[Treebase-guts] SF.net SVN: treebase:[159] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers

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

Revision: 159
          http://treebase.svn.sourceforge.net/treebase/?rev=159&view=rev
Author:   rvos
Date:     2009-07-02 10:43:46 +0000 (Thu, 02 Jul 2009)

Log Message:
-----------
Major refactoring to facilitate CQL queries and RSS1.0 result sets

Modified Paths:
--------------
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -20,13 +20,16 @@
 
 package org.cipres.treebase.web.controllers;
 
+import java.io.IOException;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.log4j.Logger;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.RangeExpression.MalformedRangeExpression;
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
 import org.cipres.treebase.domain.matrix.Matrix;
@@ -34,11 +37,21 @@
 import org.cipres.treebase.domain.search.MatrixSearchResults;
 import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
+import org.cipres.treebase.domain.search.TreeSearchResults;
 import org.cipres.treebase.web.Constants;
 import org.cipres.treebase.web.util.RequestMessageSetter;
 import org.cipres.treebase.web.util.SearchMessageSetter;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLAndNode;
+import org.z3950.zing.cql.CQLBooleanNode;
+import org.z3950.zing.cql.CQLNode;
+import org.z3950.zing.cql.CQLNotNode;
+import org.z3950.zing.cql.CQLOrNode;
+import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLParser;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 /**
  * MatrixSearchController.java
@@ -72,50 +85,162 @@
 
 		clearMessages(request);
 		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
 		
 		LOGGER.info("formName is '" + formName + "'");
-
 		
+		if ( ! TreebaseUtil.isEmpty(query) ) {
+			/*
+			CQLParser parser = new CQLParser();
+			CQLNode root = parser.parse(query);
+			root = normalizeParseTree(root);
+			Set<Matrix> queryResults = doCQLQuery(root, new HashSet<Matrix>(),request, response, errors);
+			MatrixSearchResults tsr = new MatrixSearchResults(queryResults);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, tsr); 			
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, root);
+			}
+			*/
+			return this.handleQueryRequest(request, response, errors);
+		}		
+		
 		if (formName.equals("matrixSimple")) {
 			String buttonName = request.getParameter("searchButton");
-
+			Set<Matrix> matches = new HashSet<Matrix>();
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+		 	SearchMessageSetter mSetter = new RequestMessageSetter(request);
+			MatrixSearchResults oldRes;	
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (MatrixSearchResults) sr.convertToMatrices();
+				} else {
+					oldRes = new MatrixSearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
 			if (buttonName.equals("matrixID")) {
-				return doSearch(request, response, SearchType.byID, errors);
+				matches.addAll(doSearch(request, response, SearchType.byID, errors,searchTerm));
 			} else if  (buttonName.equals("matrixTitle")) {
-				return doSearch(request, response, SearchType.byTitle, errors);
+				matches.addAll(doSearch(request, response, SearchType.byTitle, errors,searchTerm));
 			} else if  (buttonName.equals("matrixType")) {
-				return doSearch(request, response, SearchType.byType, errors);
+				matches.addAll(doSearch(request, response, SearchType.byType, errors,searchTerm));
 			} else if  (buttonName.equals("matrixNTAX")) {
-				return doSearch(request, response, SearchType.byNTAX, errors);	
+				matches.addAll(doSearch(request, response, SearchType.byNTAX, errors,searchTerm));	
 			} else if  (buttonName.equals("matrixNCHAR")) {
-				return doSearch(request, response, SearchType.byNCHAR, errors);
+				matches.addAll(doSearch(request, response, SearchType.byNCHAR, errors,searchTerm));
 			} else {
 				throw new Error("Unknown search button name '" + buttonName + "'");
 			}
-		} else { 
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				SearchResults<Matrix> newRes = intersectSearchResults(oldRes, 
+						new MatrixSearchResults(matches), mSetter, "No matching matrices found");
+				saveSearchResults(request, newRes);	
+				return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes); 
+			}
+			else {
+				return this.searchResultsAsRDF(new MatrixSearchResults(matches), request, null, "matrix", "matrix");
+			}			
+		} 
+		
+		else { 
 			return super.onSubmit(request, response, command, errors);
 		}
 	}
 	
-	private ModelAndView doSearch(
+	private Set<Matrix> doCQLQuery(
+			CQLNode node, 
+			Set<Matrix> results, 
+			HttpServletRequest request, 
+			HttpServletResponse response, 
+			BindException errors
+		) throws InstantiationException {
+		if ( node instanceof CQLBooleanNode ) {
+			Set<Matrix> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request, response, errors);
+			Set<Matrix> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request, response, errors);
+			if ( node instanceof CQLNotNode ) {
+				for ( Matrix rightMatrix : resultsRight ) {
+					if ( resultsLeft.contains(rightMatrix) )
+						resultsLeft.remove(rightMatrix);
+				}
+			}
+			else if ( node instanceof CQLOrNode ) {
+				resultsLeft.addAll(resultsRight);
+			}
+			else if ( node instanceof CQLAndNode ) {
+				Set<Matrix> resultsUnion = new HashSet<Matrix>();
+				for ( Matrix leftMatrix : resultsLeft ) {
+					if ( resultsRight.contains(leftMatrix) )
+						resultsUnion.add(leftMatrix);
+				}				
+				resultsLeft = resultsUnion;
+			}
+			results = resultsLeft;
+		}		
+		else if ( node instanceof CQLTermNode ) {
+			CQLTermNode term = (CQLTermNode)node;
+			String index = term.getIndex();				
+			if ( index.startsWith("tb.title") ) {
+				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm()));
+			} else if ( index.startsWith("tb.identifier") ) {
+				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm()));
+			} else if ( index.startsWith("tb.type") ) {
+				results.addAll(doSearch(request, response, SearchType.byType, errors, term.getTerm()));
+			} else if ( index.startsWith("tb.ntax") ) {
+				results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
+			} else if ( index.startsWith("tb.nchar") ) {
+				results.addAll(doSearch(request, response, SearchType.byNTAX, errors, term.getTerm()));
+			} else {
+				// issue warnings
+				addMessage(request, "Unsupported index: " + index);
+			}	
+		}
+		logger.debug(node);
+		return results;		
+	}		
+	
+	private CQLNode normalizeParseTree(CQLNode node) {
+		if ( node instanceof CQLBooleanNode ) {
+			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
+			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
+			return node;
+		}
+		else if ( node instanceof CQLTermNode ) {
+			String index = ((CQLTermNode)node).getIndex();
+			String term = ((CQLTermNode)node).getTerm();
+			CQLRelation relation = ((CQLTermNode)node).getRelation();
+			index = index.replaceAll("dcterms.title", "tb.title.matrix");
+			index = index.replaceAll("dcterms.identifier", "tb.identifier.matrix");
+			index = index.replaceAll("dcterms.extent", "tb.ntax.matrix");
+			return new CQLTermNode(index,relation,term);
+		}
+		logger.debug(node);
+		return node;
+	}	
+	
+	@SuppressWarnings("unchecked")
+	private Collection<Matrix> doSearch(
 			HttpServletRequest request,
 			HttpServletResponse response,
 			SearchType searchType,
-			BindException errors) throws InstantiationException {
+			BindException errors,
+			String searchTerm) throws InstantiationException {
 
