properly handle uris

CHANGELOG

@@ -3,6 +3,8 @@ minerva (14.0.12) stable; urgency=medium
   * Bug fix: removing comment from submap did not work
   * Bug fix: reaction name containing "<" character was exported inproperly to
     CellDesigner (#1227)
+  * Bug fix: doi annotation was inproperly parsed from CellDesigner file and
+    resulted in not clickable link (#1231)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 11 May 2020 17:00:00 +0200
 

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

 package lcsb.mapviewer.model.map;
 
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -911,7 +913,13 @@ public enum MiriamType {
       if (!foundUri.endsWith("/")) { // add one character for separator
         uriLength++;
       }
-      return new MiriamData(foundType, miriamUri.substring(uriLength));
+      String resource = miriamUri.substring(uriLength);
+      try {
+        resource = URLDecoder.decode(resource, "UTF-8");
+      } catch (UnsupportedEncodingException e) {
+        logger.warn("Problematic uri: " + resource, e);
+      }
+      return new MiriamData(foundType, resource);
     }
     throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
   }

model/src/test/java/lcsb/mapviewer/model/map/MiriamTypeTest.java

@@ -117,4 +117,11 @@ public class MiriamTypeTest extends ModelTestFunctions {
     }
   }
 
+  @Test
+  public void testGetMiriamForDoiUri() {
+    MiriamData md = MiriamType.getMiriamByUri("urn:miriam:doi:10.1109%2F5.771073");
+    logger.debug(md);
+    assertTrue(md.getResource().contains("/"));
+  }
+
 }