the methods that I needed. Feel free to implement
- * others.
- */
-public class NamespaceMapperStub implements NamespaceMapper {
-	// ----------------------------------------------------------------------
-	// Stub infrastructure
-	// ----------------------------------------------------------------------
-	
-	private final Map<String, String> prefixMap = new HashMap<String, String>();
-	
-	public void setPrefixForNamespace(String prefix, String namespace) {
-		prefixMap.put(prefix, namespace);
-	}
-
-	// ----------------------------------------------------------------------
-	// Stub methods
-	// ----------------------------------------------------------------------
-
-	@Override
-	public String getNamespaceForPrefix(String prefix) {
-		return prefixMap.get(prefix);
-	}
-
-	// ----------------------------------------------------------------------
-	// Un-implemented methods
-	// ----------------------------------------------------------------------
-
-	@Override
-	public void addedStatement(Statement arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.addedStatement() not implemented.");
-	}
-
-	@Override
-	public void addedStatements(Statement[] arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.addedStatements() not implemented.");
-	}
-
-	@Override
-	public void addedStatements(List<Statement> arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.addedStatements() not implemented.");
-	}
-
-	@Override
-	public void addedStatements(StmtIterator arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.addedStatements() not implemented.");
-	}
-
-	@Override
-	public void addedStatements(Model arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.addedStatements() not implemented.");
-	}
-
-	@Override
-	public void notifyEvent(Model arg0, Object arg1) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.notifyEvent() not implemented.");
-	}
-
-	@Override
-	public void removedStatement(Statement arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.removedStatement() not implemented.");
-	}
-
-	@Override
-	public void removedStatements(Statement[] arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.removedStatements() not implemented.");
-	}
-
-	@Override
-	public void removedStatements(List<Statement> arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.removedStatements() not implemented.");
-	}
-
-	@Override
-	public void removedStatements(StmtIterator arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.removedStatements() not implemented.");
-	}
-
-	@Override
-	public void removedStatements(Model arg0) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.removedStatements() not implemented.");
-	}
-
-	@Override
-	public String getPrefixForNamespace(String namespace) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.getPrefixForNamespace() not implemented.");
-	}
-
-	@Override
-	public List<String> getPrefixesForNamespace(String namespace) {
-		throw new RuntimeException(
-				"NamespaceMapperStub.getPrefixesForNamespace() not implemented.");
-	}
-
-}

webapp/web/error.jsp

@@ -13,7 +13,6 @@
             request.setAttribute("bodyJsp", "/errorbody.jsp");
             request.setAttribute("title", "Error");
             request.setAttribute("css", "");
-            request.setAttribute("appBean", appBean);
             request.setAttribute("themeDir", themeDir);
             %>
 

webapp/web/js/imageUpload/validateUpload.js

@@ -1,9 +0,0 @@
-/* $This file is distributed under the terms of the license in /doc/license.txt$ */
-
-function validate_upload_file(form_passed){
-
-    if (form_passed.datafile.value == "") {
-        alert ("Please browse and select a photo");
-        return false;
-    }
-}

webapp/web/templates/page/basicPage.jsp

@@ -38,9 +38,6 @@
         if (request.getAttribute("css") == null){
             e+="basicPage.jsp expects that request parameter 'css' be set to css to include in page.\n";
         }
-        if( request.getAttribute("appBean") == null){
-            e+="basicPage.jsp expects that request attribute 'appBean' be set.\n";
-        }
         if( e.length() > 0 ){
             throw new JspException(e);
         }

webapp/web/templates/page/blankPage.jsp

@@ -31,9 +31,6 @@
         if (request.getAttribute("css") == null){
             e+="basicPage.jsp expects that request parameter 'css' be set to css to include in page.\n";            
         }         
-        if( request.getAttribute("appBean") == null){
-            e+="basicPage.jsp expects that request attribute 'appBean' be set.\n";          
-        }
         if( e.length() > 0 ){
             throw new JspException(e);
         }