public void test13666() {
Options options = new Options();
Option dir = OptionBuilder.withDescription("dir").hasArg().create('d');
options.addOption(dir);
final PrintStream oldSystemOut = System.out;
try {
final ByteArrayOutputStream bytes = new ByteArrayOutputStream();
final PrintStream print = new PrintStream(bytes);
// capture this platform's eol symbol
print.println();
final String eol = bytes.toString();
bytes.reset();
System.setOut(new PrintStream(bytes));
try {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("dir", options);
} catch (Exception exp) {
fail("Unexpected Exception: " + exp.getMessage());
}
assertEquals("usage: dir" + eol + " -d <arg> dir" + eol, bytes.toString());
} finally {
System.setOut(oldSystemOut);
}
}
public static void main(String args[]) throws IOException, ParseException {
Options options = new Options();
options.addOption("u", "uniquehits", false, "only output hits with a single mapping");
options.addOption(
"s",
"nosuboptimal",
false,
"do not include hits whose score is not equal to the best score for the read");
CommandLineParser parser = new GnuParser();
CommandLine cl = parser.parse(options, args, false);
boolean uniqueOnly = cl.hasOption("uniquehits");
boolean filterSubOpt = cl.hasOption("nosuboptimal");
ArrayList<String[]> lines = new ArrayList<String[]>();
String line;
String lastRead = "";
BufferedReader reader = new BufferedReader(new InputStreamReader(System.in));
while ((line = reader.readLine()) != null) {
String pieces[] = line.split("\t");
if (!pieces[0].equals(lastRead)) {
printLines(lines, uniqueOnly, filterSubOpt);
lines.clear();
}
lines.add(pieces);
lastRead = pieces[0];
}
printLines(lines, uniqueOnly, filterSubOpt);
}
public void run(String[] args)
throws ParseException, TransformationException, IOException, AnalysisException {
Options options = new Options();
options.addOption("input", true, "input path");
options.addOption("output", true, "output path");
options.addOption("ext", true, "extension");
CommandLineParser parser = new DefaultParser();
CommandLine line = parser.parse(options, args);
String inDir = line.getOptionValue("input");
String outDir = line.getOptionValue("output");
String extension = line.getOptionValue("ext");
File dir = new File(inDir);
for (File f : FileUtils.listFiles(dir, new String[] {extension}, true)) {
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
List<BxPage> pages = tvReader.read(new FileReader(f));
BxDocument doc = new BxDocument().setPages(pages);
doc.setFilename(f.getName());
BxDocument rewritten = transform(doc);
File f2 = new File(outDir + doc.getFilename());
BxDocumentToTrueVizWriter wrt = new BxDocumentToTrueVizWriter();
boolean created = f2.createNewFile();
if (!created) {
throw new IOException("Cannot create file: ");
}
FileWriter fw = new FileWriter(f2);
wrt.write(fw, Lists.newArrayList(rewritten));
fw.flush();
fw.close();
}
}
public static Options constructGnuOptions() {
final Options gnuOptions = new Options();
Option aminoDefaultConfigurationOption =
new Option(
"d", "amino_default_config_path", true, "The path where the amino default file lives.");
aminoDefaultConfigurationOption.setRequired(true);
gnuOptions.addOption(aminoDefaultConfigurationOption);
gnuOptions.addOption("b", "base_dir", true, "The base directory of the running job");
gnuOptions.addOption(
"c",
"amino_config_file_path",
true,
"A CSV of filenames or paths which will be acted like a classpath setting up configurations!");
gnuOptions.addOption(
"stop",
"stop_on_first_phase",
false,
"Stop after the first phase of an AminoEnrichmentJob");
Option propertyOverride =
new Option(
"D",
"property_override",
true,
"A map of key/value configuration properties to override (ie: 'key=value')");
propertyOverride.setValueSeparator('=');
propertyOverride.setArgs(2);
gnuOptions.addOption(propertyOverride);
return gnuOptions;
}
private static boolean setOptions(String[] lcommand) {
Options loptions = new Options();
loptions.addOption(new Option("d", "debug", false, "print debug information (highly verbose)"));
loptions.addOption(new Option("o", "stdout", false, "print output files to standard output"));
loptions.addOption(new Option("w", "warning", false, "print warning messages"));
CommandLineParser clparser = new PosixParser();
try {
