search by miriam returns also elements annotated automatically

CHANGELOG

 minerva (14.0.6) stable; urgency=medium
   * Bug fix: opening map with no background overlays and search request in url
     provides proper error message (#1046)
+  * Bug fix: search by identifier didn't consider identifiers added by
+    annotators (#1047)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 18 Dec 2019 12:00:00 +0200
 
 minerva (14.0.5) stable; urgency=medium
   * Bug fix: copy-paste of genetic-variant data overlay into Add overlay 

model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java

@@ -344,7 +344,8 @@ public class ModelFullIndexed implements Model {
     Set<BioEntity> result = new HashSet<>();
     for (Element element : getElements()) {
       for (MiriamData md : element.getMiriamData()) {
-        if (md.equals(miriamData)) {
+        if (Objects.equals(md.getResource(), miriamData.getResource())
+            && Objects.equals(md.getDataType(), miriamData.getDataType())) {
           result.add(element);
         }
       }
@@ -352,7 +353,8 @@ public class ModelFullIndexed implements Model {
 
     for (Reaction element : getReactions()) {
       for (MiriamData md : element.getMiriamData()) {
-        if (md.equals(miriamData)) {
+        if (Objects.equals(md.getResource(), miriamData.getResource())
+            && Objects.equals(md.getDataType(), miriamData.getDataType())) {
           result.add(element);
         }
       }

model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java

@@ -115,6 +115,16 @@ public class ModelTest extends ModelTestFunctions {
     assertEquals(0, elements.size());
   }
 
+  @Test
+  public void testElementsByAnnotationWithAnnotator() {
+    model = createModel();
+
+    Set<BioEntity> elements = model
+        .getElementsByAnnotation(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL12345", Object.class));
+    assertNotNull(elements);
+    assertEquals(1, elements.size());
+  }
+
   private Model createModel() {
     Model model = new ModelFullIndexed(null);
 

service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java

@@ -54,7 +54,7 @@ public class SearchService implements ISearchService {
    * Default class logger.
    */
   @SuppressWarnings("unused")
-  private static Logger logger = LogManager.getLogger(SearchService.class.getName());
+  private static Logger logger = LogManager.getLogger();
 
   /**
    * Data access object for models.
@@ -91,7 +91,7 @@ public class SearchService implements ISearchService {
    * between String and List is stored. The key in this map is incomplete typed
    * word, and value list contains suggestions that should appear for this word.
    */
-  private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
+  private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<>();
 
   /**
    * Default constructor that set list of prefixes used in the search queries.