JAL-4353 wait for files to be written fully before comparing size with older file

[jalview.git] / test / jalview / bin / CommandsTest.java

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 8dae8f3..7b42737 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.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.bin;
 
 import java.io.File;
@@ -49,7 +69,7 @@ public class CommandsTest
   }
 
   @AfterMethod(alwaysRun = true)
-  public void tearDown() 
+  public void tearDown()
   {
     try
     {
@@ -96,7 +116,8 @@ public class CommandsTest
   }
   */
 
-  @Test(groups = "Functional", dataProvider = "cmdLines")
+  @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines", singleThreaded = true)
+
   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
           int numFrames, String[] sequences)
   {
@@ -111,13 +132,13 @@ public class CommandsTest
       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
               "Overall command parse and operation is false");
 
-      Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
               "Wrong number of AlignFrames");
 
       if (sequences != null)
       {
         Set<String> openedSequenceNames = new HashSet<>();
-        AlignFrame[] afs = Desktop.getAlignFrames();
+        AlignFrame[] afs = Desktop.getDesktopAlignFrames();
         for (AlignFrame af : afs)
         {
           openedSequenceNames.addAll(
@@ -147,8 +168,8 @@ public class CommandsTest
 
   @Test(
     groups =
-    { "Functional", "testTask1" },
-    dataProvider = "structureImageOutputFiles")
+    { "Functional", "testTask3" },
+    dataProvider = "structureImageOutputFiles",    singleThreaded = true)
   public void structureImageOutputTest(String cmdLine, String[] filenames)
           throws IOException
   {
@@ -171,8 +192,16 @@ public class CommandsTest
                 + "' has no content from '" + cmdLine + "'");
         // make sure the successive output files get bigger!
         if (lastFile != null)
+        {
+          waitForLastWrite(file,25);
+          
+          if (Files.size(file.toPath()) > Files
+                  .size(lastFile.toPath()))
           Assert.assertTrue(Files.size(file.toPath()) > Files
                   .size(lastFile.toPath()));
+        }
+        // remember it for next file
+        lastFile = file;
       }
     } catch (Exception x)
     {
@@ -185,7 +214,22 @@ public class CommandsTest
     }
   }
 
-  @Test(groups = "Functional", dataProvider = "argfileOutputFiles")
+  private static long waitForLastWrite(File file, int i) throws IOException
+  {
+    long lastSize,stableSize =Files.size(file.toPath());
+    // wait around until we are sure the file has been completely written.
+    do {
+      lastSize = stableSize;
+      try {
+        Thread.sleep(i);
+      } catch (Exception x) {}
+      stableSize=Files.size(file.toPath());
+    } while (stableSize!=lastSize);
+    return stableSize;
+  }
+
+  @Test(groups = "Functional", dataProvider = "argfileOutputFiles", singleThreaded = true)
+
   public void argFilesGlobAndSubstitutionsTest(String cmdLine,
           String[] filenames) throws IOException
   {
@@ -207,9 +251,13 @@ public class CommandsTest
         Assert.assertTrue(Files.size(file.toPath()) > 0, "File '" + filename
                 + "' has no content from '" + cmdLine + "'");
         // make sure the successive output files get bigger!
-        if (lastFile != null)
+        if (lastFile != null) {
           Assert.assertTrue(Files.size(file.toPath()) > Files
                   .size(lastFile.toPath()));
+          System.out.println("this file: "+file+" +"+Files.size(file.toPath()) + " greater than " +Files.size(lastFile.toPath()));
+        }
+        // remember it for next file
+        lastFile = file;
       }
     } catch (Exception x)
     {
@@ -258,6 +306,19 @@ public class CommandsTest
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
                 testfiles + "/structureimage3.png" } },
+        { "--gui --nonews --nosplash --open examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+                       
+                new String[] {
+                               testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+                }
+        },
+        { "--headless --noquit --open ./examples/1gaq.txt --append ./examples/3W5V.pdb "+"--structure examples/1gaq.txt --seqid \"1GAQ|A\" "+"--structureimage "+testfiles+"/1gaq.png --structure examples/3W5V.pdb "+"--seqid \"3W5V|A\" --structureimage "+testfiles+"/3w5v.png --overwrite",
+               
+            new String[] {
+                       testfiles+"/1gaq.png",testfiles+"/3w5v.png"
+            }
+    }
+
         /*
                 */
         //
@@ -325,7 +386,7 @@ public class CommandsTest
 
   public static boolean lookForSequenceName(String sequenceName)
   {
-    AlignFrame[] afs = Desktop.getAlignFrames();
+    AlignFrame[] afs = Desktop.getDesktopAlignFrames();
     for (AlignFrame af : afs)
     {
       for (String name : af.getViewport().getAlignment().getSequenceNames())