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

um, just mergin' in the remote changes before a push?

webapp/config/licenser/known_exceptions.txt

@@ -165,6 +165,9 @@ webapp/web/js/raphael/*
 # See /doc/3rd-party-licenses.txt for LICENSE file
 webapp/web/js/sparql/prototype.js
 
+# See /doc/3rd-party-licenses.txt for LICENSE file
+webapp/web/js/amplify/amplify.store.min.js
+
 # Apache Solr search platform. See /doc/3rd-party-licenses.txt for LICENSE file
 solr/**/*
 solr/*

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/edit/n3editing/configuration/generators/DateTimeValueFormGenerator.java

@@ -27,7 +27,7 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
         implements EditConfigurationGenerator {
 	
 	final static String vivoCore = "http://vivoweb.org/ontology/core#";
-	final static String toDateTimeValue = vivoCore + "dateTimeValue";
+	final  String toDateTimeValue = vivoCore + "dateTimeValue";
 	final static String valueType = vivoCore + "DateTimeValue";
 	final static String dateTimeValue = vivoCore + "dateTime";
 	final static String dateTimePrecision = vivoCore + "dateTimePrecision";
@@ -41,23 +41,23 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
         initPropertyParameters(vreq, session, conf);
         initObjectPropForm(conf, vreq);               
         
-        conf.setTemplate("dateTimeValueForm.ftl");
+        conf.setTemplate(this.getTemplate());
         
         conf.setVarNameForSubject("subject");
         conf.setVarNameForPredicate("toDateTimeValue");
         conf.setVarNameForObject("valueNode");
         
-        conf.setN3Optional(Arrays.asList(n3ForValue));
+        conf.setN3Optional(Arrays.asList(getN3ForValue()));
         
         conf.addNewResource("valueNode", DEFAULT_NS_FOR_NEW_RESOURCE);
         
         conf.addSparqlForExistingLiteral(
-        		"dateTimeField-value", existingDateTimeValueQuery);
+        		"dateTimeField-value", getExistingDateTimeValueQuery());
         conf.addSparqlForExistingUris(
-        		"dateTimeField-precision", existingPrecisionQuery);
+        		"dateTimeField-precision", getExistingPrecisionQuery());
-        conf.addSparqlForExistingUris("valueNode", existingNodeQuery);
+        conf.addSparqlForExistingUris("valueNode", getExistingNodeQuery());
         
-        FieldVTwo dateTimeField = new FieldVTwo().setName("dateTimeField");
+        FieldVTwo dateTimeField = new FieldVTwo().setName(this.getDateTimeFieldName());
         		dateTimeField.setEditElement(new DateTimeWithPrecisionVTwo(dateTimeField, 
         				VitroVocabulary.Precision.SECOND.uri(), 
         				VitroVocabulary.Precision.NONE.uri()));
@@ -71,30 +71,36 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
         return conf; 
 	} 
 	
-	final static String n3ForValue = 
+	
-        "?subject <" + toDateTimeValue + "> ?valueNode . \n" +
+	//Writing these as methods instead of static strings allows the method getToDateTimeValuePredicate
+	//to be called after the class has been initialized - this is important for subclasses of this generator
+	//that rely on vreq for predicate 
+	protected String getN3ForValue() {
+        return "?subject <" + this.getToDateTimeValuePredicate() + "> ?valueNode . \n" +
         "?valueNode a <" + valueType + "> . \n" +
         "?valueNode  <" + dateTimeValue + "> ?dateTimeField-value . \n" +
         "?valueNode  <" + dateTimePrecision + "> ?dateTimeField-precision ."; 
+	}
 	
-	final static String existingDateTimeValueQuery = 
+	protected String getExistingDateTimeValueQuery () {
-        "SELECT ?existingDateTimeValue WHERE { \n" +
+        return "SELECT ?existingDateTimeValue WHERE { \n" +
-        "?subject <" + toDateTimeValue + "> ?existingValueNode . \n" +
+        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
         "?existingValueNode a <" + valueType + "> . \n" +
         "?existingValueNode <" + dateTimeValue + "> ?existingDateTimeValue }";
+	}
 	
