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 init(String[] args) throws UserError {
Context.reset();
CommandLineParser globalParser = new GnuParser();
List<String> globalArgs = new ArrayList<String>();
boolean inGlobal = true;
for (String arg : args) {
if (inGlobal) {
if (arg.startsWith("--")) {
globalArgs.add(arg);
} else {
this.command = arg;
inGlobal = false;
}
} else {
commandArgs.add(arg);
}
}
try {
this.globalArguments =
globalParser.parse(globalOptions, globalArgs.toArray(new String[globalArgs.size()]));
} catch (ParseException e) {
throw new UserError("Error parsing global command line argument: " + e.getMessage());
}
}
public static Options parseArgs(String cmdArgs[]) {
CommandLineParser parser = new GnuParser();
CmdLineOptions options = getCmdLineOptions();
try {
CommandLine cmd = parser.parse(options, cmdArgs, false);
if (cmd.hasOption(HELP_OPTION)) {
printUsage(options);
System.exit(0);
}
String[] args = cmd.getArgs();
if (args.length == 0) {
System.err.println("No sstables to split");
printUsage(options);
System.exit(1);
}
Options opts = new Options(Arrays.asList(args));
opts.debug = cmd.hasOption(DEBUG_OPTION);
opts.verbose = cmd.hasOption(VERBOSE_OPTION);
opts.snapshot = !cmd.hasOption(NO_SNAPSHOT_OPTION);
opts.sizeInMB = DEFAULT_SSTABLE_SIZE;
if (cmd.hasOption(SIZE_OPTION))
opts.sizeInMB = Integer.valueOf(cmd.getOptionValue(SIZE_OPTION));
return opts;
} catch (ParseException e) {
errorMsg(e.getMessage(), options);
return null;
}
}
public static Options parseArgs(String cmdArgs[]) {
CommandLineParser parser = new GnuParser();
CmdLineOptions options = getCmdLineOptions();
try {
CommandLine cmd = parser.parse(options, cmdArgs, false);
if (cmd.hasOption(HELP_OPTION)) {
printUsage(options);
System.exit(0);
}
String[] args = cmd.getArgs();
if (args.length >= 4 || args.length < 2) {
String msg = args.length < 2 ? "Missing arguments" : "Too many arguments";
errorMsg(msg, options);
System.exit(1);
}
String keyspace = args[0];
String cf = args[1];
String snapshot = null;
if (args.length == 3) snapshot = args[2];
Options opts = new Options(keyspace, cf, snapshot);
opts.debug = cmd.hasOption(DEBUG_OPTION);
opts.keepSource = cmd.hasOption(KEEP_SOURCE);
return opts;
} catch (ParseException e) {
errorMsg(e.getMessage(), options);
return null;
}
}
public static LoaderOptions parseArgs(String cmdArgs[]) {
CommandLineParser parser = new GnuParser();
CmdLineOptions options = getCmdLineOptions();
try {
CommandLine cmd = parser.parse(options, cmdArgs, false);
if (cmd.hasOption(HELP_OPTION)) {
printUsage(options);
System.exit(0);
}
String[] args = cmd.getArgs();
if (args.length == 0) {
System.err.println("Missing sstable directory argument");
printUsage(options);
System.exit(1);
}
if (args.length > 1) {
System.err.println("Too many arguments");
printUsage(options);
System.exit(1);
}
String dirname = args[0];
File dir = new File(dirname);
if (!dir.exists()) errorMsg("Unknown directory: " + dirname, options);
if (!dir.isDirectory()) errorMsg(dirname + " is not a directory", options);
LoaderOptions opts = new LoaderOptions(dir);
opts.debug = cmd.hasOption(DEBUG_OPTION);
opts.verbose = cmd.hasOption(VERBOSE_OPTION);
opts.noProgress = cmd.hasOption(NOPROGRESS_OPTION);
if (cmd.hasOption(IGNORE_NODES_OPTION)) {
String[] nodes = cmd.getOptionValue(IGNORE_NODES_OPTION).split(",");
try {
for (String node : nodes) {
opts.ignores.add(InetAddress.getByName(node));
}
} catch (UnknownHostException e) {
errorMsg(e.getMessage(), options);
}
}
return opts;
} catch (ParseException e) {
errorMsg(e.getMessage(), options);
return null;
}
}
public static void main(String[] args) {
Main main = new Main();
main.header("Liquibase SDK");
try {
main.init(args);
if (main.command == null) {
throw new UserError("No command passed");
}
if (main.command.equals("help")) {
main.printHelp();
return;
}
VagrantControl vagrantControl;
if (main.command.equals("vagrant")) {
vagrantControl = new VagrantControl(main);
} else {
throw new UserError("Unknown command: " + main.command);
}
CommandLineParser commandParser = new GnuParser();
try {
CommandLine commandArguments =
commandParser.parse(
vagrantControl.getOptions(),
main.commandArgs.toArray(new String[main.commandArgs.size()]));
vagrantControl.execute(commandArguments);
} catch (ParseException e) {
throw new UserError("Error parsing command arguments: " + e.getMessage());
}
main.divider();
main.out("Command executed successfully");
} catch (UserError userError) {
main.out("");
main.header("ERROR EXECUTING COMMAND");
main.out(userError.getMessage());
main.out("");
main.out("");
return;
} catch (Throwable exception) {
System.out.println("Unexpected error: " + exception.getMessage());
exception.printStackTrace();
}
}
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);
}
}));
}
private void parseCmdLine(String[] args) {
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption("v", "version", false, "Q2's version");
options.addOption("d", "deploydir", true, "Deployment directory");
options.addOption("r", "recursive", false, "Deploy subdirectories recursively");
options.addOption("h", "help", false, "Usage information");
options.addOption("C", "config", true, "Configuration bundle");
options.addOption("e", "encrypt", true, "Encrypt configuration bundle");
options.addOption("i", "cli", false, "Command Line Interface");
options.addOption("c", "command", true, "Command to execute");
try {
CommandLine line = parser.parse(options, args);
if (line.hasOption("v")) {
displayVersion();
System.exit(0);
}
if (line.hasOption("h")) {
HelpFormatter helpFormatter = new HelpFormatter();
helpFormatter.printHelp("Q2", options);
System.exit(0);
}
if (line.hasOption("c")) {
cli = new CLI(this, line.getOptionValue("c"), line.hasOption("i"));
} else if (line.hasOption("i")) cli = new CLI(this, null, true);
String dir = DEFAULT_DEPLOY_DIR;
if (line.hasOption("d")) {
dir = line.getOptionValue("d");
}
recursive = line.hasOption("r");
this.deployDir = new File(dir);
if (line.hasOption("C")) deployBundle(new File(line.getOptionValue("C")), false);
if (line.hasOption("e")) deployBundle(new File(line.getOptionValue("e")), true);
} catch (MissingArgumentException e) {
System.out.println("ERROR: " + e.getMessage());
System.exit(1);
