@Test
public void testGetOptionParser() throws Exception {
OptionParser optionParser = Main.getOptionParser();
String tmpDir = systemTempDir().toString();
OptionSet optionSet =
optionParser.parse(
"-f",
"/tmp/dummy",
"-s",
"9908:976098897",
"-r",
"9908:810017902",
"-u",
"https://ap.unit4.com",
"-m",
"as2",
"-e",
tmpDir);
assertTrue(optionSet.has("u"));
assertTrue(optionSet.has("f"));
assertTrue(optionSet.has("e"));
Object e = optionSet.valueOf("e");
assertNotNull(e);
assertTrue(e instanceof File);
File f = (File) e;
assertEquals(f, new File(tmpDir));
}
public static void main(String[] args) throws Exception {
OptionParser parser = new OptionParser();
parser
.accepts("client-zone-id", "client zone id for zone routing")
.withRequiredArg()
.describedAs("zone-id")
.ofType(Integer.class);
OptionSet options = parser.parse(args);
List<String> nonOptions = options.nonOptionArguments();
if (nonOptions.size() < 2 || nonOptions.size() > 3) {
System.err.println(
"Usage: java VoldemortClientShell store_name bootstrap_url [command_file] [options]");
parser.printHelpOn(System.err);
System.exit(-1);
}
String storeName = nonOptions.get(0);
String bootstrapUrl = nonOptions.get(1);
String commandsFileName = "";
BufferedReader fileReader = null;
BufferedReader inputReader = null;
try {
if (nonOptions.size() == 3) {
commandsFileName = nonOptions.get(2);
fileReader = new BufferedReader(new FileReader(commandsFileName));
}
inputReader = new BufferedReader(new InputStreamReader(System.in));
} catch (IOException e) {
Utils.croak("Failure to open input stream: " + e.getMessage());
}
ClientConfig clientConfig =
new ClientConfig()
.setBootstrapUrls(bootstrapUrl)
.setRequestFormatType(RequestFormatType.VOLDEMORT_V3);
if (options.has("client-zone-id")) {
clientConfig.setClientZoneId((Integer) options.valueOf("client-zone-id"));
}
StoreClientFactory factory = new SocketStoreClientFactory(clientConfig);
try {
client = (DefaultStoreClient<Object, Object>) factory.getStoreClient(storeName);
} catch (Exception e) {
Utils.croak("Could not connect to server: " + e.getMessage());
}
System.out.println("Established connection to " + storeName + " via " + bootstrapUrl);
System.out.print(PROMPT);
if (fileReader != null) {
processCommands(factory, fileReader, true);
fileReader.close();
}
processCommands(factory, inputReader, false);
}
/**
* {@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);
}
@Test
public void supportsPosixlyCorrectBehavior() {
OptionParser parser = new OptionParser("i:j::k");
String[] arguments = {
"-ibar", "-i", "junk", "xyz", "-jixnay", "foo", "-k", "blah", "--", "bah"
};
OptionSet options = parser.parse(arguments);
assertTrue(options.has("i"));
assertTrue(options.has("j"));
assertTrue(options.has("k"));
assertEquals(asList("bar", "junk"), options.valuesOf("i"));
assertEquals(singletonList("ixnay"), options.valuesOf("j"));
assertEquals(asList("xyz", "foo", "blah", "bah"), options.nonOptionArguments());
parser.posixlyCorrect(true);
options = parser.parse(arguments);
assertTrue(options.has("i"));
assertFalse(options.has("j"));
assertFalse(options.has("k"));
assertEquals(asList("bar", "junk"), options.valuesOf("i"));
assertEquals(emptyList(), options.valuesOf("j"));
assertEquals(
asList("xyz", "-jixnay", "foo", "-k", "blah", "--", "bah"), options.nonOptionArguments());
}
/**
* This is the main interface to ConfigurationOptions. Passing in the arguments array will return
* an object containing all parsed arguments and default values for arguments not specified
*
* @param args the arguments array from <code>main(String[] args)</code>.
* @return A set of configuration options.
