import java.security.PermissionCollection;
import java.security.Permissions;
import java.security.Policy;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.Arg.Opt;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.BootstrapArgs;
import jalview.ext.so.SequenceOntology;
public static AlignFrame currentAlignFrame;
+ public ArgParser argparser = null;
+
+ public BootstrapArgs bootstrapArgs = null;
+
+ private boolean QUIET = false;
+
+ public static boolean quiet()
+ {
+ return Jalview.getInstance() != null && Jalview.getInstance().QUIET;
+ }
+
static
{
if (!Platform.isJS())
*/
void doMain(String[] args)
{
-
if (!Platform.isJS())
{
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();
- }
+ if (args == null)
+ args = new String[] {};
// get args needed before proper ArgParser
- BootstrapArgs bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+ bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
if (!Platform.isJS())
{
// are we being --quiet ?
if (bootstrapArgs.contains(Arg.QUIET))
{
+ QUIET = true;
OutputStream devNull = new OutputStream()
{
+
@Override
public void write(int b)
{
System.setErr(new PrintStream(devNull));
}
}
- }
- System.out
- .println("Java version: " + System.getProperty("java.version"));
- System.out.println("Java Home: " + System.getProperty("java.home"));
- System.out.println(System.getProperty("os.arch") + " "
- + System.getProperty("os.name") + " "
- + System.getProperty("os.version"));
-
- String val = System.getProperty("sys.install4jVersion");
- if (val != null)
- {
- System.out.println("Install4j version: " + val);
+ if (bootstrapArgs.contains(Arg.HELP)
+ || bootstrapArgs.contains(Arg.VERSION))
+ {
+ QUIET = true;
+ }
}
- val = System.getProperty("installer_template_version");
- if (val != 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)
{
- System.out.println("Install4j template version: " + val);
+ 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();
}
- val = System.getProperty("launcher_version");
- if (val != null)
+
+ if (!quiet() || bootstrapArgs.contains(Arg.VERSION))
{
- System.out.println("Launcher version: " + val);
+ System.out.println(
+ "Java version: " + System.getProperty("java.version"));
+ System.out.println("Java home: " + System.getProperty("java.home"));
+ System.out.println("Java arch: " + System.getProperty("os.arch") + " "
+ + System.getProperty("os.name") + " "
+ + System.getProperty("os.version"));
+
+ String val = System.getProperty("sys.install4jVersion");
+ if (val != null)
+ {
+ System.out.println("Install4j version: " + val);
+ }
+ val = System.getProperty("installer_template_version");
+ if (val != null)
+ {
+ System.out.println("Install4j template version: " + val);
+ }
+ val = System.getProperty("launcher_version");
+ if (val != null)
+ {
+ System.out.println("Launcher version: " + val);
+ }
}
if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
.bootstrapProperties(bootstrapArgs.get(Arg.PROPS));
// report Jalview version
- Cache.loadBuildProperties(true);
+ Cache.loadBuildProperties(
+ !quiet() || bootstrapArgs.contains(Arg.VERSION));
+
+ // stop now if only after --version
+ if (bootstrapArgs.contains(Arg.VERSION))
+ {
+ Jalview.exit(null, 0);
+ }
// old ArgsParser
ArgsParser aparser = new ArgsParser(args);
try
{
- String logLevel = bootstrapArgs.contains(Arg.DEBUG) ? "DEBUG" : null;
+ String logLevel = null;
+ if (bootstrapArgs.contains(Arg.TRACE))
+ {
+ logLevel = "TRACE";
+ }
+ else if (bootstrapArgs.contains(Arg.DEBUG))
+ {
+ logLevel = "DEBUG";
+ }
if (logLevel == null && !(bootstrapProperties == null))
{
logLevel = bootstrapProperties.getProperty(Cache.JALVIEWLOGLEVEL);
String usrPropsFile = bootstrapArgs.contains(Arg.PROPS)
? bootstrapArgs.get(Arg.PROPS)
: aparser.getValue("props");
+ // if usrPropsFile == null, loadProperties will use the Channel