} catch (Exception e) {
e.printStackTrace();
System.exit(1);
}
}
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();
}
}
/**
* Same as main(args) except that exceptions are thrown out instead of causing the VM to exit and
* the lookup for .groovy files can be controlled
*/
public static void commandLineCompile(String[] args, boolean lookupUnnamedFiles)
throws Exception {
Options options = createCompilationOptions();
CommandLineParser cliParser = new GroovyPosixParser();
CommandLine cli;
cli = cliParser.parse(options, args);
if (cli.hasOption('h')) {
displayHelp(options);
return;
}
if (cli.hasOption('v')) {
displayVersion();
return;
}
displayStackTraceOnError = cli.hasOption('e');
CompilerConfiguration configuration = generateCompilerConfigurationFromOptions(cli);
//
// Load the file name list
String[] filenames = generateFileNamesFromOptions(cli);
boolean fileNameErrors = filenames == null;
if (!fileNameErrors && (filenames.length == 0)) {
displayHelp(options);
return;
}
fileNameErrors = fileNameErrors && !validateFiles(filenames);
if (!fileNameErrors) {
doCompilation(configuration, null, filenames, lookupUnnamedFiles);
}
}
private static void parse_args(String[] args, String formatstr, Options opt) {
HelpFormatter formatter = new HelpFormatter();
CommandLineParser parser = new PosixParser();
CommandLine cl = null;
try {
cl = parser.parse(opt, args);
} catch (ParseException e) {
formatter.printHelp(formatstr, opt); // 如果发生异常，则打印出帮助信息
}
if (cl.hasOption("in") && cl.hasOption("out") && cl.hasOption("dd") && cl.hasOption("sw")) {
String stopWordsPath = cl.getOptionValue("sw");
String inPath = cl.getOptionValue("in");
String outPath = cl.getOptionValue("out");
String dicPath = cl.getOptionValue("dd");
processOperation(stopWordsPath, inPath, outPath, dicPath);
} else {
HelpFormatter hf = new HelpFormatter();
hf.printHelp(formatstr, "", opt, "");
return;
}
}
/**
* Given arguments specifying an SSTable, and optionally an output file, export the contents of
* the SSTable to JSON.
*
* @param args command lines arguments
* @throws ConfigurationException on configuration failure (wrong params given)
*/
public static void main(String[] args) throws ConfigurationException {
CommandLineParser parser = new PosixParser();
try {
cmd = parser.parse(options, args);
} catch (ParseException e1) {
System.err.println(e1.getMessage());
printUsage();
System.exit(1);
}
if (cmd.getArgs().length != 1) {
System.err.println("You must supply exactly one sstable");
printUsage();
System.exit(1);
}
String[] keys = cmd.getOptionValues(KEY_OPTION);
HashSet<String> excludes =
new HashSet<>(
Arrays.asList(
cmd.getOptionValues(EXCLUDE_KEY_OPTION) == null
? new String[0]
: cmd.getOptionValues(EXCLUDE_KEY_OPTION)));
String ssTableFileName = new File(cmd.getArgs()[0]).getAbsolutePath();
if (Descriptor.isLegacyFile(new File(ssTableFileName))) {
System.err.println("Unsupported legacy sstable");
System.exit(1);
}
if (!new File(ssTableFileName).exists()) {
System.err.println("Cannot find file " + ssTableFileName);
System.exit(1);
}
Descriptor desc = Descriptor.fromFilename(ssTableFileName);
try {
CFMetaData metadata = metadataFromSSTable(desc);
if (cmd.hasOption(ENUMERATE_KEYS_OPTION)) {
JsonTransformer.keysToJson(
null,
iterToStream(new KeyIterator(desc, metadata)),
cmd.hasOption(RAW_TIMESTAMPS),
metadata,
System.out);
} else {
SSTableReader sstable = SSTableReader.openNoValidation(desc, metadata);
IPartitioner partitioner = sstable.getPartitioner();
final ISSTableScanner currentScanner;
if ((keys != null) && (keys.length > 0)) {
List<AbstractBounds<PartitionPosition>> bounds =
Arrays.stream(keys)
.filter(key -> !excludes.contains(key))
.map(metadata.getKeyValidator()::fromString)
.map(partitioner::decorateKey)
.sorted()
.map(DecoratedKey::getToken)
.map(token -> new Bounds<>(token.minKeyBound(), token.maxKeyBound()))
.collect(Collectors.toList());
currentScanner = sstable.getScanner(bounds.iterator());
} else {
currentScanner = sstable.getScanner();
}
Stream<UnfilteredRowIterator> partitions =
iterToStream(currentScanner)
.filter(
i ->
excludes.isEmpty()
|| !excludes.contains(
metadata.getKeyValidator().getString(i.partitionKey().getKey())));
if (cmd.hasOption(DEBUG_OUTPUT_OPTION)) {
AtomicLong position = new AtomicLong();
partitions.forEach(
partition -> {
position.set(currentScanner.getCurrentPosition());
if (!partition.partitionLevelDeletion().isLive()) {
System.out.println(
"["
+ metadata.getKeyValidator().getString(partition.partitionKey().getKey())
+ "]@"
+ position.get()
+ " "
+ partition.partitionLevelDeletion());
}
if (!partition.staticRow().isEmpty()) {
System.out.println(
"["
+ metadata.getKeyValidator().getString(partition.partitionKey().getKey())
+ "]@"
+ position.get()
+ " "
+ partition.staticRow().toString(metadata, true));
}
partition.forEachRemaining(
row -> {
System.out.println(
"["
+ metadata
.getKeyValidator()
.getString(partition.partitionKey().getKey())
+ "]@"
+ position.get()
+ " "
+ row.toString(metadata, false, true));
position.set(currentScanner.getCurrentPosition());
});
});
} else {
JsonTransformer.toJson(
currentScanner, partitions, cmd.hasOption(RAW_TIMESTAMPS), metadata, System.out);
}
}
} catch (IOException e) {
// throwing exception outside main with broken pipe causes windows cmd to hang
e.printStackTrace(System.err);
}
System.exit(0);
}
/*
*main function
*/
public static void main(String args[]) {
String title1 = " ";
String publisher_name1 = " ";
String published_date1 = "";
String content1 = "";
int n = 0;
String str = "";
// try block starts here
try {
Options option = new Options();
option.addOption("hp", false, "help");
option.addOption("hlp", false, "help");
CommandLineParser parser = new DefaultParser();
CommandLine cmd = parser.parse(option, args);
// str=cmd.getArgs()[0];
/*prints the help message here*/
if ((cmd.hasOption("hp")) || (cmd.hasOption("hlp"))) {
System.out.println(
"this program gets an argument through commandline 'n' number of books. then reads n books from standard input"
+ "and prints them on standard output");
if (args.length <= 1) {
// exit the program
System.exit(0);
}
} // close outer if block
else {
if (args.length < 1) {
// if user not gives option and value of n then prints this message.
