From afec2b06d7d13a5ea4e2898cfd4d1987cdeafbb6 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 14 Dec 2018 11:53:02 +0100
Subject: [PATCH] mesh id with space caused exception to be thrown
---
.../mapviewer/annotation/services/MeSHParser.java | 5 ++++-
.../annotation/services/MeSHParserTest.java | 12 ++++++++++++
2 files changed, 16 insertions(+), 1 deletion(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
index 84d2a47962..e7882624e9 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java
@@ -109,6 +109,9 @@ public class MeSHParser extends CachableInterface implements IExternalService {
if (meshID == null || meshID.getResource() == null) {
throw new InvalidArgumentException("mesh cannot be null ");
}
+ if (meshID.getResource().indexOf(" ") >= 0) {
+ return null;
+ }
MeSH mesh = null;
// look for Mesh in the cache
@@ -321,7 +324,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");
for (Object object : hitsList) {
StringMap<?> hit = (StringMap<?>) object;
- String id = (String) hit.get("_id");
+ String id = (String) hit.get("_id");
result.add(new MiriamData(MiriamType.MESH_2012, id));
}
return result;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
index 8fb197d385..720bc0ebfc 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java
@@ -118,6 +118,18 @@ public class MeSHParserTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testIsValidWithSpace() throws Exception {
+ try {
+ MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "some disease");
+ assertFalse(meshParser.isValidMeshId(meshID));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testGetInvalidMesh() throws Exception {
try {
--
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