From e1348f9e5966f70d5d96ed907f9a93794529b309 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 12 Jan 2022 12:32:06 +0000
Subject: [PATCH] JAL-3703 Test that fails in Windows only, and only when the
 file handle isn't relinquished

---
 test/jalview/io/BackupFilesTest.java            |    8 +-
 test/jalview/io/WindowsFileLoadAndSaveTest.java |   93 +++++++++++++++++++++++
 2 files changed, 100 insertions(+), 1 deletion(-)
 create mode 100644 test/jalview/io/WindowsFileLoadAndSaveTest.java

diff --git a/test/jalview/io/BackupFilesTest.java b/test/jalview/io/BackupFilesTest.java
index 1386bfe..d9f28c5 100644
--- a/test/jalview/io/BackupFilesTest.java
+++ b/test/jalview/io/BackupFilesTest.java
@@ -278,7 +278,13 @@ public class BackupFilesTest
   @AfterClass(alwaysRun = true)
   private void cleanupTmpFiles()
   {
-    File newfile = new File(newFile);
+    cleanupTmpFiles(newFile, suffix, digits);
+  }
+
+  protected static void cleanupTmpFiles(String file, String mysuffix,
+          int mydigits)
+  {
+    File newfile = new File(file);
     if (newfile.exists())
     {
       newfile.delete();
diff --git a/test/jalview/io/WindowsFileLoadAndSaveTest.java b/test/jalview/io/WindowsFileLoadAndSaveTest.java
new file mode 100644
index 0000000..2dd27b4
--- /dev/null
+++ b/test/jalview/io/WindowsFileLoadAndSaveTest.java
@@ -0,0 +1,93 @@
+/*
+ * 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.io;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.datamodel.AlignmentI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+
+/**
+ * WindowsFileSaveTest simply opens an alignment file and then tries to save it.
+ * This failed in Windows from 2.11.0 to 2.11.1.6 due to a combination of the
+ * opening file handle being left open ad infinitum, causing the BackupFiles
+ * operation of moving the saved (temp) file onto the original filename to fail,
+ * but only in Windows. See: https://issues.jalview.org/browse/JAL-3628
+ * https://issues.jalview.org/browse/JAL-3703
+ * https://issues.jalview.org/browse/JAL-3935 These issues are really all fixed
+ * by JAL-3703 This test is to ensure it doesn't start again, but note that this
+ * test will only fail in Windows.
+ */
+public class WindowsFileLoadAndSaveTest
+{
+
+  private final static String fileName = "examples" + File.separator
+          + "uniref50.fa";
+
+  private final static String testFileName = fileName + "-TEST";
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  /**
+   * Test saving and re-reading in a specified format
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void loadAndSaveAlignment() throws IOException
+  {
+    File file = new File(fileName);
+    File testFile = new File(testFileName);
+    Files.copy(file.toPath(), testFile.toPath(),
+            StandardCopyOption.REPLACE_EXISTING);
+    FormatAdapter fa = new FormatAdapter();
+    AlignmentI a = fa.readFile(testFile, DataSourceType.FILE,
+            FileFormat.Fasta);
+
+    AlignFrame af = new AlignFrame(a, 500, 500);
+    af.saveAlignment(testFileName, FileFormat.Fasta);
+
+    Assert.assertTrue(af.isSaveAlignmentSuccessful());
+  }
+
+  @AfterClass(alwaysRun = true)
+  private void cleanupTmpFiles()
+  {
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    BackupFilesTest.cleanupTmpFiles(testFileName, bfpe.suffix, bfpe.digits);
+  }
+
+}
-- 
1.7.10.2