System.out.println(
"this program gets an argument through commandline 'n' number of books. then reads n books from standard input"
+ "and prints them on standard output");
System.exit(0);
}
} // close the outer else block
str = cmd.getArgs()[0];
n = Integer.parseInt(str);
} catch (Exception e) {
// System.exit(0);
// if any erroy occurs it catches here
System.out.println(e);
}
int num = 0;
Scanner sc1 = new Scanner(System.in); /*create an instance of scanner object*/
Scanner sc = new Scanner(System.in);
CmdBook b[] = new CmdBook[n]; /* create arraylist of objects of class Book*/
for (int i = 0; i < n; i++) {
// initialise the array of objects
b[i] = new CmdBook();
}
for (int i = 0; i < n; i++) {
/* take input from standard input*/
System.out.println("enter the title of the book:");
title1 = sc.next();
System.out.println("enter the name of publisher");
publisher_name1 = sc.next();
System.out.println("enter published date");
published_date1 = sc.next();
System.out.println("how many authors are");
num = sc1.nextInt();
ArrayList<String> author_name1 =
new ArrayList<String>(); /*create an ArrayList author_name1 */
for (int j = 0; j < num; j++) {
/*take input */
System.out.println("enter authorname" + (j + 1));
author_name1.add(sc.next());
}
System.out.println("enter contents of book:");
content1 = sc.next();
/* call the method bookdetail with auguments which contains from
* standard input
*/
b[i].bookdetail(title1, publisher_name1, published_date1, content1, author_name1);
}
for (int i = 0; i < n; i++) {
/*call the methode printbook withe no aurgument*/
b[i].printbook();
}
} /*end of main function here*/
private void loadArgs(String[] args) throws ParameterProblem {
logger.debug("Parsing command line arguments");
final CommandLineParser parser = new PosixParser();
final Opts opts = new Opts();
final CommandLine line;
try {
line = parser.parse(opts.getOptions(), args);
} catch (ParseException e) {
throw new ParameterProblem(e.getMessage(), e);
}
// figure action first
AdminAction theAction = null;
for (AdminAction a : AdminAction.values()) {
if (line.hasOption(a.option())) {
if (theAction == null) {
theAction = a;
} else {
throw new ParameterProblem("You may only specify a single action");
}
}
}
if (theAction == null) {
throw new ParameterProblem("You must specify an action");
}
this.action = theAction;
logger.debug("Action: " + theAction);
// short circuit for --help arg
if (theAction == AdminAction.Help) {
return;
}
// then action-specific arguments
if (theAction == AdminAction.AddNodes || theAction == AdminAction.UpdateNodes) {
this.hosts = parseHosts(line.getOptionValue(theAction.option()));
if (line.hasOption(Opts.MEMORY)) {
final String memString = line.getOptionValue(Opts.MEMORY);
if (memString == null || memString.trim().length() == 0) {
throw new ParameterProblem("Node memory value is empty");
}
this.nodeMemory = parseMemory(memString);
this.nodeMemoryConfigured = true;
}
if (line.hasOption(Opts.NETWORKS)) {
this.nodeNetworks = line.getOptionValue(Opts.NETWORKS);
}
if (line.hasOption(Opts.POOL)) {
String pool = line.getOptionValue(Opts.POOL);
if (pool == null || pool.trim().length() == 0) {
throw new ParameterProblem("Node pool value is empty");
}
this.nodePool = pool.trim();
}
final boolean active = line.hasOption(Opts.ACTIVE);
final boolean inactive = line.hasOption(Opts.INACTIVE);
if (active && inactive) {
throw new ParameterProblem(
"You cannot specify both " + Opts.ACTIVE_LONG + " and " + Opts.INACTIVE_LONG);
}
if (active) {
this.nodeActiveConfigured = true;
}
if (inactive) {
this.nodeActive = false;
this.nodeActiveConfigured = true;
}
} else if (theAction == AdminAction.RemoveNodes) {
this.hosts = parseHosts(line.getOptionValue(theAction.option()));
} else if (theAction == AdminAction.ListNodes) {
final String hostArg = line.getOptionValue(AdminAction.ListNodes.option());
if (hostArg != null) {
this.hosts = parseHosts(hostArg);
}
} else if (theAction == AdminAction.PoolAvailability) {
if (line.hasOption(Opts.POOL)) {
final String pool = line.getOptionValue(Opts.POOL);
if (pool == null || pool.trim().length() == 0) {
throw new ParameterProblem("Pool name value is empty");
}
this.nodePool = pool;
}
if (line.hasOption(Opts.FREE)) {
this.inUse = RemoteNodeManagement.FREE_ENTRIES;
}
if (line.hasOption(Opts.USED)) {
this.inUse = RemoteNodeManagement.USED_ENTRIES;
}
}
// finally everything else
if (!line.hasOption(Opts.CONFIG)) {
throw new ParameterProblem(Opts.CONFIG_LONG + " option is required");
}
String config = line.getOptionValue(Opts.CONFIG);
if (config == null || config.trim().length() == 0) {
throw new ParameterProblem("Config file path is invalid");
}
super.configPath = config.trim();
final boolean batchMode = line.hasOption(Opts.BATCH);
final boolean json = line.hasOption(Opts.JSON);
final Reporter.OutputMode mode;
if (batchMode && json) {
throw new ParameterProblem(
"You cannot specify both " + Opts.BATCH_LONG + " and " + Opts.JSON_LONG);
} else if (batchMode) {
mode = Reporter.OutputMode.Batch;
} else if (json) {
mode = Reporter.OutputMode.Json;
} else {
mode = Reporter.OutputMode.Friendly;
}
final String[] fields;
if (line.hasOption(Opts.REPORT)) {
fields = parseFields(line.getOptionValue(Opts.REPORT), theAction);
} else {
fields = theAction.fields();
}
String delimiter = null;
if (line.hasOption(Opts.DELIMITER)) {
delimiter = line.getOptionValue(Opts.DELIMITER);
}
this.reporter = new Reporter(mode, fields, delimiter);
if (line.hasOption(Opts.OUTPUT)) {
final String filename = line.getOptionValue(Opts.OUTPUT);
final File f = new File(filename);
try {
this.outStream = new FileOutputStream(f);
} catch (FileNotFoundException e) {
throw new ParameterProblem(
