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);
}
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 static String[] ginit(String[] args) {
if (System.getenv("KONOHA_DEBUG") != null) {
verboseDebug = true;
verboseGc = true;
verboseSugar = true;
verboseCode = true;
}
CommandLineParser parser = new BasicParser();
CommandLine commandLine = null;
try {
commandLine = parser.parse(longOptions, args);
} catch (ParseException e) {
// TODO
}
if(commandLine.hasOption("verbose")) {
verboseDebug = true;
System.out.println("option vervose");
}
if(commandLine.hasOption("verbose:gc")) {
verboseGc = true;
System.out.println("option vervose:gc");
}
if(commandLine.hasOption("verbose:sugar")) {
verboseSugar = true;
System.out.println("option vervose:sugar");
}
if(commandLine.hasOption("verbose:code")) {
verboseCode = true;
System.out.println("option vervose:code");
}
if(commandLine.hasOption("interactive")) {
interactiveFlag = true;
System.out.println("option interactive");
}
if(commandLine.hasOption("typecheck")) {
compileonlyFlag = true;
System.out.println("option typecheck");
}
if(commandLine.hasOption("start-with")) {
startupScript = commandLine.getOptionValue("start-with");
System.out.println("option start-with");
System.out.println(" with arg " + startupScript);
}
if(commandLine.hasOption("test")) {
testScript = commandLine.getOptionValue("test");
System.out.println(" with arg " + testScript);
}
if(commandLine.hasOption("test-with")) {
testScript = commandLine.getOptionValue("test");
System.out.println(" with arg " + testScript);
}
if(commandLine.hasOption("builtin-test")) {
builtinTest = commandLine.getOptionValue("builtin-test");
System.out.println(" with arg " + builtinTest);
}
return commandLine.getArgs();
}
private static boolean commandLine(String[] args) {
CommandLineParser cl = new CommandLineParser(args);
// see if we are asking for help
if (cl.getProperty("help") != null || cl.getProperty("-help") != null) {
usage();
return false;
}
inputImageFilename = cl.getProperty("i");
if (inputImageFilename == null) {
usage();
return false;
}
outputImageFilename = cl.getProperty("o");
if (outputImageFilename == null) {
usage();
return false;
}
encoder = cl.getProperty("e");
if (encoder == null) {
usage();
return false;
}
String tmps = cl.getProperty("cs");
if (tmps != null) tileCacheSize = Long.parseLong(tmps) * megaBytes;
return true;
}
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;
}
}
/*
*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*/
public static void main(String[] args) {
try {
// IMPORTANT HINT REGARDING STRING ENCODING
// in Java all Strings have UTF-8 as default encoding
// therefore: there are only a few references to UTF-8 encoding in this demo code
// however, if values are retrieved from a database or another program language is used, then
// one needs to
// make sure that the UTF-8 encoding is correctly implemented
// create CMD line option object
Options options = new Options();
// add CMD line options
options.addOption(
"o",
"output-dir",
true,
"specify base output directory, if none is specified a new directory will be created in the current path");
options.addOption(
"n",
"number-of-generated-receipts",
true,
"specify number of receipts to be randomly generated, 50 is default");
options.addOption(
"g",
"signature-creation-device-cannot-fail",
false,
"deactivate glitches in signature-creation-device");
options.addOption(
"s",
"no-signature-certificate-switch",
false,
"deactivate switching of signature certificates after 5 receipts");
options.addOption(
"t", "no-training-receipts", false, "deactivate random generation of training-receipts");
/// parse CMD line options
CommandLineParser parser = new DefaultParser();
CommandLine cmd = parser.parse(options, args);
boolean signatureCreationDeviceAlwaysWorks = cmd.hasOption("g");
boolean deactivateSignatureCertificateSwitching = cmd.hasOption("s");
boolean deactivateTrainingReceipts = cmd.hasOption("t");
String outputParentDirectoryString = cmd.getOptionValue("o");
if (outputParentDirectoryString == null) {
DateFormat df = new SimpleDateFormat("yyyy-MM-dd'T'HH-mm-ss");
outputParentDirectoryString = "./CashBoxDemoOutput" + df.format(new Date());
}
File OUTPUT_PARENT_DIRECTORY = new File(outputParentDirectoryString);
OUTPUT_PARENT_DIRECTORY.mkdirs();
System.out.println("Setting workdir to " + OUTPUT_PARENT_DIRECTORY.getAbsolutePath());
String numberOfReceiptsString = cmd.getOptionValue("n");