cmd = clparser.parse(loptions, lcommand);
} catch (org.apache.commons.cli.ParseException e) {
String mytoolcmd = "java -jar stave.jar";
String myoptlist = " <options> <source files>";
String myheader = "Convert JavaParser's AST to OpenJDK's AST";
String myfooter = "More info: https://github.com/pcgomes/javaparser2jctree";
HelpFormatter formatter = new HelpFormatter();
// formatter.printUsage( new PrintWriter(System.out,true), 100, "java -jar synctask.jar",
// loptions );
// formatter.printHelp( mytoolcmd + myoptlist, myheader, loptions, myfooter, false);
formatter.printHelp(mytoolcmd + myoptlist, loptions, false);
return (false);
}
return (true);
}
public void test11456() {
// Posix
Options options = new Options();
options.addOption(OptionBuilder.hasOptionalArg().create('a'));
options.addOption(OptionBuilder.hasArg().create('b'));
String[] args = new String[] {"-a", "-bvalue"};
CommandLineParser parser = new PosixParser();
try {
CommandLine cmd = parser.parse(options, args);
assertEquals(cmd.getOptionValue('b'), "value");
} catch (ParseException exp) {
fail("Unexpected Exception: " + exp.getMessage());
}
// GNU
options = new Options();
options.addOption(OptionBuilder.hasOptionalArg().create('a'));
options.addOption(OptionBuilder.hasArg().create('b'));
args = new String[] {"-a", "-b", "value"};
parser = new GnuParser();
try {
CommandLine cmd = parser.parse(options, args);
assertEquals(cmd.getOptionValue('b'), "value");
} catch (ParseException exp) {
fail("Unexpected Exception: " + exp.getMessage());
}
}
/** Add the commandline options common to any command */
static {
options.addOption("h", "help", false, "print this message");
options.addOption("p", "project", true, "project name");
options.addOption("a", "action", true, "action to run {create | remove}");
options.addOption("v", "verbose", false, "verbose messages");
options.addOption("G", "cygwin", false, "for create, indicate that the node is using cygwin");
// options.addOption("N", "nodeslist", true, "Path to arbitrary nodes.properties file");
}
private static Options createOptions() {
Options options = new Options();
options.addOption("h", "help", false, "Prints this message");
options.addOption("w", "wmprt", true, "Path to WMPRT folder");
options.addOption("o", "output", true, "Output Folder for generated code");
options.addOption("n", "namespace", true, "The desired namespace for the generated code");
return options;
}
// wrapper function to add an option
private void addOptionWrapper(Option opt, boolean isStandard) {
// for parsing command-line options
options.addOption(opt);
// for printing help messages
getOptionList().add(opt);
if (isStandard) {
optionsStandard.addOption(opt);
} else {
optionsExperimental.addOption(opt);
}
}
public void test12210() {
// create the main options object which will handle the first parameter
Options mainOptions = new Options();
// There can be 2 main exclusive options: -exec|-rep
// Therefore, place them in an option group
String[] argv = new String[] {"-exec", "-exec_opt1", "-exec_opt2"};
OptionGroup grp = new OptionGroup();
grp.addOption(new Option("exec", false, "description for this option"));
grp.addOption(new Option("rep", false, "description for this option"));
mainOptions.addOptionGroup(grp);
// for the exec option, there are 2 options...
Options execOptions = new Options();
execOptions.addOption("exec_opt1", false, " desc");
execOptions.addOption("exec_opt2", false, " desc");
// similarly, for rep there are 2 options...
Options repOptions = new Options();
repOptions.addOption("repopto", false, "desc");
repOptions.addOption("repoptt", false, "desc");
// create the parser
GnuParser parser = new GnuParser();
// finally, parse the arguments:
// first parse the main options to see what the user has specified
// We set stopAtNonOption to true so it does not touch the remaining
// options
try {
CommandLine cmd = parser.parse(mainOptions, argv, true);
// get the remaining options...
argv = cmd.getArgs();
if (cmd.hasOption("exec")) {
cmd = parser.parse(execOptions, argv, false);
// process the exec_op1 and exec_opt2...
assertTrue(cmd.hasOption("exec_opt1"));
assertTrue(cmd.hasOption("exec_opt2"));
} else if (cmd.hasOption("rep")) {
cmd = parser.parse(repOptions, argv, false);
// process the rep_op1 and rep_opt2...
