workaround for bug in JSBML library...

workaround for bug in JSBML library (https://github.com/sbmlteam/jsbml/issues/195) XMLNode.convertStringToXMLNode is not thread safe

CHANGELOG

+minerva (14.0.9) stable; urgency=medium
+  * Bug fix: simultanous export to SBML of more than one file could result in
+    500 Internal Server Error (#1110)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 3 Feb 2020 15:00:00 +0200
+
 minerva (14.0.8) stable; urgency=medium
   * Bug fix: API didn't allow to upload pluins with local url (#1084,
     regression 14.0.7)

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

 package lcsb.mapviewer.converter.model.sbml;
 
+import java.util.Collection;
+
 import javax.xml.stream.XMLStreamException;
 
 import org.apache.commons.text.StringEscapeUtils;
 import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.util.StringTools;
+import org.sbml.jsbml.xml.XMLNode;
+import org.sbml.jsbml.xml.stax.SBMLReader;
 
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.model.map.MiriamData;
 
 /**
  * This utility class parses notes from SBML node and prepares escaped string
@@ -60,4 +67,14 @@ public class NotesUtility {
     return StringEscapeUtils.escapeXml10(notes);
   }
 
+  public static XMLNode getRdfNode(Collection<MiriamData> data, String metaid) throws XMLStreamException {
+    XmlAnnotationParser parser = new XmlAnnotationParser();
+    String rdf = parser.dataSetToXmlString(data, metaid);
+    return getRdfNode(rdf);
+  }
+
+  public static XMLNode getRdfNode(String rdf) throws XMLStreamException {
+    return new SBMLReader().readNotes(StringTools.toXMLAnnotationString(rdf));
+  }
+
 }

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

@@ -13,10 +13,10 @@ import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 import org.sbml.jsbml.ext.render.*;
+import org.sbml.jsbml.xml.XMLNode;
 
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
@@ -117,10 +117,9 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     String mapKey = getSbmlIdKey(element);
     if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
       S sbmlElement = createSbmlElement(element);
-      XmlAnnotationParser parser = new XmlAnnotationParser();
-      String rdf = parser.dataSetToXmlString(element.getMiriamData(), sbmlElement.getId());
       try {
-        sbmlElement.setAnnotation(rdf);
+        XMLNode rdfNode = NotesUtility.getRdfNode(element.getMiriamData(), sbmlElement.getId());
+        sbmlElement.setAnnotation(rdfNode);
       } catch (XMLStreamException e1) {
         throw new InconsistentModelException(e1);
       }

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

@@ -104,7 +104,7 @@ public class SbmlExporter {
     String rdf = parser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(),
         model.getModificationDates(), model.getIdModel());
     try {
-      result.setAnnotation(rdf);
+      result.setAnnotation(NotesUtility.getRdfNode(rdf));
     } catch (XMLStreamException e1) {
       throw new InconsistentModelException(e1);
     }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -8,6 +8,7 @@ import java.io.File;
 import java.lang.reflect.Modifier;
 import java.util.*;
 
+import org.apache.commons.lang3.mutable.MutableBoolean;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.Test;
@@ -21,6 +22,7 @@ import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.graphics.PolylineDataComparator;
+import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;
@@ -678,5 +680,31 @@ public class SbmlExporterTest extends SbmlTestFunctions {
 
   }
 
+  @Test
+  public void testExportMultiTthreaded() throws Exception {
+    final Model originalModel = getModelAfterSerializing("testFiles/small/small_molecule.xml");
+    Set<Thread> threads = new HashSet<>();
+    MutableBoolean exceptionHappened = new MutableBoolean(false);
+    for (int i = 0; i < 20; i++) {
+      Thread thread = new Thread(new Runnable() {
+        @Override
+        public void run() {
+          try {
+            new SbmlExporter().toXml(originalModel);
+          } catch (Exception e) {
+            exceptionHappened.setTrue();
+            e.printStackTrace();
+          }
+        }
+      });
+      thread.start();
+      threads.add(thread);
+    }
+    for (Thread thread : threads) {
+      thread.join();
+    }
+
+    assertFalse(exceptionHappened.booleanValue());
+  }
 
 }