JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / ws / PDBSequenceFetcherTest.java

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 2963ef2..4b9437a 100644 (file)
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -25,6 +25,8 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.List;
@@ -37,9 +39,10 @@ public class PDBSequenceFetcherTest
 
   SequenceFetcher sf;
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // ensure 'add annotation from structure' is selected
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
@@ -49,10 +52,18 @@ public class PDBSequenceFetcherTest
     sf = new SequenceFetcher(false);
   }
 
-  @Test(groups =
-  { "Network" }, enabled = true)
+  /**
+   * 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
   {
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
     assertTrue(response != null);
@@ -61,8 +72,47 @@ public class PDBSequenceFetcherTest
     {
       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 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);
+    }
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testPdbSeqRetrieve() throws Exception
+  {
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testmmCifSeqRetrieve() throws Exception
+  {
+    StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  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())
+    {
+      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");
     }
   }