-	final static String existingPrecisionQuery = 
+	protected String getExistingPrecisionQuery() {
-        "SELECT ?existingPrecision WHERE { \n" +
+        return "SELECT ?existingPrecision WHERE { \n" +
-        "?subject <" + toDateTimeValue + "> ?existingValueNode . \n" +
+        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingValueNode . \n" +
         "?existingValueNode a <" + valueType + "> . \n" +
         "?existingValueNode <"  + dateTimePrecision + "> ?existingPrecision }";
-	
+	}
-	final static String existingNodeQuery =
+	protected String getExistingNodeQuery() {
-        "SELECT ?existingNode WHERE { \n" +
+        return "SELECT ?existingNode WHERE { \n" +
-        "?subject <" + toDateTimeValue + "> ?existingNode . \n" +
+        "?subject <" + this.getToDateTimeValuePredicate() + "> ?existingNode . \n" +
         "?existingNode a <" + valueType + "> }";
 
-	
+	}
 	public static String getNodeVar() {
 		return "valueNode";
 	}
@@ -103,6 +109,19 @@ public class DateTimeValueFormGenerator extends BaseEditConfigurationGenerator
 		return "?" + getNodeVar();
 	}
 
+	//isolating the predicate in this fashion allows this class to be subclassed for other date time value
+	//properties
+	protected String getToDateTimeValuePredicate() {
+		return this.toDateTimeValue;
+	}
+	
+	protected String getDateTimeFieldName() {
+		return "dateTimeField";
+	}
+	
+	protected String getTemplate() {
+		return "dateTimeValueForm.ftl";
+	}
 //Adding form specific data such as edit mode
 	public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
 		HashMap<String, Object> formSpecificData = new HashMap<String, Object>();

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 path = httpreq.getRequestURI();
+			String path = hreq.getRequestURI();
 			if (path != null) {
 				url = path;
 			}
 
-	        String query = httpreq.getQueryString();
+			String query = hreq.getQueryString();
 			if (!StringUtils.isEmpty(query)) {
 				url = url + "?" + query;
 			}
 
 			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/css/individual/individual-property-groups.css

@@ -0,0 +1,32 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+span#toggleContainer {
+    float:right;
+    padding:10px 8px 0 0;
+    font-size: 0.85em;
+}
+section.property-group h2 { 
+    padding: 8px 10px 4px 12px; 
+}
+.scroll-up {
+   position: absolute; 
+   width: 21px;
+   height: 30px;
+   top: 8px; /* changed for redesign, was 0 */
+   right: 12px; /* changed for redesign, was -21px;*/
+}
+section.property-group div {
+    margin-top:15px;
+    display:none;
+}
+section.property-group h2 {
+    font-size: 1.15em !important; 
+    color: #5e6363 !important; 
+    font-weight: normal !important;
+    background: #fafaf9 !important; 
+}
+/* this class is referenced in java script; the important is needed to override the color in the previous selector */
+section.property-group h2.expandedPropGroupH2 {
+    background:#e4ecf3 !important;
+    color:#2485ae !important;  
+}

webapp/web/css/individual/individual.css

@@ -32,7 +32,7 @@
 /* <------ INDIVIDUAL INTRO FOR ANY CLASS*/
 #individual-intro {
     margin-top: 15px;
-    margin-bottom: 20px;
+    margin-bottom: 0;
     position: relative;
     overflow: hidden;
 }
@@ -63,7 +63,7 @@ img#uriIcon {
     width: 166px;
     float: left;
     padding-right: 1.5em;
-    margin-bottom: 20px;
+    margin-bottom: 0;
 }
 #share-contact h3 {
     margin-top: 15px;

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/amplify/amplify.store.min.js

