chembl provide taxonomy id - we don't need to translate name to id

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

@@ -170,8 +170,14 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
         Node node = list.item(i);
         if (node.getNodeType() == Node.ELEMENT_NODE) {
           if (node.getNodeName().equalsIgnoreCase("organism")) {
-            // node with information abou organism
-            target.setOrganism(getTaxonomyBackend().getByName(node.getTextContent()));
+            // nothing to do here, we use taxonomy id
+          } else if (node.getNodeName().equalsIgnoreCase("tax_id")) {
+            String value = node.getTextContent();
+            MiriamData taxonomy = new MiriamData(MiriamType.TAXONOMY, value);
+            String organismName = getTaxonomyBackend().getNameForTaxonomy(taxonomy);
+            if (organismName != null) {
+              target.setOrganism(taxonomy);
+            }
           } else if (node.getNodeName().equalsIgnoreCase("pref_name")) {
             // node with information about name
             target.setName(node.getTextContent());
@@ -210,7 +216,7 @@ public class ChEMBLParser extends DrugAnnotation implements IExternalService {
             // nothing to do here
             continue;
           } else {
-            logger.warn("Unknown node: " + node.getNodeName());
+            logger.warn("Unknown node: " + node.getNodeName() + ";" + node.getTextContent());
           }
         }
       }

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

@@ -167,7 +167,7 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
 	 *          object representing taxonomy id
 	 * @return name for given taxonomy id
 	 * @throws TaxonomySearchException
-	 *           thrown when there is a problem with accessing external dadatabse
+	 *           thrown when there is a problem with accessing external database
 	 */
 	public String getNameForTaxonomy(MiriamData miriamData) throws TaxonomySearchException {
 		if (miriamData == null) {