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 7a0bac687e063250633d27cbd35f6a8eafa64ade..faf50e78437ab16bc9270fee817760d73db0321c 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 c49d3571497104ecd85068b4c42255fd04f3066e..546d8e83f32fe95f4883b39aca7323916fe69a8f 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 45d496c6cedef68db65b2a1b3b574ffdb391de7d..90c34bcd67f40a232deedeadb5a4653e90499b76 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); }