int NUMBER_OF_RECEIPTS = DEFAULT_NUMBER_OF_GENERATED_RECEIPTS;
if (numberOfReceiptsString != null) {
NUMBER_OF_RECEIPTS = new Integer(numberOfReceiptsString);
}
// TODO add provider independent functionality
// initialise cryptographic providers
Security.addProvider(new BouncyCastleProvider());
// prepare cashbox init parameters
CashBoxParameters cashBoxParameters = new CashBoxParameters();
// set parameter for signature certificate switching
// if > 0 then switch signature certificate after so many signatures
// this is important for demonstrating the handling of the DEP export format
// when receipts where signed with multiple signature certificates
if (deactivateSignatureCertificateSwitching) {
cashBoxParameters.setChangeSignatureCertificateAfterSoManyReceipts(-1);
} else {
cashBoxParameters.setChangeSignatureCertificateAfterSoManyReceipts(10);
}
// generate and set random cash box ID ("Kassen-ID")
// REF TO SPECIFICATION: Detailspezifikation/Abs 4
String CASH_BOX_ID = "DEMO-CASH-BOX" + Math.round(Math.random() * 1000);
cashBoxParameters.setCashBoxID(CASH_BOX_ID);
// set cashbox suite
// REF TO SPECIFICATION: Detailspezifikation/Abs 2
// AT0 is used here for demonstration purposes, see Abs 2 for details on AT0
cashBoxParameters.setRkSuite(RKSuite.R1_AT0);
// set initial receipt identifier
// in this demo cashbox integer values are used as receipt identifiers ("Belegnummer"),
// however the specification does not
// impose that limit. An arbitrary UTF-8 String could be used, the only requirement is that
// the same combination of
// the cashBox ID ("Kassen-ID") and the receipt identifier ("Belegnummer") is NEVER used for
// more than one receipt
// using the same multiple times compromises the security of the encrypted turnover value,
// which might lead
// to leaked turnover data.
// REF TO SPECIFICATION: Detailspezifikation/Abs 4, Abs 8, Abs 9, Abs 10
long initialReceiptIdentifier = Math.round(Math.random() * 1000000);
cashBoxParameters.setInitialReceiptIdentifier(initialReceiptIdentifier);
// set DEP module for storing and exporting receipts
// REF TO SPECIFICATION: Detailspezifikation/Abs 3, 11
cashBoxParameters.setDepModul(new SimpleMemoryDEPModule());
// create random AES key for turnover encryption
// REF TO SPECIFICATION: Detailspezifikation/Abs 4, Abs 8, Abs 9, Abs 10
cashBoxParameters.setTurnoverKeyAESkey(CashBoxUtils.createAESKey());
// set up signature module
// the signature module is composed of an JWS module that create the JSON Web Signature (JWS)
// and
// a low level signature module for signing the hash values.
// REF TO SPECIFICATION: Detailspezifikation/Abs 2, Abs 4, Abs 5, Abs 6
// JWSModule jwsModule = new OrgBitbucketBcJwsModule(); //requires bouncycastle provider
JWSModule jwsModule = new ManualJWSModule(); // allows for provider independent use cases
// set damage flag, which simulates the failure of the signature creation device and the
// correct handling
// of this case, obviously this is only suitable for demonstration purposes
jwsModule.setDamageIsPossible(!signatureCreationDeviceAlwaysWorks);
jwsModule.setProbabilityOfDamagedSignatureDevice(PROPABILITY_DAMAGED_SIGNATURE_DEVICE);
jwsModule.setSignatureModule(new DO_NOT_USE_IN_REAL_CASHBOX_DemoSoftwareSignatureModule());
// jwsModule.setSignatureModule(new PKCS11SignatureModule());
cashBoxParameters.setJwsModule(jwsModule);
// set printer module
// REF TO SPECIFICATION: Detailspezifikation/Abs 12, Abs 13, Abs 14, Abs 15
PrinterModule printerModule = new SimplePDFPrinterModule();
cashBoxParameters.setPrinterModule(printerModule);
// init the cash box with the parameters
DemoCashBox demoCashBox = new DemoCashBox(cashBoxParameters);
// init done, start interaction with cashbox
// create random receipt data that will be handled by the cashbox
List<RawReceiptData> receipts =
RandomReceiptGenerator.generateRandomReceipts(NUMBER_OF_RECEIPTS);
// store first receipt (Startbeleg) in cashbox
// all taxtype values are set to zero (per default in this demo)
RawReceiptData firstReceipt = new RawReceiptData();
demoCashBox.storeReceipt(firstReceipt, false, false);
// now store the other receipts
for (RawReceiptData rawReceiptData : receipts) {
// store receipt within cashbox: (prepare data-to-be-signed, sign with JWS, store signed
// receipt in DEP)
// pre-defined chance for a training receipt (just for demo purposes)
boolean isTrainingReceipt = false;