-		String searchTerm = convertStars(request.getParameter("searchTerm"));
-		String keywordSearchTerm = "%" + searchTerm + "%";
-	 	SearchMessageSetter mSetter = new RequestMessageSetter(request);
+//		String searchTerm = convertStars(request.getParameter("searchTerm"));
+//		String keywordSearchTerm = "%" + searchTerm + "%";
+//	 	SearchMessageSetter mSetter = new RequestMessageSetter(request);
 		
-		MatrixSearchResults oldRes;	
-		{
-			SearchResults<?> sr = searchResults(request);
-			if (sr != null) {
-				oldRes = (MatrixSearchResults) sr.convertToMatrices();
-			} else {
-				oldRes = new MatrixSearchResults ();   // TODO: Convert existing search results to new type	
-			}
-		}
+//		MatrixSearchResults oldRes;	
+//		{
+//			SearchResults<?> sr = searchResults(request);
+//			if (sr != null) {
+//				oldRes = (MatrixSearchResults) sr.convertToMatrices();
+//			} else {
+//				oldRes = new MatrixSearchResults ();   // TODO: Convert existing search results to new type	
+//			}
+//		}
 
 		Collection<Matrix> matches = null;
 		MatrixService matrixService = getSearchService().getMatrixService();	
@@ -164,13 +289,14 @@
 			}
 		}
 		matches.removeAll(orphanedMatrices);
-
-		SearchResults<Matrix> newRes = intersectSearchResults(oldRes, 
-				new MatrixSearchResults(matches), mSetter, "No matching matrices found");
-
-		saveSearchResults(request, newRes);
+		return matches;
 		
-		return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes); 
+//		SearchResults<Matrix> newRes = intersectSearchResults(oldRes, 
+//				new MatrixSearchResults(matches), mSetter, "No matching matrices found");
+//
+//		saveSearchResults(request, newRes);
+//		
+//		return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, newRes); 
 
 	}
 
@@ -183,4 +309,36 @@
 		return "matrixSearch.html";
 	}
 
+	@Override
+	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException {
+		String query = request.getParameter("query");				
+		CQLParser parser = new CQLParser();
+		CQLNode root = parser.parse(query);
+		root = normalizeParseTree(root);
+		Set<Matrix> queryResults = doCQLQuery(root, new HashSet<Matrix>(),request, response, errors);
+		MatrixSearchResults tsr = new MatrixSearchResults(queryResults);
+		saveSearchResults(request, tsr);
+		if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+			return new ModelAndView("search/matrixSearch", Constants.RESULT_SET, tsr); 			
+		}
+		else {
+			SearchResults<?> res = tsr;
+			String schema = null, original = "matrix";
+			if ( ! TreebaseUtil.isEmpty(request.getParameter("recordSchema")) ) {
+				schema = request.getParameter("recordSchema");
+				if ( schema.equals("tree") ) {
+					res = tsr.convertToTrees();
+				}
+				else if ( schema.equals("taxon") ) {
+					res = tsr.convertToTaxa();
+				}
+				else if ( schema.equals("study") ) {
+					res = tsr.convertToStudies();
+				}
+			}
+			this.saveSearchResults(request, res);
+			return this.searchResultsAsRDF(res, request, root, schema, original);
+		}
+	}
+
 }

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	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/PhyloWSController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -70,29 +70,33 @@
             		+ "', should be /${class}/${NamespacedGUID}");
             }
             String[] pathComponents = pathInfo.split("/");
-            String rawNamespacedGUID = pathComponents[pathComponents.length-1];
-            if ( rawNamespacedGUID.startsWith("uBio:") ) {
-            	url = uBioBaseUrl + rawNamespacedGUID.substring("uBio:".length());
-            }
-            else if ( rawNamespacedGUID.startsWith("NCBI:") ) {
-            	url = ncbiBaseUrl + rawNamespacedGUID.substring("NCBI:".length());
-            }            
-            else {
-	            NamespacedGUID namespacedGUID = new NamespacedGUID(rawNamespacedGUID);
-	            TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
-	            if ( hasWebPage(pathComponents) ) {
-	            	if ( TreebaseUtil.isEmpty(req.getParameter(format)) ) {
-	            		url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
-	            	}
-	            	else if ( req.getParameter(format).equals("html") ) {
-	            		url = domain + createUrl(tbID.getTypePrefix(),tbID.getId());
-	            	}
-	            	else {
-	            		url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
-	            	}
+            if ( pathComponents[pathComponents.length-1].equals("find") ) {
+            	url = domain + createSearchUrl(pathComponents[pathComponents.length-2],req);
+            } else {
+	            String rawNamespacedGUID = pathComponents[pathComponents.length-1];
+	            if ( rawNamespacedGUID.startsWith("uBio:") ) {
+	            	url = uBioBaseUrl + rawNamespacedGUID.substring("uBio:".length());
 	            }
+	            else if ( rawNamespacedGUID.startsWith("NCBI:") ) {
+	            	url = ncbiBaseUrl + rawNamespacedGUID.substring("NCBI:".length());
+	            }            
 	            else {
-	            	url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+		            NamespacedGUID namespacedGUID = new NamespacedGUID(rawNamespacedGUID);
+		            TreebaseIDString tbID = namespacedGUID.getTreebaseIDString();
+		            if ( hasWebPage(pathComponents) ) {
+		            	if ( TreebaseUtil.isEmpty(req.getParameter(format)) ) {
+		            		url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+		            	}
+		            	else if ( req.getParameter(format).equals("html") ) {
+		            		url = domain + createUrl(tbID.getTypePrefix(),tbID.getId());
+		            	}
+		            	else {
+		            		url = domain + createDownloadUrl(tbID.getTypePrefix(),tbID.getId(),req.getParameter(format));
+		            	}
+		            }
+		            else {
+		            	url = domain + "/treebase-web/search/study/anyObjectAsRDF.html?namespacedGUID=" + namespacedGUID.toString();
+		            }
 	            }
             }
         } catch ( MalformedTreebaseIDString e ) {
@@ -109,6 +113,20 @@
         return null;
 	}
 	
+	private String createSearchUrl(String path,HttpServletRequest request) {
+		StringBuilder sb = new StringBuilder();
+		sb
+			.append("/treebase-web/search/")
+			.append(path)
+			.append("Search.html?query=")
+			.append(request.getParameter("query"))
+			.append("&format=")
+			.append(request.getParameter("format"))
+			.append("&recordSchema=")
+			.append(request.getParameter("recordSchema"));
+		return sb.toString();
+	}
+
 	private boolean hasWebPage(String[] pathComponents) {
 		for ( int i = ( pathComponents.length - 1 ); i >= 0; i-- ) {
 			for ( int j = 0; j < classesWithPages.length; j++ ) {

