/**
* {@inheritDoc}
*
* <p>All necessary setup for the module. Populate the "processing" table in seqware_meta_db.
* Create a temporary directory.
*/
@Override
public ReturnValue init() {
ReturnValue ret = new ReturnValue();
ret.setExitStatus(ReturnValue.SUCCESS);
// fill in the [xxx] fields in the processing table
ret.setAlgorithm("TrimAllReads");
ret.setDescription("Trim all reads to a specific length.");
ret.setVersion("0.7.0");
try {
OptionParser parser = getOptionParser();
// The parameters object is actually an ArrayList of Strings created
// by splitting the command line options by space. JOpt expects a String[]
options = parser.parse(this.getParameters().toArray(new String[0]));
// create a temp directory in current working directory
// tempDir = FileTools.createTempDirectory(new File("."));
// you can write to "stdout" or "stderr" which will be persisted back to the DB
ret.setStdout(ret.getStdout() + "Output: " + (String) options.valueOf("outfastq") + "\n");
} catch (OptionException e) {
e.printStackTrace();
ret.setStderr(e.getMessage());
ret.setExitStatus(ReturnValue.INVALIDPARAMETERS);
} // catch (IOException e) {
// e.printStackTrace();
// ret.setStderr(e.getMessage());
// ret.setExitStatus(ReturnValue.DIRECTORYNOTWRITABLE);
// }
return (ret);
}
private static OptionSet parseOptions(String[] argv) throws IOException {
OptionSet args = null;
OptionParser parser = new OptionParser();
parser.acceptsAll(Arrays.asList("l", CMD_LIST), "list readers");
parser.acceptsAll(Arrays.asList("p", OPT_PROVIDER), "specify provider").withRequiredArg();
parser.acceptsAll(Arrays.asList("v", OPT_VERBOSE), "be verbose");
parser.acceptsAll(Arrays.asList("e", OPT_ERROR), "fail if not 0x9000");
parser.acceptsAll(Arrays.asList("h", OPT_HELP), "show help");
parser.acceptsAll(Arrays.asList("r", OPT_READER), "use reader").withRequiredArg();
parser.acceptsAll(Arrays.asList("a", CMD_APDU), "send APDU").withRequiredArg();
parser.acceptsAll(Arrays.asList("w", OPT_WEB), "open ATR in web");
parser.acceptsAll(Arrays.asList("V", OPT_VERSION), "show version information");
parser.accepts(OPT_DUMP, "save dump to file").withRequiredArg().ofType(File.class);
parser.accepts(OPT_REPLAY, "replay command from dump").withRequiredArg().ofType(File.class);
parser.accepts(OPT_SUN, "load SunPCSC");
parser.accepts(OPT_JNA, "load jnasmartcardio");
parser.accepts(OPT_CONNECT, "connect to host:port or URL").withRequiredArg();
parser.accepts(OPT_PINNED, "require certificate").withRequiredArg().ofType(File.class);
parser.accepts(OPT_PROVIDERS, "list providers");
parser.accepts(OPT_ALL, "process all readers");
parser.accepts(OPT_WAIT, "wait for card insertion");
parser.accepts(OPT_T0, "use T=0");
parser.accepts(OPT_T1, "use T=1");
parser.accepts(OPT_TEST_SERVER, "run a test server on port 10000").withRequiredArg();
parser.accepts(OPT_NO_GET_RESPONSE, "don't use GET RESPONSE with SunPCSC");
parser.accepts(OPT_LIB, "use specific PC/SC lib with SunPCSC").withRequiredArg();
parser.accepts(OPT_PROVIDER_TYPE, "provider type if not PC/SC").withRequiredArg();
// Parse arguments
try {
args = parser.parse(argv);
// Try to fetch all values so that format is checked before usage
for (String s : parser.recognizedOptions().keySet()) {
args.valuesOf(s);
}
} catch (OptionException e) {
if (e.getCause() != null) {
System.err.println(e.getMessage() + ": " + e.getCause().getMessage());
} else {
System.err.println(e.getMessage());
}
System.err.println();
help_and_exit(parser, System.err);
}
if (args.has(OPT_HELP)) {
help_and_exit(parser, System.out);
}
return args;
}
private OptionSet parseOptions(OptionParser p, String[] args) throws IOException {
OptionSet options = null;
try {
options = p.parse(args);
if (options.has("?")
