List of usage examples for java.lang String split
public String[] split(String regex)
From source file:mod.org.dcm4che2.tool.DcmQR.java
@SuppressWarnings("unchecked") public static void main(String[] args) { CommandLine cl = parse(args);/*w w w. j a v a 2s .c o m*/ DcmQR dcmqr = new DcmQR(cl.hasOption("device") ? cl.getOptionValue("device") : "DCMQR"); final List<String> argList = cl.getArgList(); String remoteAE = argList.get(0); String[] calledAETAddress = split(remoteAE, '@'); dcmqr.setCalledAET(calledAETAddress[0], cl.hasOption("reuseassoc")); if (calledAETAddress[1] == null) { dcmqr.setRemoteHost("127.0.0.1"); dcmqr.setRemotePort(104); } else { String[] hostPort = split(calledAETAddress[1], ':'); dcmqr.setRemoteHost(hostPort[0]); dcmqr.setRemotePort(toPort(hostPort[1])); } if (cl.hasOption("L")) { String localAE = cl.getOptionValue("L"); String[] localPort = split(localAE, ':'); if (localPort[1] != null) { dcmqr.setLocalPort(toPort(localPort[1])); } String[] callingAETHost = split(localPort[0], '@'); dcmqr.setCalling(callingAETHost[0]); if (callingAETHost[1] != null) { dcmqr.setLocalHost(callingAETHost[1]); } } if (cl.hasOption("username")) { String username = cl.getOptionValue("username"); UserIdentity userId; if (cl.hasOption("passcode")) { String passcode = cl.getOptionValue("passcode"); userId = new UserIdentity.UsernamePasscode(username, passcode.toCharArray()); } else { userId = new UserIdentity.Username(username); } userId.setPositiveResponseRequested(cl.hasOption("uidnegrsp")); dcmqr.setUserIdentity(userId); } if (cl.hasOption("connectTO")) dcmqr.setConnectTimeout(parseInt(cl.getOptionValue("connectTO"), "illegal argument of option -connectTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("reaper")) dcmqr.setAssociationReaperPeriod(parseInt(cl.getOptionValue("reaper"), "illegal argument of option -reaper", 1, Integer.MAX_VALUE)); if (cl.hasOption("cfindrspTO")) dcmqr.setDimseRspTimeout(parseInt(cl.getOptionValue("cfindrspTO"), "illegal argument of option -cfindrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cmoverspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cmoverspTO"), "illegal argument of option -cmoverspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("cgetrspTO")) dcmqr.setRetrieveRspTimeout(parseInt(cl.getOptionValue("cgetrspTO"), "illegal argument of option -cgetrspTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("acceptTO")) dcmqr.setAcceptTimeout(parseInt(cl.getOptionValue("acceptTO"), "illegal argument of option -acceptTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("releaseTO")) dcmqr.setReleaseTimeout(parseInt(cl.getOptionValue("releaseTO"), "illegal argument of option -releaseTO", 1, Integer.MAX_VALUE)); if (cl.hasOption("soclosedelay")) dcmqr.setSocketCloseDelay(parseInt(cl.getOptionValue("soclosedelay"), "illegal argument of option -soclosedelay", 1, 10000)); if (cl.hasOption("rcvpdulen")) dcmqr.setMaxPDULengthReceive( parseInt(cl.getOptionValue("rcvpdulen"), "illegal argument of option -rcvpdulen", 1, 10000) * KB); if (cl.hasOption("sndpdulen")) dcmqr.setMaxPDULengthSend( parseInt(cl.getOptionValue("sndpdulen"), "illegal argument of option -sndpdulen", 1, 10000) * KB); if (cl.hasOption("sosndbuf")) dcmqr.setSendBufferSize( parseInt(cl.getOptionValue("sosndbuf"), "illegal argument of option -sosndbuf", 1, 10000) * KB); if (cl.hasOption("sorcvbuf")) dcmqr.setReceiveBufferSize( parseInt(cl.getOptionValue("sorcvbuf"), "illegal argument of option -sorcvbuf", 1, 10000) * KB); if (cl.hasOption("filebuf")) dcmqr.setFileBufferSize( parseInt(cl.getOptionValue("filebuf"), "illegal argument of option -filebuf", 1, 