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	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -22,6 +22,9 @@
 
 package org.cipres.treebase.web.controllers;
 
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
@@ -50,6 +53,8 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.view.RedirectView;
+import org.z3950.zing.cql.CQLNode;
+import org.z3950.zing.cql.CQLParseException;
 
 
 /**
@@ -65,6 +70,8 @@
 	protected String formView;
 
 	private TaxonLabelService mTaxonLabelService;
+	
+	protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException;	
 
 	protected ModelAndView onSubmit(
 			HttpServletRequest request,
@@ -110,6 +117,33 @@
 		return selectResultsView(request);
 	}
 	
+	protected ModelAndView searchResultsAsRDF (SearchResults<?> searchResults,HttpServletRequest request,CQLNode root, String schema, String original) throws UnsupportedEncodingException {
+		//${baseURL}
+		//${phyloWSPath}
+		//${normalizedCQLQuery}
+		//${searchResults}
+		//${domainAddress}
+		String phyloWSPath = "find/" + original;
+		request.getSession().setAttribute("searchResultsThawed", searchResults);		
+		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("recordSchema", schema);
+		request.getSession().setAttribute("format", request.getParameter("format"));
+		request.getSession().setAttribute("baseURL", baseURL.toString());
+		request.getSession().setAttribute("domainAddress", domainAddress.toString());
+		request.getSession().setAttribute("phyloWSPath", phyloWSPath);
+		request.getSession().setAttribute("originalSection", original);
+		if ( null != root ) {			
+			request.getSession().setAttribute("normalizedCQLQuery", URLEncoder.encode(root.toCQL(),"UTF-8"));
+		}
+		return new ModelAndView(new RedirectView("searchResultsAsRDF.html"));
+	}
+	
 	protected <E extends TBPersistable> SearchResults<E> intersectSearchResults(
 			SearchResults<E> oldRes,
 			SearchResults<E> newRes, 
@@ -380,6 +414,10 @@
 	protected ModelAndView showForm(HttpServletRequest request,
 			HttpServletResponse response, BindException bindException, Map model)
 			throws Exception {
+		String query = request.getParameter("query");
+		if ( query != null ) {
+			return this.handleQueryRequest(request, response, bindException);
+		}
 		String action = request.getParameter("action");
 		if (action != null && action.equals("discard") && request.getMethod().equals("GET")) {
 			discardSearchResults(request);

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	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -20,27 +20,36 @@
 
 package org.cipres.treebase.web.controllers;
 
+import java.io.IOException;
 import java.util.Collection;
-import java.util.LinkedList;
-import java.util.List;
+import java.util.HashSet;
+import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.log4j.Logger;
 import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
 import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
 import org.cipres.treebase.domain.search.StudySearchResults;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.study.StudyService;
-import org.cipres.treebase.domain.taxon.TaxonLabel;
-import org.cipres.treebase.domain.taxon.TaxonVariant;
 import org.cipres.treebase.web.Constants;
 import org.cipres.treebase.web.util.RequestMessageSetter;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLAndNode;
+import org.z3950.zing.cql.CQLBooleanNode;
+import org.z3950.zing.cql.CQLNode;
+import org.z3950.zing.cql.CQLNotNode;
+import org.z3950.zing.cql.CQLOrNode;
+import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLParser;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 /**
  * StudySearchController.java
@@ -99,13 +108,41 @@
 
 		clearMessages(request);
 		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
 		
 		LOGGER.info("formName is '" + formName + "'");
 		
+		if ( ! TreebaseUtil.isEmpty(query) ) {
+			/*
+			CQLParser parser = new CQLParser();
+			CQLNode root = parser.parse(query);
+			root = normalizeParseTree(root);
+			Set<Study> queryResults = doCQLQuery(root, new HashSet<Study>(),request, response, errors);
+			StudySearchResults tsr = new StudySearchResults(queryResults);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
+				return new ModelAndView("search/studySearch", Constants.RESULT_SET, tsr);
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, root);
+			}
+			*/
+			return this.handleQueryRequest(request, response, errors);
+		}		
+		
 		if (formName.equals("searchKeyword")) {
 			SearchType searchType;
 			String buttonName = request.getParameter("searchButton");
-			
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			StudySearchResults oldRes;
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (StudySearchResults) sr.convertToStudies();
+				} else {
+					oldRes = new StudySearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
 			if (buttonName.equals("authorKeyword")) {
 				searchType = SearchType.byAuthorName;
 			} else if (buttonName.equals("studyID")) {
@@ -123,84 +160,171 @@
 			} else {
 				throw new Error("Unknown search button name '" + buttonName + "'");
 			}
-
-			return doSearch(request, response, searchType, errors);	
+			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm);	
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {				
+				SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
+				new RequestMessageSetter(request), "No matching studies found");	
+				saveSearchResults(request, newRes);
+				return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes); 		
+			}
+			else {
+				return this.searchResultsAsRDF(new StudySearchResults(matches), request, null,"study","study");
+			}
 		} else {
 			return super.onSubmit(request, response, command, errors);
 		}
 	}
 	
-	protected ModelAndView doSearch(
+	private Set<Study> doCQLQuery(
+			CQLNode node, 
+			Set<Study> results, 
+			HttpServletRequest request, 
+			HttpServletResponse response, 
+			BindException errors
+		) throws InstantiationException {
+		if ( node instanceof CQLBooleanNode ) {
+			Set<Study> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request, response, errors);
+			Set<Study> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request, response, errors);
+			if ( node instanceof CQLNotNode ) {
+				Set<Study> resultsDifference = new HashSet<Study>();
+				for ( Study leftStudy : resultsLeft ) {
+					if ( ! resultsRight.contains(leftStudy) )
+						resultsDifference.add(leftStudy);
+				}
+				resultsLeft = resultsDifference;
+			}
+			else if ( node instanceof CQLOrNode ) {
+				resultsLeft.addAll(resultsRight);
+			}
+			else if ( node instanceof CQLAndNode ) {
+				Set<Study> resultsUnion = new HashSet<Study>();
+				for ( Study leftStudy : resultsLeft ) {
+					if ( resultsRight.contains(leftStudy) )
+						resultsUnion.add(leftStudy);
+				}				
+				resultsLeft = resultsUnion;
+			}
+			results = resultsLeft;
+		}		
+		else if ( node instanceof CQLTermNode ) {
+			CQLTermNode term = (CQLTermNode)node;
+			String index = term.getIndex();
+			if ( index.startsWith("tb.title") ) {
+				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm()));
+			} else if ( index.equals("tb.identifier.study") ) {
+				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm()));
+			} else if ( index.startsWith("dcterms.contributor") ) {
+				results.addAll(doSearch(request, response, SearchType.byAuthorName, errors, term.getTerm()));
+			} else if ( index.startsWith("dcterms.abstract") ) {
+				results.addAll(doSearch(request, response, SearchType.inAbstract, errors, term.getTerm()));
+			} else if ( index.startsWith("dcterms.subject") ) {
+				results.addAll(doSearch(request, response, SearchType.byKeyword, errors, term.getTerm()));
+			} else if ( index.startsWith("dcterms.bibliographicCitation") ) {
+				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 {
+				// issue warnings
+				addMessage(request, "Unsupported index: " + index);
+			}		
+		}
+		logger.debug(node);
+		return results;		
+	}		
+	
+	private CQLNode normalizeParseTree(CQLNode node) {
+		if ( node instanceof CQLBooleanNode ) {
+			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
+			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
+			return node;
+		}
+		else if ( node instanceof CQLTermNode ) {
+			String index = ((CQLTermNode)node).getIndex();
+			String term = ((CQLTermNode)node).getTerm();
+			CQLRelation relation = ((CQLTermNode)node).getRelation();
+			index = index.replaceAll("dcterms.title", "tb.title.study");
+			index = index.replaceAll("dcterms.identifier", "tb.identifier.study");
+			return new CQLTermNode(index,relation,term);
+		}
+		logger.debug(node);
+		return node;
+	}		
+	
+	@SuppressWarnings("unchecked")
+	protected Collection<Study> doSearch(
 			HttpServletRequest request,
 			HttpServletResponse response,
 			SearchType searchType,
-			BindException errors) throws InstantiationException {
+			BindException errors,
+			String searchTerm) throws InstantiationException {
 		