@@ -0,0 +1,10 @@
+/*!
+ * Amplify Store - Persistent Client-Side Storage 1.1.0
+ * 
+ * Copyright 2011 appendTo LLC. (http://appendto.com/team)
+ * Dual licensed under the MIT or GPL licenses.
+ * http://appendto.com/open-source-licenses
+ * 
+ * http://amplifyjs.com
+ */
+(function(a,b){function e(a,e){c.addType(a,function(f,g,h){var i,j,k,l,m=g,n=(new Date).getTime();if(!f){m={},l=[],k=0;try{f=e.length;while(f=e.key(k++))d.test(f)&&(j=JSON.parse(e.getItem(f)),j.expires&&j.expires<=n?l.push(f):m[f.replace(d,"")]=j.data);while(f=l.pop())e.removeItem(f)}catch(o){}return m}f="__amplify__"+f;if(g===b){i=e.getItem(f),j=i?JSON.parse(i):{expires:-1};if(j.expires&&j.expires<=n)e.removeItem(f);else return j.data}else if(g===null)e.removeItem(f);else{j=JSON.stringify({data:g,expires:h.expires?n+h.expires:null});try{e.setItem(f,j)}catch(o){c[a]();try{e.setItem(f,j)}catch(o){throw c.error()}}}return m})}var c=a.store=function(a,b,d,e){var e=c.type;d&&d.type&&d.type in c.types&&(e=d.type);return c.types[e](a,b,d||{})};c.types={},c.type=null,c.addType=function(a,b){c.type||(c.type=a),c.types[a]=b,c[a]=function(b,d,e){e=e||{},e.type=a;return c(b,d,e)}},c.error=function(){return"amplify.store quota exceeded"};var d=/^__amplify__/;for(var f in{localStorage:1,sessionStorage:1})try{window[f].getItem&&e(f,window[f])}catch(g){}if(window.globalStorage)try{e("globalStorage",window.globalStorage[window.location.hostname]),c.type==="sessionStorage"&&(c.type="globalStorage")}catch(g){}(function(){if(!c.types.localStorage){var a=document.createElement("div"),d="amplify";a.style.display="none",document.getElementsByTagName("head")[0].appendChild(a);try{a.addBehavior("#default#userdata"),a.load(d)}catch(e){a.parentNode.removeChild(a);return}c.addType("userData",function(e,f,g){a.load(d);var h,i,j,k,l,m=f,n=(new Date).getTime();if(!e){m={},l=[],k=0;while(h=a.XMLDocument.documentElement.attributes[k++])i=JSON.parse(h.value),i.expires&&i.expires<=n?l.push(h.name):m[h.name]=i.data;while(e=l.pop())a.removeAttribute(e);a.save(d);return m}e=e.replace(/[^-._0-9A-Za-z\xb7\xc0-\xd6\xd8-\xf6\xf8-\u037d\u37f-\u1fff\u200c-\u200d\u203f\u2040\u2070-\u218f]/g,"-");if(f===b){h=a.getAttribute(e),i=h?JSON.parse(h):{expires:-1};if(i.expires&&i.expires<=n)a.removeAttribute(e);else return i.data}else f===null?a.removeAttribute(e):(j=a.getAttribute(e),i=JSON.stringify({data:f,expires:g.expires?n+g.expires:null}),a.setAttribute(e,i));try{a.save(d)}catch(o){j===null?a.removeAttribute(e):a.setAttribute(e,j),c.userData();try{a.setAttribute(e,i),a.save(d)}catch(o){j===null?a.removeAttribute(e):a.setAttribute(e,j);throw c.error()}}return m})}})(),function(){function e(a){return a===b?b:JSON.parse(JSON.stringify(a))}var a={},d={};c.addType("memory",function(c,f,g){if(!c)return e(a);if(f===b)return e(a[c]);d[c]&&(clearTimeout(d[c]),delete d[c]);if(f===null){delete a[c];return null}a[c]=f,g.expires&&(d[c]=setTimeout(function(){delete a[c],delete d[c]},g.expires));return f})}()})(this.amplify=this.amplify||{})

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/js/individual/propertyGroupControls.js

