[Treebase-guts] SF.net SVN: treebase:[708] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers

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

Revision: 708
          http://treebase.svn.sourceforge.net/treebase/?rev=708&view=rev
Author:   rvos
Date:     2010-06-02 14:42:42 +0000 (Wed, 02 Jun 2010)

Log Message:
-----------
Fixes for issue 2992932

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/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
    trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.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	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/MatrixSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -71,21 +73,7 @@
 		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);
+			return this.handleQueryRequest(request, response, errors, query);
 		}		
 		
 		if (formName.equals("matrixSimple")) {
@@ -180,27 +168,8 @@
 		}
 		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,
@@ -209,20 +178,6 @@
 			BindException errors,
 			String searchTerm) throws InstantiationException {
 
-//		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	
-//			}
-//		}
-
 		Collection<Matrix> matches = null;
 		MatrixService matrixService = getSearchService().getMatrixService();	
 
@@ -271,13 +226,6 @@
 		}
 		matches.removeAll(orphanedMatrices);
 		return matches;
-		
-//		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); 
 
 	}
 
@@ -291,8 +239,8 @@
 	}
 
 	@Override
-	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");				
+	protected ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors, String query) throws CQLParseException, IOException, InstantiationException {
+		//String query = request.getParameter("query");				
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -322,4 +270,13 @@
 		}
 	}
 
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.matrix");
+		mapping.put("dcterms.identifier", "tb.identifier.matrix");
+		mapping.put("dcterms.extent", "tb.ntax.matrix");
+		return mapping;
+	}
+
 }

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	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -35,8 +35,11 @@
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.view.RedirectView;
+import org.z3950.zing.cql.CQLBooleanNode;
 import org.z3950.zing.cql.CQLNode;
 import org.z3950.zing.cql.CQLParseException;
+import org.z3950.zing.cql.CQLRelation;
+import org.z3950.zing.cql.CQLTermNode;
 
 
 /**
@@ -46,14 +49,51 @@
 	/**
 	 * Logger for this class
 	 */
-	private static final Logger LOGGER = Logger.getLogger(SearchController.class);
-	
+	private static final Logger LOGGER = Logger.getLogger(SearchController.class);	
 	protected SearchService searchService;
 	protected String formView;
-
 	private TaxonLabelService mTaxonLabelService;
 	
-	protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors) throws CQLParseException, IOException, InstantiationException;	
+	protected abstract ModelAndView handleQueryRequest(HttpServletRequest request,HttpServletResponse response,BindException errors,String query) throws CQLParseException, IOException, InstantiationException;
+	
+	/**
+	 * Recursively traverses a CQL parse tree (presumably starting from its
+	 * root node), replacing the observed indices with ones suggested by the map
+	 * returned by getPredicateMapping(). The function of this is to allow concrete
+	 * subclasses to create specific mappings from more general ones, e.g. when a
+	 * study search query refers to the index "dcterms.identifier", the StudySearchController
+	 * can specify that within its context this index is understood to mean "tb.identifier.study",
+	 * i.e. the study ID.
+	 * @param node
+	 * @return
+	 */
+	protected 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();
+			Map<String,String> mapping = getPredicateMapping();
+			for ( String key : mapping.keySet() ) {
+				index = index.replaceAll(key, mapping.get(key));
+			}
+			return new CQLTermNode(index,relation,term);
+		}
+		logger.debug(node);
+		return node;
+	}	
+	
+	/**
+	 * Returns a mapping between more general search indices (e.g. "dcterms.identifier")
+	 * and the specific indices (e.g. "tb.identifier.study") that are understood to be used 
+	 * by the concrete subclass
+	 * @return
+	 */
+	protected abstract Map<String,String> getPredicateMapping();
 
 	protected ModelAndView onSubmit(
 			HttpServletRequest request,
@@ -399,7 +439,7 @@
 		String query = request.getParameter("query");
 		if ( query != null && ! TreebaseUtil.isEmpty(query) ) {
 			LOGGER.info("query is '"+ query +"'");
-			return this.handleQueryRequest(request, response, bindException);
+			return this.handleQueryRequest(request, response, bindException, query);
 		}
 		String action = request.getParameter("action");
 		if (action != null && action.equals("discard") && request.getMethod().equals("GET")) {