-		String searchTerm = convertStars(request.getParameter("searchTerm"));
+//		String searchTerm = convertStars(request.getParameter("searchTerm"));
 		String keywordSearchTerm = "%" + searchTerm + "%";
-		StudySearchResults oldRes;	
-
-		{
-			SearchResults<?> sr = searchResults(request);
-			if (sr != null) {
-				oldRes = (StudySearchResults) sr.convertToStudies();
-			} else {
-				oldRes = new StudySearchResults ();   // TODO: Convert existing search results to new type	
-			}
-		}
-		
-		LOGGER.info("doSearch old results contained " + oldRes.size() + " item(s)");
+//		StudySearchResults oldRes;	
+//
+//		{
+//			SearchResults<?> sr = searchResults(request);
+//			if (sr != null) {
+//				oldRes = (StudySearchResults) sr.convertToStudies();
+//			} else {
+//				oldRes = new StudySearchResults ();   // TODO: Convert existing search results to new type	
+//			}
+//		}
+//		
+//		LOGGER.info("doSearch old results contained " + oldRes.size() + " item(s)");
 		Collection<Study> matches;
 		StudyService studyService = getSearchService().getStudyService();	
 				
 		switch (searchType) {
-		case byID:
-			matches = (Collection<Study>) doSearchByIDString(request, studyService, Study.class, searchTerm);
-			break;
-		case byLegacyID:
-		{
-			TreebaseIDString legacyID = null;
-			boolean malformed = false;
-			try {
-				legacyID = new TreebaseIDString(searchTerm, Study.class);
-			} catch (MalformedTreebaseIDString e) {
-				malformed = true;
+			case byID:
+				matches = (Collection<Study>) doSearchByIDString(request, studyService, Study.class, searchTerm);
+				break;
+			case byLegacyID:
+			{
+				TreebaseIDString legacyID = null;
+				boolean malformed = false;
+				try {
+					legacyID = new TreebaseIDString(searchTerm, Study.class);
+				} catch (MalformedTreebaseIDString e) {
+					malformed = true;
+				}
+				if (malformed || legacyID.getTBClass() != Study.class) {
+					addMessage(request, "Legacy ID number '" + searchTerm + "' is not valid; try S#### or just ####");
+					matches = null;
+					break;
+				}
+				matches = (Collection<Study>) studyService.findByTBStudyID("S" + legacyID.getId().toString());
+				break;
 			}
-			if (malformed || legacyID.getTBClass() != Study.class) {
-				addMessage(request, "Legacy ID number '" + searchTerm + "' is not valid; try S#### or just ####");
-				matches = null;
+			case inAbstract:
+				matches = studyService.findByAbstract(keywordSearchTerm);
 				break;
-			}
-			matches = (Collection<Study>) studyService.findByTBStudyID("S" + legacyID.getId().toString());
-			break;
+			case inCitation:
+				matches = studyService.findByCitation(keywordSearchTerm);
+				break;
+			case byAuthorName:
+				matches = studyService.findByAuthor(searchTerm);
+				break;
+			case byTitle:
+				matches = studyService.findByTitle(keywordSearchTerm);
+				break;
+			case byKeyword:
+				matches = studyService.findByKeyword(keywordSearchTerm);
+				break;
+			default:
+				throw new Error ("Unknown search type '" + searchType + "'");
 		}
-		case inAbstract:
-			matches = studyService.findByAbstract(keywordSearchTerm);
-			break;
-		case inCitation:
-			matches = studyService.findByCitation(keywordSearchTerm);
-			break;
-		case byAuthorName:
-			matches = studyService.findByAuthor(searchTerm);
-			break;
-		case byTitle:
-			matches = studyService.findByTitle(keywordSearchTerm);
-			break;
-		case byKeyword:
-			matches = studyService.findByKeyword(keywordSearchTerm);
-			break;
-		default:
-			throw new Error ("Unknown search type '" + searchType + "'");
-		}
 		
-		SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
-				new RequestMessageSetter(request), "No matching studies found");
-		
-		saveSearchResults(request, newRes);
-
-		return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes); 
+		return matches;
+//		SearchResults<Study> newRes = intersectSearchResults(oldRes, new StudySearchResults(matches), 
+//				new RequestMessageSetter(request), "No matching studies found");
+//		
+//		saveSearchResults(request, newRes);
+//
+//		return new ModelAndView("search/studySearch", Constants.RESULT_SET, newRes); 
 	}
 
+	/*
 	private void validateTaxonSet(HttpServletRequest request,
 			HttpServletResponse response, String searchTerm,
 			BindException errors) {
@@ -256,6 +380,7 @@
 	private String titleCase(String s) {
 		return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
 	}
+	*/
 