@@ -0,0 +1,115 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+$(document).ready(function(){
+        
+    $.extend(this, individualLocalName);
+    
+    retrieveLocalStorage();
+
+    // expands/collapses the div within each property group
+    $.each($('section.property-group'), function() {
+        var groupName = $(this).attr("id");
+        $(this).children("nav").children("img").click(function() {
+            if ( $("div[id='" + groupName + "Group']").is(":visible") ) {
+                $("div[id='" + groupName + "Group']").slideUp(222);
+                $(this).attr("src", $(this).attr("src").replace("collapse-prop-group","expand-prop-group"));
+                $("section#" + groupName).children("h2").removeClass("expandedPropGroupH2");
+            }
+            else {
+                $("div[id='" + groupName + "Group']").slideDown(222);
+                $(this).attr("src", $(this).attr("src").replace("expand-prop-group","collapse-prop-group"));
+                $("section#" + groupName).children("h2").addClass("expandedPropGroupH2");
+            }
+            manageLocalStorage();
+        });
+    });
+
+
+    // expands/collapses all property groups together
+    $.each($('a#propertyGroupsToggle'), function() {
+        $('a#propertyGroupsToggle').click(function() {
+            var anchorHtml = $(this).html();
+            if ( anchorHtml.indexOf('expand') > -1 ) {
+                $.each($('section.property-group'), function() {
+                    $("div[id='" + $(this).attr("id") + "Group']").slideDown(222);
+                    var innerSrc = $(this).children("nav").children("img").attr("src");
+                    $(this).children("nav").children("img").attr("src",innerSrc.replace("expand-prop-group","collapse-prop-group"));
+                    $(this).children("h2").addClass("expandedPropGroupH2");
+                });
+                $(this).html("collapse all");
+            }
+            else {
+                $.each($('section.property-group'), function() {
+                    $("div[id='" + $(this).attr("id") + "Group']").slideUp(222);
+                    var innerSrc = $(this).children("nav").children("img").attr("src");
+                    $(this).children("nav").children("img").attr("src",innerSrc.replace("collapse-prop-group","expand-prop-group"));
+                    $(this).children("h2").removeClass("expandedPropGroupH2");
+                });
+                $(this).html("expand all");
+            }
+            manageLocalStorage();
+        });
+   }); 
+   
+    //  Next two functions --  keep track of which property group tabs have been expanded,
+    //  so if we return from a custom form or a related individual, even via the back button,
+    //  the property groups will be expanded as before.
+    function manageLocalStorage() {
+        var localName = this.individualLocalName;
+        // is this individual already stored? If not, how many have been stored?
+        // If the answer is 3, remove the first one in before adding the new one
+        var current = amplify.store(localName);
+        var profiles = amplify.store("profiles");
+        if ( current == undefined ) {
+            if ( profiles == undefined ) {
+                var lnArray = [];
+                lnArray.push(localName);
+                amplify.store("profiles", lnArray);
+            }
+            else if ( profiles != undefined && profiles.length >= 3 ) {
+                firstItem = profiles[0];
+                amplify.store(firstItem, null);
+                profiles.splice(0,1);
+                profiles.push(localName);
+                amplify.store("profiles", profiles)
+            }
+            else if ( profiles != undefined && profiles.length < 3 ) {
+                profiles.push(localName);
+                amplify.store("profiles", profiles)
+            }
+        }
+        var groups = [];
+        $.each($('section.property-group').children("nav").children("img"), function() {
+            if ( $(this).attr('src').indexOf('collapse-prop-group') > -1 ) {
+                groups.push($(this).attr('groupName'));
+            }
+        });
+        amplify.store(localName, groups);
+        var checkLength = amplify.store(localName);
+        if ( checkLength.length == 0 ) {
+            amplify.store(localName, null);
+        }
+    }
+
+    function retrieveLocalStorage() {
+        var localName = this.individualLocalName;
+        var groups = amplify.store(individualLocalName);
+            if ( groups != undefined ) {
+                for ( i = 0; i < groups.length; i++) {
+                    var groupName = groups[i];
+                    // unlikely, but it's possible a group that was previously opened and stored won't be displayed
+                    // because the object properties would have been deleted. So ensure that the group in local
+                    // storage has been rendered on the page. More likely, a user navigated from a quick view to a full
+                    // profile, opened a group, then navigated back to the quick view where the group isn't rendered.
+                    if ($("section#" + groupName).length ) {
+                        $("div[id='" + groupName + "Group']").slideDown(1);
+                        $("img[groupName='" + groupName + "']").attr("src", $("img[groupName='" + groupName + "']").attr("src").replace("expand-prop-group","collapse-prop-group"));
+                        $("section#" + groupName).children("h2").addClass("expandedPropGroupH2");
+                    }
+                }
+                if ( groups.length == $('section.property-group').length ) {
+                    $('a#propertyGroupsToggle').html('collapse all');
+                }
+            }
+        }
+});

webapp/web/templates/freemarker/body/individual/individual-vitro.ftl

@@ -49,10 +49,18 @@
 <#assign nameForOtherGroup = "other"> <#-- used by both individual-propertyGroupMenu.ftl and individual-properties.ftl -->
 
 <#-- Property group menu -->
+<#-- With release 1.6 the property group is no longer used. The include statement
+     remains in the event a particular VIVO site still wants to use it with the new
+     collapsible groups.
+     
      <#include "individual-propertyGroupMenu.ftl">
+-->
 
 <#-- Ontology properties -->
 <#include "individual-properties.ftl">
+<script>
+    var individualLocalName = "${individual.localName}";
+</script>
 