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	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/StudySearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -96,7 +98,7 @@
 		
 		if ( ! TreebaseUtil.isEmpty(query) && ! query.equals("")) {
 			LOGGER.info("query is '" + query + "'");
-			return this.handleQueryRequest(request, response, errors);
+			return this.handleQueryRequest(request, response, errors, query);
 		}		
 		
 		if (formName.equals("searchKeyword")) {
@@ -129,7 +131,9 @@
 			} else {
 				throw new Error("Unknown search button name '" + buttonName + "'");
 			}
-			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm);	
+			// XXX we now never do an exact match with terms provided through the web app. We can change
+			// this, e.g. by adding a check box whose value is the boolean argument of doSearch()
+			Collection<Study> matches = doSearch(request, response, searchType, errors,searchTerm,false);	
 			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");	
@@ -139,7 +143,8 @@
 			else {
 				return this.searchResultsAsRDF(new StudySearchResults(matches), request, null,"study","study");
 			}
-		} else {
+		} 
+		else {
 			return super.onSubmit(request, response, command, errors);
 		}
 	}
@@ -177,23 +182,24 @@
 		}		
 		else if ( node instanceof CQLTermNode ) {
 			CQLTermNode term = (CQLTermNode)node;
+			boolean exactMatch = term.getRelation().getBase().equals("==");
 			String index = term.getIndex();
 			if ( index.startsWith("tb.title") ) {
-				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byTitle, errors, term.getTerm(),exactMatch));
 			} else if ( index.equals("tb.identifier.study") ) {
-				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byID, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.contributor") ) {
-				results.addAll(doSearch(request, response, SearchType.byAuthorName, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byAuthorName, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.abstract") ) {
-				results.addAll(doSearch(request, response, SearchType.inAbstract, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.inAbstract, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.subject") ) {
-				results.addAll(doSearch(request, response, SearchType.byKeyword, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byKeyword, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("dcterms.bibliographicCitation") ) {
-				results.addAll(doSearch(request, response, SearchType.inCitation, errors, term.getTerm()));				
+				results.addAll(doSearch(request, response, SearchType.inCitation, errors, term.getTerm(),exactMatch));				
 			} else if ( index.equals("tb.identifier.study.tb1") ) {
-				results.addAll(doSearch(request, response, SearchType.byLegacyID, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byLegacyID, errors, term.getTerm(),exactMatch));
 			} else if ( index.startsWith("prism.publicationName") ) {
-				results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm()));
+				results.addAll(doSearch(request, response, SearchType.byJournal, errors, term.getTerm(),exactMatch));
 			} else {
 				// issue warnings
 				addMessage(request, "Unsupported index: " + index);
@@ -201,48 +207,18 @@
 		}
 		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,
-			String searchTerm) throws InstantiationException {
+			String searchTerm,
+			boolean exactMatch) throws InstantiationException {
 		
-//		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)");
 		Collection<Study> matches;
 		StudyService studyService = getSearchService().getStudyService();	
 				
@@ -283,79 +259,21 @@
 				matches = studyService.findByKeyword(keywordSearchTerm);
 				break;
 			case byJournal:
-				matches = studyService.findByJournal(keywordSearchTerm, false);
+			{
+				if ( exactMatch ) {
+					matches = studyService.findByJournal(searchTerm, exactMatch);
+				} else {
+					matches = studyService.findByJournal(keywordSearchTerm, exactMatch);
+				}
 				break;
+			}
 			default:
 				throw new Error ("Unknown search type '" + searchType + "'");
 		}
 		
