JAL-3210 Two fixed tests (previously not compiling)

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

diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java
index 94bf979..1706870 100644 (file)
--- a/test/jalview/ws/SequenceFetcherTest.java
+++ b/test/jalview/ws/SequenceFetcherTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws;
 
 import jalview.analysis.CrossRef;
@@ -5,43 +25,81 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 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
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    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)
@@ -52,8 +110,7 @@ public class SequenceFetcherTest
           try
           {
             testRetrieval(argv[0], sp,
-                    argv.length > 1 ? argv[1] : sp
-                    .getTestQuery());
+                    argv.length > 1 ? argv[1] : sp.getTestQuery());
           } catch (Exception e)
           {
             e.printStackTrace();
@@ -73,7 +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++)
     {
@@ -95,7 +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());
     {