} else {
fail("exec option not found");
}
} catch (ParseException exp) {
fail("Unexpected exception: " + exp.getMessage());
}
}
private static void parseArguments(String[] args) throws ParseException {
Options options = new Options();
options.addOption("input", true, "The input file path");
options.addOption("output", true, "The output file path");
options.addOption("threads", true, "The number of threads");
CommandLine commandLine = new PosixParser().parse(options, args);
inputFilePath = commandLine.getOptionValue("input", "price_moves.csv");
outputFilePath = commandLine.getOptionValue("output", "result.txt");
numberOfThreads = Integer.valueOf(commandLine.getOptionValue("threads", "1"));
}
/** Method to create command line parser */
private void createCmdLineParser() {
cmdOptions = new Options();
// add a accession option
cmdOptions.addOption(
ACCESSION_CMD, true, "a list of pride experiment accessions, separated by comma");
// add a user name option
cmdOptions.addOption(USER_NAME_CMD, true, "pride user name");
// add a password option
cmdOptions.addOption(PASSWORD_CMD, true, "pride password");
// create cmd line parser
cmdParser = new GnuParser();
}
public void test15046() throws Exception {
CommandLineParser parser = new PosixParser();
final String[] CLI_ARGS = new String[] {"-z", "c"};
Option option = new Option("z", "timezone", true, "affected option");
Options cliOptions = new Options();
cliOptions.addOption(option);
parser.parse(cliOptions, CLI_ARGS);
// now add conflicting option
cliOptions.addOption("c", "conflict", true, "conflict option");
CommandLine line = parser.parse(cliOptions, CLI_ARGS);
assertEquals(option.getValue(), "c");
assertTrue(!line.hasOption("c"));
}
public static void main(String[] args) throws Exception {
String propertyFile = null;
// create the command line parser
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption("f", "file", true, "The properties file");
options.addOption("v", "verbose", false, "Verbose logging output");
options.addOption("h", "help", false, "Help output");
try {
CommandLine line = parser.parse(options, args);
if (line.hasOption('v')) {
org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.DEBUG);
}
if (line.hasOption('h')) {
usage(options);
}
if (line.hasOption('f')) {
propertyFile = line.getOptionValue('f');
} else {
throw new Exception("Please supply -f");
}
} catch (Exception e) {
log.error("Invalid command line: " + e, e);
usage(options);
}
Properties props = new Properties();
props.load(new FileReader(propertyFile));
startFromProperties(props);
Runtime.getRuntime()
.addShutdownHook(
new Thread(
new Runnable() {
@Override
public void run() {
log.info("Received shutdown signal. Shutting down...");
server.stop(3);
}
}));
}
public void test13425() {
Options options = new Options();
Option oldpass =
OptionBuilder.withLongOpt("old-password")
.withDescription("Use this option to specify the old password")
.hasArg()
.create('o');
Option newpass =
OptionBuilder.withLongOpt("new-password")
.withDescription("Use this option to specify the new password")
.hasArg()
.create('n');
String[] args = {"-o", "-n", "newpassword"};
options.addOption(oldpass);
options.addOption(newpass);
Parser parser = new PosixParser();
try {
CommandLine line = parser.parse(options, args);
}
// catch the exception and leave the method
catch (Exception exp) {
assertTrue(exp != null);
return;
}
fail("MissingArgumentException not caught.");
}
public static Options buildCommandLineOptions(final Options options) {
Option opt = new Option("h", "help", false, "Print help");
opt.setRequired(false);
options.addOption(opt);
opt =
new Option(
"n",
"namesrvAddr",
true,
"Name server address list, eg : 192.168.0.1:9876; 192.168.0.2:9876");
opt.setRequired(false);
options.addOption(opt);
return options;
}
/* public static String optarg; //TODO import gnu.getopt.Getopt; in ginit()
public static int optind; //TODO import gnu.getopt.Getopt; in ginit();
//TODO make long_options(struct)
