Resolve "problem with caching drugs list for big projects"

Closes #2168 (closed)

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

 package lcsb.mapviewer.annotation.services.annotators;
 
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.springframework.stereotype.Service;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
 import lcsb.mapviewer.annotation.cache.QueryCacheInterface;
 import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
 import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
@@ -31,15 +20,23 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorData;
 import lcsb.mapviewer.model.user.annotator.AnnotatorInputParameter;
 import lcsb.mapviewer.model.user.annotator.AnnotatorOutputParameter;
 import lcsb.mapviewer.model.user.annotator.BioEntityField;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.springframework.stereotype.Service;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 
 /**
  * This class is responsible for connecting to
  * <a href="https://rest.genenames.org/">HGNC restfull API</a> and annotate
  * elements with information taken from this service.
- * 
- * 
+ *
  * @author Piotr Gawron
- * 
  */
 @Service
 public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator {
@@ -51,13 +48,13 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
 
   private final Logger logger = LogManager.getLogger();
 
-  private MiriamConnector miriamConnector;
+  private final MiriamConnector miriamConnector;
 
   /**
    * Constructor.
    */
   public HgncAnnotatorImpl(final MiriamConnector miriamConnector) {
-    super(HgncAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, true);
+    super(HgncAnnotator.class, new Class[]{Protein.class, Rna.class, Gene.class}, true);
     this.miriamConnector = miriamConnector;
   }
 
@@ -234,8 +231,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
   /**
    * Creates query url for given {@link MiriamType#HGNC} identifier.
    *
-   * @param id
-   *          {@link MiriamType#HGNC} identifier
+   * @param id {@link MiriamType#HGNC} identifier
    * @return url to restful api webpage for given identifier
    */
   private String getHgncIdUrl(final String id) {
@@ -245,12 +241,11 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
   /**
    * Creates query url for given {@link MiriamType#HGNC_SYMBOL}.
    *
-   * @param name
-   *          {@link MiriamType#HGNC_SYMBOL}
+   * @param name {@link MiriamType#HGNC_SYMBOL}
    * @return url to restful API web page for given HGNC symbol
    */
   private String getHgncNameUrl(final String name) {
-    String hgncSymbol = "" + name;
+    String hgncSymbol = name;
     hgncSymbol = hgncSymbol.split("\\s+")[0];
     return REST_API_URL + "symbol/" + hgncSymbol;
   }
@@ -259,12 +254,10 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
    * Converts {@link MiriamType#HGNC}/{@link MiriamType#HGNC_SYMBOL} identifier
    * into list of {@link MiriamType#UNIPROT} identifiers.
    *
-   * @param miriamData
-   *          {@link MiriamData} with {@link MiriamType#HGNC} identifier
+   * @param miriamData {@link MiriamData} with {@link MiriamType#HGNC} identifier
    * @return list of {@link MiriamData} with {@link MiriamType#UNIPROT}
-   * @throws AnnotatorException
-   *           thrown when there was problem with accessing external database or
-   *           any other unknown problem
+   * @throws AnnotatorException thrown when there was problem with accessing external database or
+   *                            any other unknown problem
    */
   @Override
   public List<MiriamData> hgncToUniprot(final MiriamData miriamData) throws AnnotatorException {
@@ -323,12 +316,10 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
    * Converts {@link MiriamType#HGNC} identifier into
    * {@link MiriamType#HGNC_SYMBOL}.
    *
-   * @param miriamData
-   *          {@link MiriamData} with {@link MiriamType#HGNC} identifier
+   * @param miriamData {@link MiriamData} with {@link MiriamType#HGNC} identifier
    * @return {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
-   * @throws AnnotatorException
-   *           thrown when there was problem with accessing external database or
-   *           any other unknown problem
+   * @throws AnnotatorException thrown when there was problem with accessing external database or
+   *                            any other unknown problem
    */
   @Override
   public MiriamData hgncIdToHgncName(final MiriamData miriamData) throws AnnotatorException {
@@ -373,13 +364,9 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
    * Returns <code>true</code> if the {@link MiriamData} given in the parameter
    * is a valid {@link MiriamType#HGNC} or {@link MiriamType#HGNC_SYMBOL}.
    *
-   * @param md
-   *          {@link MiriamData} to validate
-   * @return <code>true</code> if the {@link MiriamData} given in the parameter
-   *         is a valid {@link MiriamType#HGNC} or
-   *         {@link MiriamType#HGNC_SYMBOL}
-   * @throws AnnotatorException
-   *           thrown when there is a problem accessing HGNC restful AI
+   * @param md {@link MiriamData} to validate
+   * @return <code>true</code> if the {@link MiriamData} given in the parameter is a valid {@link MiriamType#HGNC} or {@link MiriamType#HGNC_SYMBOL}
+   * @throws AnnotatorException thrown when there is a problem accessing HGNC restful AI
    */
   @Override
   public boolean isValidHgncMiriam(final MiriamData md) throws AnnotatorException {
@@ -388,7 +375,7 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
       if (url == null) {
         return false;
       }
-      return hgncToUniprot(md).size() > 0;
+      return !hgncToUniprot(md).isEmpty();
     } else {
       return false;
     }
@@ -397,11 +384,9 @@ public class HgncAnnotatorImpl extends ElementAnnotator implements HgncAnnotator
   /**
    * Transforms HGNC symbol into {@link MiriamType#ENTREZ} identifier.
    *
-   * @param md
-   *          hgnc symbol
+   * @param md hgnc symbol
    * @return {@link MiriamType#ENTREZ} identifier for a given hgnc symbol
-   * @throws AnnotatorException
-   *           thrown when there is a problem with accessing hgnc server
+   * @throws AnnotatorException thrown when there is a problem with accessing hgnc server
    */
   @Override
   public MiriamData hgncToEntrez(final MiriamData md) throws AnnotatorException {