 	@Override
 	SearchResultsType currentSearchType() {
@@ -266,4 +391,38 @@
 	public String getDefaultViewURL() {
 		return "studySearch.html";
 	}
+
+	@Override
+	protected ModelAndView handleQueryRequest(HttpServletRequest request,
+			HttpServletResponse response, BindException errors)
+			throws CQLParseException, IOException, InstantiationException {
+		String query = request.getParameter("query");						
+		CQLParser parser = new CQLParser();
+		CQLNode root = parser.parse(query);
+		root = normalizeParseTree(root);
+		Set<Study> queryResults = doCQLQuery(root, new HashSet<Study>(),request, response, errors);
+		StudySearchResults tsr = new StudySearchResults(queryResults);
+		saveSearchResults(request, tsr);
+		if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
+			return new ModelAndView("search/studySearch", Constants.RESULT_SET, tsr);
+		}
+		else {
+			SearchResults<?> res = tsr;
+			String schema = null;
+			if ( ! TreebaseUtil.isEmpty(request.getParameter("recordSchema")) ) {
+				schema = request.getParameter("recordSchema");
+				if ( schema.equals("tree") ) {
+					res = tsr.convertToTrees();
+				}
+				else if ( schema.equals("matrix") ) {
+					res = tsr.convertToMatrices();
+				}
+				else if ( schema.equals("taxon") ) {
+					res = tsr.convertToTaxa();
+				}
+			}
+			this.saveSearchResults(request, res);
+			return this.searchResultsAsRDF(res, request, root, schema, "study");
+		}		
+	}
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -1,17 +1,20 @@
 package org.cipres.treebase.web.controllers;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Map;
+import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.log4j.Logger;
 import org.cipres.treebase.TreebaseIDString;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.TreebaseIDString.MalformedTreebaseIDString;
+import org.cipres.treebase.domain.search.MatrixSearchResults;
+import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
 import org.cipres.treebase.domain.search.SearchService;
 import org.cipres.treebase.domain.search.TaxonSearchResults;
@@ -19,16 +22,29 @@
 import org.cipres.treebase.domain.taxon.TaxonHome;
 import org.cipres.treebase.domain.taxon.TaxonLabel;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.cipres.treebase.domain.taxon.TaxonLabelService;
 import org.cipres.treebase.domain.taxon.TaxonVariant;
 import org.cipres.treebase.web.model.SearchCommand;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLAndNode;
+import org.z3950.zing.cql.CQLBooleanNode;
+import org.z3950.zing.cql.CQLNode;
+import org.z3950.zing.cql.CQLNotNode;
+import org.z3950.zing.cql.CQLOrNode;
+import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLParser;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 public class TaxonSearchController extends SearchController {
-	static final Logger LOGGER = Logger.getLogger(TreeSearchController.class);
+	static final Logger LOGGER = Logger.getLogger(TaxonSearchController.class);
 	
 	private TaxonHome mTaxonHome;
 	private TaxonLabelHome mTaxonLabelHome;
+	private enum SearchIndex { LABEL, ID };
+	private enum SearchTable { TAXON, TAXONLABEL, TAXONVARIANT };
+	private enum NamingAuthority { TREEBASE, UBIO, NCBI };
 	
 	@Override
 	protected ModelAndView onSubmit(HttpServletRequest request,
@@ -36,10 +52,56 @@
 	throws Exception {
 		clearMessages(request);
 		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
+		if ( ! TreebaseUtil.isEmpty(query) ) {
+			/*
+			CQLParser parser = new CQLParser();
+			CQLNode root = parser.parse(query);
+			root = normalizeParseTree(root);
+			Set<Taxon> queryResults = doCQLQuery(root, new HashSet<Taxon>(),request);
+			TaxonSearchResults tsr = new TaxonSearchResults(queryResults);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				return samePage(request);
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, root);
+			}
+			*/
+			return this.handleQueryRequest(request, response, errors);
+		}
 		if (formName.equals("searchByTaxonLabel")) {
 			SearchCommand newSearchCommand = (SearchCommand)searchCommand;
-			ModelAndView modelAndView = doTaxonSearch(request, response, newSearchCommand, errors);			
-			return modelAndView;	
+			String searchOn = request.getParameter("searchOn");
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			String[] searchTerms = searchTerm.split("\\r\\n");	
+			Collection<Taxon> taxa = new HashSet<Taxon>();
+			for ( int i = 0; i < searchTerms.length; i++ ) {
+				if ( searchOn.equals("TextSearch") ) {
+					taxa.addAll(doTaxonSearch(request, newSearchCommand, searchTerms[i], SearchIndex.LABEL, null));
+				}
+				else if ( searchOn.equals("Identifiers") ) {
+					String objectIdentifier = request.getParameter("objectIdentifier");
+					if ( objectIdentifier.equals("TreeBASE") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.TREEBASE));
+					}
+					else if ( objectIdentifier.equals("NCBI") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.NCBI));
+					}
+					else if ( objectIdentifier.equals("uBio") ) {
+						taxa.addAll(doTaxonSearch(request,newSearchCommand,searchTerms[i],SearchIndex.ID,NamingAuthority.UBIO));
+					}								
+				}	
+			}
+			TaxonSearchResults tsr = new TaxonSearchResults(taxa);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+				return samePage(request);
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, null,"taxon","taxon");
+			}			
+			
 		} else if (formName.equals("taxonResultsAction")) {
 			return modifySearchResults(request, response, errors);
 		} else {
@@ -47,13 +109,99 @@
 		}
 	}
 	
+	private CQLNode normalizeParseTree(CQLNode node) {
+		if ( node instanceof CQLBooleanNode ) {
+			((CQLBooleanNode)node).left = normalizeParseTree(((CQLBooleanNode)node).left);
+			((CQLBooleanNode)node).right = normalizeParseTree(((CQLBooleanNode)node).right);
+			return node;
+		}
+		else if ( node instanceof CQLTermNode ) {
+			String index = ((CQLTermNode)node).getIndex();
+			String term = ((CQLTermNode)node).getTerm();
+			CQLRelation relation = ((CQLTermNode)node).getRelation();
+			index = index.replaceAll("dcterms.title", "tb.title.taxon");
+			index = index.replaceAll("dcterms.identifier", "tb.identifier.taxon");
+			return new CQLTermNode(index,relation,term);
+		}
+		logger.debug(node);
+		return node;
+	}
+	
+	private Set<Taxon> doCQLQuery(CQLNode node, Set<Taxon> results, HttpServletRequest request) {
+		if ( node instanceof CQLBooleanNode ) {
+			Set<Taxon> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request);
+			Set<Taxon> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request);
+			if ( node instanceof CQLNotNode ) {
+				for ( Taxon rightTaxon : resultsRight ) {
+					if ( resultsLeft.contains(rightTaxon) ) {
+						resultsLeft.remove(rightTaxon);
+					}
+				}
+			}
+			else if ( node instanceof CQLOrNode ) {
+				resultsLeft.addAll(resultsRight);
+			}
+			else if ( node instanceof CQLAndNode ) {
+				Set<Taxon> resultsUnion = new HashSet<Taxon>();
+				for ( Taxon leftTaxon : resultsLeft ) {
+					if ( resultsRight.contains(leftTaxon) ) {
+						resultsUnion.add(leftTaxon);
+					}
+				}				
+				resultsLeft = resultsUnion;
+			}
+			results = resultsLeft;
+		}
+		else if ( node instanceof CQLTermNode ) {
+			CQLTermNode term = (CQLTermNode)node;
+			String index = term.getIndex();
+			if ( index.startsWith("tb.title") ) {
+				boolean exactMatch = term.getRelation().getBase().equals("==");
+				SearchTable searchTable = null;
+				if ( index.endsWith("taxonLabel") ) {
+					searchTable = SearchTable.TAXONLABEL;
+				}
+				else if ( index.endsWith("taxonVariant") ) {
+					searchTable = SearchTable.TAXONVARIANT;
+				}
+				else if ( index.endsWith("taxon") ) {
+					searchTable = SearchTable.TAXON;
+				}
+				boolean caseSensitive = true;
+				if ( ! term.getRelation().getModifiers().isEmpty() ) {
+					caseSensitive = ! term.getRelation().getModifiers().firstElement().getType().equalsIgnoreCase("ignoreCase");
+				}
+				results.addAll(doTextSearch(term.getTerm(), caseSensitive, exactMatch, searchTable));
+			}
+			else if ( index.startsWith("tb.identifier") ) {
+				NamingAuthority namingAuthority = null;
+				if ( index.endsWith("ncbi") ) {
+					namingAuthority = NamingAuthority.NCBI;
+				}
+				else if ( index.endsWith("ubio") ) {
+					namingAuthority = NamingAuthority.UBIO;
+				}
+				else {
+					namingAuthority = NamingAuthority.TREEBASE;
+				}
+				results.addAll(doIdentifierSearch(request, term.getTerm(), namingAuthority));
+			} else {
+				// issue warnings
+				addMessage(request, "Unsupported index: " + index);
+			}
+			
+		}
+		logger.debug(node);
+		return results;		
+	}
+	
 	private ModelAndView modifySearchResults(HttpServletRequest request,
 			HttpServletResponse response, BindException errors) throws InstantiationException {
 		TaxonSearchResults results = searchResults(request).convertToTaxa();
 		