|| !options.has(maxwiOptName)
|| options.nonOptionArguments().size() < 2) {
System.err.println("Usage:\nSimilarity <input_paths> <output_path> [options]");
System.err.println("Please specify " + maxwiOptName + " option\n");
p.printHelpOn(System.err);
System.exit(0);
}
} catch (OptionException e) {
System.err.println(e.getMessage());
System.exit(1);
}
return options;
}
public static void main(final String[] args) throws IOException {
final MappingTestServerOptionParser parser = new MappingTestServerOptionParser();
try {
final OptionSet options = parser.parse(args);
if (options.has("help")) {
parser.printHelpOn(System.out);
} else {
final String host = options.valueOf(parser.hostOption);
final Integer port = options.valueOf(parser.portOption);
final MappingTestServer server =
new MappingTestServer(
options.valueOf(parser.schemaOption),
options.valueOf(parser.mappingOption),
port,
host);
Runtime.getRuntime().addShutdownHook(new Thread(server::stopServer));
log.info("Starting server on {}:{}...", host, port);
server.runServer();
}
} catch (final OptionException e) {
System.err.println(e.getLocalizedMessage());
parser.printHelpOn(System.err);
}
}
public static void main(String[] args) throws Exception {
// We don't want to do the full argument parsing here as that might easily change in update
// versions
// So we only handle the absolute minimum which is APP_NAME, APP_DATA_DIR_KEY and USER_DATA_DIR
OptionParser parser = new OptionParser();
parser.allowsUnrecognizedOptions();
parser
.accepts(USER_DATA_DIR_KEY, description("User data directory", DEFAULT_USER_DATA_DIR))
.withRequiredArg();
parser
.accepts(APP_NAME_KEY, description("Application name", DEFAULT_APP_NAME))
.withRequiredArg();
OptionSet options;
try {
options = parser.parse(args);
} catch (OptionException ex) {
System.out.println("error: " + ex.getMessage());
System.out.println();
parser.printHelpOn(System.out);
System.exit(EXIT_FAILURE);
return;
}
BitsquareEnvironment bitsquareEnvironment = new BitsquareEnvironment(options);
// need to call that before BitsquareAppMain().execute(args)
initAppDir(bitsquareEnvironment.getProperty(BitsquareEnvironment.APP_DATA_DIR_KEY));
// For some reason the JavaFX launch process results in us losing the thread context class
// loader: reset it.
// In order to work around a bug in JavaFX 8u25 and below, you must include the following code
// as the first line of your realMain method:
Thread.currentThread().setContextClassLoader(BitsquareAppMain.class.getClassLoader());
new BitsquareAppMain().execute(args);
}
public static void main(String[] args) throws Exception {
OptionParser parser = new OptionParser("p:f:c:r:H:s:t:h");
OptionSet options = null;
try {
options = parser.parse(args);
} catch (OptionException ex) {
System.err.println(ex.getMessage());
System.exit(1);
}
if (options.has("h")) {
printHelp(System.out);
System.exit(0);
}
final int port;
if (options.has("p")) {
String portStr = options.valueOf("p").toString();
try {
port = Integer.parseInt(portStr);
} catch (NumberFormatException ex) {
throw new IllegalArgumentException("Invalid port number: " + portStr, ex);
}
} else {
port = -1;
System.err.println("Mandatory parameter port not given.");
System.exit(1);
}
AnyUrlServlet servlet = new AnyUrlServlet();
if (options.has("f")) {
String fileStr = options.valueOf("f").toString();
servlet.setFile(new File(fileStr));
}
if (options.has("c")) {
servlet.setContentType(options.valueOf("c").toString());
}
if (options.has("r")) {
servlet.setCharset(options.valueOf("r").toString());
}
if (options.has("H")) {
MultiValueMap headers = new MultiValueMapLinkedHashSet();
for (Object t : options.valuesOf("H")) {
final String headerLine = t.toString().trim();
final int sepIdx = headerLine.indexOf(':');
if ((sepIdx > 0) && (sepIdx < headerLine.length())) {
final String header = headerLine.substring(0, sepIdx).trim();
final String value = headerLine.substring(sepIdx + 1).trim();
// System.out.printf("\nHeader: Value => %s:%s\n", header, value);
headers.put(header, value);
}
}
servlet.setHeaders(headers);
}
if (options.has("s")) {
try {
int statusCode = Integer.parseInt(options.valueOf("s").toString());
servlet.setStatusCode(statusCode);
} catch (NumberFormatException ex) {
throw new IllegalArgumentException("Param -s must be a valid status code.");
}
}
if (options.has("t")) {
try {
long throttleMillis = Long.parseLong(options.valueOf("t").toString());
if (throttleMillis > 1) {
servlet.setThrottleMillis(throttleMillis);
} else {
throw new NumberFormatException();
}
} catch (NumberFormatException ex) {
throw new IllegalArgumentException("Param -t must be a valid number.");
}
}
Server server = new Server(port);
server.setStopAtShutdown(true);
// Attach the servlet:
ServletContextHandler ctx = new ServletContextHandler();
ctx.setContextPath("/");
server.setHandler(ctx);
ctx.addServlet(new ServletHolder(servlet), "/*");
server.start();
}
public static void main(String[] args) {
// Todo: Installation script
OptionParser parser =
