CellDesigner sometimes marked reduced notation reaction as reversible even...

CellDesigner sometimes marked reduced notation reaction as reversible even though they should not be

CHANGELOG

@@ -4,6 +4,8 @@ minerva (14.0.9) stable; urgency=medium
   * Bug fix: refresh data overlay did not hide data overlays that were removed
     and selected (#1097)
   * Bug fix: transparent complexes are shown with wrong color (#1103)
+  * Bug fix: CellDesigner sometimes marked reduced notation reaction as
+    reversible even though they were not visualized so (#1109)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 3 Feb 2020 15:00:00 +0200
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

@@ -25,6 +25,7 @@ import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.reaction.type.*;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
  * This is a part of {@link ReactionXmlParser} class functionality that allows
@@ -176,6 +177,15 @@ public class ReactionFromXml {
     } catch (InvalidStateException e) {
       throw new ReactionParserException(result, e);
     }
+    if (result instanceof ReducedNotation || result instanceof ModifierReactionNotation) {
+      // there is a bug in CellDesigner (#1109) that allows to save such reactions
+      // with reversible flag (even though it cannot be reversible)
+      if (result.isReversible()) {
+        logger.warn(
+            new ElementUtils().getElementTag(result) + "Reacion was marked as reversible but it cannot be reversible");
+        result.setReversible(false);
+      }
+    }
     return result;
   }
 
@@ -409,7 +419,7 @@ public class ReactionFromXml {
       }
       applyStylingToLine(line, result.getLine());
 
-      if (booleanLogicGateType!=null) {
+      if (booleanLogicGateType != null) {
         assignColorFromGateMembers(result, gateMembers);
       }
       if (reactantsLinkNode != null) {
@@ -951,7 +961,7 @@ public class ReactionFromXml {
                 polylines.add(result.getReactants().get(elementIndex - 1).getLine());
               }
             }
-            for (PolylineData polyline: polylines) {
+            for (PolylineData polyline : polylines) {
               polyline.setColor(line.getColor());
               polyline.setWidth(line.getWidth());
             }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -26,7 +26,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.layout.graphics.*;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.*;
 import lcsb.mapviewer.model.map.species.*;
 
 public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
@@ -874,4 +874,15 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     assertEquals(c1.getBlue(), c2.getBlue());
   }
 
+  @Test
+  public void testTrigger() throws Exception {
+    CellDesignerXmlParser parser = new CellDesignerXmlParser();
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/problematic/unknown-rections.xml"));
+    for (Reaction reaction : model.getReactions()) {
+      if (reaction instanceof ReducedNotation || reaction instanceof ModifierReactionNotation) {
+        assertFalse("Reaction cannot be reversible: " + reaction, reaction.isReversible());
+      }
+    }
+  }
+
 }