 		String buttonName = request.getParameter("taxonResultsaction");
 		if (buttonName.equals("addCheckedToResults")) {
-			Map<String,String> parameterMap = request.getParameterMap();
+//			Map<String,String> parameterMap = request.getParameterMap();
 			Collection<Taxon> newTaxa = new HashSet<Taxon> ();
 			for (String taxonIdString : request.getParameterValues("selection")) {
 				Taxon tx;
@@ -72,36 +220,40 @@
 		return samePage(request);
 	}
 
-	protected ModelAndView doTaxonSearch(HttpServletRequest request,
-			HttpServletResponse response,
-			SearchCommand searchCommand, BindException errors) throws Exception {
-		String searchTerm = convertStars(request.getParameter("searchTerm"));
-		String[] searchTerms = searchTerm.split("\\r\\n");
-		String searchOn = request.getParameter("searchOn");
-		//Collection<TaxonVariant> tvs = new ArrayList<TaxonVariant>();
+	protected Collection<Taxon> doTaxonSearch(HttpServletRequest request,
+			SearchCommand searchCommand, String searchTerm, SearchIndex searchIndex, NamingAuthority namingAuthority) throws Exception {
+		
 		Collection<Taxon> taxa = new HashSet<Taxon> ();
-		if ( searchOn.equals("TextSearch") ) {
-			taxa = doTextSearch(request,searchTerms);
+		switch(searchIndex) {
+			case LABEL:
+				String[] stringModifiers = request.getParameterValues("stringModifier");
+				boolean caseSensitive = false;
+				boolean exactMatch = false;
+				if ( stringModifiers != null ) {
+					for ( int i = 0; i < stringModifiers.length; i++ ) {
+						if ( stringModifiers[i].equals("caseSensitive") ) {
+							caseSensitive = true;
+						}
+						if ( stringModifiers[i].equals("exactMatch") ) {
+							exactMatch = true;
+						}
+					}
+				}			
+				for ( SearchTable searchTable : createSearchTableEnum(request) ) {
+					taxa.addAll(doTextSearch(searchTerm, caseSensitive, exactMatch, searchTable));
+				}
+				break;
+			case ID:
+				taxa.addAll(doIdentifierSearch(request,searchTerm, namingAuthority));
+				break;
 		}
-		else if ( searchOn.equals("Identifiers") ) {
-			taxa = doIdentifierSearch(request,searchTerms);			
-		}
 		
-		/*
-		tvs = getTaxonLabelService().findTaxonVariantByFullName(searchTerm);
-		LOGGER.debug("Found " + tvs.size() + " tvs");
-		for (TaxonVariant tv : tvs) {
-			if (tv.getTaxon() != null) taxa.add(tv.getTaxon());
-		}
-		*/
-		
 		getTaxonLabelService().resurrectAll(taxa);
 		LOGGER.debug("Found " + taxa.size() + " taxa");
-
-		TaxonSearchResults tsr = new TaxonSearchResults(taxa);
-		//saveTempSearchResults(request, tsr);
-		saveSearchResults(request, tsr);
-		return samePage(request);	
+		return taxa;
+//		TaxonSearchResults tsr = new TaxonSearchResults(taxa);
+//		saveSearchResults(request, tsr);
+//		return samePage(request);	
 	}
 	
 	/**
@@ -110,44 +262,60 @@
 	 * @param request
 	 * @param results
 	 */
-	private Collection<Taxon> doIdentifierSearch(HttpServletRequest request,String[] identifiers) {
-		String objectIdentifier = request.getParameter("objectIdentifier");
+	private Collection<Taxon> doIdentifierSearch(HttpServletRequest request, String identifier, NamingAuthority namingAuthority) {		
 		Collection<Taxon> taxaFound = new ArrayList<Taxon>();
-		if ( objectIdentifier.equals("TreeBASE") ) {
-			LOGGER.debug("Going to search for TreeBASE IDs");	
-			for ( int i = 0; i < identifiers.length; i++ ) {
+		switch(namingAuthority) {
+			case TREEBASE :
+				LOGGER.debug("Going to search for TreeBASE IDs");	
 				TreebaseIDString idstr;
 				try {
-					idstr = new TreebaseIDString(identifiers[i], Taxon.class, true);
+					idstr = new TreebaseIDString(identifier, Taxon.class, true);
+					Taxon match = getTaxonHome().findPersistedObjectByID(idstr.getTBClass(), idstr.getId());
+					if ( match != null ) {
+						taxaFound.add(match);
+					}					
 				} catch (MalformedTreebaseIDString e) {
-					addMessage(request, "Ignoring malformed taxon ID string '" + identifiers[i] + "'; try 'Tx####' or just a number");
-					continue;
+					addMessage(request, "Ignoring malformed taxon ID string '" + identifier + "'; try 'Tx####' or just a number");
 				}
-				Taxon match = getTaxonHome().findPersistedObjectByID(idstr.getTBClass(), idstr.getId());
+				break;
+			case NCBI :
+				LOGGER.debug("Going to search for NCBI taxon ids");	
+				Taxon match = getTaxonHome().findByNcbiTaxId(Integer.parseInt(identifier));
 				if ( match != null ) {
 					taxaFound.add(match);
 				}
-			}			
+				break;
+			case UBIO :
+				LOGGER.debug("Going to search for uBio nameBankIDs");
+				Taxon match1 = getTaxonHome().findByUBIOTaxId(Long.parseLong(identifier));
+				if ( match1 != null ) {
+					taxaFound.add(match1);
+				}
+				break;
 		}
-		else if ( objectIdentifier.equals("NCBI") ) {
-			LOGGER.debug("Going to search for NCBI taxon ids");	
-			for ( int i = 0; i < identifiers.length; i++ ) {
-				Taxon match = getTaxonHome().findByNcbiTaxId(Integer.parseInt(identifiers[i]));
-				if ( match != null ) {
-					taxaFound.add(match);
-				}
+		return taxaFound;
+	}
+	
+	/**
+	 * 
+	 * @param request
+	 * @return
+	 */
+	private Set<SearchTable> createSearchTableEnum(HttpServletRequest request) {
+		Set<SearchTable> results = new HashSet<SearchTable>();
+		String[] stringProperties = request.getParameterValues("stringProperty");	
+		for ( int i = 0; i < stringProperties.length; i++ ) {
+			if ( stringProperties[i].equals("taxonLabel") ) {
+				results.add(SearchTable.TAXONLABEL);
 			}
-		}
-		else if ( objectIdentifier.equals("uBio") ) {
-			LOGGER.debug("Going to search for uBio nameBankIDs");
-			for ( int i = 0; i < identifiers.length; i++ ) {
-				Taxon match = getTaxonHome().findByUBIOTaxId(Long.parseLong(identifiers[i]));
-				if ( match != null ) {
-					taxaFound.add(match);
-				}
+			else if ( stringProperties[i].equals("taxonVariant") ) {
+				results.add(SearchTable.TAXONVARIANT);
+			}
+			else if ( stringProperties[i].equals("taxon") ) {
+				results.add(SearchTable.TAXON);
 			}			
 		}
-		return taxaFound;
+		return results;
 	}
 	
