treebase-guts — Commit and tracker messages

[Treebase-guts] SF.net SVN: treebase:[566] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlObjectConverter.java

[<rv...@us...>]

Revision: 566
          http://treebase.svn.sourceforge.net/treebase/?rev=566&view=rev
Author:   rvos
Date:     2010-03-12 23:36:19 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Added logging messages.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2010-03-12 23:34:13 UTC (rev 565)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlObjectConverter.java	2010-03-12 23:36:19 UTC (rev 566)
@@ -7,6 +7,7 @@
 import java.util.Iterator;
 import java.util.Set;
 
+import org.apache.log4j.Logger;
 import org.cipres.treebase.TreebaseIDString;
 import org.cipres.treebase.NamespacedGUID;
 import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
@@ -21,6 +22,7 @@
 import org.nexml.model.OTUs;
 
 public class NexmlObjectConverter extends AbstractNexusConverter {
+	private Logger logger = Logger.getLogger(NexmlObjectConverter.class);
 	protected static URI mDCURI;
 	protected static URI mPrismURI;
 	protected static URI mTBTermsURI;
@@ -87,6 +89,7 @@
 		if ( null != tbPersistable.getId() ) {
 			//attachAnnotation(mDCIdentifier,makeNamespacedID(tbPersistable,persistableClass),mDCURI,annotatable);			
 			String uriString = getDocument().getBaseURI().toString() + tbPersistable.getPhyloWSPath().toString();
+			annotatable.addAnnotationValue("tb:resource",mTBTermsURI, URI.create(uriString));
 			annotatable.addAnnotationValue("dcterms:relation",mDCURI, URI.create(uriString));
 		}
 	}
@@ -133,8 +136,10 @@
 	}
 	
 	protected OTUs getOTUsById(Long taxonLabelSetId) {
-		for ( OTUs otus : getDocument().getOTUsList() ) {
+		logger.debug("Going to look for taxa block "+taxonLabelSetId);
+		for ( OTUs otus : getDocument().getOTUsList() ) {			
 			Long annotatedID = readTreeBaseID(otus);
+			logger.debug("Seen taxa block "+annotatedID);
 			if ( taxonLabelSetId.equals(annotatedID) ) {
 				return otus;
 			}


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[Treebase-guts] SF.net SVN: treebase:[565] trunk/treebase-core/src/main/java/org/cipres/ treebase/service/nexus/NexusServiceRDFa.java

[<rv...@us...>]

Revision: 565
          http://treebase.svn.sourceforge.net/treebase/?rev=565&view=rev
Author:   rvos
Date:     2010-03-12 23:34:13 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Flattened rdf triples. TODO: replace id attributes with purl URIs.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-03-12 23:32:59 UTC (rev 564)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/nexus/NexusServiceRDFa.java	2010-03-12 23:34:13 UTC (rev 565)
@@ -11,6 +11,8 @@
 
 import javax.xml.parsers.ParserConfigurationException;
 
+import org.apache.log4j.Logger;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.domain.nexus.NexusDataSet;
 import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
 import org.cipres.treebase.domain.study.Study;
@@ -35,46 +37,86 @@
  *
  */
 public class NexusServiceRDFa extends NexusServiceNexml {
+	private static final Logger LOGGER = Logger.getLogger(NexusServiceRDFa.class);
+	
+	/**
+	 * 
+	 */
 	public String serialize(NexusDataSet nexusDataSet,Properties properties) {
 		NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, properties);
 		return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());
 	}
+	
+	/**
+	 * 
+	 */
 	public String serialize(NexusDataSet nexusDataSet) {
-		/*
-		Document document = null;
-		try {
-			document = DocumentFactory.createDocument();
-		} catch (ParserConfigurationException e) {
-			e.printStackTrace();
-		}
-		NexmlDocumentConverter ndc = new NexmlDocumentConverter(null,getTaxonLabelHome(),document);
-		String NeXML = ndc.fromTreeBaseToXml(nexusDataSet).getXmlString();
-		return transform(NeXML);
-		*/
 		NexmlDocumentConverter ndc = getNexmlDocumentConverter(null, null);
 		return transform(ndc.fromTreeBaseToXml(nexusDataSet).getXmlString());		
 	}
 
+	/**
+	 * 
+	 */
 	public String serialize(Study study,Properties properties) {
 		NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, properties);
 		return transform(ndc.fromTreeBaseToXml(study).getXmlString());
 	}
+	
+	/**
+	 * 
+	 */
 	public String serialize(Study study) {
-		/*
-		Document document = null;
-		try {
-			document = DocumentFactory.createDocument();
-		} catch (ParserConfigurationException e) {
-			e.printStackTrace();
-		}
-		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),document);
-		String NeXML = ndc.fromTreeBaseToXml(study).getXmlString();
-		return transform(NeXML);
-		*/
 		NexmlDocumentConverter ndc = getNexmlDocumentConverter(study, null);
 		return transform(ndc.fromTreeBaseToXml(study).getXmlString());		
 	}
 	
+	/**
+	 * 
+	 * @param cdaoDoc
+	 */
+	private void normalizeCdaoDoc (org.dom4j.Document cdaoDoc) {
+		
+		LOGGER.info("inside normalizeCdaoDoc");
+		Iterator<org.dom4j.Element> parentIterator = cdaoDoc.getRootElement().elementIterator();
+		while ( parentIterator.hasNext() ) {
+			org.dom4j.Element parent = parentIterator.next();
+			QName rdfIDQName = QName.get("ID", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+			String rdfID = parent.attributeValue(rdfIDQName);
+			if ( ! TreebaseUtil.isEmpty(rdfID) ) {
+				
+				LOGGER.info("going to flatten ID "+rdfID);
+				Iterator<org.dom4j.Element> childIterator = cdaoDoc.getRootElement().elementIterator();
+				while ( childIterator.hasNext() ) {
+					org.dom4j.Element child = childIterator.next();
+					QName rdfAboutQName = QName.get("about", "rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#");
+					String rdfAbout = child.attributeValue(rdfAboutQName);
+					
+					if ( ! TreebaseUtil.isEmpty(rdfAbout) && rdfAbout.equals("#"+rdfID) ) {
+						
+						LOGGER.info("found referencing element");
+						Iterator<org.dom4j.Element> grandChildIterator = child.elementIterator();
+						while ( grandChildIterator.hasNext() ) {
+							org.dom4j.Element grandChild = grandChildIterator.next();
+							grandChild.detach();
+							parent.add(grandChild);
+						}
+						
+						childIterator.remove();
+					}
+
+				}
+			}
+		}
+
+	}
+	
+	/**
+	 * 
+	 * @param input
+	 * @return
+	 */
+	@SuppressWarnings("unchecked")
 	private String transform(String input) {
 		SAXReader reader = new SAXReader();
 		ByteArrayInputStream bs = new ByteArrayInputStream(input.getBytes());
@@ -82,6 +124,7 @@
 		try {
 			nexmlDocument = reader.read( bs );
 		} catch (DocumentException e) {
+			System.out.println(input);
 			e.printStackTrace();
 		}
 				
@@ -115,6 +158,7 @@
 			elt.detach();
 			cdaoDoc.getRootElement().add(elt);
 		}
+		normalizeCdaoDoc(cdaoDoc);
 		return cdaoDoc.asXML();		
 	}
 }


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[Treebase-guts] SF.net SVN: treebase:[564] trunk/treebase-core/src/test/java/org/cipres/ treebase/auxdata/AuxDataTest.java

[<rv...@us...>]

Revision: 564
          http://treebase.svn.sourceforge.net/treebase/?rev=564&view=rev
Author:   rvos
Date:     2010-03-12 23:32:59 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Added findByJournal auto-generated method stub, to satisfy interface requirements.

Modified Paths:
--------------
    trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java

Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java	2010-03-12 23:31:38 UTC (rev 563)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/auxdata/AuxDataTest.java	2010-03-12 23:32:59 UTC (rev 564)
@@ -336,6 +336,12 @@
 			// TODO Auto-generated method stub
 			return null;
 		}
+
+		public Collection<Study> findByJournal(String pJournal,
+				boolean pCaseSensitive) {
+			// TODO Auto-generated method stub
+			return null;
+		}
 	}
 }
 


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[Treebase-guts] SF.net SVN: treebase:[563] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/AnyObjectAsRDFController.java

[<rv...@us...>]

Revision: 563
          http://treebase.svn.sourceforge.net/treebase/?rev=563&view=rev
Author:   rvos
Date:     2010-03-12 23:31:38 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Removed unused template variables (we use purl domain instead of runtime-computed domain). Started sketching out functionality for generic annotations in rss feeds.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java	2010-03-12 23:29:53 UTC (rev 562)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/AnyObjectAsRDFController.java	2010-03-12 23:31:38 UTC (rev 563)
@@ -6,6 +6,8 @@
 import org.cipres.treebase.NamespacedGUID;
 import org.cipres.treebase.PhyloWSPath;
 import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.TreebaseUtil;
+import org.cipres.treebase.domain.Annotatable;
 import org.cipres.treebase.domain.matrix.Matrix;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.tree.PhyloTree;
@@ -45,20 +47,16 @@
 						request.setAttribute("hasRdf", true);
 					}
 					phyloWSPath = new PhyloWSPath(theClass.getPackage(),namespacedGUID);
+//					if ( theClass.isAssignableFrom(Annotatable.class) ) {
+//						request.setAttribute(arg0, arg1)
+//					}
 				}
 			}
 		}
 		request.getSession().setAttribute("namespacedGUID", namespacedGUID.toString());
 		// <c:set var="baseURL" value="http://localhost:8080/treebase-web/PhyloWS"/>
-		StringBuffer domainAddress = new StringBuffer("http://");
-		domainAddress
-			.append(request.getServerName())
-			.append(':')
-			.append(request.getServerPort());
-		StringBuffer baseURL = new StringBuffer(domainAddress);
-		baseURL.append("/treebase-web/phylows");
-		request.getSession().setAttribute("baseURL", baseURL.toString());
-		request.getSession().setAttribute("domainAddress", domainAddress.toString());
+		// treebase.purl.domain=http://purl.org/phylo/treebase/phylows/
+		request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlDomain());
 		request.getSession().setAttribute("phyloWSPath", phyloWSPath);
 		return new ModelAndView("anyObjectAsRDF");
 	}


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[Treebase-guts] SF.net SVN: treebase:[562] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/PhyloWSController.java

[<rv...@us...>]

Revision: 562
          http://treebase.svn.sourceforge.net/treebase/?rev=562&view=rev
Author:   rvos
Date:     2010-03-12 23:29:53 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Removed runtime-computed domain name and server port, which no longer work with the new tomcat configuration (would now compute "localhost"). Using relative URLs instead.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java	2010-03-12 23:27:28 UTC (rev 561)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java	2010-03-12 23:29:53 UTC (rev 562)
@@ -26,11 +26,28 @@
 	private PhyloTreeService mPhyloTreeService;
 	private StudyService mStudyService;
 	private static String format = "format";
+	
+	/* 
+	 * this array is used to identify whether a path fragment maps to an object
+	 * for which web pages are available. Maybe this should be an enum or a map
+	 * instead.
+	 */
 	private static String[] classesWithPages = { "tree", "study", "matrix" };
     
+	/**
+	 * Given an object prefix ("tree", "study" or "matrix") and an object ID, constructs
+	 * a relative URL to an HTML page about that object.
+	 * @param prefix identifies either studies, matrices or trees
+	 * @param objectId is the primary key for the requested object
+	 * @param request is the servlet request, which we need to check for reviewer access
+	 * @return a relative URL to an HTML page, or an empty string
+	 * @throws Exception
+	 */
     private String createUrl(String prefix, Long objectId,HttpServletRequest request) throws Exception {
     	String url = "";
     	StringBuffer base = new StringBuffer("/treebase-web/search/study");
+    	
+    	// requested object is a study
     	if ( prefix.equals(TreebaseIDString.getPrefixForClass(Study.class)) ) {
 			Study study = getStudyService().findByID(objectId);
 			if ( study == null ) {
@@ -54,6 +71,8 @@
 					.toString();
 			}
     	}   
+    	
+    	// requested object is a matrix
     	else if ( prefix.equals(TreebaseIDString.getPrefixForClass(Matrix.class)) ) {
     		Matrix matrix = getMatrixService().findByID(objectId);
     		if ( matrix == null ) {
@@ -67,6 +86,8 @@
     			.append(objectId)
     			.toString();
     	}
+    	
+    	// requested object is a tree
     	else if ( prefix.equals(TreebaseIDString.getPrefixForClass(PhyloTree.class)) ) {
     		PhyloTree phyloTree = getPhyloTreeService().findByID(objectId);
     		if ( phyloTree == null ) {
@@ -87,7 +108,7 @@
 		throws Exception {
         res.setContentType("text/plain");
         String url = null;
-        String domain = "http://" + req.getServerName() + ":" + req.getServerPort();
+        //String domain = "http://" + req.getServerName() + ":" + req.getServerPort();
 		if ( ! TreebaseUtil.isEmpty(req.getParameter(Constants.X_ACCESS_CODE)) ) {
 			req.getSession().setAttribute(
 				Constants.X_ACCESS_CODE, 
@@ -103,7 +124,8 @@
             }
             String[] pathComponents = pathInfo.split("/");
             if ( pathComponents[pathComponents.length-1].equals("find") ) {
-            	url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
+            	//url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
+            	url = createSearchUrl(pathComponents[pathComponents.length-2],req);
             } else {
 	            String rawNamespacedGUID = pathComponents[pathComponents.length-1];
 	            if ( rawNamespacedGUID.startsWith("uBio:") ) { // XXX be polite, use real URL
@@ -118,17 +140,17 @@
 		            if ( hasWebPage(pathComponents) ) {
 		            	String serializationFormat = createSerializationFormat(req);
 		            	if ( TreebaseUtil.isEmpty(serializationFormat) ) {
-		            		url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+		            		url = "/treebase-web/search/study/anyObjectAsRDF.rdf?namespacedGUID=" + namespacedGUID.toString();
 		            	}
 		            	else if ( serializationFormat.equals("html") ) {
-		            		url = domain + createUrl(tbID.getTypePrefix(),tbID.getId(),req);
+		            		url = createUrl(tbID.getTypePrefix(),tbID.getId(),req);
 		            	}
 		            	else {
-		            		url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
+		            		url = createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),serializationFormat);
 		            	}
 		            }
 		            else {
-		            	url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+		            	url = "/treebase-web/search/study/anyObjectAsRDF.rdf?namespacedGUID=" + namespacedGUID.toString();
 		            }
 	            }
             }
@@ -157,9 +179,8 @@
 	}
 	
 	private String createSearchUrl(String path,HttpServletRequest request) {
-		StringBuilder sb = new StringBuilder();
+		StringBuilder sb = new StringBuilder("/treebase-web/search/");
 		sb
-			.append("/treebase-web/search/")
 			.append(path)
 			.append("Search.html?query=")
 			.append(request.getParameter("query"))
@@ -170,6 +191,12 @@
 		return sb.toString();
 	}
 