new OptionParser() {
{
acceptsAll(asList("?", "help"), "Show the help");
acceptsAll(asList("c", "config"), "Properties file to use")
.withRequiredArg()
.ofType(File.class)
.defaultsTo(new File("server.properties"))
.describedAs("Properties file");
acceptsAll(asList("P", "plugins"), "Plugin directory to use")
.withRequiredArg()
.ofType(File.class)
.defaultsTo(new File("plugins"))
.describedAs("Plugin directory");
acceptsAll(asList("h", "host", "server-ip"), "Host to listen on")
.withRequiredArg()
.ofType(String.class)
.describedAs("Hostname or IP");
acceptsAll(asList("W", "world-dir", "universe", "world-container"), "World container")
.withRequiredArg()
.ofType(File.class)
.describedAs("Directory containing worlds");
acceptsAll(asList("w", "world", "level-name"), "World name")
.withRequiredArg()
.ofType(String.class)
.describedAs("World name");
acceptsAll(asList("p", "port", "server-port"), "Port to listen on")
.withRequiredArg()
.ofType(Integer.class)
.describedAs("Port");
acceptsAll(asList("o", "online-mode"), "Whether to use online authentication")
.withRequiredArg()
.ofType(Boolean.class)
.describedAs("Authentication");
acceptsAll(asList("s", "size", "max-players"), "Maximum amount of players")
.withRequiredArg()
.ofType(Integer.class)
.describedAs("Server size");
acceptsAll(
asList("d", "date-format"),
"Format of the date to display in the console (for log entries)")
.withRequiredArg()
.ofType(SimpleDateFormat.class)
.describedAs("Log date format");
acceptsAll(asList("log-pattern"), "Specfies the log filename pattern")
.withRequiredArg()
.ofType(String.class)
.defaultsTo("server.log")
.describedAs("Log filename");
acceptsAll(
asList("log-limit"), "Limits the maximum size of the log file (0 = unlimited)")
.withRequiredArg()
.ofType(Integer.class)
.defaultsTo(0)
.describedAs("Max log size");
acceptsAll(asList("log-count"), "Specified how many log files to cycle through")
.withRequiredArg()
.ofType(Integer.class)
.defaultsTo(1)
.describedAs("Log count");
acceptsAll(asList("log-append"), "Whether to append to the log file")
.withRequiredArg()
.ofType(Boolean.class)
.defaultsTo(true)
.describedAs("Log append");
acceptsAll(asList("log-strip-color"), "Strips color codes from log file");
acceptsAll(asList("b", "bukkit-settings"), "File for bukkit settings")
.withRequiredArg()
.ofType(File.class)
.defaultsTo(new File("bukkit.yml"))
.describedAs("Yml file");
acceptsAll(asList("C", "commands-settings"), "File for command settings")
.withRequiredArg()
.ofType(File.class)
.defaultsTo(new File("commands.yml"))
.describedAs("Yml file");
acceptsAll(asList("nojline"), "Disables jline and emulates the vanilla console");
acceptsAll(asList("noconsole"), "Disables the console");
acceptsAll(asList("v", "version"), "Show the CraftBukkit Version");
acceptsAll(asList("demo"), "Demo mode");
}
};
OptionSet options = null;
try {
options = parser.parse(args);
} catch (joptsimple.OptionException ex) {
Logger.getLogger(Main.class.getName()).log(Level.SEVERE, ex.getLocalizedMessage());
}
if ((options == null) || (options.has("?"))) {
try {
parser.printHelpOn(System.out);
} catch (IOException ex) {
Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
}
} else if (options.has("v")) {
System.out.println(CraftServer.class.getPackage().getImplementationVersion());
} else {
try {
// This trick bypasses Maven Shade's clever rewriting of our getProperty call when using
// String literals
String jline_UnsupportedTerminal =
new String(
new char[] {
'j', 'l', 'i', 'n', 'e', '.', 'U', 'n', 's', 'u', 'p', 'p', 'o', 'r', 't', 'e',
'd', 'T', 'e', 'r', 'm', 'i', 'n', 'a', 'l'
});
String jline_terminal =
new String(
new char[] {'j', 'l', 'i', 'n', 'e', '.', 't', 'e', 'r', 'm', 'i', 'n', 'a', 'l'});
useJline = !(jline_UnsupportedTerminal).equals(System.getProperty(jline_terminal));
if (options.has("nojline")) {
System.setProperty("user.language", "en");
useJline = false;
}
if (!useJline) {
// This ensures the terminal literal will always match the jline implementation
System.setProperty(
jline.TerminalFactory.JLINE_TERMINAL, jline.UnsupportedTerminal.class.getName());
}
if (options.has("noconsole")) {
useConsole = false;
}
// Spigot Start
int maxPermGen = 0; // In kb
for (String s :
java.lang.management.ManagementFactory.getRuntimeMXBean().getInputArguments()) {
if (s.startsWith("-XX:MaxPermSize")) {
maxPermGen = Integer.parseInt(s.replaceAll("[^\\d]", ""));
maxPermGen <<= 10 * ("kmg".indexOf(Character.toLowerCase(s.charAt(s.length() - 1))));
}
}
if (maxPermGen < (128 << 10)) // 128mb
{
System.out.println(
"Warning, your max perm gen size is not set or less than 128mb. It is recommended you restart Java with the following argument: -XX:MaxPermSize=128M");
System.out.println(
"Please see http://www.spigotmc.org/wiki/changing-permgen-size/ for more details and more in-depth instructions.");
}
// Spigot End
System.out.println("Loading libraries, please wait...");
MinecraftServer.main(options);
} catch (Throwable t) {
t.printStackTrace();
}
}
}