From a9740fef61108c68642fbeb283c691b178a03af7 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 20 Apr 2018 15:50:16 +0200
Subject: [PATCH] when exporting notes to sbml, the notes string is escaped
first
---
.../converter/model/sbml/SbmlBioEntityExporter.java | 3 ++-
.../converter/model/sbml/SbmlExporterTest.java | 13 +++++++++++++
2 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index b4bc5cab6f..6566226645 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -6,6 +6,7 @@ import java.util.Map;
import javax.xml.stream.XMLStreamException;
+import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
@@ -72,7 +73,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
sbmlElement.setName(element.getName());
try {
- sbmlElement.setNotes(element.getNotes());
+ sbmlElement.setNotes(StringEscapeUtils.escapeXml(element.getNotes()));
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 65569d1d9c..3d6832feed 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -261,4 +261,17 @@ public class SbmlExporterTest {
assertEquals(0, comparator.compare(model, model2));
}
+
+ @Test
+ public void testExportProblematicNotes() throws Exception {
+ Model model = createModelWithReaction();
+ Reaction reaction = model.getReactions().iterator().next();
+ reaction.setNotes("X=Y<Z");
+
+ Model deserializedModel = getModelAfterSerializing(model);
+ Reaction deserializedReaction = deserializedModel.getReactions().iterator().next();
+
+ assertEquals(reaction.getNotes(), deserializedReaction.getNotes());
+
+ }
}
--
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