X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=e7f9ff1288b2332899d670f3c61d0f24a6da93ae;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=fc23faadc41e0a505bf9708a6ae7c60ced42d357;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index fc23faa..e7f9ff1 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.
  * 
@@ -20,49 +20,163 @@
  */
 package jalview.ws;
 
-import static org.junit.Assert.*;
+import static org.testng.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.Arrays;
 import java.util.List;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class PDBSequenceFetcherTest
 {
 
-  SequenceFetcher sf;
-  @Before
-  public void setUp() throws Exception
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
-    sf = new SequenceFetcher(false);
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  @Test
-  public void testPdbPerChainRetrieve() throws Exception
+  SequenceFetcher sf;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp() throws Exception
   {
-    List<DbSourceProxy> sps = sf
-    .getSourceProxy("PDB");
-    AlignmentI response = sps.get(0).getSequenceRecords("1QIPA");
-    assertTrue(response!=null);
-    assertTrue(response.getHeight()==1);
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    // 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();
   }
-  @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");
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "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.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 class TestRetrieveObject
+  {
+    String id;
+
+    int expectedHeight;
+
+    public TestRetrieveObject(String id, int expectedHeight)
     {
-      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);
+      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");
+    StringBuilder errors = new StringBuilder();
+    for (TestRetrieveObject str : toRetrieve)
+    {
+      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);
+        // FIXME: should test that all residues extracted as sequences from
+        // chains in structure have a mapping to data in the structure
+        List<SequenceFeature> prev = null;
+        int lastp = -1;
+        for (int col = 1; col <= sq.getLength(); col++)
+        {
+          List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
+          if (sf.size() != 1)
+          {
+            errors.append(str.id + ": "
+                    + "Expected one feature at column (position): "
+                    + (col - 1) + " (" + sq.findPosition(col - 1) + ")"
+                    + ": saw " + sf.size());
+            errors.append("\n");
+            if (prev != null)
+            {
+              errors.append("Last Feature was at position " + lastp + ": "
+                      + prev.get(0).toString());
+              errors.append("\n");
+            }
+          }
+          else
+          {
+            prev = sf;
+            lastp = sq.findPosition(col - 1);
+          }
+        }
+      }
+    }
+    if (errors.length() > 0)
+    {
+      Assert.fail(errors.toString());
+    }
+  }
 }