X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=d020173c9f39e22a4af93fe3b5d99b446d611476;hb=52288466dd1e71946a06fd1e6ea15fa8e652c693;hp=fc23faadc41e0a505bf9708a6ae7c60ced42d357;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index fc23faa..d020173 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,48 +20,59 @@
  */
 package jalview.ws;
 
-import static org.junit.Assert.*;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.List;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PDBSequenceFetcherTest
 {
 
   SequenceFetcher sf;
-  @Before
+
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
+    // ensure 'add annotation from structure' is selected
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+
     sf = new SequenceFetcher(false);
   }
 
-  @Test
-  public void testPdbPerChainRetrieve() throws Exception
-  {
-    List<DbSourceProxy> sps = sf
-    .getSourceProxy("PDB");
-    AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
-    assertTrue(response!=null);
-    assertTrue(response.getHeight()==1);
-  }
-  @Test
+  /**
+   * Test that RNA structure can be added by a call to the RNAML service.
+   * 
+   * Note this test depends on http://arn-ibmc.in2p3.fr/api/compute/2d which is
+   * not always reliable.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
-    List<DbSourceProxy> sps = sf
-    .getSourceProxy("PDB");
+    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
-    assertTrue(response!=null);
-    assertTrue(response.getHeight()==1);
-    for (SequenceI sq:response.getSequences())
+    assertTrue(response != null);
+    assertTrue(response.getHeight() == 1);
+    for (SequenceI sq : response.getSequences())
     {
-      assertTrue("No annotation transfered to sequence.",sq.getAnnotation().length>0);
-      assertTrue("No PDBEntry on sequence.",sq.getPDBId().size()>0);
-      assertTrue("No RNA annotation on sequence.", sq.getRNA()!=null);
+      assertTrue("No annotation transfered to sequence.",
+              sq.getAnnotation().length > 0);
+      assertTrue("No PDBEntry on sequence.",
+              sq.getAllPDBEntries().size() > 0);
+      assertTrue(
+              "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
+              sq.getRNA() != null);
     }
   }