+ // preferences.file
+ Cache.loadProperties(usrPropsFile);
if (usrPropsFile != null)
{
- Cache.loadProperties(usrPropsFile);
System.out.println(
"CMD [-props " + usrPropsFile + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.PROPS,
+ "test/jalview/bin/testProps.jvprops", usrPropsFile);
}
- // new ArgParser
- ArgParser argparser;
// --argfile=... -- OVERRIDES ALL NON-BOOTSTRAP ARGS
if (bootstrapArgs.contains(Arg.ARGFILE))
{
- argparser = ArgParser
- .parseArgFiles(bootstrapArgs.getList(Arg.ARGFILE));
+ argparser = ArgParser.parseArgFiles(
+ bootstrapArgs.getList(Arg.ARGFILE),
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
}
else
{
- argparser = new ArgParser(args);
+ argparser = new ArgParser(args,
+ bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+ bootstrapArgs);
}
if (!Platform.isJS())
* @j2sIgnore
*/
{
- if (aparser.contains("help") || aparser.contains("h")
- || argparser.getBool(Arg.HELP))
+ if (bootstrapArgs.contains(Arg.HELP))
{
+ System.out.println(Arg.usage());
+ Jalview.exit(null, 0);
+ }
+ if (aparser.contains("help") || aparser.contains("h"))
+ {
+ /*
+ * Now using new usage statement.
showUsage();
+ */
+ System.out.println(Arg.usage());
Jalview.exit(null, 0);
}
{
System.setProperty("java.awt.headless", "true");
// new
- headlessArg = argparser.getBool(Arg.HEADLESS);
+ headlessArg = bootstrapArgs.getBoolean(Arg.HEADLESS);
}
if (aparser.contains("nodisplay") || aparser.contains("nogui")
|| aparser.contains("headless"))
// allow https handshakes to download intermediate certs if necessary
System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
- final String jabawsUrl = aparser.getValue("jabaws");
+ String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+ if (jabawsUrl == null)
+ jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
try
Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
System.out.println(
"CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+ testoutput(bootstrapArgs, Arg.JABAWS,
+ "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
} catch (MalformedURLException e)
{
System.err.println(
}
}
- String defs = aparser.getValue("setprop");
- while (defs != null)
+ List<String> setprops = new ArrayList<>();
+ if (bootstrapArgs.contains(Arg.SETPROP))
{
- int p = defs.indexOf('=');
+ setprops = bootstrapArgs.getList(Arg.SETPROP);
+ }
+ else
+ {
+ String sp = aparser.getValue("setprop");
+ while (sp != null)
+ {
+ setprops.add(sp);
+ sp = aparser.getValue("setprop");
+ }
+ }
+ for (String setprop : setprops)
+ {
+ int p = setprop.indexOf('=');
if (p == -1)
{
- System.err.println("Ignoring invalid setprop argument : " + defs);
+ System.err
+ .println("Ignoring invalid setprop argument : " + setprop);
}
else
{
- System.out.println("Executing setprop argument: " + defs);
+ System.out.println("Executing setprop argument: " + setprop);
if (Platform.isJS())
{
- Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
+ Cache.setProperty(setprop.substring(0, p),
+ setprop.substring(p + 1));
}
// DISABLED FOR SECURITY REASONS
// TODO: add a property to allow properties to be overriden by cli args
- // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
+ // Cache.setProperty(setprop.substring(0,p), setprop.substring(p+1));
}
- defs = aparser.getValue("setprop");
}
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
if (!(headless || headlessArg))
{
- Desktop.nosplash = aparser.contains("nosplash");
+ Desktop.nosplash = "false".equals(bootstrapArgs.get(Arg.SPLASH))
+ || aparser.contains("nosplash")
+ || Cache.getDefault("SPLASH", "true").equals("false");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
}
}
- if (!aparser.contains("nowebservicediscovery"))
+ boolean webservicediscovery = bootstrapArgs
+ .getBoolean(Arg.WEBSERVICEDISCOVERY);
+ if (aparser.contains("nowebservicediscovery"))
