synonyms are escaped html strings

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java

 package lcsb.mapviewer.annotation.services.annotators;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.net.HttpURLConnection;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -9,15 +8,11 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.log4j.Logger;
 import org.springframework.stereotype.Service;
-import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
 
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
 import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -300,7 +295,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
 						Node node = list.item(i);
 						if (node.getNodeType() == Node.ELEMENT_NODE) {
 							if (node.getNodeName().equals("Gene-ref_syn_E")) {
-								synonyms.add(node.getTextContent());
+								synonyms.add(StringEscapeUtils.unescapeHtml4(node.getTextContent()));
 							}
 						}
 					}

annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java

@@ -343,6 +343,23 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
     }
   }
 
+  @Test
+  public void testAnnotateElementWithEncodedSynonyms() throws Exception {
+    try {
+      Species proteinAlias = new GenericProtein("id");
+      proteinAlias.addMiriamData(new MiriamData(MiriamType.ENTREZ, "834106"));
+      entrezAnnotator.annotateElement(proteinAlias);
+
+      for (String synonym : proteinAlias.getSynonyms()) {
+        assertFalse("Invalid character found in synonym: " + synonym, synonym.contains("&"));
+      }
+
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseEntrezResponse() throws Exception {
     WebPageDownloader downloader = entrezAnnotator.getWebPageDownloader();