[Treebase-guts] SF.net SVN: treebase:[1103] trunk/treebase-web/src/main/java/org/cipres/ treebase/web/controllers/ClassificationSearchController.java

[<hs...@us...>]

Revision: 1103
          http://sourceforge.net/p/treebase/code/1103
Author:   hshyket
Date:     2013-06-14 00:29:39 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Adding exception handling for classification search where ncbi identifier is invalid.

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

Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java	2013-06-06 19:32:24 UTC (rev 1102)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ClassificationSearchController.java	2013-06-14 00:29:39 UTC (rev 1103)
@@ -41,14 +41,28 @@
 	
 	@SuppressWarnings("unchecked")
 	private Collection<PhyloTree> doSearch(
-			String searchTerm
-		) {
-
+			HttpServletRequest request,
+			HttpServletResponse response,
+			BindException errors,
+			String searchTerm) throws InstantiationException {
+		
 		Collection<PhyloTree> matches = null;
-		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();	
-		matches = phyloTreeService.findTreesByNCBINodes(searchTerm);
+		PhyloTreeService phyloTreeService = getSearchService().getPhyloTreeService();
+		
+		try {
+			matches = phyloTreeService.findTreesByNCBINodes(searchTerm);
+		}
+		catch ( NumberFormatException e ) {
+			addMessage(request, "Malformed NCBI identifier '" + searchTerm );
+			LOGGER.error("Couldn't parse NCBI identifier: "+e.getMessage());
+		}
+		catch ( NullPointerException e) {
+			addMessage(request, "NCBI identifier not found '" + searchTerm );
+			LOGGER.error("Couldn't find NCBI identifier: "+e.getMessage());
+			
+		}
+		
 		return matches;
-
 	}
 	
 	@Override
@@ -59,7 +73,7 @@
 		CQLParser parser = new CQLParser();
 		CQLNode root = parser.parse(query);
 		root = normalizeParseTree(root);
-		HashSet<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request);
+		HashSet<PhyloTree> queryResults = doCQLQuery(root, new HashSet<PhyloTree>(),request, response, errors);
 		TreeSearchResults tsr = new TreeSearchResults(queryResults);
 		saveSearchResults(request, tsr);
 		
@@ -86,10 +100,16 @@
 		}
 	}
 	
-	protected HashSet<PhyloTree> doCQLQuery(CQLNode node, HashSet<PhyloTree> results, HttpServletRequest request) {
+	protected HashSet<PhyloTree> doCQLQuery(
+			CQLNode node, 
+			HashSet<PhyloTree> results, 
+			HttpServletRequest request, 
+			HttpServletResponse response, 
+			BindException errors
+			) throws InstantiationException {
 		if ( node instanceof CQLBooleanNode ) {
-			HashSet<PhyloTree> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request);
-			HashSet<PhyloTree> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request);
+			HashSet<PhyloTree> resultsLeft = doCQLQuery(((CQLBooleanNode)node).left,results, request, response, errors);
+			HashSet<PhyloTree> resultsRight = doCQLQuery(((CQLBooleanNode)node).right,results, request, response, errors);
 			if ( node instanceof CQLNotNode ) {
 				for ( PhyloTree rightTree : resultsRight ) {
 					if ( resultsLeft.contains(rightTree) )
@@ -114,7 +134,10 @@
 				String index = term.getIndex();
 				if ( index.startsWith("tb.identifier") ) {
 					if ( index.endsWith("ncbi") ) {
-						results.addAll(doSearch(term.getTerm()));
+						Collection<PhyloTree> trees = doSearch(request, response, errors, term.getTerm()); 
+						if ( null != trees ) {
+							results.addAll(trees);
+						}
 					}
 					else {
 						// issue warnings

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