private static String[] long_options = { "verbose", "verbose:gc", "verbose:sugar",
"verbose:code", "interactive", "typecheck",
"start-with", "test", "test-with", "builtin-test", "NULL" };
*/
static {
longOptions = new Options();
longOptions.addOption(null, "verbose", false, null);
longOptions.addOption(null, "verbose:gc", false, null);
longOptions.addOption(null, "verbose:sugar", false, null);
longOptions.addOption(null, "verbose:code", false, null);
longOptions.addOption("i", "interactive", false, null);
longOptions.addOption("c", "typecheck", false, null);
longOptions.addOption("S", "start-with", true, null);
longOptions.addOption("T", "test", true, null);
longOptions.addOption("T", "test-with", true, null);
longOptions.addOption("B", "builtin-test", true, null);
}
public void addParameterInfo() {
/* use Object parameter of Options class to store parameter information */
parameter.addOption(
OptionBuilder.withArgName("input VCF file")
.hasArg()
.withDescription("Input vcf file containing variation info")
.create(INPUT_VCF));
parameter.addOption(
OptionBuilder.withArgName("input tabular file")
.hasArg()
.withDescription("Input tabular file containing variation info")
.create(INPUT_TAB));
parameter.addOption(
OptionBuilder.withArgName("output file")
.hasArg()
.withDescription("Output alleles p value")
.create(OUTPUT_LINE));
parameter.addOption(
OptionBuilder.withArgName("Columns for Alleles")
.hasArg()
.withDescription("columns where allele info is set")
.create(COLUMN));
parameter.addOption(
OptionBuilder.withArgName("Cache data")
.hasArg(false)
.withDescription("weather to cache data in memory or not, default no")
.create(CACHE));
parameter.addOption(
OptionBuilder.withArgName("re-partition num")
.hasArg()
.withDescription(
"even the load of each task, 1 partition for a task or 4 partitions for a task is recommended. Default, not re-partition")
.create(PARTITIONS));
parameter.addOption(
OptionBuilder.hasArg(false).withDescription("show version information").create(VERSION));
parameter.addOption(
OptionBuilder.hasArg(false)
.withDescription("print and show this information")
.create(HELP));
parameter.addOption(OptionBuilder.hasArg(false).withDescription("").create(HELP2));
}
private void parseArgs(final String[] args) throws ParseException {
final Options options = new Options();
options.addOption("c", "claim", false, "Use Try/Claim");
options.addOption("", "pubChannel", true, "Primary publishing channel");
options.addOption("", "reflectChannel", true, "Reflection channel");
final CommandLineParser parser = new GnuParser();
final CommandLine command = parser.parse(options, args);
if (command.hasOption("pubChannel")) {
pubChannel = command.getOptionValue("pubChannel", "udp://localhost:44444");
}
if (command.hasOption("reflectChannel")) {
reflectChannel = command.getOptionValue("reflectChannel", "udp://localhost:55555");
}
}
public void test15648() throws Exception {
CommandLineParser parser = new PosixParser();
final String[] args = new String[] {"-m", "\"Two Words\""};
Option m = OptionBuilder.hasArgs().create("m");
Options options = new Options();
options.addOption(m);
CommandLine line = parser.parse(options, args);
assertEquals("Two Words", line.getOptionValue("m"));
}
// TODO add exception for invalid options
private void loadCLO(String[] args) {
Options options = new Options();
String[][] clolist = {
// {"variable/optionname", "description"},
{"genConfig", "general configuration file location"},
{"inWeightsLoc", "input weights configuration file location"},
{"inDBLoc", "input database file location"},
{"outWeightsLoc", "output weights configuration file location"},
{"outDBLoc", "output database file location"},
{"p3pLocation", "adding to DB: single policy file location"},
{"p3pDirLocation", "adding to DB: multiple policy directory location"},
{"newDB", "create new database in place of old one (doesn't check for existence of old one"},
{"newPolicyLoc", "the policy object to process"},
{"userResponse", "response to specified policy"},
