From dcdf54b52932630bbc230a6e553db0a7482a2cb4 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 13 Dec 2018 09:27:46 +0000 Subject: [PATCH] JAL-3130 Attempting to fix 8 tests that pass on a Mac but not on linux (e.g. jv-bamboo) --- src/jalview/gui/Desktop.java | 158 +++++++++++++------------- src/jalview/io/FileLoader.java | 3 + test/jalview/ext/htsjdk/TestHtsContigDb.java | 20 ++-- test/jalview/util/PlatformTest.java | 11 +- 4 files changed, 100 insertions(+), 92 deletions(-) diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 9e8624a..874c619 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -381,83 +381,84 @@ public class Desktop extends jalview.jbgui.GDesktop try { - if (Platform.isAMac()) - { - if (desktopClass.getDeclaredMethod("setAboutHandler", - new Class[] - { AboutHandler.class }) != null) - { - - hdesktop.setAboutHandler(new AboutHandler() - { - @Override - public void handleAbout(AboutEvent e) - { - aboutMenuItem_actionPerformed(null); - } - }); - - } - - if (desktopClass.getDeclaredMethod("setPreferencesHandler", - new Class[] - { PreferencesHandler.class }) != null) - { - - hdesktop.setPreferencesHandler(new PreferencesHandler() - { - @Override - public void handlePreferences(PreferencesEvent e) - { - preferences_actionPerformed(null); - } - }); - - } - - if (desktopClass.getDeclaredMethod("setQuitHandler", - new Class[] - { QuitHandler.class }) != null) - { - - hdesktop.setQuitHandler(new QuitHandler() - { - @Override - public void handleQuitRequestWith(QuitEvent e, QuitResponse r) - { - boolean confirmQuit = jalview.bin.Cache - .getDefault(CONFIRM_KEYBOARD_QUIT, true); - int n; - if (confirmQuit) - { - n = JOptionPane.showConfirmDialog(null, - MessageManager.getString("label.quit_jalview"), - MessageManager.getString("action.quit"), - JOptionPane.OK_CANCEL_OPTION, - JOptionPane.PLAIN_MESSAGE, null); - } - else - { - n = JOptionPane.OK_OPTION; - } - if (n == JOptionPane.OK_OPTION) - { - System.out.println("Shortcut Quit confirmed by user"); - quit(); - r.performQuit(); // probably won't reach this line, but just in - // case - } - else - { - r.cancelQuit(); - System.out.println("Shortcut Quit cancelled by user"); - } - } - }); - hdesktop.setQuitStrategy(QuitStrategy.CLOSE_ALL_WINDOWS); - - } - } + if (Platform.isAMac()) + { + if (desktopClass.getDeclaredMethod("setAboutHandler", + new Class[] + { AboutHandler.class }) != null) + { + + hdesktop.setAboutHandler(new AboutHandler() + { + @Override + public void handleAbout(AboutEvent e) + { + aboutMenuItem_actionPerformed(null); + } + }); + + } + + if (desktopClass.getDeclaredMethod("setPreferencesHandler", + new Class[] + { PreferencesHandler.class }) != null) + { + + hdesktop.setPreferencesHandler(new PreferencesHandler() + { + @Override + public void handlePreferences(PreferencesEvent e) + { + preferences_actionPerformed(null); + } + }); + + } + + if (desktopClass.getDeclaredMethod("setQuitHandler", + new Class[] + { QuitHandler.class }) != null) + { + + hdesktop.setQuitHandler(new QuitHandler() + { + @Override + public void handleQuitRequestWith(QuitEvent e, QuitResponse r) + { + boolean confirmQuit = jalview.bin.Cache + .getDefault(CONFIRM_KEYBOARD_QUIT, true); + int n; + if (confirmQuit) + { + n = JOptionPane.showConfirmDialog(null, + MessageManager.getString("label.quit_jalview"), + MessageManager.getString("action.quit"), + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.PLAIN_MESSAGE, null); + } + else + { + n = JOptionPane.OK_OPTION; + } + if (n == JOptionPane.OK_OPTION) + { + System.out.println("Shortcut Quit confirmed by user"); + quit(); + r.performQuit(); // probably won't reach this line, but just + // in + // case + } + else + { + r.cancelQuit(); + System.out.println("Shortcut Quit cancelled by user"); + } + } + }); + hdesktop.setQuitStrategy(QuitStrategy.CLOSE_ALL_WINDOWS); + + } + } } catch (NoSuchMethodException e) { @@ -1816,8 +1817,7 @@ public class Desktop extends jalview.jbgui.GDesktop final String[] desc = new String[] { "Jalview Project", "Jalview Project (old)" }; JalviewFileChooser chooser = new JalviewFileChooser( - Cache.getProperty("LAST_DIRECTORY"), suffix, - desc, + Cache.getProperty("LAST_DIRECTORY"), suffix, desc, "Jalview Project"); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager.getString("label.restore_state")); diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 2a18b0b..78f646c 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -193,6 +193,9 @@ public class FileLoader implements Runnable Thread.sleep(500); } catch (Exception ex) { + System.out.println( + "Exception caught while waiting for FileLoader thread"); + ex.printStackTrace(); } } diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index 28c5cf0..ad9bf03 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -44,12 +44,12 @@ public class TestHtsContigDb @Test(groups = "Functional") public final void testGetSequenceProxy() throws Exception { - String pathname = "test/jalview/ext/htsjdk/pgmb.fasta"; + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta"; HtsContigDb db = new HtsContigDb("ADB", new File(pathname)); - + assertTrue(db.isValid()); assertTrue(db.isIndexed()); // htsjdk opens the .fai file - + SequenceI sq = db.getSequenceProxy("Deminut"); assertNotNull(sq); assertEquals(sq.getLength(), 606); @@ -60,7 +60,7 @@ public class TestHtsContigDb sq = db.getSequenceProxy("PPL_06716"); assertNotNull(sq); assertEquals(sq.getLength(), 602); - + // dict = db.getDictionary(f, truncate)) } @@ -73,7 +73,7 @@ public class TestHtsContigDb expectedExceptions = java.lang.IllegalArgumentException.class) public final void testGetSequenceProxy_indexed() { - String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai"; + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai"; new HtsContigDb("ADB", new File(pathname)); fail("Expected exception opening .fai file"); } @@ -92,16 +92,20 @@ public class TestHtsContigDb @Test(groups = "Functional") public void testCreateFastaSequenceIndex() throws IOException { - File fasta = new File("test/jalview/ext/htsjdk/pgmb.fasta"); - + File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta"); + /* * create .fai with no overwrite fails if it exists */ - try { + try + { HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false); fail("Expected exception"); } catch (IOException e) { + System.out.println( + "Caught IOException in testCreateFastaSequenceIndex"); + e.printStackTrace(); // expected } diff --git a/test/jalview/util/PlatformTest.java b/test/jalview/util/PlatformTest.java index 307f450..470e64d 100644 --- a/test/jalview/util/PlatformTest.java +++ b/test/jalview/util/PlatformTest.java @@ -26,7 +26,7 @@ import static org.testng.Assert.assertTrue; import jalview.gui.JvOptionPane; import java.awt.Button; -import java.awt.Event; +import java.awt.event.InputEvent; import java.awt.event.MouseEvent; import org.testng.annotations.BeforeClass; @@ -61,11 +61,11 @@ public class PlatformTest assertFalse(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = Event.CTRL_MASK; + mods = InputEvent.CTRL_DOWN_MASK; assertFalse(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = Event.META_MASK; + mods = InputEvent.META_DOWN_MASK; assertTrue(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); @@ -97,11 +97,12 @@ public class PlatformTest assertFalse(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = Event.CTRL_MASK; + mods = InputEvent.CTRL_DOWN_MASK; assertTrue(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = Event.CTRL_MASK | Event.SHIFT_MASK | Event.ALT_MASK; + mods = InputEvent.CTRL_DOWN_MASK | InputEvent.SHIFT_DOWN_MASK + | InputEvent.ALT_DOWN_MASK; clickCount = 2; buttonNo = 2; isPopupTrigger = true; -- 1.7.10.2