unused method removed

annotation/src/main/java/lcsb/mapviewer/annotation/services/MeSHParser.java

 package lcsb.mapviewer.annotation.services;
 
 import java.io.IOException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.lang3.SerializationException;
 import org.apache.http.HttpStatus;
@@ -12,7 +16,11 @@ import org.w3c.dom.Node;
 
 import com.google.gson.Gson;
 
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.CachableInterface;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
+import lcsb.mapviewer.annotation.cache.XmlSerializer;
 import lcsb.mapviewer.annotation.data.MeSH;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -60,7 +68,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
   }
 
   @Override
-  public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+  public Object refreshCacheQuery(final Object query) throws SourceNotAvailable {
     Object result = null;
     try {
       if (query instanceof String) {
@@ -92,7 +100,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
   }
 
   @Override
-  protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+  protected void setWebPageDownloader(final WebPageDownloader webPageDownloader) {
     super.setWebPageDownloader(webPageDownloader);
   }
 
@@ -103,7 +111,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    * @throws AnnotatorException
    *           thrown when there is a problem with accessing mesh database
    */
-  public MeSH getMeSH(MiriamData meshID) throws AnnotatorException {
+  public MeSH getMeSH(final MiriamData meshID) throws AnnotatorException {
     if (meshID == null || meshID.getResource() == null) {
       throw new InvalidArgumentException("mesh cannot be null ");
     }
@@ -142,7 +150,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    *          id as miriam data.
    * @return return the object.
    */
-  public String getIdentifier(MiriamData meshID) {
+  public String getIdentifier(final MiriamData meshID) {
     return MESH_PREFIX + meshID.getResource();
   }
 
@@ -155,7 +163,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    * @throws AnnotatorException
    *           thrown when there is a problem with accessing mesh db
    */
-  private MeSH getMeSHByIdFromDB(MiriamData meshID) throws IOException {
+  private MeSH getMeSHByIdFromDB(final MiriamData meshID) throws IOException {
     try {
       MeSH result = new MeSH();
       String page = getWebPageContent(URL_MESH_DATABASE + meshID.getResource());
@@ -163,7 +171,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
       Gson gson = new Gson();
 
       Map<?, ?> gsonObject = new HashMap<String, Object>();
-      gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
+      gsonObject = gson.fromJson(page, gsonObject.getClass());
       Set<String> synonyms = getSynonyms(gsonObject);
       String name = getName(gsonObject);
       String description = getDescription(gsonObject);
@@ -191,7 +199,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    *          gson to process
    * @return name of {@link MeSH} entry
    */
-  private String getName(Map<?, ?> gsonObject) {
+  private String getName(final Map<?, ?> gsonObject) {
     Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorName");
     if (descriptorTag == null) {
       descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordName");
@@ -206,7 +214,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    *          gson to process
    * @return id of {@link MeSH} entry
    */
-  private String getId(Map<?, ?> gsonObject) {
+  private String getId(final Map<?, ?> gsonObject) {
     Map<?, ?> descriptorTag = (Map<?, ?>) gsonObject.get("DescriptorUI");
     if (descriptorTag == null) {
       descriptorTag = (Map<?, ?>) gsonObject.get("SupplementalRecordUI");
@@ -221,7 +229,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    *          gson to process
    * @return description of {@link MeSH} entry
    */
-  private String getDescription(Map<?, ?> gsonObject) {
+  private String getDescription(final Map<?, ?> gsonObject) {
     Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("_generated");
     return (String) concepts.get("PreferredConceptScopeNote");
   }
@@ -233,7 +241,7 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    *          gson to process
    * @return synonyms of {@link MeSH} entry
    */
-  private Set<String> getSynonyms(Map<?, ?> gsonObject) {
+  private Set<String> getSynonyms(final Map<?, ?> gsonObject) {
     Set<String> synonyms = new HashSet<>();
     Map<?, ?> concepts = (Map<?, ?>) gsonObject.get("ConceptList");
     ArrayList<?> conceptList = (ArrayList<?>) concepts.get("Concept");
@@ -280,33 +288,14 @@ public class MeSHParser extends CachableInterface implements IExternalService {
    * @throws AnnotatorException
    *           thrown when there is problem with accessing mesh db
    */
-  public boolean isValidMeshId(MiriamData meshId) throws AnnotatorException {
+  public boolean isValidMeshId(final MiriamData meshId) throws AnnotatorException {
     if (meshId == null) {
       return false;
     }
     return getMeSH(meshId) != null;
   }
 
-  public List<MeSH> getMeshBySynonym(String synonym) throws AnnotatorException {
-    try {
-      List<MeSH> result = new ArrayList<>();
-      String page = getWebPageContent(URL_SEARCH_BY_SYNONYM + synonym);
-      Gson gson = new Gson();
-
-      Map<?, ?> gsonObject = new HashMap<String, Object>();
-      gsonObject = (Map<?, ?>) gson.fromJson(page, gsonObject.getClass());
-      Set<MiriamData> synonyms = getIdsBySynonymQuery(gsonObject);
-      for (MiriamData meshID : synonyms) {
-        result.add(getMeSH(meshID));
-      }
-
-      return result;
-    } catch (IOException e) {
-      throw new AnnotatorException(e);
-    }
-  }
-
-  private Set<MiriamData> getIdsBySynonymQuery(Map<?, ?> gsonObject) {
+  private Set<MiriamData> getIdsBySynonymQuery(final Map<?, ?> gsonObject) {
     Set<MiriamData> result = new HashSet<>();
     Map<?, ?> hits = (Map<?, ?>) gsonObject.get("hits");
     ArrayList<?> hitsList = (ArrayList<?>) hits.get("hits");

annotation/src/test/java/lcsb/mapviewer/annotation/services/MeSHParserTest.java

 package lcsb.mapviewer.annotation.services;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
 import static org.mockito.ArgumentMatchers.anyString;
 import static org.mockito.ArgumentMatchers.nullable;
 import static org.mockito.Mockito.when;
 
 import java.io.IOException;
-import java.util.List;
 
 import org.apache.http.HttpStatus;
 import org.apache.logging.log4j.LogManager;
@@ -16,7 +19,9 @@ import org.mockito.Mockito;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.*;
+import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
+import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
+import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.annotation.data.MeSH;
 import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -42,15 +47,6 @@ public class MeSHParserTest extends AnnotationTestFunctions {
     assertTrue(mesh.getSynonyms().size() > 0);
   }
 
-  @Test
-  public void testGetMeshBySynonym() throws Exception {
-    String synonym = "MPTP";
-    List<MeSH> result = meshParser.getMeshBySynonym(synonym);
-    assertEquals(1, result.size());
-    MeSH mesh = result.get(0);
-    assertTrue(mesh.getSynonyms().contains(synonym));
-  }
-
   @Test
   public void testIsValidMesh() throws Exception {
     MiriamData meshID = new MiriamData(MiriamType.MESH_2012, "D004298");