export map notes to gpml

CHANGELOG

 minerva (15.0.2) stable; urgency=medium
   * Bug fix: annotations using identifiers.org urls sometimes required http and
     sometimes required https url (#1297)
+  * Bug fix: map notes were not exported to GPML
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 29 Jun 2020 11:00:00 +0200
 

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java

@@ -805,6 +805,9 @@ public class ModelToGPML {
     StringBuilder gpml = new StringBuilder("");
     gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
     gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\" Name=\"Generated\">\n");
+    if (model.getNotes() != null) {
+      gpml.append("  <Comment>" + model.getNotes().trim() + "</Comment>\n");
+    }
     gpml.append("  <Graphics BoardWidth=\"" + model.getWidth() + "\" BoardHeight=\"" + model.getHeight() + "\"/>\n");
 
     gpml.append(getDataNodes(model));

pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java

@@ -200,7 +200,7 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
     assertEquals(reaction.isReversible(), newReaction.isReversible());
   }
 
-  private Reaction createReaction(Protein p1, Protein p2) {
+  private Reaction createReaction(Species p1, Species p2) {
     Reaction reaction = new TransportReaction("re" + (speciesCounter++));
     Reactant reactant = new Reactant(p1);
     Product product = new Product(p2);
@@ -396,4 +396,18 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
     assertEquals(0, new ModelComparator().compare(model, model2));
   }
 
+  @Test
+  public void testMapNotes() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(1000);
+    model.setHeight(1000);
+    model.setNotes("xyz");
+
+    lcsb.mapviewer.wikipathway.GpmlParser parser = new lcsb.mapviewer.wikipathway.GpmlParser();
+
+    String xml = parser.model2String(model);
+    Model model2 = parser.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(xml.getBytes())));
+
+    assertEquals(0, new ModelComparator().compare(model, model2));
+  }
 }