invisible layer is not drawn

CHANGELOG

@@ -3,6 +3,7 @@ minerva (12.3.1~beta.1) unstable; urgency=low
     name was used
   * Bug fix: plugin tab header wasn't properly resized after adding plugins 
     that introduced second line for tab selection (#758)
+  * Bug fix: invisible layer shouldn't be shown in the on th map (#813)
 
 minerva (13.1.0~beta.0) unstable; urgency=low
   * Feature: annotators are more flexible - you can define set of input and

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java

@@ -711,7 +711,9 @@ public abstract class AbstractImageGenerator {
     List<Drawable> bioEntities = new ArrayList<>();
     bioEntities.addAll(params.getModel().getBioEntities());
     for (Layer layer : params.getModel().getLayers()) {
-      bioEntities.addAll(layer.getDrawables());
+      if (layer.isVisible()) {
+        bioEntities.addAll(layer.getDrawables());
+      }
     }
     bioEntities.sort(BioEntity.Z_INDEX_COMPARATOR);
 

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/AbstractImageGeneratorTest.java

@@ -13,6 +13,8 @@ import org.junit.Before;
 import org.junit.Test;
 import org.mockito.Mockito;
 
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -68,6 +70,33 @@ public class AbstractImageGeneratorTest extends GraphicsTestFunctions {
     }
   }
 
+  @Test
+  public void testDrawMapWithInvisibleLayerNesting() throws Exception {
+    try {
+      Graphics2D graphics = createGraphicsMock();
+
+      Model model = createEmptyModel();
+      Layer layer = new Layer();
+      layer.setVisible(false);
+      LayerRect rect = new LayerRect();
+      rect.setX(10.0);
+      rect.setX(10.0);
+      rect.setWidth(20.);
+      rect.setHeight(20.);
+      layer.addLayerRect(rect);
+      model.addLayer(layer);
+
+      AbstractImageGenerator gen = createAbstractImageGeneratorMock(graphics, model);
+      gen.setParams(new AbstractImageGenerator.Params().model(model).nested(true));
+      gen.draw();
+
+      // 3 times for proteins and 4 times for reaction
+      verify(graphics, times(0)).draw(any());
+    } catch (Exception e) {
+      throw e;
+    }
+  }
+
   @Test
   public void testDrawSimpleMapWithWhenNestingHidesElement() throws Exception {
     try {
@@ -88,9 +117,7 @@ public class AbstractImageGeneratorTest extends GraphicsTestFunctions {
   }
 
   private Model createSimpleModel() {
-    Model model = new ModelFullIndexed(null);
-    model.setWidth(100);
-    model.setHeight(100);
+    Model model = createEmptyModel();
 
     GenericProtein protein1 = createProtein();
     model.addElement(protein1);
@@ -110,6 +137,13 @@ public class AbstractImageGeneratorTest extends GraphicsTestFunctions {
     return model;
   }
 
+  private Model createEmptyModel() {
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(100);
+    model.setHeight(100);
+    return model;
+  }
+
   private AbstractImageGenerator createAbstractImageGeneratorMock(Graphics2D graphics, Model model) throws Exception {
     AbstractImageGenerator result = Mockito.mock(AbstractImageGenerator.class, Mockito.CALLS_REAL_METHODS);
     result.setGraphics(graphics);

frontend-js/package-lock.json

@@ -87,6 +87,7 @@
       "version": "0.1.4",
       "resolved": "https://registry.npmjs.org/align-text/-/align-text-0.1.4.tgz",
       "integrity": "sha1-DNkKVhCT810KmSVsIrcGlDP60Rc=",
+      "optional": true,
       "requires": {
         "kind-of": "^3.0.2",
         "longest": "^1.0.1",
@@ -3309,7 +3310,8 @@
     "longest": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/longest/-/longest-1.0.1.tgz",
-      "integrity": "sha1-MKCy2jj3N3DoKUoNIuZiXtd9AJc="
+      "integrity": "sha1-MKCy2jj3N3DoKUoNIuZiXtd9AJc=",
+      "optional": true
     },
     "loose-envify": {
       "version": "1.3.1",