"Specified output file could not be opened for writing: " + f.getAbsolutePath(), e);
}
} else {
this.outStream = System.out;
}
final List leftovers = line.getArgList();
if (leftovers != null && !leftovers.isEmpty()) {
throw new ParameterProblem(
"There are unrecognized arguments, check -h to make "
+ "sure you are doing the intended thing: "
+ leftovers.toString());
}
}
public static LoaderOptions parseArgs(String cmdArgs[]) {
CommandLineParser parser = new GnuParser();
CmdLineOptions options = getCmdLineOptions();
try {
CommandLine cmd = parser.parse(options, cmdArgs, false);
if (cmd.hasOption(HELP_OPTION)) {
printUsage(options);
System.exit(0);
}
String[] args = cmd.getArgs();
if (args.length == 0) {
System.err.println("Missing sstable directory argument");
printUsage(options);
System.exit(1);
}
if (args.length > 1) {
System.err.println("Too many arguments");
printUsage(options);
System.exit(1);
}
String dirname = args[0];
File dir = new File(dirname);
if (!dir.exists()) errorMsg("Unknown directory: " + dirname, options);
if (!dir.isDirectory()) errorMsg(dirname + " is not a directory", options);
LoaderOptions opts = new LoaderOptions(dir);
opts.debug = cmd.hasOption(DEBUG_OPTION);
opts.verbose = cmd.hasOption(VERBOSE_OPTION);
opts.noProgress = cmd.hasOption(NOPROGRESS_OPTION);
if (cmd.hasOption(RPC_PORT_OPTION))
opts.rpcPort = Integer.parseInt(cmd.getOptionValue(RPC_PORT_OPTION));
if (cmd.hasOption(USER_OPTION)) opts.user = cmd.getOptionValue(USER_OPTION);
if (cmd.hasOption(PASSWD_OPTION)) opts.passwd = cmd.getOptionValue(PASSWD_OPTION);
if (cmd.hasOption(INITIAL_HOST_ADDRESS_OPTION)) {
String[] nodes = cmd.getOptionValue(INITIAL_HOST_ADDRESS_OPTION).split(",");
try {
for (String node : nodes) {
opts.hosts.add(InetAddress.getByName(node.trim()));
}
} catch (UnknownHostException e) {
errorMsg("Unknown host: " + e.getMessage(), options);
}
} else {
System.err.println("Initial hosts must be specified (-d)");
printUsage(options);
System.exit(1);
}
if (cmd.hasOption(IGNORE_NODES_OPTION)) {
String[] nodes = cmd.getOptionValue(IGNORE_NODES_OPTION).split(",");
try {
for (String node : nodes) {
opts.ignores.add(InetAddress.getByName(node.trim()));
}
} catch (UnknownHostException e) {
errorMsg("Unknown host: " + e.getMessage(), options);
}
}
// try to load config file first, so that values can be rewritten with other option values.
// otherwise use default config.
Config config;
if (cmd.hasOption(CONFIG_PATH)) {
File configFile = new File(cmd.getOptionValue(CONFIG_PATH));
if (!configFile.exists()) {
errorMsg("Config file not found", options);
}
config = new YamlConfigurationLoader().loadConfig(configFile.toURI().toURL());
} else {
config = new Config();
}
opts.storagePort = config.storage_port;
opts.sslStoragePort = config.ssl_storage_port;
opts.throttle = config.stream_throughput_outbound_megabits_per_sec;
opts.encOptions = config.client_encryption_options;
opts.serverEncOptions = config.server_encryption_options;
if (cmd.hasOption(THROTTLE_MBITS)) {
opts.throttle = Integer.parseInt(cmd.getOptionValue(THROTTLE_MBITS));
}
if (cmd.hasOption(SSL_TRUSTSTORE)) {
opts.encOptions.truststore = cmd.getOptionValue(SSL_TRUSTSTORE);
}
if (cmd.hasOption(SSL_TRUSTSTORE_PW)) {
opts.encOptions.truststore_password = cmd.getOptionValue(SSL_TRUSTSTORE_PW);
}
if (cmd.hasOption(SSL_KEYSTORE)) {
opts.encOptions.keystore = cmd.getOptionValue(SSL_KEYSTORE);
// if a keystore was provided, lets assume we'll need to use it
opts.encOptions.require_client_auth = true;
}
if (cmd.hasOption(SSL_KEYSTORE_PW)) {
opts.encOptions.keystore_password = cmd.getOptionValue(SSL_KEYSTORE_PW);
}
if (cmd.hasOption(SSL_PROTOCOL)) {
opts.encOptions.protocol = cmd.getOptionValue(SSL_PROTOCOL);
}
if (cmd.hasOption(SSL_ALGORITHM)) {
opts.encOptions.algorithm = cmd.getOptionValue(SSL_ALGORITHM);
}
if (cmd.hasOption(SSL_STORE_TYPE)) {
opts.encOptions.store_type = cmd.getOptionValue(SSL_STORE_TYPE);
}
if (cmd.hasOption(SSL_CIPHER_SUITES)) {
opts.encOptions.cipher_suites = cmd.getOptionValue(SSL_CIPHER_SUITES).split(",");
}
if (cmd.hasOption(TRANSPORT_FACTORY)) {
ITransportFactory transportFactory =
getTransportFactory(cmd.getOptionValue(TRANSPORT_FACTORY));
configureTransportFactory(transportFactory, opts);
opts.transportFactory = transportFactory;
}
return opts;
} catch (ParseException | ConfigurationException | MalformedURLException e) {
errorMsg(e.getMessage(), options);
return null;
}
}
public static void main(String[] args) {
String logConfig = System.getProperty("log-config");
if (logConfig == null) {
logConfig = "log-config.txt";
}
Options options = new Options();
options.addOption("h", "help", false, "print this message");
options.addOption("v", "version", false, "output version information and exit");
options.addOption(OptionBuilder.withDescription("trace mode").withLongOpt("trace").create());
options.addOption(OptionBuilder.withDescription("debug mode").withLongOpt("debug").create());
options.addOption(OptionBuilder.withDescription("info mode").withLongOpt("info").create());
options.addOption(
OptionBuilder.withArgName("file")
.hasArg()
.withDescription(
"file from which to read the labelled training set in tabular format (reference annotation)")
.isRequired()
.withLongOpt("labelled")
.create("l"));
options.addOption(
OptionBuilder.withArgName("file")
.hasArg()
.withDescription(
"file from which to read the translated unlabelled training set in tabular format (one sentence per line, including id)")
.isRequired()
.withLongOpt("unlabelled")
.create("u"));
options.addOption(
OptionBuilder.withArgName("file")
.hasArg()
.withDescription(
"file from which to read the translated roles (phrase table: source language \\t target language)")