+	/**
+	 * Given an array of path fragments, returns whether an HTML web page
+	 * exists for the type of object the fragments map onto
+	 * @param pathComponents
+	 * @return true of web page exists, false otherwise
+	 */
 	private boolean hasWebPage(String[] pathComponents) {
 		for ( int i = ( pathComponents.length - 1 ); i >= 0; i-- ) {
 			for ( int j = 0; j < classesWithPages.length; j++ ) {


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[Treebase-guts] SF.net SVN: treebase:[561] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchController.java

[<rv...@us...>]

Revision: 561
          http://treebase.svn.sourceforge.net/treebase/?rev=561&view=rev
Author:   rvos
Date:     2010-03-12 23:27:28 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Changed redirect view to point to .rdf extension, as opposed to .html extension.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2010-03-12 23:26:27 UTC (rev 560)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2010-03-12 23:27:28 UTC (rev 561)
@@ -123,7 +123,7 @@
 		if ( null != root ) {			
 			request.getSession().setAttribute("normalizedCQLQuery", URLEncoder.encode(root.toCQL(),"UTF-8"));
 		}
-		return new ModelAndView(new RedirectView("searchResultsAsRDF.html"));
+		return new ModelAndView(new RedirectView("searchResultsAsRDF.rdf"));
 	}
 	
 	protected <E extends TBPersistable> SearchResults<E> intersectSearchResults(


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[Treebase-guts] SF.net SVN: treebase:[560] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/SearchResultsAsRDFController.java

[<rv...@us...>]

Revision: 560
          http://treebase.svn.sourceforge.net/treebase/?rev=560&view=rev
Author:   rvos
Date:     2010-03-12 23:26:27 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Removed unused code.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java	2010-03-12 23:25:12 UTC (rev 559)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchResultsAsRDFController.java	2010-03-12 23:26:27 UTC (rev 560)
@@ -32,27 +32,10 @@
 		if ( null != frozenResults ) {
 			String phyloWSPath = request.getSession().getAttribute("originalSection") + "/find";
 			SearchResults<?> searchResults = frozenResults.thaw();
-			request.getSession().setAttribute("searchResultsThawed", searchResults);
-//			SearchResultsType searchResultsType = searchResults.getResultType();
-//			switch(searchResultsType) {
-//				case NONE   : phyloWSPath = ""; break;
-//				case STUDY  : phyloWSPath = "study/find"; break;
-//				case MATRIX : phyloWSPath = "matrix/find"; break;
-//				case TREE   : phyloWSPath = "tree/find"; break;
-//				case TAXON  : phyloWSPath = "taxon/find"; break;
-//			}
-			
-			StringBuffer domainAddress = new StringBuffer("http://");
-			domainAddress
-				.append(request.getServerName())
-				.append(':')
-				.append(request.getServerPort());
-			StringBuffer baseURL = new StringBuffer(domainAddress);
-			baseURL.append("/treebase-web/phylows");
+			request.getSession().setAttribute("searchResultsThawed", searchResults);			
 			request.getSession().setAttribute("recordSchema", request.getSession().getAttribute("recordSchema"));
 			request.getSession().setAttribute("format", "rss1");
-			request.getSession().setAttribute("baseURL", baseURL.toString());
-			request.getSession().setAttribute("domainAddress", domainAddress.toString());
+			request.getSession().setAttribute("baseURL", TreebaseUtil.getPurlDomain());
 			request.getSession().setAttribute("phyloWSPath", phyloWSPath);
 			if ( null != request.getParameter("query") ) {			
 				String query = request.getParameter("query");						
@@ -64,52 +47,6 @@
 			}
 		}
 		return new ModelAndView("searchResultsAsRDF");
-
-		
-		/*
-		
-		NamespacedGUID namespacedGUID = new NamespacedGUID(request.getParameter("namespacedGUID"));
-		TreebaseIDString treebaseIDString = null;
-		PhyloWSPath phyloWSPath = null;
-		request.setAttribute("hasWebPage", false);
-		request.setAttribute("hasNexus", false);
-		request.setAttribute("hasNeXML", false);
-		request.setAttribute("hasRdf", false);
-		try {
-			treebaseIDString = namespacedGUID.getTreebaseIDString();
-		} catch ( Exception e ) {
-			e.printStackTrace();
-		}
-		if ( null != treebaseIDString ) {
-			if ( null != treebaseIDString.getTypePrefix() ) {
-				Class<?> theClass = TreebaseIDString.getClassForPrefix(treebaseIDString.getTypePrefix());
-				if ( null != theClass ) {
-					if ( theClass.isAssignableFrom(PhyloTree.class) 
-							|| theClass.isAssignableFrom(Matrix.class) 
-							|| theClass.isAssignableFrom(Study.class) ) {
-						request.setAttribute("hasWebPage", true);
-						request.setAttribute("hasNexus", true);
-						request.setAttribute("hasNeXML", true);
-						request.setAttribute("hasRdf", true);
-					}
-					phyloWSPath = new PhyloWSPath(theClass.getPackage(),namespacedGUID);
-				}
-			}
-		}
-		request.getSession().setAttribute("namespacedGUID", namespacedGUID.toString());
-		// <c:set var="baseURL" value="http://localhost:8080/treebase-web/PhyloWS"/>
-		StringBuffer domainAddress = new StringBuffer("http://");
-		domainAddress
-			.append(request.getServerName())
-			.append(':')
-			.append(request.getServerPort());
-		StringBuffer baseURL = new StringBuffer(domainAddress);
-		baseURL.append("/treebase-web/phylows");
-		request.getSession().setAttribute("baseURL", baseURL.toString());
-		request.getSession().setAttribute("domainAddress", domainAddress.toString());
-		request.getSession().setAttribute("phyloWSPath", phyloWSPath);
-		return new ModelAndView("anyObjectAsRDF");
-		*/
 	}
 
 }


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[Treebase-guts] SF.net SVN: treebase:[559] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/StudySearchController.java

[<rv...@us...>]

Revision: 559
          http://treebase.svn.sourceforge.net/treebase/?rev=559&view=rev
Author:   rvos
Date:     2010-03-12 23:25:12 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Added mapping from CQL search predicate prism.publicationName to Study.findByJournal functionality.

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2010-03-12 23:23:11 UTC (rev 558)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2010-03-12 23:25:12 UTC (rev 559)
@@ -77,6 +77,7 @@
 		byLegacyID,
 		byTitle,
 		byKeyword,
+		byJournal
 	}
 
 	protected ModelAndView onSubmit(
@@ -191,6 +192,8 @@
 				results.addAll(doSearch(request, response, SearchType.inCitation, errors, term.getTerm()));				
 			} else if ( index.equals("tb.identifier.study.tb1") ) {
 				results.addAll(doSearch(request, response, SearchType.byLegacyID, errors, term.getTerm()));
+			} else if ( index.startsWith("prism.publicationName") ) {
+				results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm()));
 			} else {
 				// issue warnings
 				addMessage(request, "Unsupported index: " + index);
@@ -279,6 +282,9 @@
 			case byKeyword:
 				matches = studyService.findByKeyword(keywordSearchTerm);
 				break;
+			case byJournal:
+				matches = studyService.findByJournal(keywordSearchTerm, false);
+				break;
 			default:
 				throw new Error ("Unknown search type '" + searchType + "'");
 		}


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[Treebase-guts] SF.net SVN: treebase:[558] trunk/treebase-web/src/main/webapp/WEB-INF/pages /anyObjectAsRDF.jsp

[<rv...@us...>]

Revision: 558
          http://treebase.svn.sourceforge.net/treebase/?rev=558&view=rev
Author:   rvos
Date:     2010-03-12 23:23:11 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Removed superfluous feed image (we can't really compute its absolute path here, unless we hardcode things), removed superfluous forward slashes in URLs.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp	2010-03-12 23:22:09 UTC (rev 557)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/anyObjectAsRDF.jsp	2010-03-12 23:23:11 UTC (rev 558)
@@ -6,54 +6,54 @@
   xmlns:dcterms="http://purl.org/dc/terms/"
   xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns="http://purl.org/rss/1.0/">
-  <channel rdf:about="${baseURL}/${phyloWSPath}">
+  <channel rdf:about="${baseURL}${phyloWSPath}">
     <title>${phyloWSPath}</title>
     <link>${baseURL}</link>
     <description>Serializations for ${phyloWSPath}</description>
-    <image rdf:resource="${domainAddress}<fmt:message key="icons.treebase.16px"/>"/>
+    <%--image rdf:resource="<c:url value="/images/logo16px.png"/>"/--%>
     <items>
       <rdf:Seq>
-		<c:if test="${hasWebPage}"><rdf:li rdf:resource="${baseURL}/${phyloWSPath}?format=html"/></c:if>
-		<c:if test="${hasNeXML}"><rdf:li rdf:resource="${baseURL}/${phyloWSPath}?format=nexml"/></c:if>
-		<c:if test="${hasNexus}"><rdf:li rdf:resource="${baseURL}/${phyloWSPath}?format=nexus"/></c:if>
-		<c:if test="${hasRdf}"><rdf:li rdf:resource="${baseURL}/${phyloWSPath}?format=rdf"/></c:if>
+		<c:if test="${hasWebPage}"><rdf:li rdf:resource="${baseURL}${phyloWSPath}?format=html"/></c:if>
+		<c:if test="${hasNeXML}"><rdf:li rdf:resource="${baseURL}${phyloWSPath}?format=nexml"/></c:if>
+		<c:if test="${hasNexus}"><rdf:li rdf:resource="${baseURL}${phyloWSPath}?format=nexus"/></c:if>
+		<c:if test="${hasRdf}"><rdf:li rdf:resource="${baseURL}${phyloWSPath}?format=rdf"/></c:if>
       </rdf:Seq>
     </items>
   </channel>
-  <image rdf:about="${domainAddress}<fmt:message key="icons.treebase.16px"/>">
+  <%--image rdf:about="<c:url value="/images/logo16px.png"/>">
     <title>${phyloWSPath}</title>
     <link>${baseURL}</link>
-    <url>${domainAddress}<fmt:message key="icons.treebase.16px"/></url>
-  </image>
+    <url><c:url value="/images/logo16px.png"/></url>
+  </image--%>
   <c:if test="${hasWebPage}">
-  <item rdf:about="${baseURL}/${phyloWSPath}?format=html">
+  <item rdf:about="${baseURL}${phyloWSPath}?format=html">
     <title>Web page</title>
-    <link>${baseURL}/${phyloWSPath}?format=html</link>
+    <link>${baseURL}${phyloWSPath}?format=html</link>
     <description>A human-readable version of the resource</description>
     <dc:format>text/html</dc:format>
     <dc:language>EN-US</dc:language>
   </item>
   </c:if>
   <c:if test="${hasNeXML}">
-  <item rdf:about="${baseURL}/${phyloWSPath}?format=nexml">
+  <item rdf:about="${baseURL}${phyloWSPath}?format=nexml">
     <title>NeXML file</title>
-    <link>${baseURL}/${phyloWSPath}?format=nexml</link>
+    <link>${baseURL}${phyloWSPath}?format=nexml</link>
     <description>A NeXML serialization of the resource</description>
     <dc:format>application/xml</dc:format>
   </item>
   </c:if>  
   <c:if test="${hasNexus}">
-  <item rdf:about="${baseURL}/${phyloWSPath}?format=nexus">
+  <item rdf:about="${baseURL}${phyloWSPath}?format=nexus">
     <title>Nexus file</title>
-    <link>${baseURL}/${phyloWSPath}?format=nexus</link>
+    <link>${baseURL}${phyloWSPath}?format=nexus</link>
     <description>A Nexus serialization of the resource</description>
     <dc:format>text/plain</dc:format>
   </item>
   </c:if>   
   <c:if test="${hasRdf}">
-  <item rdf:about="${baseURL}/${phyloWSPath}?format=rdf">
+  <item rdf:about="${baseURL}${phyloWSPath}?format=rdf">
     <title>RDF file</title>
-    <link>${baseURL}/${phyloWSPath}?format=rdf</link>
+    <link>${baseURL}${phyloWSPath}?format=rdf</link>
     <description>An RDF/XML serialization of the resource</description>
     <dc:format>application/rdf+xml</dc:format>
   </item>


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[Treebase-guts] SF.net SVN: treebase:[557] trunk/treebase-web/src/main/webapp/WEB-INF/pages /searchResultsAsRDF.jsp

[<rv...@us...>]

