new implementation of miriam resolver

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

@@ -94,25 +94,6 @@ public final class MiriamConnector extends CachableInterface implements IExterna
     } catch (Exception e) {
       throw new AnnotationException("Problem with accessing identifiers.org", e);
     }
-    // Document document = XmlParser.getXmlDocumentFromString(page);
-    // Node uri = XmlParser.getNode("uri", document.getChildNodes());
-    // return XmlParser.getNodeValue(uri);
-
-    // String[] urls = getLink().getLocations(uri);
-    // if (urls == null) {
-    // result = null;
-    // } else if (urls.length > 0) {
-    // result = urls[0];
-    // }
-    // if (result != null) {
-    // setCacheValue(query, result);
-    // return result;
-    // } else {
-    // logger.warn("Cannot find url for miriam: " + miriamData);
-    // // if url cannot be found then mark miriam data as invalid for one day
-    // setCacheValue(query, INVALID_LINK, 1);
-    // return null;
-    // }
   }
 
   @Override

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

@@ -313,4 +313,5 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
       throw e;
     }
   }
+
 }

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

@@ -3,6 +3,9 @@ package lcsb.mapviewer.model.map;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -359,8 +362,8 @@ public enum MiriamType {
    */
   MESH_2012("MeSH",
       "http://www.nlm.nih.gov/mesh/",
-      new String[] { "urn:miriam:mesh" },
-      new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000560", 
+      new String[] { "urn:miriam:mesh", "urn:miriam:mesh.2012" },
+      new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000560",
       new Class<?>[] {},
       "mesh",
       "D010300"),
@@ -718,6 +721,7 @@ public enum MiriamType {
       "wb",
       "WBGene00000001");
 
+  private static Logger logger = LogManager.getLogger(MiriamType.class);
   /**
    * User friendly name.
    */
@@ -801,8 +805,10 @@ public enum MiriamType {
    * @param classes
    *          {@link #validClass}
    */
-  MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier, Class<?>[] requiredClasses, String namespace, String exampleIdentifier) {
-    this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier, requiredClasses, namespace, exampleIdentifier);
+  MiriamType(String commonName, String dbHomePage, String uri, Class<?>[] classes, String registryIdentifier,
+      Class<?>[] requiredClasses, String namespace, String exampleIdentifier) {
+    this(commonName, dbHomePage, new String[] { uri }, classes, registryIdentifier, requiredClasses, namespace,
+        exampleIdentifier);
   }
 
   /**
@@ -844,6 +850,7 @@ public enum MiriamType {
         }
       }
     }
+    logger.warn("Unknown miriam type: " + uri);
     return null;
   }