Merge branch '467-creating-user-s-overlay-type' into 'devel_12.0.x'

Resolve "creating user's overlay TYPE = PROTEIN is not working"

See merge request !365

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

@@ -221,7 +221,14 @@ public class ColorModelCommand extends ModelCommand {
         }
       }
       for (MiriamData md : schema.getMiriamData()) {
-        if (!element.getMiriamData().contains(md)) {
+        boolean found = false;
+        for (MiriamData elementMiriamData : element.getMiriamData()) {
+          if (elementMiriamData.getDataType().equals(md.getDataType())
+              && elementMiriamData.getResource().equals(md.getResource())) {
+            found = true;
+          }
+        }
+        if (!found) {
           return false;
         }
       }

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

@@ -360,6 +360,61 @@ public class ColorModelCommandTest extends CommandTestFunctions {
 
   }
 
+  @Test
+  public void testSpeciesMatchWithMiriamData() throws Exception {
+    try {
+      GenericColorSchema colorSchema = new GenericColorSchema();
+      colorSchema.setName("s1");
+      colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+      GenericColorSchema colorSchema2 = new GenericColorSchema();
+      colorSchema2.setName("s1");
+      colorSchema2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
+
+      GenericProtein species = new GenericProtein("id");
+      species.setName("s1");
+      species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+      List<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(colorSchema);
+
+      ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+      assertTrue(factory.match(species, colorSchema));
+      assertFalse(factory.match(species, colorSchema2));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
+  @Test
+  public void testSpeciesMatchWithMiriamDataDifferentAnnotator() throws Exception {
+    try {
+      GenericColorSchema colorSchema = new GenericColorSchema();
+      colorSchema.setName("s1");
+      colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+      GenericProtein species = new GenericProtein("id");
+      species.setName("s1");
+      species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA", Object.class));
+
+      List<ColorSchema> schemas = new ArrayList<>();
+      schemas.add(colorSchema);
+
+      ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+      assertTrue(factory.match(species, colorSchema));
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+
+  }
+
   @Test
   public void testReactionMatchWithProteinMiriamData() throws Exception {
     try {