Revision: 557
          http://treebase.svn.sourceforge.net/treebase/?rev=557&view=rev
Author:   rvos
Date:     2010-03-12 23:22:09 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Changed mime type from application/rdf+xml to application/rss+xml (safari likes this), removed superfluous feed image (we can't really compute its absolute path here, unless we hardcode things), removed superfluous forward slashes in URLs.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp	2010-03-12 23:19:29 UTC (rev 556)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/searchResultsAsRDF.jsp	2010-03-12 23:22:09 UTC (rev 557)
@@ -1,33 +1,33 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <%@ include file="/common/taglibs.jsp"%>
-<% response.setContentType("application/rdf+xml"); %>
+<% response.setContentType("application/rss+xml"); %>
 <rdf:RDF
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:dcterms="http://purl.org/dc/terms/"
   xmlns:dc="http://purl.org/dc/elements/1.1/"
   xmlns="http://purl.org/rss/1.0/">
-  <channel rdf:about="${baseURL}/${phyloWSPath}?query=<c:out value="${normalizedCQLQuery}" escapeXml="true"/>&amp;format=${format}&amp;recordSchema=${recordSchema}">
+  <channel rdf:about="${baseURL}${phyloWSPath}?query=<c:out value="${normalizedCQLQuery}" escapeXml="true"/>&amp;format=${format}&amp;recordSchema=${recordSchema}">
     <title>${phyloWSPath}</title>
     <link>${baseURL}</link>
     <description>${searchResultsThawed.description}</description>
-    <image rdf:resource="${domainAddress}<fmt:message key="icons.treebase.16px"/>"/>
+    <%--image rdf:resource="${domainAddress}<fmt:message key="icons.treebase.16px"/>"/--%>
     <items>
       <rdf:Seq>      
 		<c:forEach var="result" items="${searchResultsThawed.results}" varStatus="status">
-			<rdf:li rdf:resource="${baseURL}/<c:out value="${result.phyloWSPath}"/>"/>
+			<rdf:li rdf:resource="${baseURL}<c:out value="${result.phyloWSPath}"/>"/>
 		</c:forEach>      
       </rdf:Seq>
     </items>
   </channel>
-  <image rdf:about="${domainAddress}<fmt:message key="icons.treebase.16px"/>">
+  <%--image rdf:about="${domainAddress}<fmt:message key="icons.treebase.16px"/>">
     <title>${phyloWSPath}</title>
     <link>${baseURL}</link>
     <url>${domainAddress}<fmt:message key="icons.treebase.16px"/></url>
-  </image>
+  </image--%>
   <c:forEach var="result" items="${searchResultsThawed.results}" varStatus="status">
-  <item rdf:about="${baseURL}/<c:out value="${result.phyloWSPath}"/>">
+  <item rdf:about="${baseURL}<c:out value="${result.phyloWSPath}"/>">
     <title><c:out value="${result.namespacedGUID}"/></title>
-    <link>${baseURL}/<c:out value="${result.phyloWSPath}"/></link>
+    <link>${baseURL}<c:out value="${result.phyloWSPath}"/></link>
     <description><c:out value="${result.namespacedGUID}"/></description>
   </item>  
   </c:forEach>


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[Treebase-guts] SF.net SVN: treebase:[556] trunk/treebase-web/src/main/webapp/WEB-INF/ treebase-servlet.xml

[<rv...@us...>]

Revision: 556
          http://treebase.svn.sourceforge.net/treebase/?rev=556&view=rev
Author:   rvos
Date:     2010-03-12 23:19:29 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Changed extension for *AsRDF* jsps to .rdf

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-12 23:18:17 UTC (rev 555)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-12 23:19:29 UTC (rev 556)
@@ -950,9 +950,9 @@
 			    <prop key="/search/study/analysis.html">searchSummaryController</prop>
 			    <prop key="/search/study/taxa.html">searchSummaryController</prop>
 			    <prop key="/search/study/rowSegments.html">searchSummaryController</prop>
-			    <prop key="/search/study/anyObjectAsRDF.html">anyObjectAsRDFController</prop>
+			    <prop key="/search/study/anyObjectAsRDF.rdf">anyObjectAsRDFController</prop>
 			    
-			    <prop key="/search/searchResultsAsRDF.html">searchResultsAsRDFController</prop>
+			    <prop key="/search/searchResultsAsRDF.rdf">searchResultsAsRDFController</prop>
 				<prop key="/search/matrixRowList.html">listMatrixRowController</prop>
 				<prop key="/search/taxonList.html">listTaxaSearchController</prop>
 				<prop key="/search/downloadAStudy.html">downloadAStudyController</prop>				


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[Treebase-guts] SF.net SVN: treebase:[555] trunk/treebase-web/src/main/webapp/WEB-INF/web. xml

[<rv...@us...>]

Revision: 555
          http://treebase.svn.sourceforge.net/treebase/?rev=555&view=rev
Author:   rvos
Date:     2010-03-12 23:18:17 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Added servlet mapping for .rdf extension, so that rss feeds can be generated with this extension (as opposed to the default .html extension). It seems that this way safari knows to render the feed correctly.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/web.xml

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-03-12 19:34:05 UTC (rev 554)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-03-12 23:18:17 UTC (rev 555)
@@ -173,9 +173,13 @@
 	<servlet-mapping>
 		<servlet-name>treebase</servlet-name>
 		<url-pattern>*.html</url-pattern>
-	</servlet-mapping>
+	</servlet-mapping>
 	<servlet-mapping>
 		<servlet-name>treebase</servlet-name>
+		<url-pattern>*.rdf</url-pattern>
+	</servlet-mapping>	
+	<servlet-mapping>
+		<servlet-name>treebase</servlet-name>
 		<url-pattern>/phylows/*</url-pattern>
 	</servlet-mapping>
 	


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[Treebase-guts] SF.net SVN: treebase:[554] trunk/treebase-core/db/cleaning

[<vga...@us...>]

Revision: 554
          http://treebase.svn.sourceforge.net/treebase/?rev=554&view=rev
Author:   vgapeyev
Date:     2010-03-12 19:34:05 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Miscellaneous post-migration data fixes (see README) 

Added Paths:
-----------
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/README.txt
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/all_postload_fixes.sql
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/field_defaults.sql
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/matrix_ntax_nchar.sql
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasedev.txt
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasestage.txt
    trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/user_tb1import.sql

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/README.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/README.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/README.txt	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,20 @@
+Miscellaneous data fixes applied after all TB1 nexus data was imported. 
+To run them all, use 
+    all_postload_fixes.sql 
+    
+ Were applied to treebasedev and treebasestage (the reference instance at the time)
+ on 2010-03-12 -- see out_*.txt files for output.    
+ 
+    
+Notes on the individual fixes: 
+
+user_tb1import.sql
+   Assigns the special user 'tb1import' to all studies and submissions with null user_id. 
+
+field_defaults.sql 
+   Puts default values into phylotree.treekind, phylotree.treequality, and matrix.description. 
+
+matrix_ntax_nchar.sql 
+   Updates matrix.{ntax,nchar} to the actual counts of rows and columns.  
+
+   
\ No newline at end of file

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/all_postload_fixes.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/all_postload_fixes.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/all_postload_fixes.sql	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,9 @@
+
+\echo  'Assigning the special user tb1import to all studies and submissions with null user_id...'
+\i user_tb1import.sql
+
+\echo 'Putting default values into phylotree.treekind, phylotree.treequality, and matrix.description...'
+\i field_defaults.sql 
+
+\echo 'Updating matrix.{ntax,nchar} to the actual counts of rows and columns...'
+\i matrix_ntax_nchar.sql 

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/field_defaults.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/field_defaults.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/field_defaults.sql	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,16 @@
+BEGIN transaction; 
+
+update phylotree 
+   set treekind_id = 1 
+where treekind_id is null; 
+
+update phylotree 
+   set treequality_id = 1 
+where treequality_id is null; 
+
+update matrix
+  set description = 'Legacy TreeBASE Matrix ID = ' || tb_matrixid
+where description is null 
+  and tb_matrixid is not null; 
+
+COMMIT; 
\ No newline at end of file

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/matrix_ntax_nchar.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/matrix_ntax_nchar.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/matrix_ntax_nchar.sql	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,17 @@
+BEGIN transaction; 
+
+update matrix as m 
+   set nTax  = r.rows_counted,
+       nChar = c.columns_counted
+from (select matrix_id, count(*) as rows_counted 
+      from matrixrow group by matrix_id) as r, 
+     (select matrix_id, count(*) as columns_counted 
+      from matrixcolumn group by matrix_id) as c  
+where m.matrix_id = r.matrix_id and m.matrix_id = c.matrix_id 
+  and ((m.ntax is null or m.ntax <> r.rows_counted) or
+       (m.nchar is null or m.nchar <> c.columns_counted)) 
+returning m.matrix_id, m.tb_matrixid, m.nexusfilename, m.published, 
+          m.nTax  as new_ntax,
+          m.nChar as new_nchar;  
+
+COMMIT; 
\ No newline at end of file

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasedev.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasedev.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasedev.txt	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,32 @@
+treebasedev=> \i ./all_postload_fixes.sql
+BEGIN
+UPDATE 2079
+UPDATE 2044
+COMMIT
+BEGIN
+UPDATE 7
+UPDATE 7
+UPDATE 53
+COMMIT
+BEGIN
+ matrix_id |     tb_matrixid      |      nexusfilename       | published | new_ntax | new_nchar 
+-----------+----------------------+--------------------------+-----------+----------+-----------
+      4050 |                      | 18S-28S                  | f         |       72 |      1818
+      4070 |                      | zztip                    | f         |       12 |       542
+      4090 | M1728                | M1728.nex                | f         |       26 |        30
+      4091 | M1729                | M1729.nex                | f         |       46 |        30
+      4092 | M2056                | M2056.nex                | f         |       49 |       161
+      4093 | M2313                | M2313.nex                | f         |       43 |      1902
+      4094 | M2765                | M2765.nex                | f         |       74 |      2266
+      4095 | M2767                | M2767.nex                | f         |       66 |       806
+      4096 | M62c1x28x96c15c56c19 | M62c1x28x96c15c56c19.nex | f         |       72 |        82
+      4097 | M644                 | M644.nex                 | f         |       28 |        86
+      4098 | M64c1x28x96c16c00c36 | M64c1x28x96c16c00c36.nex | f         |       46 |        84
+      4099 | M76c1x29x96c15c31c23 | M76c1x29x96c15c31c23.nex | f         |       15 |        31
+      4110 |                      | M2496.nex                | f         |       34 |     16837
+      4130 |                      | 12Tx432C.nex             | f         |       12 |       432
+      4150 |                      | withstates.nex           | f         |        7 |        28
+(15 rows)
+
+UPDATE 15
+COMMIT

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasestage.txt
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasestage.txt	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/out_treebasestage.txt	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,39 @@
+treebasestage=> \i ./all_postload_fixes.sql
+Assigning the special user tb1import to all studies and submissions with null user_id...
+BEGIN
+UPDATE 2451
+UPDATE 2427
+COMMIT
+Putting default values into phylotree.treekind, phylotree.treequality, and matrix.description...
+BEGIN
+UPDATE 983
+UPDATE 983
+UPDATE 834
+COMMIT
+Updating matrix.{ntax,nchar} to the actual counts of rows and columns...
+BEGIN
+
+
+ matrix_id |     tb_matrixid      |      nexusfilename       | published | new_ntax | new_nchar 
+-----------+----------------------+--------------------------+-----------+----------+-----------
+      4050 |                      | 18S-28S                  | f         |       72 |      1818
+      4070 |                      | zztip                    | f         |       12 |       542
+      4090 | M1728                | M1728.nex                | f         |       26 |        30
+      4091 | M1729                | M1729.nex                | f         |       46 |        30
+      4092 | M2056                | M2056.nex                | f         |       49 |       161
+      4093 | M2313                | M2313.nex                | f         |       43 |      1902
+      4094 | M2765                | M2765.nex                | f         |       74 |      2266
+      4095 | M2767                | M2767.nex                | f         |       66 |       806
+      4096 | M62c1x28x96c15c56c19 | M62c1x28x96c15c56c19.nex | f         |       72 |        82
+      4097 | M644                 | M644.nex                 | f         |       28 |        86
+      4098 | M64c1x28x96c16c00c36 | M64c1x28x96c16c00c36.nex | f         |       46 |        84
+      4099 | M76c1x29x96c15c31c23 | M76c1x29x96c15c31c23.nex | f         |       15 |        31
+      4110 |                      | M2496.nex                | f         |       34 |     16837
+      4130 |                      | 12Tx432C.nex             | f         |       12 |       432
+      4150 |                      | withstates.nex           | f         |        7 |        28
+      4374 | M4524                | M4524.nex                | f         |      205 |     11335
+      4622 | M4460                | M4460.nex                | f         |       54 |      9173
+(17 rows)
+
+UPDATE 17
+COMMIT

Added: trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/user_tb1import.sql
===================================================================
--- trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/user_tb1import.sql	                        (rev 0)
+++ trunk/treebase-core/db/cleaning/2010-03-12_postload_fixes/user_tb1import.sql	2010-03-12 19:34:05 UTC (rev 554)
@@ -0,0 +1,15 @@
+BEGIN transaction; 
+
+update study as s
+  set user_id = u.user_id
+from "user" as u  
+where s.user_id is null
+  and u.username = 'tb1import'; 
+
+update submission as s
+  set user_id = u.user_id
+from "user" as u  
+where s.user_id is null
+  and u.username = 'tb1import'; 
+
+COMMIT; 


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[Treebase-guts] SF.net SVN: treebase:[553] trunk/treebase-core/src/main/java/org/cipres/ treebase

[<rv...@us...>]

Revision: 553
          http://treebase.svn.sourceforge.net/treebase/?rev=553&view=rev
Author:   rvos
Date:     2010-03-12 18:24:41 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Added findByJournal search method, which is needed so that we can create RSS feeds for journals.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java
    trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java	2010-03-12 11:38:21 UTC (rev 552)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/dao/study/StudyDAO.java	2010-03-12 18:24:41 UTC (rev 553)
@@ -19,6 +19,7 @@
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
 import org.cipres.treebase.domain.tree.PhyloTree;
 import org.hibernate.Criteria;
+import org.hibernate.Query;
 import org.hibernate.SQLQuery;
 import org.hibernate.criterion.Expression;
 import org.hibernate.criterion.Restrictions;
@@ -364,5 +365,19 @@
 		return studies;
 	}
 
+	/*
+	 * (non-Javadoc)
+	 * @see org.cipres.treebase.domain.study.StudyHome#findByJournal(java.lang.String)
+	 */
+	public Collection<Study> findByJournal(String pJournal) {
+		Collection<Study> returnVal = new ArrayList<Study>();
+		if (pJournal != null) {
+			Query q = getSession().createQuery("select study from Citation where lower(journal) like :mStr");
+			q.setString("mStr", pJournal.trim().toLowerCase() + '%');
+			returnVal = q.list();			
+		}
+		return returnVal;
+	}
 
+
 }

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java	2010-03-12 11:38:21 UTC (rev 552)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyHome.java	2010-03-12 18:24:41 UTC (rev 553)
@@ -45,6 +45,14 @@
 	 * @return Set<Study>
 	 */
 	Collection<Study> findByAuthor(Person pAuthor);
+	
+	/**
+	 * Find studies by journal name.
+	 * 
+	 * @param pJournal
+	 * @return Collection<Study>
+	 */
+	Collection<Study> findByJournal(String pJournal);
 
 	/**
 	 * Find studies submitted by an user. Return an empty set if no match is found.

