Merge branch '1126-minervanet-error-report-169' into 'master'

Resolve "MINERVANET - Error Report 169"

Closes #1126

See merge request !1080

CHANGELOG

@@ -6,6 +6,7 @@ minerva (15.0.0~beta.2) stable; urgency=medium
     structured log form
   * Bug fix: antisenseRNA shape is infered from SBGN when antisenseRNA text is
     present in glyph label (#1114)
+  * Bug fix: export to SBGN sometimes crashed due to concurrency issues (#1126)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 27 Feb 2020 14:00:00 +0200
 

model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java

@@ -277,11 +277,10 @@ public class CopyCommand extends NewModelCommand {
    *          original reaction
    * @return copy of the reaction
    */
-  private Reaction createCopy(Reaction reaction) {
+  Reaction createCopy(Reaction reaction) {
     Reaction copy = reaction.copy();
-    reaction.getNodes().clear();
-    for (AbstractNode node : copy.getNodes()) {
-      reaction.addNode(node);
+    for (AbstractNode node : reaction.getNodes()) {
+      node.setReaction(reaction);
     }
     copy.getNodes().clear();
 

model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java

@@ -3,8 +3,9 @@ package lcsb.mapviewer.commands;
 import static org.junit.Assert.*;
 
 import java.awt.geom.Point2D;
-import java.util.Calendar;
+import java.util.*;
 
+import org.apache.commons.lang3.mutable.MutableBoolean;
 import org.junit.*;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -18,6 +19,7 @@ import lcsb.mapviewer.model.map.layout.graphics.Layer;
 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.TransportReaction;
 import lcsb.mapviewer.model.map.species.*;
 
 public class CopyCommandTest extends CommandTestFunctions {
@@ -312,4 +314,47 @@ public class CopyCommandTest extends CommandTestFunctions {
     assertEquals(0, comparator.compare(copy, model));
   }
 
+  @Test
+  public void testMultithreadedCopyReaction() throws Exception {
+    MutableBoolean exceptionHappened = new MutableBoolean(false);
+    Reaction r = new TransportReaction("x");
+    r.addReactant(new Reactant(createProtein()));
+    r.addReactant(new Reactant(createProtein()));
+    r.addReactant(new Reactant(createProtein()));
+    r.addReactant(new Reactant(createProtein()));
+    r.addProduct(new Product(createProtein()));
+    for (AbstractNode node : r.getNodes()) {
+      node.setLine(new PolylineData(new Point2D.Double(0.0, 0.0), new Point2D.Double(110.0, 10.0)));
+    }
+
+    List<Thread> threads = new ArrayList<>();
+    for (int i = 0; i < 100; i++) {
+      threads.add(new Thread(new Runnable() {
+
+        @Override
+        public void run() {
+          try {
+            new CopyCommand(null).createCopy(r);
+          } catch (Exception e) {
+            e.printStackTrace();
+            exceptionHappened.setTrue();
+          }
+        }
+      }));
+    }
+    for (Thread thread : threads) {
+      thread.start();
+    }
+    for (Thread thread : threads) {
+      thread.join();
+    }
+
+    assertFalse(exceptionHappened.booleanValue());
+
+    for (AbstractNode node : r.getNodes()) {
+      assertEquals(r, node.getReaction());
+    }
+
+  }
+
 }