* @throws Exception
*/
static ConfigurationOptions parse(String[] args) throws Exception {
ConfigurationOptions cfg = new ConfigurationOptions();
OptionParser parser = setupParser();
processOptions(parser.parse(args), cfg);
return cfg;
}
@Test
public void senderAndReceiverIsOptional() throws Exception {
OptionParser optionParser = Main.getOptionParser();
OptionSet optionSet =
optionParser.parse("-f", "/tmp/dummy", "-u", "https://ap.unit4.com", "-m", "as2");
assertFalse(optionSet.has("-r"));
assertFalse(optionSet.has("-s"));
}
public static void parseArgs(String args[]) throws java.io.IOException {
parser.acceptsAll(asList("h", "?"), "show help then exit");
OptionSpec<String> CMD = parser.accepts("c", "command").withRequiredArg().ofType(String.class);
OptionSpec<String> LOGIN =
parser.accepts("u", "LoginId").withRequiredArg().ofType(String.class);
OptionSpec<String> PASSWORD =
parser.accepts("p", "password").withRequiredArg().ofType(String.class);
OptionSpec<String> ISSUER =
parser.accepts("i", "IssuerDN").withRequiredArg().ofType(String.class);
OptionSpec<String> SUBJECT =
parser.accepts("s", "SubjectDN").withRequiredArg().ofType(String.class);
OptionSpec<String> CONTEXT =
parser
.accepts("C", "context:UNITTEST,DEVELOPMENT,SDK,PRODUCTION")
.withRequiredArg()
.ofType(String.class);
OptionSet options = parser.parse(args);
// check for help
if (options.has("?")) {
parser.printHelpOn(System.out);
System.exit(0);
}
if (options.has(CMD)) {
cmd = options.valueOf(CMD);
} else {
System.out.println("a -c cmd argument is required");
parser.printHelpOn(System.out);
System.exit(0);
}
if (options.has(LOGIN)) {
loginName = options.valueOf(LOGIN);
}
if (options.has(PASSWORD)) {
password = options.valueOf(PASSWORD);
}
if (options.has(ISSUER)) {
issuer = options.valueOf(ISSUER);
}
if (options.has(SUBJECT)) {
subject = options.valueOf(SUBJECT);
}
if (options.has(CONTEXT)) {
context = options.valueOf(CONTEXT);
if (!context.equals("UNITTEST")
&& !context.equals("SDK")
&& !context.equals("DEVELOPMENT")
&& !context.equals("PRODUCTION")) {
System.out.println("unrecognized CONTEXT value: " + context);
System.exit(-1);
}
}
}
private OptionParser buildOptionParser() {
OptionParser parser = new OptionParser();
parser
.accepts(ARGUMENT_EXPERIMENT, "Pre selected experiment")
.withRequiredArg()
.ofType(String.class);
parser.accepts(ARGUMENT_EXPERIMENT_LIST, "Retrieves the current list of available experiments");
parser.accepts(ARGUMENT_HELP, "Displays this help").forHelp();
parser.allowsUnrecognizedOptions();
return parser;
}
/**
* {@inheritDoc}
*
* <p>A method used to return the syntax for this module
*/
@Override
public String get_syntax() {
OptionParser parser = getOptionParser();
StringWriter output = new StringWriter();
try {
parser.printHelpOn(output);
return (output.toString());
} catch (IOException e) {
e.printStackTrace();
return (e.getMessage());
}
}
private void unschedule(String[] args) throws Exception {
String[] ONE_REQUIRED = {OPT_RESOURCEID, OPT_GROUPID};
OptionParser p = getOptionParser();
p.accepts(OPT_RESOURCEID, "The id of the resource to unschedule from maintenance")
.withRequiredArg()
.ofType(Integer.class);
p.accepts(OPT_GROUPID, "The id of the group to unschedule from maintenance")
.withRequiredArg()
.ofType(Integer.class);
OptionSet options = getOptions(p, args);
int criteria = 0;
for (String opt : ONE_REQUIRED) {
if (options.has(opt)) {
criteria++;
}
}
if (criteria == 0) {
System.err.println("One of " + Arrays.toString(ONE_REQUIRED) + " is required.");
System.exit(-1);
} else if (criteria > 1) {
System.err.println("Only one of " + Arrays.toString(ONE_REQUIRED) + " may be specified");
System.exit(-1);
}
HQApi api = getApi(options);
MaintenanceApi maintenanceApi = api.getMaintenanceApi();
StatusResponse response = null;
Integer id = null;
if (options.has(OPT_GROUPID)) {
id = (Integer) getRequired(options, OPT_GROUPID);
response = maintenanceApi.unschedule(id);
} else if (options.has(OPT_RESOURCEID)) {
id = (Integer) getRequired(options, OPT_RESOURCEID);
ResourceResponse resourceResponse = api.getResourceApi().getResource(id, false, false);
checkSuccess(resourceResponse);
response = maintenanceApi.unschedule(resourceResponse.getResource());
}
checkSuccess(response);
if (options.has(OPT_GROUPID)) {
System.out.println("Maintenance for group " + id + " unscheduled.");