10000) * KB); dcmqr.setPackPDV(!cl.hasOption("pdv1")); dcmqr.setTcpNoDelay(!cl.hasOption("tcpdelay")); dcmqr.setMaxOpsInvoked(cl.hasOption("async") ? parseInt(cl.getOptionValue("async"), "illegal argument of option -async", 0, 0xffff) : 1); dcmqr.setMaxOpsPerformed(cl.hasOption("cstoreasync") ? parseInt(cl.getOptionValue("cstoreasync"), "illegal argument of option -cstoreasync", 0, 0xffff) : 0); if (cl.hasOption("C")) dcmqr.setCancelAfter( parseInt(cl.getOptionValue("C"), "illegal argument of option -C", 1, Integer.MAX_VALUE)); if (cl.hasOption("lowprior")) dcmqr.setPriority(CommandUtils.LOW); if (cl.hasOption("highprior")) dcmqr.setPriority(CommandUtils.HIGH); if (cl.hasOption("cstore")) { String[] storeTCs = cl.getOptionValues("cstore"); for (String storeTC : storeTCs) { String cuid; String[] tsuids; int colon = storeTC.indexOf(':'); if (colon == -1) { cuid = storeTC; tsuids = DEF_TS; } else { cuid = storeTC.substring(0, colon); String ts = storeTC.substring(colon + 1); try { tsuids = TS.valueOf(ts).uids; } catch (IllegalArgumentException e) { tsuids = ts.split(","); } } try { cuid = CUID.valueOf(cuid).uid; } catch (IllegalArgumentException e) { // assume cuid already contains UID } dcmqr.addStoreTransferCapability(cuid, tsuids); } if (cl.hasOption("cstoredest")) dcmqr.setStoreDestination(cl.getOptionValue("cstoredest")); } dcmqr.setCFind(!cl.hasOption("nocfind")); dcmqr.setCGet(cl.hasOption("cget")); if (cl.hasOption("cmove")) dcmqr.setMoveDest(cl.getOptionValue("cmove")); if (cl.hasOption("evalRetrieveAET")) dcmqr.setEvalRetrieveAET(true); dcmqr.setQueryLevel(cl.hasOption("P") ? QueryRetrieveLevel.PATIENT : cl.hasOption("S") ? QueryRetrieveLevel.SERIES : cl.hasOption("I") ? QueryRetrieveLevel.IMAGE : QueryRetrieveLevel.STUDY); if (cl.hasOption("noextneg")) dcmqr.setNoExtNegotiation(true); if (cl.hasOption("rel")) dcmqr.setRelationQR(true); if (cl.hasOption("datetime")) dcmqr.setDateTimeMatching(true); if (cl.hasOption("fuzzy")) dcmqr.setFuzzySemanticPersonNameMatching(true); if (!cl.hasOption("P")) { if (cl.hasOption("retall")) dcmqr.addPrivate(UID.PrivateStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("blocked")) dcmqr.addPrivate(UID.PrivateBlockedStudyRootQueryRetrieveInformationModelFIND); if (cl.hasOption("vmf")) dcmqr.addPrivate(UID.PrivateVirtualMultiframeStudyRootQueryRetrieveInformationModelFIND); } if (cl.hasOption("cfind")) { String[] cuids = cl.getOptionValues("cfind"); for (int i = 0; i < cuids.length; i++) dcmqr.addPrivate(cuids[i]); } if (!cl.hasOption("nodefret")) dcmqr.addDefReturnKeys(); if (cl.hasOption("r")) { String[] returnKeys = cl.getOptionValues("r"); for (int i = 0; i < returnKeys.length; i++) dcmqr.addReturnKey(Tag.toTagPath(returnKeys[i])); } if (cl.hasOption("q")) { String[] matchingKeys = cl.getOptionValues("q"); for (int i = 1; i < matchingKeys.length; i++, i++) dcmqr.addMatchingKey(Tag.toTagPath(matchingKeys[i - 1]), matchingKeys[i]); } dcmqr.configureTransferCapability(cl.hasOption("ivrle")); int repeat = cl.hasOption("repeat") ? parseInt(cl.getOptionValue("repeat"), "illegal argument of option -repeat", 1, Integer.MAX_VALUE) : 0; int interval = cl.hasOption("repeatdelay") ? parseInt(cl.getOptionValue("repeatdelay"), "illegal argument of option -repeatdelay", 1, Integer.MAX_VALUE) : 0; boolean closeAssoc = cl.hasOption("closeassoc"); if (cl.hasOption("tls")) { String cipher = cl.getOptionValue("tls"); if ("NULL".equalsIgnoreCase(cipher)) { dcmqr.setTlsWithoutEncyrption(); } else if ("3DES".equalsIgnoreCase(cipher)) { dcmqr.setTls3DES_EDE_CBC(); } else if ("AES".equalsIgnoreCase(cipher)) { dcmqr.setTlsAES_128_CBC(); } else { exit("Invalid parameter for option -tls: " + cipher); } if (cl.hasOption("tls1")) { dcmqr.setTlsProtocol(TLS1); } else if (cl.hasOption("ssl3")) { dcmqr.setTlsProtocol(SSL3); } else if (cl.hasOption("no_tls1")) { dcmqr.setTlsProtocol(NO_TLS1); } else if (cl.hasOption("no_ssl3")) { dcmqr.setTlsProtocol(NO_SSL3); } else if (cl.hasOption("no_ssl2")) { dcmqr.setTlsProtocol(NO_SSL2); } dcmqr.setTlsNeedClientAuth(!cl.hasOption("noclientauth")); if (cl.hasOption("keystore")) { dcmqr.setKeyStoreURL(cl.getOptionValue("keystore")); } if (cl.hasOption("keystorepw")) { dcmqr.setKeyStorePassword(cl.getOptionValue("keystorepw")); } if (cl.hasOption("keypw")) { dcmqr.setKeyPassword(cl.getOptionValue("keypw")); } if (cl.hasOption("truststore")) { dcmqr.setTrustStoreURL(cl.getOptionValue("truststore")); } if (cl.hasOption("truststorepw")) { dcmqr.setTrustStorePassword(cl.getOptionValue("truststorepw")); } long t1 = System.currentTimeMillis(); try { dcmqr.initTLS(); } catch (Exception e) { System.err.println("ERROR: Failed to initialize TLS context:" + e.getMessage()); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Initialize TLS context in {} s", Float.valueOf((t2 - t1) / 1000f)); } try { dcmqr.start(); } catch (Exception e) { System.err.println( "ERROR: Failed to start server for receiving " + "requested objects:" + e.getMessage()); System.exit(2); } try { long t1 = System.currentTimeMillis(); try { dcmqr.open(); } catch (Exception e) { LOG.error("Failed to establish association:", e); System.exit(2); } long t2 = System.currentTimeMillis(); LOG.info("Connected to {} in {} s", remoteAE, Float.valueOf((t2 - t1) / 1000f)); for (;;) { List<DicomObject> result; if (dcmqr.isCFind()) { result = dcmqr.query(); long t3 = System.currentTimeMillis(); LOG.info("Received {} matching entries in {} s", Integer.valueOf(result.size()), Float.valueOf((t3 - t2) / 1000f)); t2 = t3; } else { result = Collections.singletonList(dcmqr.getKeys()); } if (dcmqr.isCMove() || dcmqr.isCGet()) { if (dcmqr.isCMove()) dcmqr.move(result); else dcmqr.get(result); long t4 = System.currentTimeMillis(); LOG.info("Retrieved {} objects (warning: {}, failed: {}) in {}s", new Object[] { Integer.valueOf(dcmqr.getTotalRetrieved()), Integer.valueOf(dcmqr.getWarning()), Integer.valueOf(dcmqr.getFailed()), Float.valueOf((t4 - t2) / 1000f) }); } if (repeat == 0 || closeAssoc) { try { dcmqr.close(); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } LOG.info("Released connection to {}", remoteAE); } if (repeat-- == 0) break; Thread.sleep(interval); long t4 = System.currentTimeMillis(); dcmqr.open(); t2 = System.currentTimeMillis(); LOG.info("Reconnect or reuse connection to {} in {} s", remoteAE, Float.valueOf((t2 - t4) / 1000f)); } } catch (IOException e) { LOG.error(e.getMessage(), e); } catch (InterruptedException e) { LOG.error(e.getMessage(), e); } catch (ConfigurationException e) { LOG.error(e.getMessage(), e); } finally { dcmqr.stop(); } }
From source file:com.basho.contact.ContactConsole.java
public static void main(String[] args) throws IOException { CommandLine commandLine = processArgs(args); ConsoleReader reader = new ConsoleReader(); reader.setBellEnabled(false);// w w w .j a v a 2s . com reader.setExpandEvents(false); // TODO: look into this // TODO: Pasting in text with tabs prints out a ton of completions //reader.addCompleter(new jline.console.completer.StringsCompleter(keywords)); String line; PrintWriter out = new PrintWriter(System.out); DefaultConnectionProvider connections = new DefaultConnectionProvider(); RuntimeContext ctx = new RuntimeContext(connections, System.out, System.err); if (!commandLine.hasOption("nosignals")) { ConsoleSignalHander.install("INT", ctx); } ContactWalker walker = new ContactWalker(ctx); ContactAdminWalker adminWalker = new ContactAdminWalker(ctx); List<ContactBaseListener> walkers = new ArrayList<ContactBaseListener>(); walkers.add(walker); walkers.add(adminWalker); boolean nextLinePrompt = false; ANSIBuffer buf = new ANSIBuffer(); buf.setAnsiEnabled(!commandLine.hasOption("nocolor")); buf.blue("Welcome to Riak Contact\n"); buf.blue("(c) 2013 Dave Parfitt\n"); System.out.println(buf.toString()); if (!commandLine.hasOption("noconfig")) { String config = null; try { config = readConfig(); } catch (Exception e) { e.printStackTrace(); } if (config != null && !config.trim().isEmpty()) { processInput(config, walkers, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); } } if (commandLine.hasOption("infile")) { String filename = commandLine.getOptionValue("infile"); readInputFile(filename, walkers, ctx); ctx.getActionListener().term(); System.exit(0); } StringBuffer lines = new StringBuffer(); ANSIBuffer ansiprompt = new ANSIBuffer(); ansiprompt.setAnsiEnabled(true); ansiprompt.green("> "); String prompt = ansiprompt.toString(!commandLine.hasOption("nocolor")); boolean inHereDoc = false; while ((line = reader.readLine(nextLinePrompt ? "" : prompt)) != null) { out.flush(); String chunks[] = line.split(" "); String consoleCommandCheck = chunks[0].toLowerCase().trim(); if (consoleOnlyCommands.containsKey(consoleCommandCheck)) { consoleOnlyCommands.get(consoleCommandCheck).run(line, reader); continue; } if (line.contains("~%~") && !line.contains("\\~%~")) { inHereDoc = !inHereDoc; } if (!line.trim().endsWith(";")) { nextLinePrompt = true; lines.append(line); lines.append("\n"); } else if (line.trim().endsWith(";") && !inHereDoc) { lines.append(line); String input = lines.toString(); nextLinePrompt = false; processInput(input, walkers, ctx); processOutput(ctx, out, !commandLine.hasOption("nocolor")); lines = new StringBuffer(); } else if (inHereDoc) { lines.append(line); lines.append("\n"); } } ctx.getActionListener().term(); }
From source file:DataCrawler.OpenAIRE.XMLGenerator.java
public static void main(String[] args) { String text = ""; try {/*from ww w .ja v a 2 s. c om*/ if (args.length < 4) { System.out.println("<command> template_file csv_file output_dir log_file [start_id]"); } // InputStream fis = new FileInputStream("E:/Downloads/result-r-00000"); InputStream fis = new FileInputStream(args[1]); BufferedReader br = new BufferedReader(new InputStreamReader(fis, Charset.forName("UTF-8"))); // String content = new String(Files.readAllBytes(Paths.get("publications_template.xml"))); String content = new String(Files.readAllBytes(Paths.get(args[0]))); Document doc = Jsoup.parse(content, "UTF-8", Parser.xmlParser()); // String outputDirectory = "G:/"; String outputDirectory = args[2]; // PrintWriter logWriter = new PrintWriter(new FileOutputStream("publication.log",false)); PrintWriter logWriter = new PrintWriter(new FileOutputStream(args[3], false)); Element objectId = null, title = null, publisher = null, dateofacceptance = null, bestlicense = null, resulttype = null, originalId = null, originalId2 = null; boolean start = true; // String startID = "dedup_wf_001::207a098867b64f3b5af505fa3aeecd24"; String startID = ""; if (args.length >= 5) { start = false; startID = args[4]; } String previousText = ""; while ((text = br.readLine()) != null) { /* For publications: 0. dri:objIdentifier context 9. title context 12. publisher context 18. dateofacceptance 19. bestlicense @classname 21. resulttype @classname 26. originalId context (Notice that the prefix is