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;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.ChannelProperties;
import jalview.util.HttpUtils;
+import jalview.util.IdUtils;
+import jalview.util.IdUtils.IdType;
import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
* @author $author$
* @version $Revision$
*/
-public class Jalview
+public class Jalview implements JalviewObjectI
{
static
{
protected Commands cmds;
- public static AlignFrame currentAlignFrame;
+ public AlignFrame currentAlignFrame = null;
private ArgParser argparser = null;
public void addFetcher(final AlignFrame af,
final Vector<String> dasSources)
{
- final long id = System.currentTimeMillis();
+ final long id = IdUtils.newId(IdType.PROGRESS);
queued++;
final FeatureFetcher us = this;
new Thread(new Runnable()
// stop now if only after --version
if (bootstrapArgs.contains(Arg.VERSION))
{
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
// old ArgsParser
}
else if (bootstrapArgs.contains(Arg.DEBUG))
{
- logLevel = "DEBUG";
+ logLevel = bootstrapArgs.getBoolean(Arg.DEBUG) ? "DEBUG" : "INFO";
}
if (logLevel == null && !(bootstrapProperties == null))
{
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
.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"))
{
showUsage();
*/
Console.outPrintln(Arg.usage());
- Jalview.exit(null, 0);
+ Jalview.exit(null, ExitCode.OK);
}
// new CLI
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;
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
+ mixedCliWarning();
+
try
{
JalviewTaskbar.setTaskbar(this);
}
}
}
- // Run Commands from cli
- cmds = new Commands(argparser, headlessArg);
- cmds.processArgs();
- boolean commandsSuccess = cmds.argsWereParsed();
+ else
+ {
- if (commandsSuccess)
+ 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
+ boolean commandsSuccess = false;
+ if (!(argparser.isMixedStyle() || argparser.isOldStyle()))
{
- if (headlessArg)
+ cmds = new Commands(argparser, headlessArg);
+ cmds.processArgs();
+ commandsSuccess = cmds.argsWereParsed();
+
+ if (commandsSuccess)
{
- if (argparser.getBoolean(Arg.NOQUIT))
- {
- Console.warn(
- "Completed " + Arg.HEADLESS.getName() + " commands, but "
- + Arg.NOQUIT + " is set so not quitting!");
- }
- else
+ if (headlessArg)
{
- Jalview.exit("Successfully completed commands in headless mode",
- 0);
+ if (argparser.getBoolean(Arg.NOQUIT))
+ {
+ Console.warn("Completed " + Arg.HEADLESS.getName()
+ + " commands, but " + Arg.NOQUIT
+ + " is set so not quitting!");
+ }
+ else
+ {
+ Jalview.exit("Successfully completed commands in headless mode",
+ ExitCode.OK);
+ }
}
+ Console.info("Successfully completed commands");
}
- Console.info("Successfully completed commands");
- }
- else
- {
- if (headlessArg)
+ else
{
- Jalview.exit("Error when running Commands in headless mode", 1);
+ if (headlessArg)
+ {
+ Jalview.exit("Error when running Commands in headless mode",
+ ExitCode.ERROR_RUNNING_COMMANDS);
+ }
+ Console.warn("Error when running commands");
}
- Console.warn("Error when running commands");
}
// Check if JVM and compile version might cause problems and log if it
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;
desktop.setProgressBar(
MessageManager
.getString("status.processing_commandline_args"),
- progress = System.currentTimeMillis());
+ progress = IdUtils.newId(IdType.PROGRESS));
}
Console.outPrintln("CMD [-open " + file + "] executed successfully!");
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 + "'");
}
}
desktop.setInBatchMode(false);
}
+
+ cliWarning();
}
private static void setLookAndFeel()
PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
"USAGESTATS",
MessageManager.getString("prompt.analytics_title"),
- MessageManager.getString("prompt.analytics"),
- new Runnable()
+ MessageManager.getString("prompt.analytics"), new Runnable()
{
@Override
public void run()
}
try
{
+ JalviewObjectI j = new JalviewObject(this);
Map<String, java.lang.Object> 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);
.errPrintln("Exception Whilst trying to execute file " + sfile
+ " as a groovy script.");
e.printStackTrace(System.err);
-
}
}
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;
}
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!
}
}
+ 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
* @param a
* - Arg currently being processed
* @param s1
- * - expected
+ * - expected
* @param s2
*/
protected static void testoutput(ArgParser ap, Arg a, String s1,
}
/**
- * conditionally (on @param yes) report that expected value s1 was set during CommandsTest 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)
{
public static boolean isBatchMode()
{
- return getInstance()!=null && (getInstance().desktop == null || getInstance().desktop.isInBatchMode());
+ 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 = "<a href=\"https://www.jalview.org/help/html/features/commandline.html\">https://www.jalview.org/help/html/features/commandline.html</a>";
+ 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<String> 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);
+ }
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff