From fd64c343e17a21eb50bcbd1a4e6bf2021a3a81b1 Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 31 May 2017 11:08:24 +0100
Subject: [PATCH] Fixed failing tests

---
 src/jalview/io/AppletFormatAdapter.java   |   17 +++++++--
 test/jalview/ext/jmol/JmolViewerTest.java |   54 +----------------------------
 test/jalview/io/FileLoaderTest.java       |   10 +++---
 3 files changed, 19 insertions(+), 62 deletions(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index c5a80e3..907ff46 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -407,15 +407,26 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public static DataSourceType checkProtocol(String file)
+  /**
+   * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+   * data
+   *
+   * @param data
+   * @return the protocol for the input data
+   */
+  public static DataSourceType checkProtocol(String data)
   {
-    DataSourceType protocol = DataSourceType.FILE;
-    String ft = file.toLowerCase().trim();
+    DataSourceType protocol = DataSourceType.PASTE;
+    String ft = data.toLowerCase().trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
+    else if (new File(data).exists())
+    {
+      protocol = DataSourceType.FILE;
+    }
     return protocol;
   }
 
diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 4a59044..792f7ad 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -33,7 +33,6 @@ import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 
-import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -117,56 +116,5 @@ public class JmolViewerTest
     }
   }
 
-  @Test(groups = { "Functional", "Network" })
-  public void testStructureLoadingViaURL()
-  {
-    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
-    String inFile = "http://www.jalview.org/builds/develop/examples/3W5V.pdb";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.URL);
-    assertTrue("Didn't read input file " + inFile, af != null);
-    for (SequenceI sq : af.getViewport().getAlignment().getSequences())
-    {
-      SequenceI dsq = sq.getDatasetSequence();
-      while (dsq.getDatasetSequence() != null)
-      {
-        dsq = dsq.getDatasetSequence();
-      }
-      if (dsq.getAllPDBEntries() != null
-              && dsq.getAllPDBEntries().size() > 0)
-      {
-        for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
-        {
-          final StructureViewer structureViewer = new StructureViewer(af
-                  .getViewport().getStructureSelectionManager());
-          structureViewer.setViewerType(ViewerType.JMOL);
-          JalviewStructureDisplayI jmolViewer = structureViewer
-                  .viewStructures(dsq.getAllPDBEntries().elementAt(q),
-                          new SequenceI[] { sq }, af.getCurrentView()
-                                  .getAlignPanel());
-          /*
-          * Wait for viewer load thread to complete
-          */
-          try
-          {
-            while (!jmolViewer.getBinding().isFinishedInit())
-            {
-              Thread.sleep(500);
-            }
-          } catch (InterruptedException e)
-          {
-          }
-          // System.out.println(">>>>>>>>>>>>>>>>> "
-          // + jmolViewer.getBinding().getPdbFile());
-          String[] expectedModelFiles = new String[] { "http://www.jalview.org/builds/develop/examples/3W5V.pdb" };
-          String[] actualModelFiles = jmolViewer.getBinding().getStructureFiles();
-          Assert.assertEqualsNoOrder(actualModelFiles, expectedModelFiles);
-          jmolViewer.closeViewer(true);
-          // todo: break here means only once through this loop?
-          break;
-        }
-        break;
-      }
-    }
-  }
+
 }
diff --git a/test/jalview/io/FileLoaderTest.java b/test/jalview/io/FileLoaderTest.java
index 0e21f6e..968901f 100644
--- a/test/jalview/io/FileLoaderTest.java
+++ b/test/jalview/io/FileLoaderTest.java
@@ -14,11 +14,9 @@ public class FileLoaderTest
     fileLoader.LoadFileWaitTillLoaded(urlFile, DataSourceType.URL,
             FileFormat.PDB);
     Assert.assertNotNull(fileLoader.file);
-    // The FileLoader's file is expected to a temporary file different from the
-    // original URL.
-    Assert.assertNotEquals(urlFile, fileLoader.file);
-    // Data source type expected to be updated from DataSourceType.URL to
-    // DataSourceType.FILE
-    Assert.assertEquals(DataSourceType.FILE, fileLoader.protocol);
+    // The FileLoader's file is expected to be same as the original URL.
+    Assert.assertEquals(urlFile, fileLoader.file);
+    // Data source type expected to be DataSourceType.URL
+    Assert.assertEquals(DataSourceType.URL, fileLoader.protocol);
   }
 }
-- 
1.7.10.2