X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=e343b0fc4cdf3f0713badb2b1c8e6d283752f909;hb=ccc53e88e3260886f5d3bdacc619c0f374be9b8f;hp=810d835cc4982039dd4fb9e623c7fee1b59b0a25;hpb=bbbc584f24167856ceb7cb298be72a62647feca8;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 810d835..e343b0f 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -73,9 +73,12 @@ import jalview.bin.argparser.Arg.Opt; import jalview.bin.argparser.Arg.Type; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.BootstrapArgs; +import jalview.bin.groovy.JalviewObject; +import jalview.bin.groovy.JalviewObjectI; import jalview.ext.so.SequenceOntology; import jalview.gui.AlignFrame; import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; import jalview.gui.PromptUserConfig; import jalview.gui.QuitHandler; import jalview.gui.QuitHandler.QResponse; @@ -117,7 +120,7 @@ import jalview.ws.jws2.Jws2Discoverer; * @author $author$ * @version $Revision$ */ -public class Jalview +public class Jalview implements JalviewObjectI { static { @@ -137,11 +140,11 @@ public class Jalview protected Commands cmds; - public static AlignFrame currentAlignFrame; + public AlignFrame currentAlignFrame = null; - public ArgParser argparser = null; + private ArgParser argparser = null; - public BootstrapArgs bootstrapArgs = null; + private BootstrapArgs bootstrapArgs = null; private boolean QUIET = false; @@ -426,7 +429,7 @@ public class Jalview // stop now if only after --version if (bootstrapArgs.contains(Arg.VERSION)) { - Jalview.exit(null, 0); + Jalview.exit(null, ExitCode.OK); } // old ArgsParser @@ -446,7 +449,7 @@ public class Jalview } else if (bootstrapArgs.contains(Arg.DEBUG)) { - logLevel = "DEBUG"; + logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO"; } if (logLevel == null && !(bootstrapProperties == null)) { @@ -458,7 +461,7 @@ public class Jalview error.printStackTrace(); String message = "\nEssential logging libraries not found." + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"; - Jalview.exit(message, 0); + Jalview.exit(message, ExitCode.OK); } // register SIGTERM listener @@ -545,7 +548,7 @@ public class Jalview .getList(Arg.HELP); Console.outPrintln(Arg.usage(helpArgs.stream().map(e -> e.getKey()) .collect(Collectors.toList()))); - Jalview.exit(null, 0); + Jalview.exit(null, ExitCode.OK); } if (aparser.contains("help") || aparser.contains("h")) { @@ -554,7 +557,7 @@ public class Jalview showUsage(); */ Console.outPrintln(Arg.usage()); - Jalview.exit(null, 0); + Jalview.exit(null, ExitCode.OK); } // new CLI @@ -641,14 +644,12 @@ public class Jalview try { Console.initLogger(); - } catch ( - - NoClassDefFoundError error) + } catch (NoClassDefFoundError error) { error.printStackTrace(); String message = "\nEssential logging libraries not found." + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"; - Jalview.exit(message, 0); + Jalview.exit(message, ExitCode.NO_LOGGING); } desktop = null; @@ -673,6 +674,8 @@ public class Jalview desktop = new Desktop(); desktop.setInBatchMode(true); // indicate we are starting up + mixedCliWarning(); + try { JalviewTaskbar.setTaskbar(this); @@ -809,8 +812,33 @@ public class Jalview } } } + else + { + + if (getArgParser().isMixedStyle()) + { + String warning = MessageManager.formatMessage( + "warning.using_mixed_command_line_arguments", + getArgParser().getMixedExamples()); + Console.warn(warning); + Jalview.exit( + "Exiting due to mixed old and new command line arguments", + ExitCode.INVALID_ARGUMENT); + } + if (getArgParser().isOldStyle()) + { + String warning = MessageManager + .getString("warning.using_old_command_line_arguments") + .replace("\n", " ") + + "https://www.jalview.org/help/html/features/commandline.html"; + Console.warn(warning); + } + + } + // Run Commands from cli cmds = new Commands(argparser, headlessArg); + cmds.processArgs(); boolean