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java	2010-03-12 11:38:21 UTC (rev 552)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/study/StudyService.java	2010-03-12 18:24:41 UTC (rev 553)
@@ -50,6 +50,15 @@
 	 * @return Collection<Study>
 	 */
 	Collection<Study> findByName(String pStudyName, boolean pCaseSensitive);
+	
+	
+	/**
+	 * Find studies by journal name. Return an empty set if no match is found.
+	 * @param pJournal
+	 * @param pCaseSensitive
+	 * @return Collection<Study>
+	 */
+	Collection<Study> findByJournal(String pJournal, boolean pCaseSensitive);
 
 	/**
 	 * Advanced study query by criteria.

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java	2010-03-12 11:38:21 UTC (rev 552)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/study/StudyServiceImpl.java	2010-03-12 18:24:41 UTC (rev 553)
@@ -8,6 +8,7 @@
 import java.io.IOException;
 import java.sql.Clob;
 import java.util.Collection;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.LinkedHashSet;
 import java.util.Set;
@@ -529,4 +530,9 @@
 	public Class defaultResultClass() {
 		return Study.class;
 	}
+
+	public Collection<Study> findByJournal(String pJournal,
+			boolean pCaseSensitive) {
+		return getStudyHome().findByJournal(pJournal);
+	}
 }


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[Treebase-guts] [ treebase-Bugs-2960910 ] Phylowidget does not run

[SourceForge.net <no...@so...>]

Bugs item #2960910, was opened at 2010-02-28 18:32
Message generated for change (Comment added) made by vgapeyev
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2960910&group_id=248804

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: ui
Group: None
>Status: Closed
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: Vladimir Gapeyev (vgapeyev)
Summary: Phylowidget does not run

Initial Comment:
Using dev server, I'm unable to look at any trees (clicking the magnifying glass, which is supposed to fire-up phylowdiget, fails to work). Causes "Error. Click for details" with the result "The application failed to run"

----------------------------------------------------------------------

>Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-03-12 10:28

Message:
As suggested earlier, PhyloWidget.jar is now deployed inside
treebase-web.war. 

Phylowidget works on Safari, but not on Firefox (where loading the page
with the applet hangs the whole browser). I believe, this problem was
present with the previous PhyloWidget deployment method as well.  I could
not see any hints of what the problem may be in any obvious places (Firefox
error console, Tomcat logs), so figuring it out is likely to require
substantial effort or/and familiarity with this piece of the codebase. 

----------------------------------------------------------------------

Comment By: Vladimir Gapeyev (vgapeyev)
Date: 2010-03-01 16:53

Message:
I am trying to understand what is going on here... 

Apparently, before I and Jon showed up, the arrangement was to run the
"publish" script, which would take Phylowidget.jar and place it inside the
exploded WAR, at treebase-web/test/phylowidget.  This location already
contains several jars (core.jar,itext.jar,jgrapht-jdk1.5.jar,pdf.jar),
which are also required by the client (see
treebase-web/src/main/webapp/WEB-INF/pages/newPhylowidget.jsp).  These jars
come packed inside treebase-web.war

So, why can't we just put Phylowidget.jar inside the WAR archive,
alongside the other 4 jars?  


----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-03-01 11:12

Message:
This is almost certainly because PhyloWidget.jar isn't in the right
location. This jar is unlike all the others in the project because it is a
client side applet that is run in a browser window, which means the web
server needs to make this jar available to the client. Apparently, the new
dev/prod/stage server configuration hasn't taken this into account. Since
only Jon has access to the server itself I suppose he's the only one who
can fix it.

----------------------------------------------------------------------

Comment By: Rutger Vos (rvos)
Date: 2010-03-01 11:12

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=2960910&group_id=248804

[Treebase-guts] SF.net SVN: treebase:[552] trunk/treebase-web/src/main/webapp/styles/styles .css

[<rv...@us...>]

Revision: 552
          http://treebase.svn.sourceforge.net/treebase/?rev=552&view=rev
Author:   rvos
Date:     2010-03-12 11:38:21 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Updated styles for h3 headings and paragraphs in submission and search.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/styles/styles.css

Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 11:37:20 UTC (rev 551)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 11:38:21 UTC (rev 552)
@@ -52,7 +52,7 @@
 	background-image: url("../images/footer_bg.gif")
 }
 
-#contentRight h2, #contentRight h3, #contentRight p {
+#contentRight h2, #contentRight h3, #contentRight p, #content p, #content h3 {
 	padding-left: 15px !important;
 	padding-right: 15px !important;	
 	padding-top: 15px !important		


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[Treebase-guts] SF.net SVN: treebase:[551] trunk/treebase-web/src/main/webapp/styles/ submissionSummary.css

[<rv...@us...>]

Revision: 551
          http://treebase.svn.sourceforge.net/treebase/?rev=551&view=rev
Author:   rvos
Date:     2010-03-12 11:37:20 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Changed decoration for "notes" section to use a post-it note icon instead of a comment balloon.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/styles/submissionSummary.css

Modified: trunk/treebase-web/src/main/webapp/styles/submissionSummary.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/submissionSummary.css	2010-03-12 01:05:21 UTC (rev 550)
+++ trunk/treebase-web/src/main/webapp/styles/submissionSummary.css	2010-03-12 11:37:20 UTC (rev 551)
@@ -22,7 +22,7 @@
 }
 li.menubar a.standalone, li.menubar { background: url('../images/blank.gif')              no-repeat 0px 0px !important }
 li.Home a.Home {                 background: url('../images/icons/house.png')             no-repeat 0px 0px !important }
-li.Notes a.Notes {               background: url('../images/icons/comment.png')           no-repeat 0px 0px !important }
+li.Notes a.Notes {               background: url('../images/icons/note.png')              no-repeat 0px 0px !important }
 li.Citation a.Citation {         background: url('../images/icons/report.png')            no-repeat 0px 0px !important }
 li.Authors a.Authors {           background: url('../images/icons/group.png')             no-repeat 0px 0px !important }
 li.Upload a.Upload {             background: url('../images/icons/page_white_get.png')    no-repeat 0px 0px !important }


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[Treebase-guts] SF.net SVN: treebase:[550] trunk/treebase-web/src/main/webapp/styles/styles .css

[<rv...@us...>]

Revision: 550
          http://treebase.svn.sourceforge.net/treebase/?rev=550&view=rev
Author:   rvos
Date:     2010-03-12 01:05:21 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Updated #content h2 style.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/styles/styles.css

Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 00:57:42 UTC (rev 549)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 01:05:21 UTC (rev 550)
@@ -39,8 +39,10 @@
 }
 
 #content h2 {
-	background: #BED1E5 url("../images/off_bg.gif") repeat-x left top;
-	padding: 5px !important
+	margin: 0px;
+	padding: 15px !important;
+	border-top: 1px solid #3d649f;
+	background-image: url("../images/footer_bg.gif")
 }
 
 #contentRight h1 {


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[Treebase-guts] SF.net SVN: treebase:[549] trunk/treebase-web/src/main/resources/ ApplicationResources.properties

[<rv...@us...>]

Revision: 549
          http://treebase.svn.sourceforge.net/treebase/?rev=549&view=rev
Author:   rvos
Date:     2010-03-12 00:57:42 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Made TreeBASE capitalization consistent

Modified Paths:
--------------
    trunk/treebase-web/src/main/resources/ApplicationResources.properties

Modified: trunk/treebase-web/src/main/resources/ApplicationResources.properties
===================================================================
--- trunk/treebase-web/src/main/resources/ApplicationResources.properties	2010-03-12 00:27:51 UTC (rev 548)
+++ trunk/treebase-web/src/main/resources/ApplicationResources.properties	2010-03-12 00:57:42 UTC (rev 549)
@@ -91,11 +91,11 @@
 
 #-- top navigation menu --
 nav.personalinfo = Personal Information
-nav.submissions=Treebase Submissions
+nav.submissions=TreeBASE Submissions
 nav.submission.progress=Submissions in Progress
 nav.submission.ready=Submissions Ready
 nav.submission.prior=Prior Submissions
-nav.home =TreeBase Home
+nav.home =TreeBASE Home
 nav.logout=Logout
 nav.login=Login
 
@@ -136,12 +136,12 @@
 user.status="<i>Logged in: </i>"
 
 # -- login --
-login.title=TreeBase Login 
+login.title=TreeBASE Login 
 login.message=Please fill the following information to log in
 login.signup=New to Treebase? Click here to <a href="{0}">Signup</a>
 
 # -- signup --
-userform.title=TreeBase User Registration
+userform.title=TreeBASE User Registration
 create.profile=Please fill the following information to complete new user registration
 update.profile= Please update the following user profile information
 user.username=Username
@@ -161,11 +161,11 @@
 user.password.sent.successful=Your password has been sent to your email address
 user.password.sent.failed=Failed to send password
 
-user.list.title =List of Treebase Users
+user.list.title =List of TreeBASE Users
 user.delete =Delete this user
 
 #-- search --
-search.title = Search Treebase
+search.title = Search TreeBASE
 search.result.title = Search Query Result
 search.type = Search for
 search.no.criteria.selected = No search criteria has been selected.  Please try again
@@ -173,8 +173,8 @@
 search.by.submission.id = Search Submission
 
 #-- submission list --
-submission.list.title = List of Treebase Submissions
-submission.mainmenu.title= Treebase Submission Menu
+submission.list.title = List of TreeBASE Submissions
+submission.mainmenu.title= TreeBASE Submission Menu
 submission.id = Submission Id
 submission.accession = Submission Id
 
@@ -206,7 +206,7 @@
 citation.update.success = Citation has been updated successfully
 
 #-- study --
-study.title = Treebase Submission Information
+study.title = TreeBASE Submission Information
 study.update.title = Update Treebase Submission
 study.id = Submission ID
 study.name = Name of study
@@ -405,7 +405,7 @@
 person.merge = Merge Person Records
 person.merge.confirm = Merge Person Records Confirmation
 person.id = Person Record Id
-person.list.title = List of TreeBase Persons
+person.list.title = List of TreeBASE Persons
 
 #-- delete
 delete.delete = Delete


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[Treebase-guts] SF.net SVN: treebase:[548] trunk/treebase-web/src/main/webapp/styles/styles .css

[<rv...@us...>]

Revision: 548
          http://treebase.svn.sourceforge.net/treebase/?rev=548&view=rev
Author:   rvos
Date:     2010-03-12 00:27:51 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Fixed some CSS validation errors.

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/styles/styles.css

Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 00:02:30 UTC (rev 547)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 00:27:51 UTC (rev 548)
@@ -46,7 +46,7 @@
 #contentRight h1 {
 	margin: 0px;
 	padding: 15px;
-	border-top: 1px solid silver;
+	border-top: 1px solid #3d649f;
 	background-image: url("../images/footer_bg.gif")
 }
 
@@ -57,7 +57,7 @@
 }
 
 #contentRight h2 {
-	border-top: 1px solid silver
+	border-top: 1px solid #3d649f
 }
 
 /* Page Structure/Layout 
@@ -262,7 +262,6 @@
     float: right;
  	font-family: "Lucida Grande", sans-serif;
  	font-style: italic;
-//	font-size: 118%;
 	display: block;
 	margin: 0 1px 0 0;
 	height: inherit;
@@ -346,18 +345,12 @@
 	margin-left: 15px;	
 }
 
-#navlist li {
-//	border-left: 5px solid #3863a4
-}
-
 #contentRight {
 	background-color: white
 }
 
 #sidebarLeftGutter {
-	background-color: #f0f0f0;
-	border-right: 1px solid silver;
-	border-bottom: 1px solid silver
+	background-color: #e8e8e8
 }
 /* Login Area Styles  
 *******************************************************************************************/


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[Treebase-guts] SF.net SVN: treebase:[547] trunk/treebase-web/src/main/webapp

[<rv...@us...>]

Revision: 547
          http://treebase.svn.sourceforge.net/treebase/?rev=547&view=rev
Author:   rvos
Date:     2010-03-12 00:02:30 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
BIG COMMIT: THIS CHANGES MUCH OF THE STATIC PAGE STYLES

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
    trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
    trunk/treebase-web/src/main/webapp/common/footer.jsp
    trunk/treebase-web/src/main/webapp/common/header.jsp
    trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
    trunk/treebase-web/src/main/webapp/styles/displaytag.css
    trunk/treebase-web/src/main/webapp/styles/styles.css

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
    trunk/treebase-web/src/main/webapp/images/TreeBASE.png
    trunk/treebase-web/src/main/webapp/images/architecture.jpeg
    trunk/treebase-web/src/main/webapp/images/gradient.jpg
    trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
    trunk/treebase-web/src/main/webapp/images/nescent_logo.png
    trunk/treebase-web/src/main/webapp/images/people/
    trunk/treebase-web/src/main/webapp/images/people/anon.jpg
    trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
    trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
    trunk/treebase-web/src/main/webapp/images/people/krice.gif
    trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
    trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
    trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
    trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
    trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
    trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml	2010-03-12 00:02:30 UTC (rev 547)
@@ -10,6 +10,7 @@
         <pattern>/about.html</pattern>
         <pattern>/urlAPI.html</pattern>
         <pattern>/people.html</pattern>
+        <pattern>/technology.html</pattern>
     </decorator>
 	