{"userIO", "user interface"},
{"userInit", "initialization via user interface"},
{"policyDB", "PolicyDatabase backend"},
{"cbrV", "CBR to use"},
{"blanketAccept", "automatically accept the user suggestion"},
{"loglevel", "level of things save to the log- see java logging details"},
{"policyDB", "PolicyDatabase backend"},
{"NetworkRType", "Network Resource type"},
{"NetworkROptions", "Network Resource options"},
{"confidenceLevel", "Confidence threshold for consulting a networked resource"},
{"useNet", "use networking options"},
{"loglocation", "where to save the log file"},
{"loglevel", "the java logging level to use. See online documentation for enums."}
};
for (String[] i : clolist) {
options.addOption(i[0], true, i[1]);
}
CommandLineParser parser = new PosixParser();
CommandLine cmd = null;
try {
cmd = parser.parse(options, args);
} catch (ParseException e) {
System.err.println("Error parsing commandline arguments.");
e.printStackTrace();
System.exit(3);
}
/*
for(String i : args)
{
System.err.println(i);
}
*/
for (String[] i : clolist) {
if (cmd.hasOption(i[0])) {
System.err.println("found option i: " + i);
genProps.setProperty(i[0], cmd.getOptionValue(i[0]));
}
}
System.err.println(genProps);
}
static Options options() {
Options options = new Options();
options.addOption(LIST, false, "List current monitors");
options.addOption(ALARMS, false, "Show alarms");
options.addOption(PERIOD, true, "Period to cover when showing alarms");
options.addOption(THRESHOLD, true, "Minimum duration when showing alarms");
options.addOption(DELETE, true, "Delete monitor by ID");
options.addOption(START, false, "Start monitors (use with 'wait' and 'timeout')");
options.addOption(WAIT, true, "Wait duration in milliseconds between each poll cycle");
options.addOption(TIMEOUT, true, "Timeout duration in milliseconds for a poll");
return options;
}
protected CommandLine getCommand(String[] args) throws ParseException {
Options options = new Options();
Option opt = new Option("maxMaps", true, "max number of maps to use for this copy");
opt.setRequired(true);
options.addOption(opt);
opt = new Option("sourcePaths", true, "comma separtated list of source paths to be copied");
opt.setRequired(true);
options.addOption(opt);
opt = new Option("targetPath", true, "target path");
opt.setRequired(true);
options.addOption(opt);
opt = new Option("falconFeedStorageType", true, "feed storage type");
opt.setRequired(true);
options.addOption(opt);
return new GnuParser().parse(options, args);
}
public void test19383() {
Options options = new Options();
options.addOption(new Option("a", "aaa", false, "aaaaaaa"));
options.addOption(new Option(null, "bbb", false, "bbbbbbb"));
options.addOption(new Option("c", null, false, "ccccccc"));
HelpFormatter formatter = new HelpFormatter();
String SEP = System.getProperty("line.separator");
StringWriter out = new StringWriter();
formatter.printHelp(new PrintWriter(out), 80, "foobar", "", options, 2, 2, "", true);
assertEquals(
"usage: foobar [-a] [--bbb] [-c]"
+ SEP
+ " -a,--aaa aaaaaaa"
+ SEP
+ " --bbb bbbbbbb"
+ SEP
+ " -c ccccccc"
+ SEP,
out.toString());
}
public void test11680() {
Options options = new Options();
options.addOption("f", true, "foobar");
options.addOption("m", true, "missing");
String[] args = new String[] {"-f", "foo"};
CommandLineParser parser = new PosixParser();
try {
CommandLine cmd = parser.parse(options, args);
try {
cmd.getOptionValue("f", "default f");
cmd.getOptionValue("m", "default m");
} catch (NullPointerException exp) {
fail("NullPointer caught: " + exp.getMessage());
}
} catch (ParseException exp) {
fail("Unexpected Exception: " + exp.getMessage());
}
}
public static void main(String[] args) {
String formatstr = "ws [--in][--out][--dd][--sw][-h]";
Options opt = new Options();
// opt.addOption(OptionBuilder.withArgName("in").hasArg().withDescription("search for buildfile
// towards the root of the filesystem and use it").create("O"));
opt.addOption(
OptionBuilder.withLongOpt("in")