commandsSuccess = cmds.argsWereParsed(); if (commandsSuccess) @@ -826,7 +854,7 @@ public class Jalview else { Jalview.exit("Successfully completed commands in headless mode", - 0); + ExitCode.OK); } } Console.info("Successfully completed commands"); @@ -835,7 +863,8 @@ public class Jalview { if (headlessArg) { - Jalview.exit("Error when running Commands in headless mode", 1); + Jalview.exit("Error when running Commands in headless mode", + ExitCode.ERROR_RUNNING_COMMANDS); } Console.warn("Error when running commands"); } @@ -866,7 +895,7 @@ public class Jalview if (file == null && desktop == null && !commandsSuccess) { - Jalview.exit("No files to open!", 1); + Jalview.exit("No files to open!", ExitCode.NO_FILES); } long progress = -1; @@ -896,7 +925,8 @@ public class Jalview if (headless) { Jalview.exit( - "Can't find file '" + file + "' in headless mode", 1); + "Can't find file '" + file + "' in headless mode", + ExitCode.FILE_NOT_FOUND); } Console.warn("Can't find file'" + file + "'"); } @@ -1220,6 +1250,8 @@ public class Jalview } desktop.setInBatchMode(false); } + + cliWarning(); } private static void setLookAndFeel() @@ -1600,9 +1632,8 @@ public class Jalview */ PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop, "USAGESTATS", - MessageManager.getString("prompt.plausible_analytics_title"), - MessageManager.getString("prompt.plausible_analytics"), - new Runnable() + MessageManager.getString("prompt.analytics_title"), + MessageManager.getString("prompt.analytics"), new Runnable() { @Override public void run() @@ -1720,12 +1751,11 @@ public class Jalview } try { + JalviewObjectI j = new JalviewObject(this); Map vbinding = new HashMap<>(); - vbinding.put("Jalview", this); - if (af != null) - { - vbinding.put("currentAlFrame", af); - } + vbinding.put(JalviewObjectI.jalviewObjectName, j); + vbinding.put(JalviewObjectI.currentAlFrameName, + af != null ? af : getCurrentAlignFrame()); Binding gbinding = new Binding(vbinding); GroovyScriptEngine gse = new GroovyScriptEngine(new URL[] { sfile }); gse.run(sfile.toString(), gbinding); @@ -1741,7 +1771,6 @@ public class Jalview .errPrintln("Exception Whilst trying to execute file " + sfile + " as a groovy script."); e.printStackTrace(System.err); - } } @@ -1755,39 +1784,42 @@ public class Jalview return false; } + @Override public AlignFrame[] getAlignFrames() { return desktop == null ? new AlignFrame[] { getCurrentAlignFrame() } - : Desktop.getAlignFrames(); - + : Desktop.getDesktopAlignFrames(); } /** * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit */ + @Override public void quit() { // System.exit will run the shutdownHook first - Jalview.exit("Quitting now. Bye!", 0); + Jalview.exit("Quitting now. Bye!", ExitCode.OK); } - public static AlignFrame getCurrentAlignFrame() + @Override + public AlignFrame getCurrentAlignFrame() { - return Jalview.currentAlignFrame; + return currentAlignFrame; } - public static void setCurrentAlignFrame(AlignFrame currentAlignFrame) + public void setCurrentAlignFrame(AlignFrame af) { - Jalview.currentAlignFrame = currentAlignFrame; + this.currentAlignFrame = af; } - protected Commands getCommands() + public Commands getCommands() { return cmds; } - public static void exit(String message, int exitcode) + public static void exit(String message, ExitCode ec) { + int exitcode = ec == ExitCode.OK ? 