From 93ef0a630b90d832d92be659786b44ecbc52bac4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Jun 2017 16:20:36 +0200
Subject: [PATCH] error handling for problems with cache improved
---
.../annotation/services/DrugbankHTMLParser.java | 9 +++++++--
.../src/main/java/lcsb/mapviewer/common/XmlParser.java | 7 ++++++-
2 files changed, 13 insertions(+), 3 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index 07b0a36856..6eac22a514 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -9,6 +9,7 @@ import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.apache.commons.lang3.SerializationException;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@@ -474,8 +475,12 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
@Override
public Drug findDrug(String drugName) throws DrugSearchException {
String query = DRUG_NAME_PREFIX + drugName;
-
- Drug drug = getDrugSerializer().xmlToObject(getCacheNode(query));
+ Drug drug = null;
+ try {
+ drug = getDrugSerializer().xmlToObject(getCacheNode(query));
+ } catch (SerializationException e) {
+ logger.error("Problem with deserializing element by query: " + query);
+ }
if (drug != null) {
return drug;
}
diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 0f0530880c..4df8104320 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -210,7 +210,12 @@ public class XmlParser {
protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
InputSource is = new InputSource();
is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is);
+ try {
+ return getXmlDocumentFromInputSource(is);
+ } catch (NullPointerException e) {
+ logger.error("Problem with input xml: " + text);
+ throw new InvalidXmlSchemaException(e);
+ }
}
/**
--
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