 	<!-- decoration page for search pages -->

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/about.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,103 +1,105 @@
-<div class="gutter">
-	<h1>Overview</h1>
-	<p>
-		TreeBASE is a relational database designed to manage and explore information on 
-		phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996; 
-		Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data 
-		matrices, together with information about the relevant publication, taxa, 
-		morphological and sequence-based characters, and published analyses. 
-	</p>
-	<p>
-		The database is designed to allow retrieval of trees and data from different 
-		studies so that existing phylogenetic results may be reassessed, compared, 
-		combined and reused. Applications include:
-	</p>
-	<ul>
-		<li>
-			to locate information on the phylogeny of particular groups of interest.
-		</li>
-		<li>
-			to obtain datasets for studies of character evolution, including general 
-			patterns across many groups, such as patterns of homoplasy.
-		</li>
-		<li>
-			in studies of biogeography -- to retrieve trees with representatives in 
-			particular geographical areas.
-		</li>
-		<li>
-			in studies of coevolution -- to retrieve information on host and parasite 
-			phylogenies.
-		</li>
-		<li>
-			in studies of congruence and combination of data -- to retrieve all molecular 
-			and morphological phylogenies for particular groups.
-		</li>
-		<li>
-			in studies of phylogenetic methods -- to retrieve all parsimony or maximum 
-			likelihood reconstructions, for example, or to download datasets of various 
-			sorts to test methods.
-		</li>
-		<li>
-			to link together trees of particular groups into more inclusive phylogenies.
-		</li>
-		<li>
-			to discover understudied groups -- a resource for students, funding agencies, 
-			etc.
-		</li>
-		<li>
-			to retrieve phylogenetic information for use in conservation biology and the 
-			management of natural resources.
-		</li>
-	</ul>
-	<h2>History, Funding, and Governance</h2>
-	<p>
-		The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994, 
-		Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype 
-		database of phylogenetic studies").  The database underwent a complete 
-		redevelopment and redesign with funding from the <a href="http://www.phylo.org">
-		Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654: 
-		"Building the Tree of Life -- A National Resource for Phyloinformatics and 
-		Computational Phylogenetics"). 
-	</p>
-	<p>
-		TreeBASE was released in March 2010 as one of the main products of The 
-		Phyloinformatics Research Foundation, Inc., a Connecticut non-profit 
-		corporation. The Foundation provides direction, governance, and continuity for 
-		software, data sharing, and communication standards to promote phyloinformatic 
-		research for the scientific community.
-	</p>
-	<p>
-		The current version of the database is 2.0 (released March 2010), and is hosted 
-		by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
-		NESCent</a>). In previous years the database has been hosted by the 
-		<a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the 
-		<a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the 
-		<a href="http://www.buffalo.edu">University at Buffalo</a>, 
-		<a href="http://www.harvard.edu">Harvard University</a>, 
-		<a href="http://www.leiden.edu">Leiden University</a>, and the 
-		<a href="http://www.ucdavid.edu">University of California, Davis</a>. 
-	</p>
-	<h2>Related resources</h2>
-	<ul>
-		<li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an 
-		online reference source and database for every one of the 1.8 million species that 
-		are named and known on this planet.</li>
-		<li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative 
-		effort of biologists and nature enthusiasts from around the world. On more than 
-		10,000 World Wide Web pages, the project provides information about biodiversity, 
-		the characteristics of different groups of organisms, and their evolutionary history</li>
-		<li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular 
-		software for evolutionary biology, designed to help biologists analyze comparative 
-		data about organisms in a phylogenetic context. 
-		</li>
-	</ul>
-	<h2>Logo</h2>
-	<p>
-		The logo displayed on the TreeBASE web-application has been adapted to match the 
-		color style of the website. Please use the logo shown here for linking to or citing 
-		TreeBASE.
-		<center>
-			<img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
-		</center>		
-	</p>
+<div id="contentRight">
+	<div class="gutter">
+		<h1>Overview</h1>
+		<p>
+			TreeBASE is a relational database designed to manage and explore information on 
+			phylogenetic relationships (Sanderson et al., 1993, 1994; Piel et al., 1996; 
+			Morel, 1996; Piel et al., 2000). It includes phylogenetic trees and data 
+			matrices, together with information about the relevant publication, taxa, 
+			morphological and sequence-based characters, and published analyses. 
+		</p>
+		<p>
+			The database is designed to allow retrieval of trees and data from different 
+			studies so that existing phylogenetic results may be reassessed, compared, 
+			combined and reused. Applications include:
+		</p>
+		<ul>
+			<li>
+				to locate information on the phylogeny of particular groups of interest.
+			</li>
+			<li>
+				to obtain datasets for studies of character evolution, including general 
+				patterns across many groups, such as patterns of homoplasy.
+			</li>
+			<li>
+				in studies of biogeography -- to retrieve trees with representatives in 
+				particular geographical areas.
+			</li>
+			<li>
+				in studies of coevolution -- to retrieve information on host and parasite 
+				phylogenies.
+			</li>
+			<li>
+				in studies of congruence and combination of data -- to retrieve all molecular 
+				and morphological phylogenies for particular groups.
+			</li>
+			<li>
+				in studies of phylogenetic methods -- to retrieve all parsimony or maximum 
+				likelihood reconstructions, for example, or to download datasets of various 
+				sorts to test methods.
+			</li>
+			<li>
+				to link together trees of particular groups into more inclusive phylogenies.
+			</li>
+			<li>
+				to discover understudied groups -- a resource for students, funding agencies, 
+				etc.
+			</li>
+			<li>
+				to retrieve phylogenetic information for use in conservation biology and the 
+				management of natural resources.
+			</li>
+		</ul>
+		<h2>History, Funding, and Governance</h2>
+		<p>
+			The prototype for TreeBASE was first launched in 1994 (Sanderson et al. 1994, 
+			Piel et al., 2002) with funding from NSF SGER (NSF DEB 9318325: "A prototype 
+			database of phylogenetic studies").  The database underwent a complete 
+			redevelopment and redesign with funding from the <a href="http://www.phylo.org">
+			Cyberinfrastructure for Phylogenetic Research project</a> (NSF EF 0331654: 
+			"Building the Tree of Life -- A National Resource for Phyloinformatics and 
+			Computational Phylogenetics"). 
+		</p>
+		<p>
+			TreeBASE was released in March 2010 as one of the main products of The 
+			Phyloinformatics Research Foundation, Inc., a Connecticut non-profit 
+			corporation. The Foundation provides direction, governance, and continuity for 
+			software, data sharing, and communication standards to promote phyloinformatic 
+			research for the scientific community.
+		</p>
+		<p>
+			The current version of the database is 2.0 (released March 2010), and is hosted 
+			by the National Evolutionary Synthesis Center (<a href="http://www.nescent.org">
+			NESCent</a>). In previous years the database has been hosted by the 
+			<a href="http://www.peabody.yale.edu/">Yale Peabody Museum</a>, the 
+			<a href="http://www.sdsc.edu">San Diego Supercomputer Center</a>, the 
+			<a href="http://www.buffalo.edu">University at Buffalo</a>, 
+			<a href="http://www.harvard.edu">Harvard University</a>, 
+			<a href="http://www.leiden.edu">Leiden University</a>, and the 
+			<a href="http://www.ucdavid.edu">University of California, Davis</a>. 
+		</p>
+		<h2>Related resources</h2>
+		<ul>
+			<li><a href="http://eol.org">Encyclopedia of Life</a>: A new project to create an 
+			online reference source and database for every one of the 1.8 million species that 
+			are named and known on this planet.</li>
+			<li><a href="http://tolweb.org">Tree of Life Web Project</a>: A collaborative 
+			effort of biologists and nature enthusiasts from around the world. On more than 
+			10,000 World Wide Web pages, the project provides information about biodiversity, 
+			the characteristics of different groups of organisms, and their evolutionary history</li>
+			<li><a href="http://mesquiteproject.org">Mesquite</a>: Experimental, modular 
+			software for evolutionary biology, designed to help biologists analyze comparative 
+			data about organisms in a phylogenetic context. 
+			</li>
+		</ul>
+		<h2>Logo</h2>
+		<p>
+			The logo displayed on the TreeBASE web-application has been adapted to match the 
+			color style of the website. Please use the logo shown here for linking to or citing 
+			TreeBASE.
+			<center>
+				<img src="images/TreeBASE.png" alt="TreeBASE Logo" width="108" height="66" />
+			</center>		
+		</p>
+	</div>
 </div>
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/home.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,33 +1,36 @@
-<div class="gutter">
-<p>
-TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and 
-the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, 
-trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the 
-public if they are used in a publication that is in press or published in a peer-reviewed scientific 
-journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or 
-in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using 
-a special access code.
-</p>
-<p id="sponsors">
-	<img src="images/aem.gif" alt="AEM" width="80" height="26" />
-	<img src="images/whs.gif" alt="WHS" width="80" height="26" />
-	<img src="images/evo.gif" alt="Evolution" width="80" height="26" />
-	<img src="images/fgb.gif" alt="FGB" width="80" height="26" />
-	<img src="images/gpprcg.gif" alt="GPPRCG"  width="80" height="26" />
-	<img src="images/invsys.gif" alt="Invertebrate Systematics" width="80" height="26" />
-	<img src="images/psa.gif" alt="PSA" width="80" height="26" />
-	<img src="images/tl.gif" alt="Lichenologist" width="80" height="26" />
-	<img src="images/mpe.gif" alt="MPE" width="80" height="26" />
-	<img src="images/msa.gif" alt="Mycologia" width="80" height="26" />
-	<img src="images/mpg.jpg" alt="Mycological Progress" width="80" height="26" />
-	<img src="images/myc.gif" alt="Mycological Research" width="80" height="26" />
-	<img src="images/mycsci.gif" alt="Myoscience" width="80" height="26" />
-	<img src="images/ode.gif" alt="ODE" width="80" height="26" />
-	<img src="images/aps.jpg" alt="APS" width="80" height="26" />
-	<img src="images/nebs.gif" alt="Rhodora" width="80" height="26" />
-	<img src="images/stmyc.gif" alt="Mycology" width="80" height="26" />
-	<img src="images/ssb.gif" alt="SSB" width="80" height="26" />
-	<img src="images/aspt.gif" alt="Systematic Botany" width="80" height="26" />
-	<img src="images/tq.gif" alt="Technical Quarterly" width="80" height="26" />
-</p>  
+<div id="contentRight">
+	<div class="gutter">
+		<h1>Welcome to TreeBASE</h1>
+		<p>
+			TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and 
+			the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, 
+			trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the 
+			public if they are used in a publication that is in press or published in a peer-reviewed scientific 
+			journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or 
+			in review can be submitted to TreeBASE but are only available to the publication editors or reviewers using 
+			a special access code.
+		</p>
+		<p id="sponsors">
+			<img src="images/aem.gif" alt="AEM" width="80" height="26" />
+			<img src="images/whs.gif" alt="WHS" width="80" height="26" />
+			<img src="images/evo.gif" alt="Evolution" width="80" height="26" />
+			<img src="images/fgb.gif" alt="FGB" width="80" height="26" />
+			<img src="images/gpprcg.gif" alt="GPPRCG"  width="80" height="26" />
+			<img src="images/invsys.gif" alt="Invertebrate Systematics" width="80" height="26" />
+			<img src="images/psa.gif" alt="PSA" width="80" height="26" />
+			<img src="images/tl.gif" alt="Lichenologist" width="80" height="26" />
+			<img src="images/mpe.gif" alt="MPE" width="80" height="26" />
+			<img src="images/msa.gif" alt="Mycologia" width="80" height="26" />
+			<img src="images/mpg.jpg" alt="Mycological Progress" width="80" height="26" />
+			<img src="images/myc.gif" alt="Mycological Research" width="80" height="26" />
+			<img src="images/mycsci.gif" alt="Myoscience" width="80" height="26" />
+			<img src="images/ode.gif" alt="ODE" width="80" height="26" />
+			<img src="images/aps.jpg" alt="APS" width="80" height="26" />
+			<img src="images/nebs.gif" alt="Rhodora" width="80" height="26" />
+			<img src="images/stmyc.gif" alt="Mycology" width="80" height="26" />
+			<img src="images/ssb.gif" alt="SSB" width="80" height="26" />
+			<img src="images/aspt.gif" alt="Systematic Botany" width="80" height="26" />
+			<img src="images/tq.gif" alt="Technical Quarterly" width="80" height="26" />
+		</p>  
+	</div>
 </div>
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,115 +1,118 @@
-<div class="gutter">
-	<table class="peopleTable">
-		<thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
-		<tr>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
-				<br/><strong>Vladimir Gapeyev</strong>
-				<br/>Developer
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
-				<br/><strong>Youjun Guo</strong>
-				<br/>Developer
-			</td>			
-			<td>
-				<img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
-				<br/><strong>Hilmar Lapp</strong>
-				<br/>Deployment Manager
-			</td>
-			<td>
-				<img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
-				<br/><strong>William Piel</strong>
-				<br/>Data Editor
-				<br />Prototype Developer
-			</td>
-			<td>
-				<img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
-				<br/><strong>Val Tannen</strong>
-				<br/>Development Leader
-			</td>
-			<td>
-				<img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
-				<br/><strong>Rutger Vos</strong>
-				<br/>Developer
-				<br/>API Design
-			</td>
-		</tr>
-	</table>
-	
-	<table class="peopleTable">	
-		<thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>	
-		<tr>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
-				<br/><strong>Lucie Chan</strong>
-				<br/>Developer
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
-				<br/><strong>Shirley Cohen</strong>
-				<br/>Student Researcher
-			</td>
-			<td>
-				<img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
-				<br/><strong>Mark J. Dominus</strong>
-				<br/>Developer
-			</td>
-			<td>
-				<img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
-				<br/><strong>Michael Donoghue</strong>
-				<br/>Conceptual Issues
-			</td>
-			<td>
-				<img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
-				<br/><strong>Torsten Eriksson</strong>
-				<br/>Prototype Developer
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
-				<br/><strong>Madhusudan Gujral</strong>
-				<br/>Developer
-			</td>
-		</tr>
-		<tr>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
-				<br/><strong>Chris Henze</strong>
-				<br/>Prototype Developer
-			</td>
-			<td>
-				<img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
-				<br/><strong>Ken Rice</strong>
-				<br/>Prototype Developer
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
-				<br/><strong>Jin Ruan</strong>
-				<br/>Developer
-			</td>
-			<td>
-				<img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
-				<br/><strong>Mike Sanderson</strong>
-				<br/>Conceptual Issues
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
-				<br/><strong>Can van Tran</strong>
-				<br/>Developer
-			</td>
-			<td>
-				<img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
-				<br/><strong>Tracy Zhao</strong>
-				<br/>Developer
-			</td>
-		</tr>
-	</table>
-	
-	<h2>Phyloinformatics Research Foundation Inc, Board</h2>
-	<ul>
-		<li>Michael Donoghue</li>
-		<li>David Maddison</li>
-		<li>William Piel</li>
-		<li>Val Tannen</li>		
-	</ul>
+<div id="contentRight">
+	<div class="gutter">
+		<h1>People</h1>
+		<table class="peopleTable">
+			<thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+			<tr>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+					<br/><strong>Vladimir Gapeyev</strong>
+					<br/>Developer
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+					<br/><strong>Youjun Guo</strong>
+					<br/>Developer
+				</td>			
+				<td>
+					<img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+					<br/><strong>Hilmar Lapp</strong>
+					<br/>Deployment Manager
+				</td>
+				<td>
+					<img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
+					<br/><strong>William Piel</strong>
+					<br/>Data Editor
+					<br />Prototype Developer
+				</td>
+				<td>
+					<img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+					<br/><strong>Val Tannen</strong>
+					<br/>Development Leader
+				</td>
+				<td>
+					<img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+					<br/><strong>Rutger Vos</strong>
+					<br/>Developer
+					<br/>API Design
+				</td>
+			</tr>
+		</table>
+		
+		<table class="peopleTable">	
+			<thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>	
+			<tr>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+					<br/><strong>Lucie Chan</strong>
+					<br/>Developer
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+					<br/><strong>Shirley Cohen</strong>
+					<br/>Student Researcher
+				</td>
+				<td>
+					<img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+					<br/><strong>Mark J. Dominus</strong>
+					<br/>Developer
+				</td>
+				<td>
+					<img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+					<br/><strong>Michael Donoghue</strong>
+					<br/>Conceptual Issues
+				</td>
+				<td>
+					<img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+					<br/><strong>Torsten Eriksson</strong>
+					<br/>Prototype Developer
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+					<br/><strong>Madhusudan Gujral</strong>
+					<br/>Developer
+				</td>
+			</tr>
+			<tr>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+					<br/><strong>Chris Henze</strong>
+					<br/>Prototype Developer
+				</td>
+				<td>
+					<img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+					<br/><strong>Ken Rice</strong>
+					<br/>Prototype Developer
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+					<br/><strong>Jin Ruan</strong>
+					<br/>Developer
+				</td>
+				<td>
+					<img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+					<br/><strong>Mike Sanderson</strong>
+					<br/>Conceptual Issues
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+					<br/><strong>Can van Tran</strong>
+					<br/>Developer
+				</td>
+				<td>
+					<img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+					<br/><strong>Tracy Zhao</strong>
+					<br/>Developer
+				</td>
+			</tr>
+		</table>
+		
+		<h2>Phyloinformatics Research Foundation Inc, Board</h2>
+		<ul>
+			<li>Michael Donoghue</li>
+			<li>David Maddison</li>
+			<li>William Piel</li>
+			<li>Val Tannen</li>		
+		</ul>
+	</div>
 </div>
\ No newline at end of file

Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp	                        (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/technology.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -0,0 +1,152 @@
+<div id="contentRight">
+	<div class="gutter">
+		<h1>Technology</h1>
+		<h2>Data Content</h2>
+		<p>
+			The primary data objects in TreeBASE are bibliographic references to published 
+			phylogenetic studies, taxon by character data matrices, and phylogenetic trees 
+			resulting from the analysis of such data matrices. Information is also 
+			available that links data matrices and trees, including types of analyses 
+			performed, software used, etc. Wherever possible, taxon labels are mapped to 
+			uBio's name services and NCBI's taxonomy. 
+		</p>
+		<h2>Implementation Technologies</h2>
+		<ul>
+			<li>Database: <a href="http://www.postgresql.org/">PostgreSQL 8.3</a></li>
+			<li>Programming language: Java (web-application), Perl (data migration and 
+			maintenance)</li>
+			<li>Database ORM: <a href="http://www.hibernate.org/">Hibernate</a></li>
+			<li>Web-application framework: <a href="http://www.springsource.org/">
+			Spring</a></li>
+			<li>Submission file parsing: <a href="http://mesquiteproject.org/">
+			Mesquite</a></li>
+			<li>Tree Visualization: <a href="http://www.phylowidget.org/">
+			PhyloWidget</a></li>	
+		</ul>
+		<h2>Source Code</h2>
+		<p>
+			Development of <a href="https://sourceforge.net/projects/treebase/">TreeBASE 
+			is hosted at SourceForge</a>. All source code can be downloaded from the 
+			<a href="https://sourceforge.net/projects/treebase/develop">TreeBASE 
+			subversion repository</a> at SourceForge under a BSD license. 
+			Documentation on installing and running TreeBASE can be 
+			found at the <a href="https://sourceforge.net/apps/mediawiki/treebase/index.php?title=Main_Page"> 
+			TreeBASE wiki</a>.	
+		</p>
+		<h2>Architecture</h2>
+		<p>
+			TreeBASE has a tiered Java-based architecture using the Hibernate and Spring 
+			frameworks built on a PostgreSQL database. The following schematic illustrates 
+			the content and features of this software stack:
+		</p>
+		<img src="images/architecture.jpeg"/>
+		<ol>
+			<li>
+				TreeBASE stores alignments, character matrices, and trees used for research 
+				that is published in peer-reviewed journals and books.
+			</li>
+			<li>
+				Each study has one or more analyses; each analysis has one or more steps; 
+				each step associates matrices and trees with algorithms and software. 
+			</li>
+			<li>
+				Each row of sequence alignments or coded characters has a taxon label that 
+				maps to leaf nodes on associated trees. Trees are hashed to allow topological 
+				querying.
+			</li>
+			<li>
+				Each row in a character matrix can be subdivided into one or more row segments; 
+				each row segment can have associated specimen, tissue, or gene sequence metadata.
+			</li> 
+			<li>
+				Names in the rows of a matrix and in row segment metadata can independently 
+				map to a dictionary of name variants, which maps to a taxonomy. This taxonomy will 
+				be mapped to a classification tree in the next release.
+			</li> 	
+		</ol>
+		<h2>Reference</h2>
+		<p>
+			<strong>Blake, J. A., C. J. Bult, M. J. Donoghue, J. Humphries, and C. Fields.</strong> 
+			1994. Interoperability of biological databases: a meeting report. 
+			<em>Syst. Biol.</em> <strong>43</strong>:585-589.
+		</p>
+		<p>
+			<strong>Donoghue, M. J.</strong>
+			1994. Progress and prospects in reconstructing plant phylogeny. 
+			<em>Ann. Missouri Bot. Gard.</em> <strong>81</strong>:405-418.
+		</p>
+		<p>
+			<strong>Donoghue, M. J. and D. D. Ackerly.</strong> 
+			1996. Phylogenetic uncertainties and sensitivity analyses in comparative biology. 
+			<em>Phil. Trans. R. Soc. London B (in press).</em>
+		</p>
+		<p>
+			<strong>Maddison, W. P. and D. R. Maddison.</strong>
+			 1992. 
+			 <em>MacClade: Interactive Analysis of Phylogeny and Character Evolution, Vers. 3.0.</em>
+			  Sunderland, MA: Sinauer Assoc.
+		</p>
+		<p>
+			<strong>Morell, V.</strong>
+			 1996. TreeBASE: the roots of phylogeny. 
+			 <em>Science</em> <strong>273</strong>: 569.	
+		</p>
+		<p>
+			<strong>Piel, W. H.</strong>
+			 2003. "Phyloinformatics and Tree Networks." In: 
+			 <strong>Wu, C. H., P. Wang, and J. T. L. Wang,</strong> eds. 
+			 <em>Computational Biology and Genome Informatics</em>. World Scientific Press.
+		</p>
+		<p>		
+			<strong>Piel, W. H., M. J. Donoghue, and M. J. Sanderson.</strong>
+			 2002. "TreeBASE: a database of phylogenetic knowledge." Pp. 41-47. In: 
+			 <strong>Shimura, J., K. L. Wilson, and D. Gordon,</strong> eds. 
+			 <em>To the interoperable "Catalog of Life" with partners Species 2000 Asia Oceanea.</em> 
+			 Research Report from the National Institute for Environmental Studies No. 171, Tsukuba, Japan.
+		</p>
+		<p>
+			<strong>Piel, W. H., M. J. Sanderson, and M. J. Donoghue.</strong>
+			 2003. The Small-World Dynamics of Tree Networks and Data Mining in Phyloinformatics. 
+			 <em>Bioinformatics</em>, <strong>19</strong>(9): 1162-1168.
+		</p>
+		<p>
+			<strong>Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson, 
+			J. M. Porter, C. Von Dohlen, M. F. Wojciechowski & M. J. Donoghue.
+			</strong> 1993. The growth of phylogenetic information and the need for a phylogenetic database. 
+			<em>Syst. Biol.</em> <strong>42</strong>:562-568.
+		</p>
+		<p>
+			<strong>Sanderson, M. J. and M. J. Donoghue.</strong>
+			 1996. The relationship between homoplasy and confidence in a phylogenetic tree. In: 
+			 <em>Homoplasy and the Evolutionary Process</em> (<strong>M. Sanderson and L. Hufford</strong>, eds.). 
+			 San Diego: Academic Press.
+		</p>
+		<p>
+			<strong>Sanderson, M. J., M. J. Donoghue, W. Piel, and T. Eriksson.</strong>
+			 1994. TreeBASE: a prototype database of phylogenetic analyses and an interactive 
+			 tool for browsing the phylogeny of life. 
+			 <em>American Journal of Botany</em>, <strong>81</strong>(6): 183.
+		</p>
+		<p>
+			<strong>Shan, H., K. G. Herbert, W. H. Piel, D. Shasha and J. T. L. Wang.</strong>
+			 2002. A Structure-Based Search Engine for Phylogenetic Databases. 
+			 <em>Proceedings of the 14th International Conference on Scientific and Statistical 
+			 Database Management (SSDBM 2002),</em> Edinburgh, Scotland, pp. 7-10.
+		</p>
+		<p>
+			<strong>Swofford, D. L.</strong>
+			 1993. 
+			 <em>PAUP: Phylogenetic Analysis Using Parsimony, Vers. 3.1.1.</em> Washington, DC: Smithsonian Institution.
+		</p>
+		<p>
+			<strong>Wang, J. T. L., H. Shan, D. Shasha, and W. H. Piel.</strong>
+			 2003. TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases. 
+			 <em>Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003),</em> Cambridge, MA, pp. 171-180.
+		</p>
+		<p>
+			<strong>Wang, J. T. L., H. Shan, D. Shasha and W. H. Piel.</strong>
+			 2005. Fast Structural Search in Phylogenetic Databases. 
+			 <em>Evolutionary Bioinformatics Online</em>, <strong>1</strong>: 37-46.
+		</p>
+	</div>
+</div>
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/urlAPI.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,109 +1,122 @@
-<div class="gutter">
-<h2>URL API</h2>
-<p>
-	The TreeBASE2 website provides users with simple ways to navigate the underlying data
-	programmatically. This page describes the stateless web service interface and URL architecture
-	that can be used to search the web site and obtain data in a variety of formats with rich semantics. 
-</p>
-<h3>PhyloWS support</h3>
-<p>
-	The site structure described here is designed to be compliant with the emerging 
-	<a href="http://evoinfo.nescent.org/PhyloWS">PhyloWS</a> standard. One of the tenets of the
-	standard is that URLs contain a <strong>/phylows/</strong> delimiter below which the standard
-	recommends a <a href="https://www.nescent.org/wg_evoinfo/PhyloWS/REST">simple API</a> to derefence 
-	phylogenetic data by their accession numbers. In the examples below, the url fragments come 
-	immediately below the <strong>/phylows/</strong> delimiter (everything between the 
-	<strong>http://</strong> and <strong>phylows</strong> is considered
-	subject to change, likely to be stabilized using <a href="http://purl.org">purl</a> addresses).
-</p>
-<h3>Site sections</h3>
-<p>The data on the TreeBASE2 website are organized in four subsections:</p>
-<ul>
-	<li><strong>taxon/</strong> <em>operational taxonomic units, taxonomic mappings and outlinks</em></li>
-	<li><strong>matrix/</strong> <em>character state matrices, morphological character definitions</em></li>
-	<li><strong>tree/</strong> <em>contains trees and tree nodes</em></li>
-	<li><strong>study/</strong> <em>full submission records, including citation and analysis records</em></li>
-</ul>
-<p>
-	Within those four sections, every item in the TreeBASE2 database can be de-referenced by appending
-	the item's full identifier to the right section name. For example, <strong>tree/TB2:Tr2227</strong> 
-	represents a tree (and returns a simple RDF file to describe the tree). For some classes of objects, 
-	these short addresses can be passed a <strong>format</strong>
-	parameter to specify in which data format to represent the object: 
-	<a href="/treebase-web/phylows/study/TB2:S1787?format=html">study/TB2:S1787?format=html</a>.
-	Identifiers that match any of the following expressions can be represented as <strong>nexml</strong>, 
-	<strong>nexus</strong>, <strong>rdf</strong> or <strong>html</strong> (i.e. in a web page):
-</p>
-<ul>
-	<li><strong>matrix/TB2:M[0-9]+</strong> <em>character state matrix</em></li>
-	<li><strong>tree/TB2:Tr[0-9]+</strong> <em>phylogenetic tree</em></li>
-	<li><strong>study/TB2:S[0-9]+</strong> <em>study record</em></li>
-</ul>
-<h3>NeXML support</h3>
-<p>
-	The <strong>nexml</strong> and the <strong>rdf</strong> download options both use output 
-	generated by the java support libraries available from the 
-	<a href="http://nexml.org/nexml/java">nexml website</a>. The website uses the nexml annotation 
-	feature extensively to transmit all the metadata stored by the database. Nexml annotations
-	are <a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a> compliant element structures
-	that use <a href="http://www.w3.org/TR/curie/">CURIE</a> strings to identify metadata properties, 
-	and @content attributes to store the property value. For example, this (simplified) annotation:
-	<strong>
-	&lt;meta content="uBio:2538170" property="tb:identifier.ubio"/&gt;
-	</strong>
-	means that the element that encloses it has a special kind of identifier attached to it, namely
-	one that TreeBASE recognizes as originating in <a href="/treebase-web/phylows/taxon/uBio:2538170">uBio</a>. 
-</p>
-<p>
-	The salient part is
-	the CURIE string predicate <strong>tb:identifier.ubio</strong>, which is one of a 
-	<a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">long list</a> of
-	proposed predicates that are written in TreeBASE's NeXML output and can be used as 
-	<a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> search predicates. The predicates
-	proposed (and now experimentally transmitted) are intended to be subclasses of predicates
-	from commonly used vocabularies. For example, <strong>tb:identifier.ubio</strong> inherits from
-	<a href="http://dublincore.org/documents/dcmi-terms/#terms-identifier">dcterms:identifier</a> and
-	so any of the latter's semantics apply to the former, which is refined to indicate that the
-	value is a uBio namebank ID.
-</p>
-<h3>Searching</h3>
-<p>
-	The TreeBASE website can be searched using a subset of constructs from the 
-	<a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. Specifically,
-	the predicates 
-	<a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">listed here with 
-	an asterisk</a> can be used in statements in the site section they apply to, such that, for example
-	a taxon can be retrieved by its ncbi ID like so:
-	<div style="background-color:;padding:10px">
-		<strong>taxon/find?query=tb.identifier.ncbi=<em>&lt;ncbi taxon id&gt;</em></strong>
+<div id="contentRight">
+	<div class="gutter">
+		<h1>Data Access</h1>
+		<h2>URL API</h2>
+		<p>
+			The TreeBASE2 website provides users with simple ways to navigate the underlying data
+			programmatically. This page describes the stateless web service interface and URL architecture
+			that can be used to search the web site and obtain data in a variety of formats with rich semantics. 
+		</p>
+		<h3>PhyloWS support</h3>
+		<p>
+			The site structure described here is designed to be compliant with the emerging 
+			<a href="http://evoinfo.nescent.org/PhyloWS">PhyloWS</a> standard. One of the tenets of the
+			standard is that URLs contain a <strong>/phylows/</strong> delimiter below which the standard
+			recommends a <a href="https://www.nescent.org/wg_evoinfo/PhyloWS/REST">simple API</a> to derefence 
+			phylogenetic data by their accession numbers. In the examples below, the url fragments come 
+			immediately below the <strong>/phylows/</strong> delimiter (everything between the 
+			<strong>http://</strong> and <strong>phylows</strong> is considered
+			subject to change, likely to be stabilized using <a href="http://purl.org">purl</a> addresses).
+		</p>
+		<h3>Site sections</h3>
+		<p>The data on the TreeBASE2 website are organized in four subsections:</p>
+		<ul>
+			<li><strong>taxon/</strong> <em>operational taxonomic units, taxonomic mappings and outlinks</em></li>
+			<li><strong>matrix/</strong> <em>character state matrices, morphological character definitions</em></li>
+			<li><strong>tree/</strong> <em>contains trees and tree nodes</em></li>
+			<li><strong>study/</strong> <em>full submission records, including citation and analysis records</em></li>
+		</ul>
+		<p>
+			Within those four sections, every item in the TreeBASE2 database can be de-referenced by appending
+			the item's full identifier to the right section name. For example, <strong>tree/TB2:Tr2227</strong> 
+			represents a tree (and returns a simple RDF file to describe the tree). For some classes of objects, 
+			these short addresses can be passed a <strong>format</strong>
+			parameter to specify in which data format to represent the object: 
+			<a href="/treebase-web/phylows/study/TB2:S1787?format=html">study/TB2:S1787?format=html</a>.
+			Identifiers that match any of the following expressions can be represented as <strong>nexml</strong>, 
+			<strong>nexus</strong>, <strong>rdf</strong> or <strong>html</strong> (i.e. in a web page):
+		</p>
+		<ul>
+			<li><strong>matrix/TB2:M[0-9]+</strong> <em>character state matrix</em></li>
+			<li><strong>tree/TB2:Tr[0-9]+</strong> <em>phylogenetic tree</em></li>
+			<li><strong>study/TB2:S[0-9]+</strong> <em>study record</em></li>
+		</ul>
+		<h3>NeXML support</h3>
+		<p>
+			The <strong>nexml</strong> and the <strong>rdf</strong> download options both use output 
+			generated by the java support libraries available from the 
+			<a href="http://nexml.org/nexml/java">nexml website</a>. The website uses the nexml annotation 
+			feature extensively to transmit all the metadata stored by the database. Nexml annotations
+			are <a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a> compliant element structures
+			that use <a href="http://www.w3.org/TR/curie/">CURIE</a> strings to identify metadata properties, 
+			and @content attributes to store the property value. For example, this (simplified) annotation:
+			<strong>
+			&lt;meta content="uBio:2538170" property="tb:identifier.ubio"/&gt;
+			</strong>
+			means that the element that encloses it has a special kind of identifier attached to it, namely
+			one that TreeBASE recognizes as originating in <a href="/treebase-web/phylows/taxon/uBio:2538170">uBio</a>. 
+		</p>
+		<p>
+			The salient part is
+			the CURIE string predicate <strong>tb:identifier.ubio</strong>, which is one of a 
+			<a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">long list</a> of
+			proposed predicates that are written in TreeBASE's NeXML output and can be used as 
+			<a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> search predicates. The predicates
+			proposed (and now experimentally transmitted) are intended to be subclasses of predicates
+			from commonly used vocabularies. For example, <strong>tb:identifier.ubio</strong> inherits from
+			<a href="http://dublincore.org/documents/dcmi-terms/#terms-identifier">dcterms:identifier</a> and
+			so any of the latter's semantics apply to the former, which is refined to indicate that the
+			value is a uBio namebank ID.
+		</p>
+		<h3>Searching</h3>
+		<p>
+			The TreeBASE website can be searched using a subset of constructs from the 
+			<a href="http://www.loc.gov/standards/sru/specs/cql.html">CQL</a> specification. Specifically,
+			the predicates 
+			<a href="http://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw">listed here with 
+			an asterisk</a> can be used in statements in the site section they apply to, such that, for example
+			a taxon can be retrieved by its ncbi ID like so:
+		</p>
+		<div style="background-color:;padding:10px">
+			<strong>taxon/find?query=tb.identifier.ncbi=<em>&lt;ncbi taxon id&gt;</em></strong>
+		</div>
+		<p>
+			or by its name like so:
+		</p>
+		<div style="background-color:;padding:10px">
+			<strong>taxon/find?query=tb.title.taxon=<em>&lt;name&gt;</em></strong>
+		</div>
+		<p>
+			or using an exact match 
+			(<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
+			can be combined with boolean <strong>and</strong>, <strong>or</strong> and <strong>not</strong>.
+			For example:
+		</p>
+		<div style="background-color:;padding:10px">
+			<strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
+		</div>
+		<p>
+			Finally, searching can be modified to project the results from one section info those of another. The
+			effect is roughly the same as switching between tabs in the search section: if the results are a
+			list of tree and you click on the matrix search tab, the trees are converted to the set of matrices
+			on which the trees are based. This behaviour can be used by specifying the 
+			<strong>recordSchema=&lt;section&gt;</strong> argument, i.e.:
+		</p>
+		<div style="background-color:;padding:10px">
+			<strong>taxon/find?query=dcterms.title=="Homo sapiens"&amp;recordSchema=tree</strong>
+		</div>
+		<p>	
+			returns all the trees that have <em>Homo sapiens</em> in them.
+			By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
+			the search results are listed in an RDF compatible RSS1.0 file, i.e.:
+		</p>
+		<div style="background-color:;padding:10px">
+			<strong>taxon/find?query=tb.title.taxon=<em>&lt;name&gt;</em>&amp;format=rss1</strong>
+		</div>
+		<p>	
+			The returned results in RSS1.0 use the short urls of the form <strong>&lt;section&gt;/&lt;id&gt;</strong>, whose
+			returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
+			this</a> one) need to be scanned to discover suitable serialization formats. 
+		</p>
 	</div>
-	or by its name like so:
-	<div style="background-color:;padding:10px">
-		<strong>taxon/find?query=tb.title.taxon=<em>&lt;name&gt;</em></strong>
-	</div>
-	or using an exact match 
-	(<strong>==</strong>) or a case-insensitive one (<strong>=/ignoreCase</strong>). These statements
-	can be combined with boolean <strong>and</strong>, <strong>or</strong> and <strong>not</strong>.
-	For example:
-	<div style="background-color:;padding:10px">
-		<strong>study/find?query=dcterms.contributor=Huelsenbeck or dcterms.contributor=Ronquist</strong>
-	</div>
-	Finally, searching can be modified to project the results from one section info those of another. The
-	effect is roughly the same as switching between tabs in the search section: if the results are a
-	list of tree and you click on the matrix search tab, the trees are converted to the set of matrices
-	on which the trees are based. This behaviour can be used by specifying the 
-	<strong>recordSchema=&lt;section&gt;</strong> argument, i.e.:
-	<div style="background-color:;padding:10px">
-		<strong>taxon/find?query=dcterms.title=="Homo sapiens"&amp;recordSchema=tree</strong>
-	</div>	
-	returns all the trees that have <em>Homo sapiens</em> in them.
-	By default, all these queries return a web page, but with a <strong>format=rss1</strong> argument
-	the search results are listed in an RDF compatible RSS1.0 file, i.e.:
-	<div style="background-color:;padding:10px">
-		<strong>taxon/find?query=tb.title.taxon=<em>&lt;name&gt;</em>&amp;format=rss1</strong>
-	</div>	
-	The returned results in RSS1.0 use the short urls of the form <strong>&lt;section&gt;/&lt;id&gt;</strong>, whose
-	returned resource descriptions (like <a href="/treebase-web/phylows/tree/TB2:Tr2227">
-	this</a> one) need to be scanned to discover suitable serialization formats. 
-</p>
 </div>
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-12 00:02:30 UTC (rev 547)
@@ -859,6 +859,7 @@
 				<prop key="/login.html">filenameController</prop>
 				<prop key="/urlAPI.html">filenameController</prop>
 				<prop key="/people.html">filenameController</prop>
+				<prop key="/technology.html">filenameController</prop>
 				