 		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) {
-		String[] taxonStrings = getTaxonStrings(searchTerm);
-		List<String> unrecognizedTaxa = new LinkedList<String> ();
-		List<String> recognizedTaxa = new LinkedList<String> ();
-
-		Collection<TaxonLabel> taxonLabels = stringsToTaxonLabels(taxonStrings);
-		request.setAttribute("taxonLabelSetOverride", taxonLabels);
-		
-		for (TaxonLabel tl : taxonLabels) {
-			TaxonVariant variant = getTaxonLabelService().findTaxonVariant(tl);
-			if (variant == null) {
-				variant = getTaxonLabelService().createFromUBIOService(tl);
-				if (variant == null) {
-					unrecognizedTaxa.add(tl.getTaxonLabel());
-				} else {
-					recognizedTaxa.add(tl.getTaxonLabel());
-				}
-			} else {
-				recognizedTaxa.add(variant.getName());
-			}
-		}
-		
-		LOGGER.info("validateTaxonSet: of " 
-				+ taxonStrings.length 
-				+ " entered taxa, "
-				+ unrecognizedTaxa.size()
-				+ " was/were unrecognized: "
-				+ unrecognizedTaxa.toString());
-		
-		request.setAttribute("unrecognizedTaxa", unrecognizedTaxa);
-		request.setAttribute("taxonLabels", joinStrings(recognizedTaxa));
-		return;
-	}
-
-	private String joinStrings(Collection<String> strings) {
-		String result = "";
-		for (String s : strings) {
-			result = result + s + "\n";
-		}
-		return result;
-	}
-
-	private Collection<TaxonLabel> stringsToTaxonLabels(String[] taxonStrings) {
-		Collection<TaxonLabel> tls = new LinkedList<TaxonLabel>();
-		for (String s : taxonStrings) {
-			tls.add(new TaxonLabel(titleCase(s)));
-		}
-		return tls;
-	}
-
-	private String titleCase(String s) {
-		return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase();
-	}
-	*/
-
 	@Override
 	SearchResultsType currentSearchType() {
 		return SearchResultsType.STUDY;
@@ -368,9 +286,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors,String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");						
+		//String query = request.getParameter("query");						
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -399,4 +317,12 @@
 			return this.searchResultsAsRDF(res, request, root, schema, "study");
 		}		
 	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.study");
+		mapping.put("dcterms.identifier", "tb.identifier.study");
+		return mapping;
+	}
 }

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	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TaxonSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -54,21 +56,7 @@
 		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);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
 		if (formName.equals("searchByTaxonLabel")) {
 			SearchCommand newSearchCommand = (SearchCommand)searchCommand;
@@ -109,24 +97,6 @@
 		}
 	}
 	
-	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);
@@ -401,9 +371,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");
+		//String query = request.getParameter("query");
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -432,4 +402,12 @@
 			return this.searchResultsAsRDF(res, request, root,schema,"taxon");
 		}
 	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.taxon");
+		mapping.put("dcterms.identifier", "tb.identifier.taxon");		
+		return mapping;
+	}
 }

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	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -3,7 +3,9 @@
 
 import java.io.IOException;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -69,21 +71,7 @@
 		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);
+			return this.handleQueryRequest(request, response, errors, query);
 		}
 		
 		if (formName.equals("treeSimple")) {
@@ -180,25 +168,6 @@
 		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.tree");
-			index = index.replaceAll("dcterms.identifier", "tb.identifier.tree");
-			index = index.replaceAll("dcterms.extent", "tb.ntax.tree");
-			return new CQLTermNode(index,relation,term);
-		}
-		logger.debug(node);
-		return node;
-	}	
 
 	@SuppressWarnings("unchecked")
 	private Collection<PhyloTree> doSearch(
@@ -208,18 +177,6 @@
 			BindException errors,
 			String searchTerm) throws InstantiationException {
 
-//		String searchTerm = convertStars(request.getParameter("searchTerm"));
-//		String keywordSearchTerm = "%" + searchTerm + "%";
-//		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	
-//			}
-//		}
-
 		Collection<PhyloTree> matches = null;
 		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();	
 
@@ -279,9 +236,9 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
-		String query = request.getParameter("query");
+		//String query = request.getParameter("query");
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
@@ -311,4 +268,13 @@
 		}
 	}
 
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		Map<String,String> mapping = new HashMap<String,String>();
+		mapping.put("dcterms.title", "tb.title.tree");
+		mapping.put("dcterms.identifier", "tb.identifier.tree");
+		mapping.put("dcterms.extent", "tb.ntax.tree");		
+		return mapping;
+	}
+
 }

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java	2010-06-02 13:27:57 UTC (rev 707)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/TreeTopSearchController.java	2010-06-02 14:42:42 UTC (rev 708)
@@ -5,6 +5,7 @@
 import java.util.Collection;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import javax.servlet.http.HttpServletRequest;
@@ -20,6 +21,7 @@
 import org.cipres.treebase.web.Constants;
 import org.springframework.validation.BindException;
 import org.springframework.web.servlet.ModelAndView;
+import org.z3950.zing.cql.CQLNode;
 import org.z3950.zing.cql.CQLParseException;
 
 /**
@@ -189,10 +191,22 @@
 
 	@Override
 	protected ModelAndView handleQueryRequest(HttpServletRequest request,
-			HttpServletResponse response, BindException errors)
+			HttpServletResponse response, BindException errors, String query)
 			throws CQLParseException, IOException, InstantiationException {
 		// TODO Auto-generated method stub
 		return null;
 	}
 
+	@Override
+	protected CQLNode normalizeParseTree(CQLNode node) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	protected Map<String, String> getPredicateMapping() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
 }


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