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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