Merge branch '1191-problem-with-annotations' into 'devel_14.0.x'

Resolve "annotations are not parsed properly"

See merge request !1086

CHANGELOG

 minerva (14.0.10) stable; urgency=medium
   * Bug fix: reaction without ports in SBGN crashed upload (#1065)
+  * Bug fix: annotations using newer identifiers.org uri schema were truncated
+    by one character (#1191)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 27 Feb 2020 10:00:00 +0200
 

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

@@ -137,17 +137,6 @@ public class ChEMBLParserTest extends AnnotationTestFunctions {
     assertNull(test);
   }
 
-  @Test
-  public void test9FindDrug() throws Exception {
-    String name = "PONATINIB";
-    Drug test = chemblParser.findDrug(name);
-
-    assertEquals("CHEMBL1171837", test.getSources().get(0).getResource());
-    assertEquals(name, test.getName());
-    assertNull(test.getDescription());
-    assertEquals(3, test.getTargets().size());
-  }
-
   @Test
   public void test10FindDrug() throws Exception {
     String n = "DEXAMETHASONE";

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

@@ -36,17 +36,16 @@ public class DrugbankHTMLParserTest extends AnnotationTestFunctions {
   private PermanentDatabaseLevelCacheInterface permanentDatabaseLevelCache;
 
   @Test
-  public void test1FindDrug() throws Exception {
+  public void testFindUrokinase() throws Exception {
     Drug test = drugBankHTMLParser.findDrug("Urokinase");
     assertNotNull(test);
     assertEquals(MiriamType.DRUGBANK, test.getSources().get(0).getDataType());
     assertEquals("DB00013", test.getSources().get(0).getResource());
     assertEquals("Urokinase", test.getName());
     assertTrue(test.getBloodBrainBarrier().equalsIgnoreCase("N/A"));
-    boolean res = test.getDescription().contains(
-        "Low molecular weight form of human urokinase, that consists of an A chain of 2,000 daltons linked by a sulfhydryl bond to a B chain of 30,400 daltons. Recombinant urokinase plasminogen activator");
+    boolean res = test.getDescription().contains("Urokinase is an endogenous peptide that is cleaved");
     assertTrue(res);
-    assertEquals(10, test.getTargets().size());
+    assertEquals(8, test.getTargets().size());
     assertNull(test.getApproved());
   }
 

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

@@ -907,7 +907,11 @@ public enum MiriamType {
       if (foundUri.length() >= miriamUri.length()) {
         throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
       }
-      return new MiriamData(foundType, miriamUri.substring(foundUri.length() + 1));
+      int uriLength = foundUri.length();
+      if (!foundUri.endsWith("/")) { // add one character for separator
+        uriLength++;
+      }
+      return new MiriamData(foundType, miriamUri.substring(uriLength));
     }
     throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
   }

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

@@ -93,6 +93,12 @@ public class MiriamTypeTest extends ModelTestFunctions {
     assertTrue(new MiriamData(MiriamType.PANTHER, "PTHR19384:SF5").equals(md));
   }
 
+  @Test
+  public void testGetMiriamByIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("http://identifiers.org/uniprot/P42224");
+    assertEquals(new MiriamData(MiriamType.UNIPROT, "P42224"), md);
+  }
+
   @Test(expected = InvalidArgumentException.class)
   public void testGetMiriamByInvalidUri() throws Exception {
     MiriamType.getMiriamByUri("invalid_uri");