JAL-1805 test envirionment separation

[jalview.git] / test / jalview / ws / seqfetcher / DbRefFetcherTest.java

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 07167bd..abaa7ec 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.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.
  * 
@@ -20,19 +20,23 @@
  */
 package jalview.ws.seqfetcher;
 
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
-import jalview.ws.DBRefFetcher;
+import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
@@ -47,6 +51,7 @@ public class DbRefFetcherTest
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
@@ -57,7 +62,7 @@ public class DbRefFetcherTest
   {
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testStandardProtDbs()
   {
     String[] defdb = DBRefSource.PROTEINDBS;
@@ -94,4 +99,45 @@ public class DbRefFetcherTest
             uniprot != null && i < 2);
   }
 
+  @Test(groups =
+  { "External" })
+  public void testEmblUniprotProductRecovery() throws Exception
+  {
+    String retrievalId = "CAA23748"; // "V00488";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  @Test(groups =
+  { "External" })
+  public void testEmblCDSUniprotProductRecovery() throws Exception
+  {
+    String retrievalId = "AAH29712";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+            DBRefSource.EMBLCDS).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  private void verifyProteinNucleotideXref(String retrievalId,
+          DbSourceProxy embl) throws Exception
+  {
+    AlignmentI alsq = embl.getSequenceRecords(retrievalId);
+    assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
+    assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
+    DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
+    assertNotNull(dr);
+    assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+    assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+            .getMap().getMappedWidth(), 1);
+    assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+            .getMap().getWidth(), 3);
+    AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
+    assertNotNull(
+            "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
+            sprods);
+    
+    
+  }
 }