 	/**
@@ -156,88 +324,50 @@
 	 * @param request
 	 * @param results
 	 */
-	private Collection<Taxon> doTextSearch(HttpServletRequest request, String[] stringPatterns) {
+	private Collection<Taxon> doTextSearch(String pattern, boolean caseSensitive, boolean exactMatch, SearchTable searchTable) {
 		LOGGER.debug("Going to search for strings");
+		LOGGER.debug("Case sensitive? " + caseSensitive);
+		LOGGER.debug("Exact match? " + exactMatch);		
+		TaxonLabelService tls = getTaxonLabelService();
 		Collection<Taxon> taxaFound = new ArrayList<Taxon>();
-		String[] stringProperties = request.getParameterValues("stringProperty");	
-		String[] stringModifiers = request.getParameterValues("stringModifier");
-		boolean caseSensitive = false;
-		boolean exactMatch = false;
-		if ( stringModifiers != null ) {
-			for ( int i = 0; i < stringModifiers.length; i++ ) {
-				if ( stringModifiers[i].equals("caseSensitive") ) {
-					caseSensitive = true;
+		switch(searchTable) {
+			case TAXONLABEL :
+				LOGGER.debug("Will search taxon labels");
+				Collection<TaxonLabel> labelsFound = exactMatch 
+					? tls.findByExactString(pattern) 
+					: tls.findBySubstring(pattern, caseSensitive);
+				for ( TaxonLabel label : labelsFound ) {
+					if ( label.getTaxonVariant() != null && label.getTaxonVariant().getTaxon() != null ) {
+						taxaFound.add(label.getTaxonVariant().getTaxon());
+					}
 				}
-				if ( stringModifiers[i].equals("exactMatch") ) {
-					exactMatch = true;
-				}
-			}
-		}
-		LOGGER.debug("Case sensitive? " + caseSensitive);
-		LOGGER.debug("Exact match? " + exactMatch);
-		if ( stringProperties != null ) {
-			for ( int i = 0; i < stringProperties.length; i++ ) {
-				for ( int j = 0; j < stringPatterns.length; j++ ) {
-					if ( stringProperties[i].equals("taxonLabel") ) {
-						LOGGER.debug("Will search taxon labels");
-						Collection<TaxonLabel> labelsFound = new ArrayList<TaxonLabel>();
-						if ( exactMatch ) {
-							labelsFound = getTaxonLabelService().findByExactString(stringPatterns[j]);
-						}
-						else {
-							labelsFound = getTaxonLabelService().findBySubstring(stringPatterns[j], caseSensitive);							
-						}
-						Iterator<TaxonLabel> labelsIterator = labelsFound.iterator();
-						while ( labelsIterator.hasNext() ) {
-							TaxonLabel label = labelsIterator.next();
-							TaxonVariant variant = label.getTaxonVariant();
-							if ( variant != null ) {
-								Taxon taxon = variant.getTaxon();
-								if ( taxon != null ) {
-									taxaFound.add(taxon);
-								}
-							}
-						}
+				break;
+			case TAXONVARIANT :
+				LOGGER.debug("Will search taxon variants");
+				Collection<TaxonVariant> variantsFound = exactMatch 
+					? tls.findTaxonVariantByFullName(pattern) 
+					: tls.findTaxonVariantWithSubstring(pattern, caseSensitive);
+				for ( TaxonVariant variant : variantsFound ) {
+					if ( variant.getTaxon() != null ) {
+						taxaFound.add(variant.getTaxon());
 					}
-					if ( stringProperties[i].equals("taxonVariant") ) {
-						LOGGER.debug("Will search taxon variants");
-						Collection<TaxonVariant> variantsFound = new ArrayList<TaxonVariant>();
-						if ( exactMatch ) {
-							variantsFound = getTaxonLabelService().findTaxonVariantByFullName(stringPatterns[j]);
-						}
-						else {
-							variantsFound = getTaxonLabelService().findTaxonVariantWithSubstring(stringPatterns[j], caseSensitive);
-						}		
-						Iterator<TaxonVariant> variantsIterator = variantsFound.iterator();
-						while ( variantsIterator.hasNext() ) {
-							TaxonVariant variant = variantsIterator.next();
-							Taxon taxon = variant.getTaxon();
-							if ( taxon != null ) {
-								taxaFound.add(taxon);
-							}
-						}
-					}
-					if ( stringProperties[i].equals("taxon") ) {
-						LOGGER.debug("Will search taxa");
-						Collection<Taxon> tmpTaxaFound = new ArrayList<Taxon>();
-						if ( exactMatch ) {
-							tmpTaxaFound = getTaxonLabelService().findTaxaByName(stringPatterns[j]);
-						}
-						else {
-							tmpTaxaFound = getTaxonLabelService().findTaxaBySubstring(stringPatterns[j], caseSensitive);
-						}
-						taxaFound.addAll(tmpTaxaFound);
-					}
 				}
-			}
+				break;
+			case TAXON :
+				LOGGER.debug("Will search taxa");
+				Collection<Taxon> tmpTaxaFound = exactMatch 
+					? tls.findTaxaByName(pattern) 
+					: tls.findTaxaBySubstring(pattern, caseSensitive);
+				taxaFound.addAll(tmpTaxaFound);
+				break;
 		}
 		return taxaFound;
 	}
 