null and will use space to separate two different "originalId") */ if (!previousText.isEmpty()) { text = previousText + text; start = true; previousText = ""; } String[] items = text.split("!"); for (int i = 0; i < items.length; ++i) { items[i] = StringUtils.strip(items[i], "#"); } if (objectId == null) objectId = doc.getElementsByTag("dri:objIdentifier").first(); objectId.text(items[0]); if (!start && items[0].equals(startID)) { start = true; } if (title == null) title = doc.getElementsByTag("title").first(); title.text(items[9]); if (publisher == null) publisher = doc.getElementsByTag("publisher").first(); if (items.length < 12) { previousText = text; continue; } publisher.text(items[12]); if (dateofacceptance == null) dateofacceptance = doc.getElementsByTag("dateofacceptance").first(); dateofacceptance.text(items[18]); if (bestlicense == null) bestlicense = doc.getElementsByTag("bestlicense").first(); bestlicense.attr("classname", items[19]); if (resulttype == null) resulttype = doc.getElementsByTag("resulttype").first(); resulttype.attr("classname", items[21]); if (originalId == null || originalId2 == null) { Elements elements = doc.getElementsByTag("originalId"); String[] context = items[26].split(" "); if (elements.size() > 0) { if (elements.size() >= 1) { originalId = elements.get(0); if (context.length >= 1) { int indexOfnull = context[0].trim().indexOf("null"); String value = ""; if (indexOfnull != -1) { if (context[0].trim().length() >= (indexOfnull + 5)) value = context[0].trim().substring(indexOfnull + 5); } else { value = context[0].trim(); } originalId.text(value); } } if (elements.size() >= 2) { originalId2 = elements.get(1); if (context.length >= 2) { int indexOfnull = context[1].trim().indexOf("null"); String value = ""; if (indexOfnull != -1) { if (context[1].trim().length() >= (indexOfnull + 5)) value = context[1].trim().substring(indexOfnull + 5); } else { value = context[1].trim(); } originalId2.text(value); } } } } else { String[] context = items[26].split(" "); if (context.length >= 1) { int indexOfnull = context[0].trim().indexOf("null"); String value = ""; if (indexOfnull != -1) { if (context[0].trim().length() >= (indexOfnull + 5)) value = context[0].trim().substring(indexOfnull + 5); } else { value = context[0].trim(); } originalId.text(value); } if (context.length >= 2) { int indexOfnull = context[1].trim().indexOf("null"); String value = ""; if (indexOfnull != -1) { if (context[1].trim().length() >= (indexOfnull + 5)) value = context[1].trim().substring(indexOfnull + 5); } else { value = context[1].trim(); } originalId2.text(value); } } if (start) { String filePath = outputDirectory + items[0].replace(":", "#") + ".xml"; PrintWriter writer = new PrintWriter(new FileOutputStream(filePath, false)); logWriter.write(filePath + " > Start" + System.lineSeparator()); writer.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>" + System.lineSeparator()); writer.write(doc.getElementsByTag("response").first().toString()); writer.close(); logWriter.write(filePath + " > OK" + System.lineSeparator()); logWriter.flush(); } } logWriter.close(); } catch (Exception e) { e.printStackTrace(); } }
From source file:AwsConsoleApp.java
