Merge branch '341-handling-mesh-identifiers' into 'master'

Resolve "Handling MeSH identifiers"

Closes #341

See merge request !419

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

@@ -82,17 +82,12 @@ public final class MiriamConnector extends CachableInterface implements IExterna
       }
       return result;
     }
-    // hard-coded specific treatment for mesh
-    if (MiriamType.MESH_2012.equals(miriamData.getDataType())) {
-      result = "http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=" + miriamData.getResource();
-    } else {
-      String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
-      String[] urls = getLink().getLocations(uri);
-      if (urls == null) {
-        result = null;
-      } else if (urls.length > 0) {
-        result = urls[0];
-      }
+    String uri = miriamData.getDataType().getUris().get(0) + ":" + miriamData.getResource();
+    String[] urls = getLink().getLocations(uri);
+    if (urls == null) {
+      result = null;
+    } else if (urls.length > 0) {
+      result = urls[0];
     }
     if (result != null) {
       setCacheValue(query, result);

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

@@ -728,6 +728,7 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
   public void testGetEmptySuggestedQueryList() throws Exception {
     try {
       Project project = new Project();
+      project.setId(-2);
 
       List<String> result = drugBankHTMLParser.getSuggestedQueryList(project, TaxonomyBackend.HUMAN_TAXONOMY);
 

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

@@ -22,7 +22,6 @@ import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.annotation.AnnotationTestFunctions;
 import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.GeneralCacheWithExclusion;
 import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
 import lcsb.mapviewer.annotation.cache.WebPageDownloader;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -66,9 +65,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
     try {
       MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.MESH_2012, "D004249");
 
-      String pageContent = getWebpage(miriamConnector.getUrlString(md));
-      assertTrue(pageContent.contains("DNA Damage"));
-
+      assertNotNull(getWebpage(miriamConnector.getUrlString(md)));
     } catch (Exception e) {
       e.printStackTrace();
       throw e;

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

@@ -253,9 +253,9 @@ public enum MiriamType {
   /**
    * MeSH 2012: http://www.nlm.nih.gov/mesh/.
    */
-  MESH_2012("MeSH 2012", //
+  MESH_2012("MeSH", //
       "http://www.nlm.nih.gov/mesh/", //
-      new String[] { "urn:miriam:mesh.2012", "urn:miriam:mesh" }, //
+      new String[] { "urn:miriam:mesh" }, //
       new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000270"), //
 
   /**