.isRequired()
.withLongOpt("roles")
.create("r"));
options.addOption(
OptionBuilder.withArgName("file")
.hasArg()
.withDescription(
"file in which to write the translated labelled training set in tabular format (aligned with the reference annotation)")
.isRequired()
.withLongOpt("output")
.create("o"));
options.addOption(
OptionBuilder.withArgName("int")
.hasArg()
.withDescription("example from which to start from")
.withLongOpt("start")
.create());
CommandLineParser parser = new PosixParser();
CommandLine commandLine = null;
try {
commandLine = parser.parse(options, args);
Properties defaultProps = new Properties();
try {
defaultProps.load(new InputStreamReader(new FileInputStream(logConfig), "UTF-8"));
} catch (Exception e) {
defaultProps.setProperty("log4j.appender.stdout", "org.apache.log4j.ConsoleAppender");
defaultProps.setProperty(
"log4j.appender.stdout.layout.ConversionPattern", "[%t] %-5p (%F:%L) - %m %n");
defaultProps.setProperty("log4j.appender.stdout.layout", "org.apache.log4j.PatternLayout");
defaultProps.setProperty("log4j.appender.stdout.Encoding", "UTF-8");
}
if (commandLine.hasOption("trace")) {
defaultProps.setProperty("log4j.rootLogger", "trace,stdout");
} else if (commandLine.hasOption("debug")) {
defaultProps.setProperty("log4j.rootLogger", "debug,stdout");
} else if (commandLine.hasOption("info")) {
defaultProps.setProperty("log4j.rootLogger", "info,stdout");
} else {
if (defaultProps.getProperty("log4j.rootLogger") == null) {
defaultProps.setProperty("log4j.rootLogger", "info,stdout");
}
}
PropertyConfigurator.configure(defaultProps);
if (commandLine.hasOption("help") || commandLine.hasOption("version")) {
throw new ParseException("");
}
File labelled = new File(commandLine.getOptionValue("labelled"));
File unlabelled = new File(commandLine.getOptionValue("unlabelled"));
File roles = new File(commandLine.getOptionValue("roles"));
File output = new File(commandLine.getOptionValue("output"));
try {
if (commandLine.hasOption("start")) {
int start = Integer.parseInt(commandLine.getOptionValue("start"));
new AnnotationMigration(labelled, unlabelled, roles, output, start);
} else {
new AnnotationMigration(labelled, unlabelled, roles, output);
}
} catch (IOException e) {
logger.error(e);
}
} catch (ParseException exp) {
if (exp.getMessage().length() > 0) {
System.err.println("Parsing failed: " + exp.getMessage() + "\n");
}
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp(
200,
"java -Dfile.encoding=UTF-8 -cp dist/dirha.jar org.fbk.cit.hlt.dirha.AnnotationMigration",
"\n",
options,
"\n",
true);
System.exit(1);
}
}
public static void main(String[] args) throws Exception {
String inputFileName = "";
String inputFileName2 = "";
String outputFileName = "";
String solrServerHost = "";
String keepListFileName = "";
String filterListFileName = "";
String searchTerm = "";
HashMap<String, String> keepGrayList = new HashMap<String, String>();
HashMap<String, String> filterGrayList = new HashMap<String, String>();
boolean useAlias = false;
CommandLineParser parser = new GnuParser();
Options options = createCLIOptions();
try {
CommandLine line = parser.parse(options, args);
if (line.hasOption("f1")) {
// get the input file
inputFileName = line.getOptionValue("f1");
}
if (line.hasOption("f2")) {
inputFileName2 = line.getOptionValue("f2");
}
if (line.hasOption("o")) {
// get the output file
outputFileName = line.getOptionValue("o");
}
if (line.hasOption("s")) {
// get the server host name
solrServerHost = line.getOptionValue("s");
}
if (line.hasOption("term")) {
searchTerm = line.getOptionValue("term");
}
if (line.hasOption("a")) {
useAlias = true;
}
if (line.hasOption("k")) {
keepListFileName = line.getOptionValue("k");
}
if (line.hasOption("r")) {
filterListFileName = line.getOptionValue("r");
}
} catch (ParseException exp) {
log.warning("Command line parsing failed. Reason:" + exp.getMessage());
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("pubcrawl", options);
System.exit(1);
}
if (isEmpty(outputFileName) || isEmpty(inputFileName) && isEmpty(searchTerm)) {
// missing required elements, print usage and exit
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("pubcrawl", options);
System.exit(1);
}
if (!isEmpty(keepListFileName)) {
// need to load the keepList hashmap
FileReader inputReader = new FileReader(keepListFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String keepTerm = bufReader.readLine();
while (keepTerm != null) {
String[] keepInfoArr = keepTerm.trim().split("\t");
keepGrayList.put(keepInfoArr[0].toLowerCase(), keepInfoArr[1]);
keepTerm = bufReader.readLine();
}
bufReader.close();
}
log.info("loading filterlist filename");
if (!isEmpty(filterListFileName)) {
// need to load the filterlist hashmap
FileReader inputReader = new FileReader(filterListFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String filterTerm = bufReader.readLine();
while (filterTerm != null) {
String[] filterInfoArr = filterTerm.trim().split("\t");
filterGrayList.put(filterInfoArr[0].toLowerCase(), filterInfoArr[1]);
filterTerm = bufReader.readLine();
}
bufReader.close();
}
SolrServer server = getSolrServer(solrServerHost);
String logname = outputFileName + "_log.out";
// create output files
FileWriter logFileStream = new FileWriter(logname);
BufferedWriter logFileOut = new BufferedWriter(logFileStream);
FileWriter dataResultsStream = new FileWriter(outputFileName);
BufferedWriter dataResultsOut = new BufferedWriter(dataResultsStream);
final Map<String, Integer> singleCountMap = new HashMap<String, Integer>();
final List<String> term2List = new ArrayList<String>();
// now load the appropriate list of gene terms - if the second file name wasn't entered