0 : ec.ordinal() + 1; if (Console.log == null) { // Don't start the logger just to exit! @@ -1824,14 +1856,35 @@ public class Jalview } } + public enum ExitCode + { + // only add new ones to the end of the list (to preserve ordinal values) + OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT, + INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS, + ERROR_RUNNING_COMMANDS, NO_LOGGING, GROOVY_ERROR; + } + /****************************** * * TEST OUTPUT METHODS * + * these operate only when Arg.TESTOUTPUT has been passed, and variously check + * if an expected value / arg was set and report it to the test framework. + * ******************************/ /** - * method for reporting string values parsed/processed during tests + * report string values parsed/processed during tests When the Bootstrap + * argument Arg.TESTOUTPUT is present - reports on debug if given s1 is not + * null and not equals s2, warns if given argument is not set, and calls + * testoutput(true,a,s1,s2) to report processing progress. * + * @param ap + * - ArgParser handling parsing + * @param a + * - Arg currently being processed + * @param s1 + * - expected + * @param s2 */ protected static void testoutput(ArgParser ap, Arg a, String s1, String s2) @@ -1856,7 +1909,9 @@ public class Jalview } /** - * method for reporting string values parsed/processed during tests + * report values passed via bootstrap arguments + * + * TODO: significant code duplication with testouput(Argparser...) - move it */ protected static void testoutput(BootstrapArgs bsa, Arg a, String s1, @@ -1884,7 +1939,8 @@ public class Jalview } /** - * report value set for string values parsed/processed during tests + * conditionally (on @param yes) report that expected value s1 was set during + * CommandsTest tests */ private static void testoutput(boolean yes, Arg a, String s1, String s2) { @@ -1951,4 +2007,88 @@ public class Jalview } Console.outPrintln("[TESTOUTPUT] arg " + message); } + + public ArgParser getArgParser() + { + return argparser; + } + + public BootstrapArgs getBootstrapArgs() + { + return bootstrapArgs; + } + + public static boolean isBatchMode() + { + return getInstance() != null && (getInstance().desktop == null + || getInstance().desktop.isInBatchMode()); + } + + /** + * Warning about old or mixed command line arguments + */ + private void mixedCliWarning() + { + Jalview j = Jalview.getInstance(); + boolean mixedStyle = j.getArgParser() != null + && j.getArgParser().isMixedStyle(); + String title = MessageManager.getString("label.command_line_arguments"); + if (mixedStyle) + { + String warning = MessageManager.formatMessage( + "warning.using_mixed_command_line_arguments", + j.getArgParser().getMixedExamples()); + String quit = MessageManager.getString("action.quit"); + + Desktop.instance.nonBlockingDialog(title, warning, null, quit, + JvOptionPane.WARNING_MESSAGE, false, false, true, 30000); + + Jalview.exit( + "Exiting due to mixed old and new command line arguments.", + ExitCode.MIXED_CLI_ARGUMENTS); + } + } + + private void cliWarning() + { + Jalview j = Jalview.getInstance(); + Commands c = j.getCommands(); + boolean oldStyle = j.getArgParser() != null + && j.getArgParser().isOldStyle(); + String title = MessageManager.getString("label.command_line_arguments"); + if (oldStyle) + { + String warning = MessageManager + .getString("warning.using_old_command_line_arguments"); + String url = "https://www.jalview.org/help/html/features/commandline.html"; + if (Desktop.instance != null) + { + String cont = MessageManager.getString("label.continue"); + + Desktop.instance.nonBlockingDialog(title, warning, url, cont, + JvOptionPane.WARNING_MESSAGE, false, true, true, 30000); + } + } + if (j.getCommands() != null && j.getCommands().getErrors().size() > 0) + { + if (Desktop.instance != null) + { + String message = MessageManager + .getString("warning.the_following_errors"); + String ok = MessageManager.getString("action.ok"); + int shortest = 60; + List errors = j.getCommands().getErrors(); + for (int i = 0; i < errors.size(); i++) + { + shortest = Math.min(shortest, errors.get(i).length()); + } + Desktop.instance.nonBlockingDialog( + Math.max(message.length(), Math.min(60, shortest)), + Math.min(errors.size(), 20), title, message, + j.getCommands().errorsToString(), ok, + JvOptionPane.WARNING_MESSAGE, true, false, true, -1); + } + } + } + }