X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FSequenceFetcherTest.java;h=c643d6baa88f457e26b3f4c4d0c9870042d74ded;hb=dd91395fac6acce3696a962e03fb932d1b8c66d5;hp=32afd5f7ab3beaa5a328e576e31fcdac3f676fc8;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 32afd5f..c643d6b 100644
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -30,10 +30,14 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 public class SequenceFetcherTest
 {
@@ -45,33 +49,57 @@ public class SequenceFetcherTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @Test(groups = "Functional")
+  public void testNoDuplicatesInFetchDbRefs()
+  {
+    Map<String, List<DbSourceProxy>> seen = new HashMap<>();
+    jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher();
+    String dupes = "";
+    // for (String src : sfetcher.getOrderedSupportedSources())
+    for (String src : sfetcher.getNonAlignmentSources())
+    {
+      List<DbSourceProxy> seenitem = seen.get(src);
+      if (seenitem != null)
+      {
+        dupes += (dupes.length() > 0 ? "," : "") + src;
+      }
+      else
+      {
+        seen.put(src, sfetcher.getSourceProxy(src));
+      }
+    }
+    if (dupes.length() > 0)
+    {
+      Assert.fail("Duplicate sources : " + dupes);
+    }
+  }
+
   /**
    * simple run method to test dbsources.
    * 
    * @param argv
+   * @j2sIgnore
    */
   public static void main(String[] argv)
   {
-    // TODO: extracted from SequenceFetcher - convert to proper unit test with
+    // TODO: extracted from SequenceFetcher - convert to network dependent
+    // functional integration test with
     // assertions
 
     String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
             + "With no arguments, all DbSources will be queried with their test Accession number.\n"
             + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
-            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
-            + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
-    boolean withDas = true;
-    if (argv != null && argv.length > 0
-            && argv[0].toLowerCase().startsWith("-nodas"))
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
+
+    if (argv != null && argv.length > 0)
     {
-      withDas = false;
       String targs[] = new String[argv.length - 1];
       System.arraycopy(argv, 1, targs, 0, targs.length);
       argv = targs;
     }
     if (argv != null && argv.length > 0)
     {
-      List<DbSourceProxy> sps = new SequenceFetcher(withDas)
+      List<DbSourceProxy> sps = new SequenceFetcher()
               .getSourceProxy(argv[0]);
 
       if (sps != null)
@@ -102,7 +130,7 @@ public class SequenceFetcherTest
       System.out.println(usage);
       return;
     }
-    ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
+    ASequenceFetcher sfetcher = new SequenceFetcher();
     String[] dbSources = sfetcher.getSupportedDb();
     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
@@ -124,7 +152,7 @@ public class SequenceFetcherTest
           String testQuery)
   {
     AlignmentI ds = null;
-    Vector<Object[]> noProds = new Vector<Object[]>();
+    Vector<Object[]> noProds = new Vector<>();
     System.out.println("Source: " + sp.getDbName() + " (" + db
             + "): retrieving test:" + sp.getTestQuery());
     {
@@ -148,23 +176,24 @@ public class SequenceFetcherTest
               System.out.println("Type: " + source);
               SequenceI[] prod = crossRef.findXrefSequences(source, dna)
                       .getSequencesArray();
-              System.out.println("Found "
-                      + ((prod == null) ? "no" : "" + prod.length)
-                      + " products");
+              System.out.println(
+                      "Found " + ((prod == null) ? "no" : "" + prod.length)
+                              + " products");
               if (prod != null)
               {
                 for (int p = 0; p < prod.length; p++)
                 {
-                  System.out.println("Prod " + p + ": "
-                          + prod[p].getDisplayId(true));
+                  System.out.println(
+                          "Prod " + p + ": " + prod[p].getDisplayId(true));
                 }
               }
             }
           }
           else
           {
-            noProds.addElement((dna ? new Object[] { al, al }
-                    : new Object[] { al }));
+            noProds.addElement(
+                    (dna ? new Object[]
+                    { al, al } : new Object[] { al }));
           }
 
         }
@@ -238,8 +267,8 @@ public class SequenceFetcherTest
           // present)
           for (int p = 0; p < prod.length; p++)
           {
-            System.out.println("Prod " + p + ": "
-                    + prod[p].getDisplayId(true));
+            System.out.println(
+                    "Prod " + p + ": " + prod[p].getDisplayId(true));
           }
         }
       }