import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStreamReader;
+import java.io.OutputStream;
import java.io.OutputStreamWriter;
+import java.io.PrintStream;
import java.io.PrintWriter;
import java.net.MalformedURLException;
import java.net.URI;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.bin.ArgParser.Arg;
+import jalview.bin.ArgParser.BootstrapArgs;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
private Desktop desktop;
+ protected Commands cmds;
+
public static AlignFrame currentAlignFrame;
static
System.setSecurityManager(null);
}
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
// get args needed before proper ArgParser
- Map<String, String> bootstrapArgs = ArgParser.bootstrapArgs(args);
+ BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+
+ if (!Platform.isJS())
+ {
+ // are we being --quiet ?
+ if (bootstrapArgs.contains(Arg.QUIET))
+ {
+ OutputStream devNull = new OutputStream()
+ {
+ @Override
+ public void write(int b)
+ {
+ // DO NOTHING
+ }
+ };
+ System.setOut(new PrintStream(devNull));
+ // redirecting stderr not working
+ if (bootstrapArgs.getList(Arg.QUIET).size() > 1)
+ {
+ System.setErr(new PrintStream(devNull));
+ }
+ }
+ }
System.out
.println("Java version: " + System.getProperty("java.version"));
// get bootstrap properties (mainly for the logger level)
Properties bootstrapProperties = Cache
- .bootstrapProperties(bootstrapArgs.get("props"));
+ .bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
// report Jalview version
Cache.loadBuildProperties(true);
// old ArgsParser
ArgsParser aparser = new ArgsParser(args);
+ // old
boolean headless = false;
+ // new
+ boolean headlessArg = false;
try
{
- String logLevel = bootstrapArgs.containsKey("debug") ? "DEBUG" : null;
+ String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
if (logLevel == null && !(bootstrapProperties == null))
{
logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
- System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
- System.exit(0);
+ String message = "\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+ Jalview.exit(message, 0);
}
// register SIGTERM listener
}
});
- String usrPropsFile = bootstrapArgs.containsKey("props")
- ? bootstrapArgs.get("props")
+ String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
+ ? bootstrapArgs.get(Arg.PROPS)
: aparser.getValue("props");
Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
}
// new ArgParser
- ArgParser argparser = new ArgParser(args);
-
- if (argparser.isSet(Arg.HEADLESS))
- headless = argparser.getBool(Arg.HEADLESS);
- boolean commandsSuccess = Commands.processArgs(argparser, headless);
- if (commandsSuccess)
+ ArgParser argparser;
+ // --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
+ if (bootstrapArgs.contains(Arg.ARGFILE))
{
- Console.info("Successfully completed commands");
- if (headless)
- System.exit(0);
+ argparser = ArgParser
+ .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
}
else
{
- Console.warn("Error when running commands");
- if (headless)
- System.exit(1);
+ argparser = new ArgParser(args);
}
if (!Platform.isJS())
* @j2sIgnore
*/
{
- if (argparser.isSet(Arg.HEADLESS))
+ if (aparser.contains("help") || aparser.contains("h")
+ || argparser.getBool(Arg.HELP))
{
- headless = argparser.getBool(Arg.HEADLESS);
+ showUsage();
+ Jalview.exit(null, 0);
}
- if (aparser.contains("help") || aparser.contains("h"))
+ if (bootstrapArgs.contains(Arg.HEADLESS))
{
- showUsage();
- System.exit(0);
+ System.setProperty("java.awt.headless", "true");
+ // new
+ headlessArg = argparser.getBool(Arg.HEADLESS);
}
- if (headless || aparser.contains("nodisplay")
- || aparser.contains("nogui") || aparser.contains("headless"))
+ if (aparser.contains("nodisplay") || aparser.contains("nogui")
+ || aparser.contains("headless"))
{
System.setProperty("java.awt.headless", "true");
+ // old
headless = true;
}
// anything else!
NoClassDefFoundError error)
{
error.printStackTrace();
- System.out.println("\nEssential logging libraries not found."
- + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
- System.exit(0);
+ String message = "\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
+ Jalview.exit(message, 0);
}
desktop = null;
- setLookAndFeel();
+ if (!(headless || headlessArg))
+ setLookAndFeel();
/*
* configure 'full' SO model if preferences say to, else use the default (full SO)
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
- if (!headless)
+ if (!(headless || headlessArg))
{
Desktop.nosplash = aparser.contains("nosplash");
desktop = new Desktop();
}
}
}
+ // Run Commands from cli
+ cmds = new Commands(argparser, headlessArg);
+ boolean commandsSuccess = cmds.argsWereParsed();
+ if (commandsSuccess)
+ {
+ if (headlessArg)
+ {
+ Jalview.exit("Successfully completed commands in headless mode", 0);
+ }
+ Console.info("Successfully completed commands");
+ }
+ else
+ {
+ if (headlessArg)
+ {
+ Jalview.exit("Error when running Commands in headless mode", 1);
+ }
+ Console.warn("Error when running commands");
+ }
// Check if JVM and compile version might cause problems and log if it
// might.
+ LaunchUtils.getJavaCompileVersion() + ".");
}
- // Move any new getdown-launcher-new.jar into place over old
- // getdown-launcher.jar
- String appdirString = System.getProperty("getdownappdir");
- if (appdirString != null && appdirString.length() > 0)
- {
- final File appdir = new File(appdirString);
- new Thread()
- {
- @Override
- public void run()
- {
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
- }
- }.start();
- }
-
String file = null, data = null;
FileFormatI format = null;
if (file == null && desktop == null)
{
- System.out.println("No files to open!");
- System.exit(1);
+ Jalview.exit("No files to open!", 1);
}
long progress = -1;
{
if (!(new File(file)).exists())
{
- System.out.println("Can't find " + file);
if (headless)
{
- System.exit(1);
+ Jalview.exit(
+ "Can't find file '" + file + "' in headless mode", 1);
}
+ Console.warn("Can't find file'" + file + "'");
}
}
}
if (cs != null)
{
System.out.println(
- "CMD [-color " + data + "] executed successfully!");
+ "CMD [-colour " + data + "] executed successfully!");
}
af.changeColour(cs);
}
// ////////////////////
if (!Platform.isJS() && !headless && file == null
- && Cache.getDefault("SHOW_STARTUP_FILE", true))
+ && Cache.getDefault("SHOW_STARTUP_FILE", true)
+ && !cmds.commandArgsProvided())
+ // don't open the startup file if command line args have been processed
+ // (&& !Commands.commandArgsProvided())
/**
* Java only
*
public void quit()
{
// System.exit will run the shutdownHook first
- System.exit(0);
+ Jalview.exit("Quitting now. Bye!", 0);
}
public static AlignFrame getCurrentAlignFrame()
{
Jalview.currentAlignFrame = currentAlignFrame;
}
+
+ protected Commands getCommands()
+ {
+ return cmds;
+ }
+
+ public static void exit(String message, int exitcode)
+ {
+ System.err.println("####### EXITING HERE!");
+ Console.debug("Using Jalview.exit");
+ if (message != null)
+ if (exitcode == 0)
+ Console.info(message);
+ else
+ Console.error(message);
+ if (exitcode > -1)
+ System.exit(exitcode);
+ }
}
git://source.jalview.org / jalview.git / blobdiff