-	private void saveTempSearchResults(HttpServletRequest request,
-			TaxonSearchResults taxonSearchResults) {
-		request.getSession().setAttribute("taxonSearchResults", taxonSearchResults);
-	}
+//	private void saveTempSearchResults(HttpServletRequest request,
+//			TaxonSearchResults taxonSearchResults) {
+//		request.getSession().setAttribute("taxonSearchResults", taxonSearchResults);
+//	}
 
 	public void setSearchService(SearchService searchService) {
 		this.searchService = searchService;
@@ -268,4 +398,38 @@
 	public void setTaxonLabelHome(TaxonLabelHome taxonLabelHome) {
 		mTaxonLabelHome = taxonLabelHome;
 	}
+
+	@Override
+	protected ModelAndView handleQueryRequest(HttpServletRequest request,
+			HttpServletResponse response, BindException errors)
+			throws CQLParseException, IOException, InstantiationException {
+		String query = request.getParameter("query");
+		CQLParser parser = new CQLParser();
+		CQLNode root = parser.parse(query);
+		root = normalizeParseTree(root);
+		Set<Taxon> queryResults = doCQLQuery(root, new HashSet<Taxon>(),request);
+		TaxonSearchResults tsr = new TaxonSearchResults(queryResults);
+		saveSearchResults(request, tsr);
+		if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {
+			return samePage(request);
+		}
+		else {
+			SearchResults<?> res = tsr;
+			String schema = null;
+			if ( ! TreebaseUtil.isEmpty(request.getParameter("recordSchema")) ) {
+				schema = request.getParameter("recordSchema");
+				if ( schema.equals("tree" ) ) {
+					res = tsr.convertToTrees();
+				}
+				else if ( schema.equals("matrix") ) {
+					res = tsr.convertToMatrices();
+				}
+				else if ( schema.equals("study") ) {
+					res = tsr.convertToStudies();
+				}
+			}
+			this.saveSearchResults(request, res);
+			return this.searchResultsAsRDF(res, request, root,schema,"taxon");
+		}
+	}
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2009-07-02 10:41:25 UTC (rev 158)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2009-07-02 10:43:46 UTC (rev 159)
@@ -20,25 +20,35 @@
 
 package org.cipres.treebase.web.controllers;
 
-import java.util.ArrayList;
+import java.io.IOException;
 import java.util.Collection;
+import java.util.HashSet;
+import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.log4j.Logger;
+import org.cipres.treebase.TreebaseUtil;
 import org.cipres.treebase.RangeExpression.MalformedRangeExpression;
 import org.cipres.treebase.domain.search.SearchResults;
 import org.cipres.treebase.domain.search.SearchResultsType;
-import org.cipres.treebase.domain.search.StudySearchResults;
 import org.cipres.treebase.domain.search.TreeSearchResults;
-import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.tree.PhyloTree;
 import org.cipres.treebase.domain.tree.PhyloTreeService;
 import org.cipres.treebase.web.Constants;
 import org.cipres.treebase.web.util.RequestMessageSetter;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLAndNode;
+import org.z3950.zing.cql.CQLBooleanNode;
+import org.z3950.zing.cql.CQLNode;
+import org.z3950.zing.cql.CQLNotNode;
+import org.z3950.zing.cql.CQLOrNode;
+import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLParser;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 /**
  * TreeSearchController.java
@@ -73,50 +83,161 @@
 
 		clearMessages(request);
 		String formName = request.getParameter("formName");
+		String query = request.getParameter("query");
 		
 		LOGGER.info("formName is '" + formName + "'");
-
 		
+		if ( ! TreebaseUtil.isEmpty(query) ) {
+			/*
+			CQLParser parser = new CQLParser();
+			CQLNode root = parser.parse(query);
+			root = normalizeParseTree(root);
+			Set<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request, response, errors);
+			TreeSearchResults tsr = new TreeSearchResults(queryResults);
+			saveSearchResults(request, tsr);
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
+				return new ModelAndView("search/treeSearch", Constants.RESULT_SET, tsr);
+			}
+			else {
+				return this.searchResultsAsRDF(tsr, request, root);
+			}
+			*/
+			return this.handleQueryRequest(request, response, errors);
+		}
+		
 		if (formName.equals("treeSimple")) {
 			String buttonName = request.getParameter("searchButton");
-
+			String searchTerm = convertStars(request.getParameter("searchTerm"));
+			Collection<PhyloTree> matches = null;
+			TreeSearchResults oldRes;	
+			{
+				SearchResults<?> sr = searchResults(request);
+				if (sr != null) {
+					oldRes = (TreeSearchResults) sr.convertToTrees();
+				} else {
+					oldRes = new TreeSearchResults ();   // TODO: Convert existing search results to new type	
+				}
+			}			
 			if (buttonName.equals("treeID")) {
-				return doSearch(request, response, SearchType.byID, errors);
+				matches = doSearch(request, response, SearchType.byID, errors, searchTerm);
 			} else if  (buttonName.equals("treeTitle")) {
-				return doSearch(request, response, SearchType.byTitle, errors);
+				matches =  doSearch(request, response, SearchType.byTitle, errors, searchTerm);
 			} else if  (buttonName.equals("treeType")) {
-				return doSearch(request, response, SearchType.byType, errors);
+				matches = doSearch(request, response, SearchType.byType, errors, searchTerm);
 			} else if  (buttonName.equals("treeKind")) {
-				return doSearch(request, response, SearchType.byKind, errors);
+				matches = doSearch(request, response, SearchType.byKind, errors, searchTerm);
 			} else if  (buttonName.equals("treeQuality")) {
-				return doSearch(request, response, SearchType.byQuality, errors);
+				matches = doSearch(request, response, SearchType.byQuality, errors, searchTerm);
 			} else if  (buttonName.equals("treeNTAX")) {
-				return doSearch(request, response, SearchType.byNTAX, errors);
+				matches = doSearch(request, response, SearchType.byNTAX, errors, searchTerm);
 			} else {
 				throw new Error("Unknown search button name '" + buttonName + "'");
 			}
+			SearchResults<PhyloTree> newRes = intersectSearchResults(oldRes, new TreeSearchResults(matches), 
+			new RequestMessageSetter(request), "No matching trees found");	
+			saveSearchResults(request, newRes);	
+			if ( TreebaseUtil.isEmpty(request.getParameter("format")) || ! request.getParameter("format").equals("rss1") ) {			
+				return new ModelAndView("search/treeSearch", Constants.RESULT_SET, newRes); 			
+			}
+			else {
+				return this.searchResultsAsRDF(newRes, request, null,"tree","tree");
+			}
 		} else { 
 			return super.onSubmit(request, response, command, errors);
 		}
 	}
 
-	private ModelAndView doSearch(
+	private Set<PhyloTree> doCQLQuery(
+			CQLNode node, 
+			Set<PhyloTree> results, 
+			HttpServletRequest request, 
+			HttpServletResponse response, 
+			BindException errors
+		) throws InstantiationException {
+		if ( node instanceof CQLBooleanNode ) {
+			Set<PhyloTree> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request, response, erro...
 
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