From 84a716b511911423fc9179b76990625477900415 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 4 Jan 2019 10:43:46 +0100
Subject: [PATCH] with null notes there is fallback to empty string
---
.../mapviewer/converter/model/sbml/NotesUtility.java | 9 ++++++++-
.../converter/model/sbml/SbmlBioEntityExporter.java | 3 +--
.../mapviewer/converter/model/sbml/SbmlExporter.java | 3 +--
3 files changed, 10 insertions(+), 5 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
index 7a0bac687e..faf50e7843 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
@@ -2,12 +2,13 @@ package lcsb.mapviewer.converter.model.sbml;
import javax.xml.stream.XMLStreamException;
+import org.apache.commons.lang3.StringEscapeUtils;
import org.sbml.jsbml.AbstractNamedSBase;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
public class NotesUtility {
- public static String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
+ public static String extractNotes(AbstractNamedSBase sbmlElement) throws InvalidInputDataExecption {
String notes = "";
try {
notes = sbmlElement.getNotesString();
@@ -28,5 +29,11 @@ public class NotesUtility {
return notes;
}
+ public static String prepareEscapedXmlNotes(String notes) {
+ if (notes == null) {
+ return "";
+ }
+ return StringEscapeUtils.escapeXml(notes);
+ }
}
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 c49d357149..546d8e83f3 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
@@ -9,7 +9,6 @@ import java.util.Set;
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.SBasePlugin;
@@ -116,7 +115,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
}
sbmlElement.setName(element.getName());
try {
- sbmlElement.setNotes(StringEscapeUtils.escapeXml(element.getNotes()));
+ sbmlElement.setNotes(NotesUtility.prepareEscapedXmlNotes(element.getNotes()));
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 45d496c6ce..90c34bcd67 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -9,7 +9,6 @@ import java.util.Set;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
@@ -80,7 +79,7 @@ public class SbmlExporter {
Model result = doc.createModel(model.getIdModel());
result.setName(model.getName());
try {
- result.setNotes(StringEscapeUtils.escapeXml(model.getNotes()));
+ result.setNotes(NotesUtility.prepareEscapedXmlNotes(model.getNotes()));
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
--
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