+ webservicediscovery = false;
+ if (webservicediscovery)
{
desktop.startServiceDiscovery();
}
- if (!aparser.contains("nousagestats"))
+ else
+ {
+ testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
+ }
+
+ boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+ if (aparser.contains("nousagestats"))
+ usagestats = false;
+ if (usagestats)
{
startUsageStats(desktop);
+ testoutput(argparser, Arg.USAGESTATS);
}
else
{
- System.err.println("CMD [-nousagestats] executed successfully!");
+ System.out.println("CMD [-nousagestats] executed successfully!");
+ testoutput(argparser, Arg.USAGESTATS);
}
- if (!aparser.contains("noquestionnaire"))
+ boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+ if (aparser.contains("noquestionnaire"))
+ questionnaire = false;
+ if (questionnaire)
{
String url = aparser.getValue("questionnaire");
if (url != null)
}
else
{
- System.err
+ System.out
.println("CMD [-noquestionnaire] executed successfully!");
+ testoutput(argparser, Arg.QUESTIONNAIRE);
}
- if (!aparser.contains("nonews")
- || Cache.getProperty("NONEWS") == null)
+ if ((!aparser.contains("nonews")
+ && Cache.getProperty("NONEWS") == null
+ && !"false".equals(bootstrapArgs.get(Arg.NEWS)))
+ || "true".equals(bootstrapArgs.get(Arg.NEWS)))
{
desktop.checkForNews();
}
if (!aparser.contains("nohtmltemplates")
- || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ && Cache.getProperty("NOHTMLTEMPLATES") == null)
{
BioJsHTMLOutput.updateBioJS();
}
* the Jalview Desktop object passed in to the groovy binding as the
* 'Jalview' object.
*/
- private void executeGroovyScript(String groovyscript, AlignFrame af)
+ protected void executeGroovyScript(String groovyscript, AlignFrame af)
{
/**
* for scripts contained in files
if (exitcode > -1)
System.exit(exitcode);
}
+
+ /*
+ * testoutput for string values
+ */
+ protected static void testoutput(ArgParser ap, Arg a, String s1,
+ String s2)
+ {
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+ {
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
+ }
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(true, a, s1, s2);
+ }
+
+ protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+ String s2)
+ {
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+ {
+ Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+ + s2 + "' for arg " + a.argString());
+ return;
+ }
+ if (!a.hasOption(Opt.BOOTSTRAP))
+ {
+ Console.error("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(true, a, s1, s2);
+ }
+
+ private static void testoutput(boolean yes, Arg a, String s1, String s2)
+ {
+ if (yes && ((s1 == null && s2 == null)
+ || (s1 != null && s1.equals(s2))))
+ {
+ System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+ + "' was set");
+ }
+ }
+
+ /*
+ * testoutput for boolean values
+ */
+ protected static void testoutput(ArgParser ap, Arg a)
+ {
+ if (ap == null)
+ return;
+ BootstrapArgs bsa = ap.getBootstrapArgs();
+ if (bsa == null)
+ return;
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+ : ap.getBoolean(a);
+ boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+ : ap.isSet(a);
+ if (!isset)
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(val, a);
+ }
+
+ protected static void testoutput(BootstrapArgs bsa, Arg a)
+ {
+ if (!bsa.getBoolean(Arg.TESTOUTPUT))
+ return;
+ if (!a.hasOption(Opt.BOOTSTRAP))
+ {
+ Console.warn("Non-bootstrap Arg '" + a.getName()
+ + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
+
+ }
+ if (!bsa.contains(a))
+ {
+ Console.warn("Arg '" + a.getName() + "' not set at all");
+ return;
+ }
+ testoutput(bsa.getBoolean(a), a);
+ }
+
+ private static void testoutput(boolean yes, Arg a)
+ {
+ System.out.println("[TESTOUTPUT] arg "
+ + (yes ? a.argString() : a.negateArgString()) + " was set");
+ }
}
git://source.jalview.org / jalview.git / blobdiff