export to SBGN fixed

CHANGELOG

@@ -11,6 +11,8 @@ minerva (14.0.8) stable; urgency=medium
     information (#1062)
   * Bug fix: import of stimulation modifiers from SBGN-ML crashed converter
     (#1063)
+  * Bug fix: export to SBGN files created from newt source produced corrupted
+    disconnected reactions
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 23 Jan 2020 12:00:00 +0200
 

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

@@ -192,7 +192,7 @@ public class SbgnmlXmlExporter {
       }
     }
 
-    sourceTargetMap.put(newGlyph.getId(), newGlyph);
+    sourceTargetMap.put(element.getElementId(), newGlyph);
     return newGlyph;
   }
 
@@ -844,6 +844,7 @@ public class SbgnmlXmlExporter {
       if (!node.getLine().getEndAtd().getArrowType().equals(ArrowType.NONE)) {
         arc.setTarget(sourceTargetMap.get(node.getReaction().getIdReaction()));
       } else {
+        boolean found = false;
         for (NodeOperator operator : node.getReaction().getOperators()) {
           if (operator.getInputs().contains(node)) {
             if (!parsedOperators.contains(operator)) {
@@ -851,8 +852,13 @@ public class SbgnmlXmlExporter {
               glyphList.add(newOperator);
             }
             arc.setTarget(sourceTargetMap.get(operatorIds.get(operator).concat(".1")));
+            found = true;
           }
         }
+        if (!found) {
+          throw new InvalidArgumentException(
+              new ElementUtils().getElementTag((Modifier) node) + "Problem with exportin modifier");
+        }
       }
     } else if (node instanceof NodeOperator) {
       if ((node instanceof DissociationOperator) || (node instanceof AssociationOperator)) {
@@ -873,7 +879,7 @@ public class SbgnmlXmlExporter {
         }
       }
     }
-
+    
     List<Point2D> arcPoints = node.getLine().getPoints();
     Start start = new Start();
     if ((node instanceof Product) || (node instanceof NodeOperator)) {

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java

@@ -3,6 +3,7 @@ package lcsb.mapviewer.converter.model.sbgnml;
 import static org.junit.Assert.*;
 
 import java.awt.geom.Point2D;
+import java.io.InputStream;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -13,6 +14,7 @@ import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.species.Complex;
 import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -116,7 +118,35 @@ public class SbgnmlXmlParserTest2 extends SbgnmlTestFunctions {
     logger.debug(sbgn);
     assertTrue("State variable is missing", sbgn.contains("state variable"));
     assertTrue("State variable doesn't contain variable", sbgn.contains("variable=\"g\""));
-    
+
+  }
+
+  @Test
+  public void testStimulationModification() throws Exception {
+    Converter converter = new SbgnmlXmlConverter();
+
+    Model model = converter.createModel(
+        new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/stimulation_modification.sbgn"));
+    for (Reaction r : model.getReactions()) {
+      assertEquals(1, r.getModifiers().size());
+    }
+  }
+
+  @Test
+  public void testExportStimulationModification() throws Exception {
+    Converter converter = new SbgnmlXmlConverter();
+
+    Model model = converter.createModel(
+        new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/stimulation_modification.sbgn"));
+
+    InputStream is = converter.model2InputStream(model);
+
+    Model model2 = converter.createModel(new ConverterParams().inputStream(is));
+
+    for (Reaction r : model2.getReactions()) {
+      assertEquals(1, r.getModifiers().size());
+    }
+
   }
 
 }