 				<prop key="/user/viewXML.html">filenameController</prop>
 				<prop key="/test/phylowidget.html">filenameController</prop>

Modified: trunk/treebase-web/src/main/webapp/common/footer.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/footer.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/footer.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,8 +1,30 @@
 <%@ include file="/common/taglibs.jsp" %>
 
-<p style="text-align:center"><!-- Revision <%=  org.cipres.treebase.Version.VCSID %>  -->
-<br />
-	<a href="http://validator.w3.org/check?uri=referer"><img src="<fmt:message key="icons.xhtml" />" alt="XHTML" title="Validate page markup" class="iconButton" style="vertical-align:middle"/></a> 
-	<a href="http://jigsaw.w3.org/css-validator/check/referer"><img src="<fmt:message key="icons.css"/>" alt="CSS" title="Validate page styles" class="iconButton"  style="vertical-align:middle"/></a><br />
-	<a href="http://www.nescent.org/"><img src="<c:url value="/images/nescent_logo.gif"/>" alt="NESCent" width="101" height="83" border="0" /></a>
-</p>	
\ No newline at end of file
+<p class="footerLogo"><!-- Revision <%=  org.cipres.treebase.Version.VCSID %>  -->
+	<a href="http://www.nescent.org/">
+		<img 
+			src="<c:url value="/images/nescent_logo.png"/>" 
+			alt="NESCent" 
+			width="83" 
+			height="83" 
+			border="0" />
+	</a>
+</p>	
+<p style="text-align:center">
+	<a href="http://validator.w3.org/check?uri=referer">
+		<img 
+			src="<fmt:message key="icons.xhtml" />" 
+			alt="XHTML" 
+			title="Validate page markup" 
+			class="iconButton" 
+			style="vertical-align:middle"/>
+	</a> 
+	<a href="http://jigsaw.w3.org/css-validator/check/referer">
+		<img 
+			src="<fmt:message key="icons.css"/>" 
+			alt="CSS" 
+			title="Validate page styles" 
+			class="iconButton"  
+			style="vertical-align:middle"/>
+	</a>
+</p>
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/common/header.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/header.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/header.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,4 +1,8 @@
 <%@ include file="/common/taglibs.jsp"%>
 
-<h1><a href="<c:url value="/home.html"/>"><img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" /></a></h1>
-
+<h1>
+	<a href="<c:url value="/home.html"/>">
+	<img src="<c:url value="/images/logo.gif"/>" alt="TreeBase Logo" width="523" height="112" border="0" />
+	</a>
+</h1>
+<img src="images/gradient.jpg" style="width:100%;height:10px"/>

Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,20 +1,22 @@
 <%@ include file="/common/taglibs.jsp"%>
-
-<div class="gutter">
-	<div id="navcontainer">
-		<ul id="navlist">
-			<li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
-			<li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>					
-			<li><span style="font-weight:bold;border-bottom: 1px solid #CCC;padding:3px;display:block"><fmt:message key="nav.about"/></span>
-				<ul id="innerNavlist">
-					<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
-					<li><a href="#"><fmt:message key="nav.technology"/></a></li>
-					<li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
-					<li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
-				</ul>
-			</li>			
-			<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
-			<li><a href="#"><fmt:message key="nav.contact"/></a></li>			
-		</ul>
+<div>
+	<div class="gutter" id="sidebarLeftGutter">
+		<div id="navcontainer">
+			<ul id="navlist">
+				<li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
+				<li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>					
+				<li><span class="navlistHeading"><fmt:message key="nav.about"/></span>
+					<ul id="innerNavlist">
+						<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
+						<li><a href="<c:url value="/technology.html"/>"><fmt:message key="nav.technology"/></a></li>
+						<li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
+						<li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
+					</ul>
+				</li>			
+				<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
+				<li><a href="#"><fmt:message key="nav.contact"/></a></li>			
+			</ul>
+		</div>
 	</div>
-</div>
+	<img src="<c:url value="images/footer_bg.gif"/>" style="width:100%"/>
+</div>
\ No newline at end of file