 <#assign rdfUrl = individual.rdfUrl>
 

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

@@ -1,7 +1,27 @@
 <#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
 
-<#-- Default individual profile page template -->
+<#-- Default VIVO individual profile page template (extends individual.ftl in vitro) -->
 
 <#include "individual-setup.ftl">
+<#import "lib-vivo-properties.ftl" as vp>
+
+<#assign individualProductExtension>
+    <#-- Include for any class specific template additions -->
+    ${classSpecificExtension!}
+    <@vp.webpages propertyGroups editable />
+    <!--PREINDIVIDUAL OVERVIEW.FTL-->
+    <#include "individual-overview.ftl">
+        </section> <!-- #individual-info -->
+    </section> <!-- #individual-intro -->
+    <!--postindiviudal overiew tfl-->
+</#assign>
 
 <#include "individual-vitro.ftl">
+
+${stylesheets.add('<link rel="stylesheet" href="${urls.base}/css/individual/individual-vivo.css" />',
+                  '<link rel="stylesheet" href="${urls.base}/css/individual/individual-property-groups.css" />')}
+
+${headScripts.add('<script type="text/javascript" src="${urls.base}/js/jquery_plugins/jquery.truncator.js"></script>',
+                  '<script type="text/javascript" src="${urls.base}/js/amplify/amplify.store.min.js"></script>')}
+${scripts.add('<script type="text/javascript" src="${urls.base}/js/individual/individualUtils.js"></script>',
+              '<script type="text/javascript" src="${urls.base}/js/individual/propertyGroupControls.js"></script>')}

webapp/web/templates/freemarker/body/partials/individual/individual-properties.ftl

@@ -4,27 +4,35 @@
 
 <#import "lib-properties.ftl" as p>
 <#assign subjectUri = individual.controlPanelUrl()?split("=") >
+
+<#if ( propertyGroups.all?size > 1 ) >
+    <span id="toggleContainer">
+        <a id="propertyGroupsToggle" href="javascript:" title="expand all groups">expand all</a>
+    </span>
+<#else>
+    <p style="clear:both"><br /></p> 
+</#if>
 <#list propertyGroups.all as group>
     <#assign groupName = group.getName(nameForOtherGroup)>
     <#assign verbose = (verbosePropertySwitch.currentValue)!false>
-    
-    <section class="property-group" role="region">
-        <nav class="scroll-up" role="navigation">
-            <a href="#branding" title="scroll up">
-                <img src="${urls.images}/individual/scroll-up.gif" alt="scroll to property group menus" />
-            </a>
-        </nav>
-        
-        <#-- Display the group heading --> 
     <#if groupName?has_content>
 		<#--the function replaces spaces in the name with underscores, also called for the property group menu-->
     	<#assign groupNameHtmlId = p.createPropertyGroupHtmlId(groupName) >
-            <h2 id="${groupNameHtmlId}">${groupName?capitalize}</h2>
     <#else>
-            <h2 id="properties">Properties</h2>
+        <#assign groupName = "Properties">
+    	<#assign groupNameHtmlId = "properties" >
     </#if>
     
+    <section id="${groupNameHtmlId}" class="property-group" role="region">
+        <nav class="scroll-up" role="navigation">
+            <img src="${urls.images}/individual/expand-prop-group.png" groupName="${groupNameHtmlId}" alt="expand property group" title="expand this property group"/>
+        </nav>
+        
+        <#-- Display the group heading --> 
+            <h2 id="${groupNameHtmlId}">${groupName?capitalize}</h2>
+        
         <#-- List the properties in the group -->
+            <div id="${groupNameHtmlId}Group" >
             <#list group.properties as property>
                 <article class="property" role="article">
                     <#-- Property display name -->
@@ -61,5 +69,16 @@
                     </ul>
                 </article> <!-- end property -->
             </#list>
+        </div>
     </section> <!-- end property-group -->
 </#list>
+<script>
+var propGroupCount = ${propertyGroups.all?size};
+if ( propGroupCount == 1 ) {
+    $('section.property-group').find('div').show();
+    $('section.property-group').find("h2").addClass("expandedPropGroupH2");
+    $('section.property-group').children("nav").children("img").hide();
+//    var innerSrc = $('section.property-group').children("nav").children("img").attr("src");
+//    $('section.property-group').children("nav").children("img").attr("src",innerSrc.replace("expand-prop-group","collapse-prop-group"));
+}
+</script>

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);
         }