} else {
System.out.println("Maintenance for resource " + id + " unscheduled.");
}
}
@Test
public void allowsDifferentFormsOfPairingArgumentWithOption() {
OptionParser parser = new OptionParser();
parser.accepts("count").withRequiredArg();
parser.accepts("level").withOptionalArg();
OptionSet options = parser.parse("--count", "4", "--level=3");
assertTrue(options.has("count"));
assertTrue(options.hasArgument("count"));
assertEquals("4", options.valueOf("count"));
assertTrue(options.has("level"));
assertTrue(options.hasArgument("level"));
assertEquals("3", options.valueOf("level"));
}
@Test
public void supportsOptionSynonyms() {
OptionParser parser = new OptionParser();
List<String> synonyms = asList("message", "blurb", "greeting");
parser.acceptsAll(synonyms).withRequiredArg();
String expectedMessage = "Hello";
OptionSet options = parser.parse("--message", expectedMessage);
for (String each : synonyms) {
assertTrue(each, options.has(each));
assertTrue(each, options.hasArgument(each));
assertEquals(each, expectedMessage, options.valueOf(each));
assertEquals(each, asList(expectedMessage), options.valuesOf(each));
}
}
public static void printUsage(PrintStream out, OptionParser parser, String msg)
throws IOException {
out.println(msg);
out.println(usageStr);
parser.printHelpOn(out);
System.exit(1);
}
private static void printHelp(OptionParser parser) {
try {
parser.printHelpOn(System.out);
} catch (Exception exception) {
exception.printStackTrace();
}
}
@Override
protected void customizeOptionParsing(OptionParser parser) {
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();
parser
.accepts(APP_DATA_DIR_KEY, description("Application data directory", DEFAULT_APP_DATA_DIR))
.withRequiredArg();
parser
.acceptsAll(
asList(APP_DATA_DIR_CLEAN_KEY, "clean"),
description("Clean application data directory", DEFAULT_APP_DATA_DIR_CLEAN))
.withRequiredArg()
.ofType(boolean.class);
parser
.accepts(ProgramArguments.NAME_KEY, description("Name of this node", null))
.withRequiredArg();
// use a fixed port as arbitrator use that for his ID
parser
.accepts(ProgramArguments.PORT_KEY, description("Port to listen on", 9999))
.withRequiredArg()
.ofType(int.class);
parser
.accepts(
ProgramArguments.USE_LOCALHOST,
description("Use localhost network for development", false))
.withRequiredArg()
.ofType(boolean.class);
parser
.accepts(ProgramArguments.DEV_TEST, description("Enable arbitrator dev priv key", false))
.withRequiredArg()
.ofType(boolean.class);
parser
.accepts(BitcoinNetwork.KEY, description("Bitcoin network", BitcoinNetwork.DEFAULT))
.withRequiredArg()
.ofType(BitcoinNetwork.class)
.withValuesConvertedBy(new EnumValueConverter(BitcoinNetwork.class));
parser
.accepts(RegTestHost.KEY, description("", RegTestHost.DEFAULT))
.withRequiredArg()
.ofType(RegTestHost.class)
.withValuesConvertedBy(new EnumValueConverter(RegTestHost.class));
}
private static void printUsage(OptionParser parser, String errorCommand) throws IOException {
parser.printHelpOn(System.err);
Utils.croak(
"Usage: $MILE_HOME/bin/run-class.sh "
+ Benchmark.class.getName()
+ " [options] config-file ops-count\n "
+ errorCommand);
}
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;
}
private void printHelp(OptionParser parser) {
try {
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
parser.printHelpOn(byteArrayOutputStream);
System.out.println(byteArrayOutputStream.toString());
} catch (IOException ex) {
Logger.getLogger(Runner.class.getName()).log(Level.SEVERE, null, ex);
}
}
@Test
public void testInitOptionsWithHelp_optionalArgument() {
parser.accepts("argName", "Funky description");
OptionSet options = initOptionsWithHelp(parser, new String[] {"--argName"});
assertNotNull(options);
assertEquals(1, options.specs().size());
assertTrue(options.has("argName"));
}
public final void parseAndExecute(final String[] cmds) throws IOException {
opts = parser.parse(cmds);
if (opts.has(HELP)) {
parser.printHelpOn(System.out);
return;
}
Indexing.STORE = opts.has(STORE);
Indexing.COMMIT = (Integer) opts.valueOf(COMMIT);
// FORMAT
if (opts.has(FORMAT)) {
format = (Format) opts.valueOf(FORMAT);
} else printError(FORMAT);
// DUMPS_DIR
if (opts.has(DUMPS_DIR)) {
dumpsDir = (File) opts.valueOf(DUMPS_DIR);
} else printError(DUMPS_DIR);
// INDEX_DIR
if (opts.has(INDEX_DIR)) {
indexDir = (File) opts.valueOf(INDEX_DIR);