if (Math.random() < PROPABILITY_TRAINING_RECEIPT && !deactivateTrainingReceipts) {
isTrainingReceipt = true;
}
// pre-defined chance for a storno receipt
boolean isStornoReceipt = false;
if (Math.random() < PROPABILITY_OF_STORNO_RECEIPT) {
isStornoReceipt = true;
}
demoCashBox.storeReceipt(rawReceiptData, isTrainingReceipt, isStornoReceipt);
}
// dump machine readable code of receipts (this "code" is used for the QR-codes)
// REF TO SPECIFICATION: Detailspezifikation/Abs 12
// dump to File
File qrCoreRepExportFile = new File(OUTPUT_PARENT_DIRECTORY, "qr-code-rep.txt");
List<ReceiptPackage> receiptPackages = demoCashBox.getStoredReceipts();
PrintWriter writer = new PrintWriter(new FileWriter(qrCoreRepExportFile));
System.out.println("------------QR-CODE-REP------------");
for (ReceiptPackage receiptPackage : receiptPackages) {
System.out.println(receiptPackage.getQRCodeRepresentation());
writer.println(receiptPackage.getQRCodeRepresentation());
}
System.out.println("");
writer.close();
// dump OCR code of receipts
// REF TO SPECIFICATION: Detailspezifikation/Abs 14
// dump to File
File ocrCoreRepExportFile = new File(OUTPUT_PARENT_DIRECTORY, "ocr-code-rep.txt");
writer = new PrintWriter(new FileWriter(ocrCoreRepExportFile));
System.out.println("------------OCR-CODE-REP------------");
for (ReceiptPackage receiptPackage : receiptPackages) {
System.out.println(receiptPackage.getOcrCodeRepresentation());
writer.println(receiptPackage.getOcrCodeRepresentation());
}
System.out.println("");
writer.close();
// export DEP from cashbox
// REF TO SPECIFICATION: Detailspezifikation/Abs 3
DEPExportFormat depExportFormat = demoCashBox.exportDEP();
// get JSON rep and dump export format to file/std output
Gson gson = new GsonBuilder().setPrettyPrinting().create();
String exportFormatJSONString = gson.toJson(depExportFormat);
System.out.println("------------DEP-EXPORT-FORMAT------------");
System.out.println(exportFormatJSONString);
System.out.println("");
// dump DEP export to file
File depExportFile = new File(OUTPUT_PARENT_DIRECTORY, "dep-export.txt");
FileOutputStream outputStream = new FileOutputStream(depExportFile);
outputStream.write(exportFormatJSONString.getBytes());
outputStream.close();
// export receipts as PDF (QR-CODE)
// REF TO SPECIFICATION: Detailspezifikation/Abs 12, Abs 13
File qrCodeDumpDirectory = new File(OUTPUT_PARENT_DIRECTORY, "qr-code-dir-pdf");
qrCodeDumpDirectory.mkdirs();
List<byte[]> printedQRCodeReceipts =
demoCashBox.printReceipt(receiptPackages, ReceiptPrintType.QR_CODE);
CashBoxUtils.writeReceiptsToFiles(printedQRCodeReceipts, "QR-", qrCodeDumpDirectory);
// export receipts as PDF (OCR)
// REF TO SPECIFICATION: Detailspezifikation/Abs 14, Abs 15
File ocrCodeDumpDirectory = new File(OUTPUT_PARENT_DIRECTORY, "ocr-code-dir-pdf");
ocrCodeDumpDirectory.mkdirs();
List<byte[]> printedOCRCodeReceipts =
demoCashBox.printReceipt(receiptPackages, ReceiptPrintType.OCR);
CashBoxUtils.writeReceiptsToFiles(printedOCRCodeReceipts, "OCR-", ocrCodeDumpDirectory);
// store signature certificates (so that they can be used for verification purposes)
// only for demonstration purposes
List<String> signatureCertificates = new ArrayList<>();
List<List<String>> certificateChains = new ArrayList<>();
DEPBelegDump[] belegDumps = depExportFormat.getBelegPackage();
for (DEPBelegDump depBelegDump : belegDumps) {
signatureCertificates.add(depBelegDump.getSignatureCertificate());
certificateChains.add(Arrays.asList(depBelegDump.getCertificateChain()));
}
File signatureCertificatesOutputFile =
new File(OUTPUT_PARENT_DIRECTORY, "signatureCertificates.txt");
String signatureCertificatesJSON = gson.toJson(signatureCertificates);
BufferedOutputStream bufferedOutputStream =
new BufferedOutputStream(new FileOutputStream(signatureCertificatesOutputFile));
ByteArrayInputStream bIn = new ByteArrayInputStream(signatureCertificatesJSON.getBytes());
IOUtils.copy(bIn, bufferedOutputStream);
bufferedOutputStream.close();
// store certificate chains (so that they can be used for verification purposes)
// only for demonstration purposes
File signatureCertificateChainsOutputFile =
new File(OUTPUT_PARENT_DIRECTORY, "signatureCertificateChains.txt");
String signatureCertificateChainsJSON = gson.toJson(certificateChains);
bufferedOutputStream =
new BufferedOutputStream(new FileOutputStream(signatureCertificateChainsOutputFile));
bIn = new ByteArrayInputStream(signatureCertificateChainsJSON.getBytes());