if (isEmpty(inputFileName2)) {
String sql = "Select term1,count from singletermcount";
if (useAlias) {
sql = "Select alias,count from singletermcount_alias";
}
JdbcTemplate jdbcTemplate = getJdbcTemplate();
jdbcTemplate.query(
sql,
new ResultSetExtractor() {
public Object extractData(ResultSet rs) throws SQLException, DataAccessException {
while (rs.next()) {
String geneName = rs.getString(1).trim();
int count = rs.getInt(2);
singleCountMap.put(geneName.toLowerCase(), count);
if (count > 0) {
term2List.add(geneName.toLowerCase());
}
}
return null;
}
});
} else { // have a second input file, so read the file in and put those as the terms in the
// term2List, set the SingleCountMap to empty
FileReader inputReader2 = new FileReader(inputFileName2);
BufferedReader bufReader2 = new BufferedReader(inputReader2);
String searchTerm2 = bufReader2.readLine();
while (searchTerm2 != null) {
term2List.add(searchTerm2.trim().toLowerCase());
searchTerm2 = bufReader2.readLine();
}
}
Long totalDocCount = getTotalDocCount(server);
logFileOut.write("Total doc count: " + totalDocCount);
Pubcrawl p = new Pubcrawl();
if (isEmpty(inputFileName)) { // entered term option, just have one to calculate
SearchTermAndList searchTermArray = getTermAndTermList(searchTerm.trim(), useAlias, false);
Long searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
ExecutorService pool = Executors.newFixedThreadPool(32);
Set<Future<NGDItem>> set = new HashSet<Future<NGDItem>>();
Date firstTime = new Date();
for (String secondTerm : term2List) {
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
}
Date secondTime = new Date();
logFileOut.write(
"First set of queries took "
+ (secondTime.getTime() - firstTime.getTime()) / 1000
+ " seconds.\n");
logFileOut.flush();
logFileOut.close();
dataResultsOut.flush();
dataResultsOut.close();
pool.shutdown();
} else {
FileReader inputReader = new FileReader(inputFileName);
BufferedReader bufReader = new BufferedReader(inputReader);
String fileSearchTerm = bufReader.readLine();
SearchTermAndList searchTermArray = getTermAndTermList(fileSearchTerm, useAlias, false);
Long searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
// do this once with a lower amount of threads, in case we are running on a server where new
// caching is taking place
ExecutorService pool = Executors.newFixedThreadPool(32);
List<Future<NGDItem>> set = new ArrayList<Future<NGDItem>>();
long firstTime = currentTimeMillis();
int count = 0;
for (String secondTerm : term2List) {
count++;
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
if (count > 5000) {
for (Future<NGDItem> futureItem : set) {
dataResultsOut.write(futureItem.get().printItem());
futureItem = null;
}
count = 0;
set.clear();
}
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
}
long secondTime = currentTimeMillis();
logFileOut.write(
"First set of queries took " + (secondTime - firstTime) / 1000 + " seconds.\n");
logFileOut.flush();
set.clear();
pool = Executors.newFixedThreadPool(32);
fileSearchTerm = bufReader.readLine();
count = 0;
while (fileSearchTerm != null) {
searchTermArray = getTermAndTermList(fileSearchTerm, useAlias, false);
searchTermCount =
getTermCount(server, singleCountMap, searchTermArray, filterGrayList, keepGrayList);
secondTime = currentTimeMillis();
for (String secondTerm : term2List) {
SearchTermAndList secondTermArray = getTermAndTermList(secondTerm, useAlias, false);
long secondTermCount =
getTermCount(server, singleCountMap, secondTermArray, filterGrayList, keepGrayList);
Callable<NGDItem> callable =
p
.new SolrCallable(
searchTermArray,
secondTermArray,
searchTermCount,
secondTermCount,
server,
useAlias,
filterGrayList,
keepGrayList,
totalDocCount);
Future<NGDItem> future = pool.submit(callable);
set.add(future);
count++;
if (count > 5000) {
for (Future<NGDItem> futureItem : set) {
dataResultsOut.write(futureItem.get().printItem());
futureItem = null;
}
count = 0;
set.clear();
}
}
for (Future<NGDItem> future : set) {
dataResultsOut.write(future.get().printItem());
future = null;
}
logFileOut.write("Query took " + (currentTimeMillis() - secondTime) / 1000 + " seconds.\n");
logFileOut.flush();
set.clear();
fileSearchTerm = bufReader.readLine();
}
long fourthTime = currentTimeMillis();
logFileOut.write("Final time: " + (fourthTime - firstTime) / 1000 + " seconds.\n");
bufReader.close();
logFileOut.flush();
logFileOut.close();
dataResultsOut.flush();
dataResultsOut.close();
pool.shutdown();
}
System.exit(0);
}
public static void main(String[] args) throws Exception {
boolean isInteractive = false;
classUrl = MynaInstaller.class.getResource("MynaInstaller.class").toString();
isJar = (classUrl.indexOf("jar") == 0);
if (!isJar) {
System.err.println("Installer can only be run from inside a Myna distribution war file");
System.exit(1);
}
Thread.sleep(1000);
Console console = System.console();
String response = null;
CommandLineParser parser = new PosixParser();
// create the Options
Options options = new Options();
options.addOption(
"c", "context", true, "Webapp context. Must Start with \"/\" Default: " + webctx);
options.addOption("h", "help", false, "Displays help.");
options.addOption(
"w",
"webroot",
true,
"Webroot to use. Will be created if webroot/WEB-INF does not exist. Default: " + webroot);
options.addOption(
"l",
"logfile",
true,
"Log file to use. Will be created if it does not exist. Default: ./<context>.log");
options.addOption(
"s",
"servername",
true,
"Name of this instance. Will also be the name of the init script. Defaults to either \"myna\" or the value of <context> if defined");
// options.addOption( "P", "purpose", true, "Purpose of the Server, such as DEV,PROD,TRAIN, etc.