} else printError(INDEX_DIR);
logger.info(
"Creating index at {} from the files at {}",
indexDir.getAbsolutePath(),
dumpsDir.getAbsolutePath());
final Indexing indexing;
switch (format) {
case SINDICE_DE:
indexing = new SindiceDEIndexing(dumpsDir, FSDirectory.open(indexDir));
break;
case SINDICE_ED:
indexing = new SindiceEDIndexing(dumpsDir, FSDirectory.open(indexDir));
break;
default:
throw new IllegalArgumentException("No such dataset format: " + format);
}
indexing.indexIt();
indexing.close();
logger.info("Finished indexing");
}
@Test(expected = CommandLineExitException.class)
public void testInitOptionsWithHelp_missingArgument() {
parser
.accepts("argName", "Funky description")
.withRequiredArg()
.ofType(String.class)
.defaultsTo("nope");
initOptionsWithHelp(parser, new String[] {"--argName"});
}
public static void main(String[] args) throws IOException, TException {
OptionParser parser = new OptionParser();
parser.accepts("c", "configuration file").withRequiredArg().ofType(String.class);
parser.accepts("help", "print help statement");
OptionSet options = parser.parse(args);
if (options.has("help")) {
parser.printHelpOn(System.out);
System.exit(-1);
}
// Logger configuration: log to the console
BasicConfigurator.configure();
LOG.setLevel(Level.DEBUG);
LOG.debug("debug logging on");
Configuration conf = new PropertiesConfiguration();
if (options.has("c")) {
String configFile = (String) options.valueOf("c");
try {
conf = new PropertiesConfiguration(configFile);
} catch (ConfigurationException e) {
}
}
// Start backend server
BackendService.Processor<BackendService.Iface> processor =
new BackendService.Processor<BackendService.Iface>(new ProtoBackend());
int listenPort = conf.getInt("listen_port", DEFAULT_LISTEN_PORT);
NM_PORT = conf.getInt("node_monitor_port", NodeMonitorThrift.DEFAULT_NM_THRIFT_PORT);
TServers.launchThreadedThriftServer(listenPort, THRIFT_WORKER_THREADS, processor);
// Register server
client = TClients.createBlockingNmClient(NM_HOST, NM_PORT);
try {
client.registerBackend(APP_ID, "localhost:" + listenPort);
LOG.debug("Client successfullly registered");
} catch (TTransportException e) {
LOG.debug("Error while registering backend: " + e.getMessage());
}
}
private static void checkRequiredArgs(
OptionParser parser, OptionSet options, OptionSpec[] required) throws IOException {
for (OptionSpec arg : required) {
if (!options.has(arg)) {
System.err.println("Missing required argument \"" + arg + "\"");
parser.printHelpOn(System.err);
System.exit(1);
}
}
}
public static void main(String[] args) throws Exception {
SaraTouchClient client = new SaraTouchClient();
OptionParser parser = new OptionParser("ch:p:t");
OptionSet options = null;
try {
options = parser.parse(args);
} catch (Exception e) {
System.out.println("Could not parse command-line options:\n" + e);
System.out.println();
System.out.println("-h <host> Server host");
System.out.println("-p <port> Server port");
System.out.println("-t Send TUIO events instead of mouse events");
System.out.println("-c Connect after starting up");
System.out.println();
System.exit(-1);
}
if (options.has("h")) {
Object o = options.valueOf("h");
if (o != null) {
String s = (String) o;
client.setHost(s);
}
}
if (options.has("p")) {
Object o = options.valueOf("p");
if (o != null) {
int i = Integer.parseInt((String) o);
client.setPort(i);
}
}
if (options.has("t")) client.setModeToTUIO();
if (options.has("c")) client.connect();
client.setSize(600, 500);
client.setVisible(true);
}
static void checkRequiredArgs(
OptionParser parser, OptionSet options, OptionSpec<?>... optionSepcs) throws IOException {
for (OptionSpec<?> arg : optionSepcs) {
if (!options.has(arg)) {
System.err.println("Missing required argument " + arg);
// parser.formatHelpWith(new MyFormatter());
parser.printHelpOn(System.err);
System.exit(1);
}
}
}
// For passing args in Netbeans 7.3, see http://forums.netbeans.org/ptopic46048.html. Doesn't work
// as of 17-09-2013 (it is ignored).
public static void main(String[] args) {
EmmaBiblioJOB emmaBiblioJob = new EmmaBiblioJOB();
int retVal = 0;
OptionParser optionParser = new OptionParser();
optionParser.accepts("a"); // validate all biblios.
optionParser.accepts(
"v"); // validate update candidate biblios (whose 'updated' flag is not 'Y').
optionParser.accepts("u"); // update candidate biblios that pass validation.