Added: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/TreeBASE.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/architecture.jpeg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/gradient.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/gradient.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/logo_bg.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/nescent_logo.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/anon.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/bpiel.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/hlapp.jpeg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/krice.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/krice.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/mdonoghue.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/mjdominus.jpeg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/msanderson.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/rvos.jpg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/teriksson.gif
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/images/people/vtannen.jpeg
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Modified: trunk/treebase-web/src/main/webapp/styles/displaytag.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/displaytag.css	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/displaytag.css	2010-03-12 00:02:30 UTC (rev 547)
@@ -15,8 +15,6 @@
     width: 80%;
 }
 
-
-
 table.list {
     border: 1px solid #808080;
     border-collapse: collapse;
@@ -24,18 +22,18 @@
     width: 100%;
     background: white;
 }
+
 table.list td {
-    padding-left: 3px;  
+    padding-left: 3px
 }
 
-
 table.list th {
     background-color: silver;
     padding: 2px;
     padding-left: 3px;
     border-bottom: 1px solid black;
     text-align: left;
-    color: black;
+    color: black;
     white-space: nowrap
 }
 
@@ -162,4 +160,4 @@
 table.detail th {
     text-align: right;
     padding: 0px 3px 0px 0px;
-}
+}
\ No newline at end of file

Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-11 16:55:59 UTC (rev 546)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-12 00:02:30 UTC (rev 547)
@@ -1,31 +1,32 @@
 body {
 	margin: 0;
 	padding: 0;
-	font-family: Verdana, sans-serif;
-	font-size: small;
+	font-family: "Helvetica Neue", GillSans, helvetica, "lucida sans", arial, sans-serif;
+	font-size: 80%;
+	line-height: 1.5em
 }
 
 /* Link Styles  
 *******************************************************************************************/
 
-#content a:link {
+#content a:link, #contentRight a:link {
 	color: #003366;
 	text-decoration: none;
 	font-weight: bold
 }
 
-#content a:visited {
+#content a:visited, #contentRight a:visited {
 	color: #3863a4;
 	text-decoration: none;
 	font-weight: bold
 }
 
-#content a:hover {
+#content a:hover, #contentRight a:hover {
 	border-bottom: 2px solid orangered;
 	font-weight: bold
 }
 
-#content a:active {
+#content a:active, #contentRight a:active {
 	text-decoration: underline;
 	font-weight: bold
 }
@@ -34,44 +35,59 @@
 *******************************************************************************************/
 	
 h1, h2, h3 {
-	color: #003366;
+	color: #003366
 }
 
 #content h2 {
-	background: #BED1E5 url(../img/off_bg.gif) repeat-x left top;
+	background: #BED1E5 url("../images/off_bg.gif") repeat-x left top;
 	padding: 5px !important
 }
 
+#contentRight h1 {
+	margin: 0px;
+	padding: 15px;
+	border-top: 1px solid silver;
+	background-image: url("../images/footer_bg.gif")
+}
+
+#contentRight h2, #contentRight h3, #contentRight p {
+	padding-left: 15px !important;
+	padding-right: 15px !important;	
+	padding-top: 15px !important		
+}
+
+#contentRight h2 {
+	border-top: 1px solid silver
+}
+
 /* Page Structure/Layout 
 ***************************...
 
[truncated message content]

[Treebase-guts] SF.net SVN: treebase:[546] trunk/treebase-web/src/main/webapp/test/ phylowidget/PhyloWidget.jar

[<vga...@us...>]

Revision: 546
          http://treebase.svn.sourceforge.net/treebase/?rev=546&view=rev
Author:   vgapeyev
Date:     2010-03-11 16:55:59 +0000 (Thu, 11 Mar 2010)

Log Message:
-----------
Put PhyloWidget.jar inside treebase-web.war, alongside the other similar jars (itext.jar, pdf.jar, etc)

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar

Added: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
===================================================================
(Binary files differ)


Property changes on: trunk/treebase-web/src/main/webapp/test/phylowidget/PhyloWidget.jar
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[545] trunk/treebase-web/src/main/webapp

[<rv...@us...>]

Revision: 545
          http://treebase.svn.sourceforge.net/treebase/?rev=545&view=rev
Author:   rvos
Date:     2010-03-11 16:44:59 +0000 (Thu, 11 Mar 2010)

Log Message:
-----------
Adding people page as per http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
    trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
    trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
    trunk/treebase-web/src/main/webapp/styles/styles.css

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml	2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/decorators.xml	2010-03-11 16:44:59 UTC (rev 545)
@@ -9,6 +9,7 @@
         <pattern>/home.html</pattern>
         <pattern>/about.html</pattern>
         <pattern>/urlAPI.html</pattern>
+        <pattern>/people.html</pattern>
     </decorator>
 	
 	<!-- decoration page for search pages -->

Modified: trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/treebase-servlet.xml	2010-03-11 16:44:59 UTC (rev 545)
@@ -858,6 +858,8 @@
 				<prop key="/home.html">filenameController</prop>
 				<prop key="/login.html">filenameController</prop>
 				<prop key="/urlAPI.html">filenameController</prop>
+				<prop key="/people.html">filenameController</prop>
+				
 				<prop key="/user/viewXML.html">filenameController</prop>
 				<prop key="/test/phylowidget.html">filenameController</prop>
 				<prop key="/test/newPhylowidget.html">filenameController</prop>

Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-11 16:44:59 UTC (rev 545)
@@ -9,7 +9,7 @@
 				<ul id="innerNavlist">
 					<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
 					<li><a href="#"><fmt:message key="nav.technology"/></a></li>
-					<li><a href="#"><fmt:message key="nav.people"/></a></li>
+					<li><a href="<c:url value="/people.html"/>"><fmt:message key="nav.people"/></a></li>
 					<li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
 				</ul>
 			</li>			

Modified: trunk/treebase-web/src/main/webapp/styles/styles.css
===================================================================
--- trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-11 16:44:23 UTC (rev 544)
+++ trunk/treebase-web/src/main/webapp/styles/styles.css	2010-03-11 16:44:59 UTC (rev 545)
@@ -281,6 +281,22 @@
 	vertical-align: middle	
 }
 
+/* People tables
+*******************************************************************************************/
+table.peopleTable td {
+	width: 130px;
+	text-align: center;
+	vertical-align: top;
+	padding-bottom: 20px;
+	padding-top: 20px;
+}
+
+table.peopleTable img {
+	border: 1px solid silver;
+	padding: 5px;
+	background-color: white;
+}
+
 	
 /* Left Sidebar Navigation Menu 
 *******************************************************************************************/


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

[Treebase-guts] SF.net SVN: treebase:[544] trunk/treebase-web/src/main/webapp/WEB-INF/pages /people.jsp

[<rv...@us...>]

Revision: 544
          http://treebase.svn.sourceforge.net/treebase/?rev=544&view=rev
Author:   rvos
Date:     2010-03-11 16:44:23 +0000 (Thu, 11 Mar 2010)

Log Message:
-----------
Adding people page as per http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en

Added Paths:
-----------
    trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp

Added: trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	                        (rev 0)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/people.jsp	2010-03-11 16:44:23 UTC (rev 544)
@@ -0,0 +1,115 @@
+<div class="gutter">
+	<table class="peopleTable">
+		<thead><tr><th colspan="6"><h2>Current contributors</h2></th></tr></thead>
+		<tr>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Vladimir Gapeyev"/>
+				<br/><strong>Vladimir Gapeyev</strong>
+				<br/>Developer
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Youjun Guo"/>
+				<br/><strong>Youjun Guo</strong>
+				<br/>Developer
+			</td>			
+			<td>
+				<img src="images/people/hlapp.jpeg" width="81" height="108" alt="Hilmar Lapp"/>
+				<br/><strong>Hilmar Lapp</strong>
+				<br/>Deployment Manager
+			</td>
+			<td>
+				<img src="images/people/bpiel.gif" width="81" height="108" alt="William Piel"/>
+				<br/><strong>William Piel</strong>
+				<br/>Data Editor
+				<br />Prototype Developer
+			</td>
+			<td>
+				<img src="images/people/vtannen.jpeg" width="81" height="108" alt="Val Tannen"/>
+				<br/><strong>Val Tannen</strong>
+				<br/>Development Leader
+			</td>
+			<td>
+				<img src="images/people/rvos.jpg" width="81" height="108" alt="Rutger Vos"/>
+				<br/><strong>Rutger Vos</strong>
+				<br/>Developer
+				<br/>API Design
+			</td>
+		</tr>
+	</table>
+	
+	<table class="peopleTable">	
+		<thead><tr><th colspan="6"><h2>Past contributors</h2></th></tr></thead>	
+		<tr>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Lucie Chan"/>
+				<br/><strong>Lucie Chan</strong>
+				<br/>Developer
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Shirley Cohen"/>
+				<br/><strong>Shirley Cohen</strong>
+				<br/>Student Researcher
+			</td>
+			<td>
+				<img src="images/people/mjdominus.jpeg" width="81" height="108" alt="Mark J. Dominus"/>
+				<br/><strong>Mark J. Dominus</strong>
+				<br/>Developer
+			</td>
+			<td>
+				<img src="images/people/mdonoghue.gif" width="81" height="108" alt="Michael Donoghue"/>
+				<br/><strong>Michael Donoghue</strong>
+				<br/>Conceptual Issues
+			</td>
+			<td>
+				<img src="images/people/teriksson.gif" width="81" height="108" alt="Torsten Eriksson"/>
+				<br/><strong>Torsten Eriksson</strong>
+				<br/>Prototype Developer
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Madhusudan Gujral"/>
+				<br/><strong>Madhusudan Gujral</strong>
+				<br/>Developer
+			</td>
+		</tr>
+		<tr>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Chris Henze"/>
+				<br/><strong>Chris Henze</strong>
+				<br/>Prototype Developer
+			</td>
+			<td>
+				<img src="images/people/krice.gif" width="81" height="108" alt="Ken Rice"/>
+				<br/><strong>Ken Rice</strong>
+				<br/>Prototype Developer
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Jin Ruan"/>
+				<br/><strong>Jin Ruan</strong>
+				<br/>Developer
+			</td>
+			<td>
+				<img src="images/people/msanderson.gif" width="81" height="108" alt="Mike Sanderson"/>
+				<br/><strong>Mike Sanderson</strong>
+				<br/>Conceptual Issues
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Can van Tran"/>
+				<br/><strong>Can van Tran</strong>
+				<br/>Developer
+			</td>
+			<td>
+				<img src="images/people/anon.jpg" width="81" height="108" alt="Tracy Zhao"/>
+				<br/><strong>Tracy Zhao</strong>
+				<br/>Developer
+			</td>
+		</tr>
+	</table>
+	
+	<h2>Phyloinformatics Research Foundation Inc, Board</h2>
+	<ul>
+		<li>Michael Donoghue</li>
+		<li>David Maddison</li>
+		<li>William Piel</li>
+		<li>Val Tannen</li>		
+	</ul>
+</div>
\ No newline at end of file


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[Treebase-guts] SF.net SVN: treebase:[541] trunk/treebase-web/src/main/webapp/common/ sidebarLeft.jsp

[<rv...@us...>]

Revision: 541
          http://treebase.svn.sourceforge.net/treebase/?rev=541&view=rev
Author:   rvos
Date:     2010-03-11 14:36:37 +0000 (Thu, 11 Mar 2010)

Log Message:
-----------
Expanded top level, left-hand navigation menu as per http://docs.google.com/Doc?docid=0AXEQpupFgwYiZGg4bXF6bl82NmZwdm50cmRz&hl=en

Modified Paths:
--------------
    trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp

Modified: trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-11 14:36:12 UTC (rev 540)
+++ trunk/treebase-web/src/main/webapp/common/sidebarLeft.jsp	2010-03-11 14:36:37 UTC (rev 541)
@@ -3,14 +3,18 @@
 <div class="gutter">
 	<div id="navcontainer">
 		<ul id="navlist">
-			<li><a href="#" class="active"><fmt:message key="nav.introduction"/></a></li>
-			<li><a href="#"><fmt:message key="nav.why"/></a></li>
-			<li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search"/></a></li>
-			<li><a href="#"><fmt:message key="nav.contact"/></a></li>
-			<li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>
-			<li><a href="#"><fmt:message key="nav.stats"/></a></li>
-			<li><a href="#"><fmt:message key="nav.referee"/></a></li>
-			<li><a href="/treebase-web/help/urlAPI.jsp"><fmt:message key="nav.urlapi"/></a></li>
+			<li><a href="<c:url value="/search/studySearch.html"/>"><fmt:message key="nav.search.treebase"/></a></li>
+			<li><a href="<c:url value="/user/processUser.html"/>"><fmt:message key="nav.submit"/></a></li>					
+			<li><span style="font-weight:bold;border-bottom: 1px solid #CCC;padding:3px;display:block"><fmt:message key="nav.about"/></span>
+				<ul id="innerNavlist">
+					<li><a href="<c:url value="/about.html"/>"><fmt:message key="nav.overview"/></a></li>
+					<li><a href="#"><fmt:message key="nav.technology"/></a></li>
+					<li><a href="#"><fmt:message key="nav.people"/></a></li>
+					<li><a href="#"><fmt:message key="nav.partnerships"/></a></li>
+				</ul>
+			</li>			
+			<li><a href="<c:url value="/urlAPI.html"/>"><fmt:message key="nav.dataaccess"/></a></li>
+			<li><a href="#"><fmt:message key="nav.contact"/></a></li>			
 		</ul>
 	</div>
 </div>


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