// Defaults to DEV" );
options.addOption("p", "port", true, "HTTP port. Set to 0 to disable HTTP. Default: " + port);
options.addOption(
"sp", "ssl-port", true, "SSL (HTTPS) port. Set to 0 to disable SSL, Default: 0");
options.addOption(
"ks", "keystore", true, "keystore path. Default: <webroot>/WEB-INF/myna/myna_keystore");
options.addOption("ksp", "ks-pass", true, "keystore password. Default: " + ksPass);
options.addOption("ksa", "ks-alias", true, "certificate alias. Default: " + ksAlias);
modeOptions.add("upgrade");
modeOptions.add("install");
options.addOption(
"m",
"mode",
true,
"Mode: one of "
+ modeOptions.toString()
+ ". \n"
+ "\"upgrade\": Upgrades myna installation in webroot and exits. "
+ "\"install\": Unpacks to webroot, and installs startup files");
options.addOption(
"u",
"user",
true,
"User to own and run the Myna installation. Only applies to unix installs. Default: nobody");
HelpFormatter formatter = new HelpFormatter();
String cmdSyntax = "java -jar myna-X.war -m <mode> [options]";
try {
CommandLine line = parser.parse(options, args);
Option option;
if (args.length == 0) {
formatter.printHelp(cmdSyntax, options);
response = console.readLine("\nContinue with Interactive Install? (y/N)");
if (response.toLowerCase().equals("y")) {
isInteractive = true;
} else System.exit(1);
}
// Help
if (line.hasOption("help")) {
formatter.printHelp(cmdSyntax, options);
System.exit(1);
}
// mode
if (line.hasOption("mode")) {
mode = line.getOptionValue("mode");
if (!modeOptions.contains(mode)) {
System.err.println(
"Invalid Arguments. Reason: Mode must be in " + modeOptions.toString());
formatter.printHelp(cmdSyntax, options);
System.exit(1);
}
} else if (isInteractive) {
option = options.getOption("mode");
console.printf("\n" + option.getDescription());
do {
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + mode + "): ");
if (!response.isEmpty()) mode = response;
} while (!modeOptions.contains(mode));
}
// webroot
if (line.hasOption("webroot")) {
webroot = line.getOptionValue("webroot");
} else if (isInteractive) {
option = options.getOption("webroot");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + webroot + "): ");
if (!response.isEmpty()) webroot = response;
}
// port
if (line.hasOption("port")) {
port = Integer.parseInt(line.getOptionValue("port"));
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("port");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + port + "): ");
if (!response.isEmpty()) port = Integer.parseInt(response);
}
// context
if (line.hasOption("context")) {
webctx = line.getOptionValue("context");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("context");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + webctx + "): ");
if (!response.isEmpty()) webctx = response;
}
if (!webctx.startsWith("/")) {
webctx = "/" + webctx;
}
// servername (depends on context)
if (!webctx.equals("/")) {
serverName = webctx.substring(1);
}
if (line.hasOption("servername")) {
serverName = line.getOptionValue("servername");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("servername");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + serverName + "): ");
if (!response.isEmpty()) serverName = response;
}
// user
if (line.hasOption("user")) {
user = line.getOptionValue("user");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("user");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + user + "): ");
if (!response.isEmpty()) user = response;
}
// logfile
logFile = "myna.log";
if (!webctx.equals("/")) {
logFile = webctx.substring(1) + ".log";
}
if (line.hasOption("logfile")) {
logFile = line.getOptionValue("logfile");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("logfile");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "path(" + logFile + "): ");
if (!response.isEmpty()) logFile = response;
}
// ssl-port
if (line.hasOption("ssl-port")) {
sslPort = Integer.parseInt(line.getOptionValue("ssl-port"));
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("ssl-port");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + sslPort + "): ");
if (!response.isEmpty()) sslPort = Integer.parseInt(response);
}
// ks-pass
if (line.hasOption("ks-pass")) {
ksPass = line.getOptionValue("ks-pass");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("ks-pass");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + ksPass + "): ");
if (!response.isEmpty()) ksPass = response;
}
// ks-alias
if (line.hasOption("ks-alias")) {
ksAlias = line.getOptionValue("ks-alias");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("ks-alias");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + ksAlias + "): ");
if (!response.isEmpty()) ksAlias = response;
}
// keystore
String appBase = new File(webroot).getCanonicalPath();
if (keystore == null) {
keystore = appBase + "/WEB-INF/myna/myna_keystore";
}
if (line.hasOption("keystore")) {
keystore = line.getOptionValue("keystore");
} else if (isInteractive && mode.equals("install")) {
option = options.getOption("keystore");
console.printf("\n" + option.getDescription());
response = console.readLine("\nEnter " + option.getLongOpt() + "(" + keystore + "): ");
if (!response.isEmpty()) keystore = response;
}
javaOpts = line.getArgList();
} catch (ParseException exp) {
System.err.println("Invalid Arguments. Reason: " + exp.getMessage());
formatter.printHelp(cmdSyntax, options);
System.exit(1);
}
if (isInteractive) {
System.out.println("\nProceeed with the following settings?:\n");
System.out.println("mode = " + mode);
System.out.println("webroot = " + webroot);
if (mode.equals("install")) {
System.out.println("port = " + port);
System.out.println("context = " + webctx);
System.out.println("servername = " + serverName);
System.out.println("user = "******"logfile = " + logFile);
System.out.println("ssl-port = " + sslPort);
System.out.println("ks-pass = "******"ks-alias = " + ksAlias);
System.out.println("keystore = " + keystore);
}
response = console.readLine("Continue? (Y/n)");
if (response.toLowerCase().equals("n")) System.exit(1);
}
File wrFile = new File(webroot);
webroot = wrFile.toString();
if (mode.equals("install")) {
adminPassword = console.readLine("\nCreate an Admin password for this installation: ");
}
// unpack myna if necessary
if (!wrFile.exists() || mode.equals("upgrade") || mode.equals("install")) {
upgrade(wrFile);
}
if (mode.equals("install")) {
File propertiesFile = new File(wrFile.toURI().resolve("WEB-INF/classes/general.properties"));
FileInputStream propertiesFileIS = new FileInputStream(propertiesFile);
Properties generalProperties = new Properties();
generalProperties.load(propertiesFileIS);
propertiesFileIS.close();
if (!adminPassword.isEmpty()) {
org.jasypt.util.password.StrongPasswordEncryptor cryptTool =
new org.jasypt.util.password.StrongPasswordEncryptor();
generalProperties.setProperty("admin_password", cryptTool.encryptPassword(adminPassword));
}
generalProperties.setProperty("instance_id", serverName);
generalProperties.store(
new java.io.FileOutputStream(propertiesFile), "Myna General Properties");
String javaHome = System.getProperty("java.home");