OptionSet options = optionParser.parse(args);
if (options.has("a")) retVal = Math.max(retVal, emmaBiblioJob.validateAll());
if (options.has("v")) retVal = Math.max(retVal, emmaBiblioJob.validateUpdateCandidates());
if (options.has("u")) retVal = Math.max(retVal, emmaBiblioJob.update());
if (!((options.has("a")) || (options.has("v")) || (options.has("u")))) usage();
System.exit(retVal);
}
private static OptionParser buildParser() {
final OptionParser parser =
new OptionParser() {
{
acceptsAll(asList(HELP_OPTION_SHORT, HELP_OPTION_LONG), "This help").forHelp();
acceptsAll(
asList(UNINSTALL_OPTION_SHORT, UNINSTALL_OPTION_LONG), "Remove registry settings");
acceptsAll(
asList(VERBOSE_OPTION_SHORT, VERBOSE_OPTION_LONG),
"Enable verbose application messages");
acceptsAll(asList(FILE_OPTION_SHORT, FILE_OPTION_LONG), "File to load at start")
.withRequiredArg()
.ofType(File.class);
accepts(PASSWORD_OPTION, "Password for a local File, server or client")
.withRequiredArg();
acceptsAll(
asList(PORTABLE_OPTION_SHORT, PORTABLE_OPTION_LONG), "Enable portable preferences");
accepts(PORTABLE_FILE_OPTION, "Enable portable preferences and specify the file")
.withRequiredArg()
.ofType(File.class);
accepts(
PORT_OPTION,
"Network port server is running on (default: "
+ JpaNetworkServer.DEFAULT_PORT
+ ")")
.withRequiredArg()
.ofType(Integer.class);
accepts(HOST_OPTION, "Server host name or address")
.requiredIf(PORT_OPTION)
.withRequiredArg();
accepts(SERVER_OPTION, "Runs as a server using the specified file")
.withRequiredArg()
.ofType(File.class);
}
};
parser.allowsUnrecognizedOptions();
return parser;
}
public void run() {
Reflections.log = null;
printVersion();
OptionParser parser = buildOptionParser();
OptionSet options = parser.parse(arguments);
if (options.has(ARGUMENT_EXPERIMENT)) {
runExperiment(options.valueOf(ARGUMENT_EXPERIMENT).toString());
System.exit(0);
}
if (options.has(ARGUMENT_EXPERIMENT_LIST)) {
printExperimentList();
System.exit(0);
}
if (options.has(ARGUMENT_HELP)) {
printHelp(parser);
System.exit(0);
}
printHelp(parser);
}
public static void main(String[] args) {
OptionParser p = new OptionParser("fc:q::");
p.accepts("ftp");
p.accepts("user").requiredIf("ftp").withRequiredArg();
p.accepts("pass").requiredIf("ftp").withRequiredArg();
OptionSet opt = p.parse(args);
if (opt.has("f")) {
System.out.println("-f exist");
System.out.println("-f with : " + opt.valueOf("f"));
}
if (opt.has("c")) {
System.out.println("-c exist with:" + opt.valueOf("c"));
}
if (opt.has("ftp")) {
// we know username and password
// existe if -ftp is set
String user = (String) opt.valueOf("user");
String pwd = (String) opt.valueOf("pass");
System.out.println("user:"******" pass:" + pwd);
}
}
/**
* getOptionParser is an internal method to parse command line args.
*
* @return OptionParser this is used to get command line options
*/
protected OptionParser getOptionParser() {
OptionParser parser = new OptionParser();
parser.accepts("infastq", "input: reads in fastq format").withRequiredArg();
parser.accepts("outfastq", "output: trimmed reads in fastq format").withRequiredArg();
parser.accepts("readsize", "length (in bases) of output reads").withRequiredArg();
parser.accepts("perl", "Path to perl").withRequiredArg();
parser.accepts("script", "Path to perl script: sw_module_TrimAllReads.pl").withRequiredArg();
return (parser);
}