.withDescription("file path of those files need to be processed")
.withValueSeparator('=')
.hasArg()
.create());
opt.addOption(
OptionBuilder.withLongOpt("out")
.withDescription("file path to store result")
.withValueSeparator('=')
.hasArg()
.create());
opt.addOption(
OptionBuilder.withLongOpt("dd")
.withDescription("file path of dictionary")
.withValueSeparator('=')
.hasArg()
.create());
opt.addOption(
OptionBuilder.withLongOpt("sw")
.withDescription("file path of stop words")
.withValueSeparator('=')
.hasArg()
.create());
opt.addOption("h", "help", false, "print help for the command.");
if (args.length == 0) {
HelpFormatter hf = new HelpFormatter();
hf.printHelp(formatstr, "", opt, "");
return;
} else {
parse_args(args, formatstr, opt);
}
}
public void test14786() throws Exception {
Option o = OptionBuilder.isRequired().withDescription("test").create("test");
Options opts = new Options();
opts.addOption(o);
opts.addOption(o);
CommandLineParser parser = new GnuParser();
String[] args = new String[] {"-test"};
CommandLine line = parser.parse(opts, args);
assertTrue(line.hasOption("test"));
}
private static Options buildOptions() {
Options options = new Options();
Option tokenService =
OptionBuilder.withArgName("service")
.hasArg()
.withDescription("set the name of calling service")
.isRequired()
.create("service");
options.addOption(tokenService);
return options;
}
public static void main(String[] args) {
Options options = new Options();
options.addOption("v", true, "Input Vector folder"); // yearly vector data
options.addOption("p", true, "Points folder"); // yearly mds (rotate) output
options.addOption("d", true, "Destination folder");
options.addOption("o", true, "Original stock file"); // global 10 year stock file
options.addOption(
"s",
true,
"Sector file"); // If Histogram true then set this as the folder to histogram output
options.addOption("h", false, "Gen from histogram");
options.addOption("e", true, "Extra classes file"); // a file containing fixed classes
options.addOption("ci", true, "Cluster input file");
options.addOption("co", true, "Cluster output file");
CommandLineParser commandLineParser = new BasicParser();
try {
CommandLine cmd = commandLineParser.parse(options, args);
String vectorFile = cmd.getOptionValue("v");
String pointsFolder = cmd.getOptionValue("p");
String distFolder = cmd.getOptionValue("d");
String originalStocks = cmd.getOptionValue("o");
String sectorFile = cmd.getOptionValue("s");
boolean histogram = cmd.hasOption("h");
String fixedClasses = cmd.getOptionValue("e");
String clusterInputFile = cmd.getOptionValue("ci");
String clusterOutputFile = cmd.getOptionValue("co");
LabelApply program =
new LabelApply(
vectorFile,
pointsFolder,
distFolder,
originalStocks,
sectorFile,
histogram,
fixedClasses,
clusterInputFile,
clusterOutputFile);
program.process();
} catch (ParseException e) {
e.printStackTrace();
}
}
public static void main(String[] args)
throws TransformationException, IOException, AnalysisException, ParseException,
CloneNotSupportedException {
Options options = new Options();
options.addOption("input", true, "input path");
options.addOption("output", true, "output path");
CommandLineParser parser = new GnuParser();
CommandLine line = parser.parse(options, args);
String inDir = line.getOptionValue("input");
String outDir = line.getOptionValue("output");
File dir = new File(inDir);
for (File f : FileUtils.listFiles(dir, new String[] {"xml"}, true)) {
TrueVizToBxDocumentReader tvReader = new TrueVizToBxDocumentReader();
List<BxPage> pages = tvReader.read(new FileReader(f));
BxDocument doc = new BxDocument().setPages(pages);
doc.setFilename(f.getName());
int all = 0;
int good = 0;
for (BxZone z : doc.asZones()) {
all++;
if (!z.getLabel().equals(BxZoneLabel.OTH_UNKNOWN)) {
good++;
}
}
int intcov = 0;
if (all > 0) {
intcov = good * 100 / all;
}
System.out.println(doc.getFilename() + " " + intcov);
File f2 = new File(outDir + doc.getFilename() + "." + intcov);
FileUtils.copyFile(f, f2);
}
}