apache commons-text added to replace deprecated escapeXml functionality

commons/pom.xml

@@ -22,6 +22,11 @@
 			<artifactId>commons-io</artifactId>
 			<version>${commons-io.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-text</artifactId>
+			<version>${apache.commons-text.version}</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>

commons/src/main/java/lcsb/mapviewer/common/XmlParser.java

@@ -21,7 +21,7 @@ import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.w3c.dom.Document;
 import org.w3c.dom.NamedNodeMap;
@@ -416,7 +416,7 @@ public class XmlParser {
       return null;
     }
     // quite expensive
-    return StringEscapeUtils.escapeXml(string).replaceAll("\n", "
").replace("\r", "
");
+    return StringEscapeUtils.escapeXml10(string).replaceAll("\n", "
").replace("\r", "
");
   }
 
   public List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java

@@ -15,7 +15,7 @@ import java.nio.charset.StandardCharsets;
 import javax.xml.bind.JAXBException;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.apache.log4j.spi.LoggingEvent;
 import org.sbgn.SbgnUtil;
@@ -74,7 +74,7 @@ public class SbgnmlXmlConverter implements IConverter {
             throw new ConverterException("problematic output sbgn. Cannot find map tag");
           }
           String notesNode = "<notes><html:body xmlns:html=\"http://www.w3.org/1999/xhtml\">" +
-              StringEscapeUtils.escapeXml(notes.toString()) + "\n</html:body></notes> ";
+              StringEscapeUtils.escapeXml10(notes.toString()) + "\n</html:body></notes> ";
           xml = xml.substring(0, position) + notesNode + xml.substring(position, xml.length());
         }
         result = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));

converter-sbml/pom.xml

@@ -104,7 +104,7 @@
 					<groupId>commons-logging</groupId>
 					<artifactId>commons-logging</artifactId>
 				</exclusion>
-			<!-- https://github.com/sbmlteam/jsbml/issues/156 -->
+				<!-- https://github.com/sbmlteam/jsbml/issues/156 -->
 				<exclusion>
 					<groupId>org.sbml.jsbml</groupId>
 					<artifactId>jsbml-core</artifactId>
@@ -153,6 +153,12 @@
 			<scope>test</scope>
 		</dependency>
 
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-text</artifactId>
+			<version>${apache.commons-text.version}</version>
+		</dependency>
+		
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java

 package lcsb.mapviewer.converter.model.sbml;
+
 import javax.xml.stream.XMLStreamException;
 
-import org.apache.commons.lang3.StringEscapeUtils;
+import org.apache.commons.text.StringEscapeUtils;
 import org.sbml.jsbml.AbstractNamedSBase;
 
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -56,7 +57,7 @@ public class NotesUtility {
     if (notes == null) {
       return "";
     }
-    return StringEscapeUtils.escapeXml(notes);
+    return StringEscapeUtils.escapeXml10(notes);
   }
 
 }

pom.xml

@@ -43,6 +43,8 @@
 
 		<apache.commons-lang3.version>3.8.1</apache.commons-lang3.version>
 
+		<apache.commons-text.version>1.6</apache.commons-text.version>
+
 		<commons-cli.version>1.4</commons-cli.version>
 
 		<batik.version>1.10</batik.version>