webroot = new File(webroot).getCanonicalPath();
if (serverName.length() == 0) serverName = "myna";
if (java.lang.System.getProperty("os.name").toLowerCase().indexOf("win") >= 0) {
if (!new File(logFile).isAbsolute()) {
logFile = new File(wrFile.toURI().resolve("WEB-INF/" + logFile)).toString();
}
File templateFile =
new File(
wrFile.toURI().resolve("WEB-INF/myna/install/windows/update_myna_service.cmd"));
String initScript =
FileUtils.readFileToString(templateFile)
.replaceAll("\\{webctx\\}", webctx)
.replaceAll("\\{server\\}", Matcher.quoteReplacement(serverName))
.replaceAll("\\{webroot\\}", Matcher.quoteReplacement(webroot))
.replaceAll("\\{logfile\\}", Matcher.quoteReplacement(logFile))
.replaceAll("\\{javahome\\}", Matcher.quoteReplacement(javaHome))
.replaceAll("\\{port\\}", new Integer(port).toString())
.replaceAll("\\{sslPort\\}", new Integer(sslPort).toString())
.replaceAll("\\{keystore\\}", Matcher.quoteReplacement(keystore))
.replaceAll("\\{ksPass\\}", Matcher.quoteReplacement(ksPass))
.replaceAll("\\{ksAlias\\}", Matcher.quoteReplacement(ksAlias));
File scriptFile =
new File(wrFile.toURI().resolve("WEB-INF/myna/install/update_myna_service.cmd"));
FileUtils.writeStringToFile(scriptFile, initScript);
// Runtime.getRuntime().exec("cmd /c start " + scriptFile.toString()).waitFor();
System.out.println(
"\nInstalled Service 'Myna App Server " + serverName + "' the following settings:\n");
System.out.println(
"\nInit script '" + scriptFile + "' created with the following settings:\n");
System.out.println("memory=256MB");
System.out.println("serverName=" + serverName);
System.out.println("javaHome=" + javaHome);
System.out.println("context=" + webctx);
System.out.println("port=" + port);
System.out.println("myna_home=" + webroot);
System.out.println("logfile=" + logFile);
System.out.println("sslPort=" + sslPort);
System.out.println("keyStore=" + keystore);
System.out.println("ksPass="******"ksAlias=" + ksAlias);
System.out.println(
"\nEdit and and run the command file in " + scriptFile + " to update this service");
} else {
String curUser = java.lang.System.getProperty("user.name");
if (!curUser.equals("root")) {
System.out.println("Install mode must be run as root.");
System.exit(1);
}
if (!new File(logFile).isAbsolute()) {
logFile = new File(wrFile.toURI().resolve("WEB-INF/" + logFile)).toString();
}
File templateFile =
new File(wrFile.toURI().resolve("WEB-INF/myna/install/linux/init_script"));
String initScript =
FileUtils.readFileToString(templateFile)
.replaceAll("\\{webctx\\}", webctx)
.replaceAll("\\{server\\}", serverName)
.replaceAll("\\{user\\}", user)
.replaceAll("\\{webroot\\}", webroot)
.replaceAll("\\{javahome\\}", javaHome)
.replaceAll("\\{logfile\\}", logFile)
.replaceAll("\\{port\\}", new Integer(port).toString())
.replaceAll("\\{sslPort\\}", new Integer(sslPort).toString())
.replaceAll("\\{keystore\\}", keystore)
.replaceAll("\\{ksPass\\}", ksPass)
.replaceAll("\\{ksAlias\\}", ksAlias);
File scriptFile = new File(wrFile.toURI().resolve("WEB-INF/myna/install/" + serverName));
FileUtils.writeStringToFile(scriptFile, initScript);
if (new File("/etc/init.d").exists()) {
exec("chown -R " + user + " " + webroot);
exec("chown root " + scriptFile.toString());
exec("chmod 700 " + scriptFile.toString());
exec("cp " + scriptFile.toString() + " /etc/init.d/");
System.out.println(
"\nInit script '/etc/init.d/"
+ serverName
+ "' created with the following settings:\n");
} else {
System.out.println(
"\nInit script '" + scriptFile + "' created with the following settings:\n");
}
System.out.println("user="******"memory=256MB");
System.out.println("server=" + serverName);
System.out.println("context=" + webctx);
System.out.println("port=" + port);
System.out.println("myna_home=" + webroot);
System.out.println("logfile=" + logFile);
System.out.println("sslPort=" + sslPort);
System.out.println("keyStore=" + keystore);
System.out.println("ksPass="******"ksAlias=" + ksAlias);
System.out.println("\nEdit this file to customize startup behavior");
}
}
}
public static void main(String[] argv)
throws IOException, CmdLineParser.UnknownOptionException,
CmdLineParser.IllegalOptionValueException {
if (argv.length < 4) {
System.out.println("Usage: hictools pre <options> <inputFile> <outputFile> <genomeID>");
System.out.println(" <options>: -d only calculate intra chromosome (diagonal) [false]");
System.out.println(
" : -o calculate densities (observed/expected), write to file [false]");
System.out.println(" : -t <int> only write cells with count above threshold t [0]");
System.out.println(
" : -c <chromosome ID> only calculate map on specific chromosome");
System.exit(0);
}
Globals.setHeadless(true);
CommandLineParser parser = new CommandLineParser();
parser.parse(argv);
String[] args = parser.getRemainingArgs();
if (args[0].equals("sort")) {
AlignmentsSorter.sort(args[1], args[2], null);
} else if (args[0].equals("pairsToBin")) {
String ifile = args[1];
String ofile = args[2];
String genomeId = args[3];
List<Chromosome> chromosomes = loadChromosomes(genomeId);
AsciiToBinConverter.convert(ifile, ofile, chromosomes);
} else if (args[0].equals("binToPairs")) {
String ifile = args[1];
String ofile = args[2];
AsciiToBinConverter.convertBack(ifile, ofile);
} else if (args[0].equals("printmatrix")) {
if (args.length < 5) {
System.err.println(
"Usage: hictools printmatrix <observed/oe/pearson> hicFile chr1 chr2 binsize");
System.exit(-1);
}
String type = args[1];
String file = args[2];
String chr1 = args[3];
String chr2 = args[4];
String binSizeSt = args[5];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
dumpMatrix(file, chr1, chr2, binSize, type);
} else if (args[0].equals("eigenvector")) {
if (args.length < 4) {
System.err.println("Usage: hictools eigenvector hicFile chr binsize");
}
String file = args[1];
String chr = args[2];
String binSizeSt = args[3];
int binSize = 0;
try {
binSize = Integer.parseInt(binSizeSt);
} catch (NumberFormatException e) {
System.err.println("Integer expected. Found: " + binSizeSt);
System.exit(-1);
}
calculateEigenvector(file, chr, binSize);
} else if (args[0].equals("pre")) {
String genomeId = "";
try {
genomeId = args[3];
} catch (ArrayIndexOutOfBoundsException e) {
System.err.println("No genome ID given");
System.exit(0);
}
List<Chromosome> chromosomes = loadChromosomes(genomeId);
long genomeLength = 0;
for (Chromosome c : chromosomes) {
if (c != null) genomeLength += c.getSize();
}
chromosomes.set(0, new Chromosome(0, "All", (int) (genomeLength / 1000)));
String[] tokens = args[1].split(",");
List<String> files = new ArrayList<String>(tokens.length);
for (String f : tokens) {
files.add(f);
}
Preprocessor preprocessor = new Preprocessor(new File(args[2]), chromosomes);
preprocessor.setIncludedChromosomes(parser.getChromosomeOption());
preprocessor.setCountThreshold(parser.getCountThresholdOption());
preprocessor.setNumberOfThreads(parser.getThreadedOption());
preprocessor.setDiagonalsOnly(parser.getDiagonalsOption());
preprocessor.setLoadDensities(parser.getDensitiesOption());
preprocessor.preprocess(files);
}
}