IOUtils.copy(bIn, bufferedOutputStream);
bufferedOutputStream.close();
// store AES key as BASE64 String (for demonstration purposes: to allow decryption of turnover
// value)
// ATTENTION, this is only for demonstration purposes, the AES key must be stored in a secure
// area
byte[] aesKey = cashBoxParameters.getTurnoverKeyAESkey().getEncoded();
String aesKeyBase64 = CashBoxUtils.base64Encode(aesKey, false);
writer = new PrintWriter(new File(OUTPUT_PARENT_DIRECTORY, "aesKeyBase64.txt"));
writer.print(aesKeyBase64);
writer.close();
} catch (IOException e) {
e.printStackTrace();
} catch (ParseException e) {
e.printStackTrace();
}
}
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);
}
}
/**
* Parses the command line arguments and sets the respective fields accordingly. This function
* sets the input source and target files, the source and target language, the running mode (gb or
* bb), the additional files required by the GB feature extractor, the rebuild and log options
*
* @param args The command line arguments
*/
public void parseArguments(String[] args) {
Option help =
OptionBuilder.withArgName("help")
.hasArg()
.withDescription("print project help information")
.isRequired(false)
.create("help");
Option input = OptionBuilder.withArgName("input").hasArgs(3).isRequired(true).create("input");
Option lang = OptionBuilder.withArgName("lang").hasArgs(2).isRequired(false).create("lang");
Option feat = OptionBuilder.withArgName("feat").hasArgs(1).isRequired(false).create("feat");
Option gb =
OptionBuilder.withArgName("gb")
.withDescription("GlassBox input files")
.hasOptionalArgs(2)
.hasArgs(3)
.create("gb");
Option mode =
OptionBuilder.withArgName("mode")
.withDescription("blackbox features, glassbox features or both")
.hasArgs(1)
.isRequired(true)
.create("mode");
Option config =
OptionBuilder.withArgName("config")
.withDescription("cofiguration file")
.hasArgs(1)
.isRequired(false)
.create("config");
Option rebuild = new Option("rebuild", "run all preprocessing tools");
rebuild.setRequired(false);
// separate 17 BB from 79 BB
Option baseline = new Option("baseline", "only 17 baseline feature will be calculated");
baseline.setRequired(false);
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption(help);
options.addOption(input);
options.addOption(mode);
options.addOption(lang);
options.addOption(feat);
options.addOption(gb);
options.addOption(rebuild);
options.addOption(config);
options.addOption(baseline);
try {
// parse the command line arguments
CommandLine line = parser.parse(options, args);
if (line.hasOption("config")) {
resourceManager = new PropertiesManager(line.getOptionValue("config"));
} else {
resourceManager = new PropertiesManager();
}
if (line.hasOption("input")) {
// print the value of block-size
String[] files = line.getOptionValues("input");
sourceFile = files[0];
targetFile = files[1];
}
if (line.hasOption("lang")) {
String[] langs = line.getOptionValues("lang");
sourceLang = langs[0];
targetLang = langs[1];
} else {
sourceLang = resourceManager.getString("sourceLang.default");
targetLang = resourceManager.getString("targetLang.default");
}
if (line.hasOption("gb")) {
String[] gbOpt = line.getOptionValues("gb");
for (String s : gbOpt) System.out.println(s);
if (gbOpt.length > 1) {
mtSys = MOSES;
nbestInput = gbOpt[0];
onebestPhrases = gbOpt[1];
onebestLog = gbOpt[2];
gbMode = 1;
} else {
File f = new File(gbOpt[0]);
if (f.isDirectory()) {
mtSys = IBM;
wordLattices = gbOpt[0];
gbMode = 1;
} else {
gbMode = 0;
gbXML = gbOpt[0];
}
}
}
if (line.hasOption("mode")) {
String[] modeOpt = line.getOptionValues("mode");
setMod(modeOpt[0].trim());
System.out.println(getMod());
configPath = resourceManager.getString("featureConfig." + getMod());
System.out.println("feature config:" + configPath);
featureManager = new FeatureManager(configPath);
}
if (line.hasOption("feat")) {
// print the value of block-size
features = line.getOptionValue("feat");
featureManager.setFeatureList(features);
} else {
featureManager.setFeatureList("all");
}
if (line.hasOption("rebuild")) {
forceRun = true;
}
if (line.hasOption("baseline")) {
isBaseline = true;
}
} catch (ParseException exp) {
System.out.println("Unexpected exception:" + exp.getMessage());
}
}
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);
}
}
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 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");
}
}
}