diff --git a/commons/pom.xml b/commons/pom.xml index 5874d03b056716a978a4974e4516c718749e064b..92f50c5630c2faac555ca47ddb9755c1e83500d4 100644 --- a/commons/pom.xml +++ b/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> diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java index a6d9f1f72195de50940341398df56b19c958602a..0d5ab74603a074c3ba1b4dab1a38ad7b8d920a6e 100644 --- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java +++ b/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) { diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java index ee8b701a4e731ca7fdf5eb785acd43fe049ef506..ffdc1fdfc09fae44b22cb99b17a76fb617488a72 100644 --- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java +++ b/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)); diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml index 92fec0b1eb8f7d7f16ae8c84f0f953d676e3c08f..f3c2a5ec22b5b2701bb9a7124504455306fe9d89 100644 --- a/converter-sbml/pom.xml +++ b/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> 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 d1ca33fbdaabcc01a7409241573e546a247bb3c9..7f2b00aa02466b613d84eefbc2a552062acfe72e 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 @@ -1,7 +1,8 @@ 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); } } diff --git a/pom.xml b/pom.xml index 28413ac14f095f02810c946ab04102bf15fdaa45..c6cbff9814714288b971db5f98a5802f5e44f3a7 100644 --- a/pom.xml +++ b/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>