Merge branch '1359-identifiers-org-url-not-processed' into 'master'

Resolve "identifiers.org url not processed"

Closes #1359

See merge request !1239

CHANGELOG

 minerva (15.1.0~beta.1) unstable; urgency=medium
+  * Small improvement: "Human Disease Ontology", "IUPHAR ligand" and "Protein
+    Modification Ontology" annotation types are handled (#1359)
   * Bug fix: SBML import - label aligned to top of species was inproperly drawn
     (#1354)
   * Bug fix: SBML text  labels that were referencing layout aliases using
     layout:graphicalObject attribute were not handled properly (#1356)
+  * Bug fix: miriam urls in new format
+   (like: https://identifiers.org/kegg.compound:197020) are parsed properly for
+    all know identifier types (#1359)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 17 Aug 2020 16:00:00 +0200
 

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

@@ -109,6 +109,24 @@ public class MiriamTypeGenericTest extends ModelTestFunctions {
     }
   }
 
+  @Test
+  public void testNewHttpAndHttpsForIdentifiersOrg() {
+    if (!deprecated) {
+      boolean httpIdentifiersOrgUriExists = false;
+      boolean httpsIdentifiersOrgUriExists = false;
+      for (String uri : miriamType.getUris()) {
+        if (uri.toLowerCase().startsWith("http://identifiers.org/") && !uri.endsWith("/")) {
+          httpIdentifiersOrgUriExists = true;
+        }
+        if (uri.toLowerCase().startsWith("https://identifiers.org/") && !uri.endsWith("/")) {
+          httpsIdentifiersOrgUriExists = true;
+        }
+      }
+      assertTrue("Http identifiers.org url does not exists for: " + miriamType, httpIdentifiersOrgUriExists);
+      assertTrue("Https identifiers.org url does not exists for: " + miriamType, httpsIdentifiersOrgUriExists);
+    }
+  }
+
   @Test
   public void testGetMiriamByIncompleteUri() throws Exception {
     for (String uri : miriamType.getUris()) {

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

@@ -123,4 +123,33 @@ public class MiriamTypeTest extends ModelTestFunctions {
     assertTrue(md.getResource().contains("/"));
   }
 
+  @Test
+  public void testGetMiriamByKeggCompoundIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("https://identifiers.org/kegg.compound:197020");
+    assertEquals(new MiriamData(MiriamType.KEGG_COMPOUND, "197020"), md);
+  }
+
+  @Test
+  public void testGetMiriamByEcoIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("https://identifiers.org/ECO:0000006");
+    assertEquals(new MiriamData(MiriamType.ECO, "ECO:0000006"), md);
+  }
+
+  @Test
+  public void testGetMiriamByMgiIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("https://identifiers.org/MGI:2442292");
+    assertEquals(new MiriamData(MiriamType.MGD, "MGI:2442292"), md);
+  }
+
+  @Test
+  public void testGetMiriamByPatoIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("https://identifiers.org/PATO:0001998");
+    assertEquals(new MiriamData(MiriamType.PATO, "PATO:0001998"), md);
+  }
+
+  @Test
+  public void testGetMiriamBySboIdentifiersOrgUri() throws Exception {
+    MiriamData md = MiriamType.getMiriamByUri("https://identifiers.org/SBO:0000262");
+    assertEquals(new MiriamData(MiriamType.SBO_TERM, "SBO:0000262"), md);
+  }
 }