From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 18 Oct 2017 14:14:46 +0000 (+0100)
Subject: JAL-2780 JAL-2781 refactored PDB fetch network tests to add in 4IM2 - this test now... 
X-Git-Tag: Release_2_10_4~68^2~45
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a47d3497273497061faecb889117682d09339675;p=jalview.git

JAL-2780 JAL-2781 refactored PDB fetch network tests to add in 4IM2 - this test now fails due to JAL-2780 and JAL-2781. Also note JAL-2224 - the test relies on SequenceI.getEnd()-SequenceI.getStart()+1 == length, which fails for these two test cases.
---

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 95863e7..0572c85 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
@@ -30,6 +31,7 @@ import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -106,23 +108,45 @@ public class PDBSequenceFetcherTest
     testRetrieveProteinSeqFromPDB();
   }
 
+  private class TestRetrieveObject
+  {
+    String id;
+
+    int expectedHeight;
+
+    public TestRetrieveObject(String id, int expectedHeight)
+    {
+      super();
+      this.id = id;
+      this.expectedHeight = expectedHeight;
+    }
+
+  }
+
+  private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+          new TestRetrieveObject("1QIP", 4),
+          new TestRetrieveObject("4IM2", 1));
+
   private void testRetrieveProteinSeqFromPDB() throws Exception
   {
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
-    AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
-    assertTrue(response != null);
-    assertTrue(response.getHeight() == 4);
-    for (SequenceI sq : response.getSequences())
+    for (TestRetrieveObject str : toRetrieve)
     {
-      assertTrue("No annotation transfered to sequence.",
-              sq.getAnnotation().length > 0);
-      assertTrue("No PDBEntry on sequence.",
-              sq.getAllPDBEntries().size() > 0);
-      org.testng.Assert
-              .assertEquals(sq.getEnd() - sq.getStart() + 1,
-                      sq.getLength(),
-                      "Sequence start/end doesn't match number of residues in sequence");
+      AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+      assertTrue("No aligment for " + str.id, response != null);
+      assertEquals(response.getHeight(), str.expectedHeight,
+              "Number of chains for " + str.id);
+      for (SequenceI sq : response.getSequences())
+      {
+        assertTrue("No annotation transfered to sequence " + sq.getName(),
+                sq.getAnnotation().length > 0);
+        assertTrue("No PDBEntry on sequence " + sq.getName(),
+                sq.getAllPDBEntries().size() > 0);
+        org.testng.Assert.assertEquals(sq.getEnd() - sq.getStart() + 1,
+                sq.getLength(),
+                "Sequence start/end doesn't match number of residues in sequence for "
+                        + sq.getName());
+      }
     }
   }
-
 }