public static void main(String[] args) throws Exception { System.out.println("==========================================="); System.out.println("Welcome to the AWS VPN connection creator"); System.out.println("==========================================="); init();//from w w w . j a v a 2 s. com List<String> CIDRblocks = new ArrayList<String>(); String vpnType = null; String vpnGatewayId = null; String customerGatewayId = null; String customerGatewayInfoPath = null; String routes = null; options.addOption("h", "help", false, "show help."); options.addOption("vt", "vpntype", true, "Set vpn tunnel type e.g. (ipec.1)"); options.addOption("vgw", "vpnGatewayId", true, "Set AWS VPN Gateway ID e.g. (vgw-eca54d85)"); options.addOption("cgw", "customerGatewayId", true, "Set AWS Customer Gateway ID e.g. (cgw-c16e87a8)"); options.addOption("r", "staticroutes", true, "Set static routes e.g. cutomer subnet 10.77.77.0/24"); options.addOption("vi", "vpninfo", true, "path to vpn info file c:\\temp\\customerGatewayInfo.xml"); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; // Parse command line options try { cmd = parser.parse(options, args); if (cmd.hasOption("h")) help(); if (cmd.hasOption("vt")) { log.log(Level.INFO, "Using cli argument -vt=" + cmd.getOptionValue("vt")); vpnType = cmd.getOptionValue("vt"); // Whatever you want to do with the setting goes here } else { log.log(Level.SEVERE, "Missing vt option"); help(); } if (cmd.hasOption("vgw")) { log.log(Level.INFO, "Using cli argument -vgw=" + cmd.getOptionValue("vgw")); vpnGatewayId = cmd.getOptionValue("vgw"); } else { log.log(Level.SEVERE, "Missing vgw option"); help(); } if (cmd.hasOption("cgw")) { log.log(Level.INFO, "Using cli argument -cgw=" + cmd.getOptionValue("cgw")); customerGatewayId = cmd.getOptionValue("cgw"); } else { log.log(Level.SEVERE, "Missing cgw option"); help(); } if (cmd.hasOption("r")) { log.log(Level.INFO, "Using cli argument -r=" + cmd.getOptionValue("r")); routes = cmd.getOptionValue("r"); String[] routeItems = routes.split(","); CIDRblocks = Arrays.asList(routeItems); } else { log.log(Level.SEVERE, "Missing r option"); help(); } if (cmd.hasOption("vi")) { log.log(Level.INFO, "Using cli argument -vi=" + cmd.getOptionValue("vi")); customerGatewayInfoPath = cmd.getOptionValue("vi"); } else { log.log(Level.SEVERE, "Missing vi option"); help(); } } catch (ParseException e) { log.log(Level.SEVERE, "Failed to parse comand line properties", e); help(); } /* * Amazon VPC * Create and delete VPN tunnel to customer VPN hardware */ try { //String vpnType = "ipsec.1"; //String vpnGatewayId = "vgw-eca54d85"; //String customerGatewayId = "cgw-c16e87a8"; //List<String> CIDRblocks = new ArrayList<String>(); //CIDRblocks.add("10.77.77.0/24"); //CIDRblocks.add("172.16.1.0/24"); //CIDRblocks.add("172.18.1.0/24"); //CIDRblocks.add("10.66.66.0/24"); //CIDRblocks.add("10.8.1.0/24"); //String customerGatewayInfoPath = "c:\\temp\\customerGatewayInfo.xml"; Boolean staticRoutesOnly = true; List<String> connectionIds = new ArrayList<String>(); List<String> connectionIdList = new ArrayList<String>(); connectionIdList = vpnExists(connectionIds); if (connectionIdList.size() == 0) { CreateVpnConnectionRequest vpnReq = new CreateVpnConnectionRequest(vpnType, customerGatewayId, vpnGatewayId); CreateVpnConnectionResult vpnRes = new CreateVpnConnectionResult(); VpnConnectionOptionsSpecification vpnspec = new VpnConnectionOptionsSpecification(); vpnspec.setStaticRoutesOnly(staticRoutesOnly); vpnReq.setOptions(vpnspec); System.out.println("Creating VPN connection"); vpnRes = ec2.createVpnConnection(vpnReq); String vpnConnId = vpnRes.getVpnConnection().getVpnConnectionId(); String customerGatewayInfo = vpnRes.getVpnConnection().getCustomerGatewayConfiguration(); //System.out.println("Customer Gateway Info:" + customerGatewayInfo); // Write Customer Gateway Info to file System.out.println("Writing Customer Gateway Info to file:" + customerGatewayInfoPath); try (PrintStream out = new PrintStream(new FileOutputStream(customerGatewayInfoPath))) { out.print(customerGatewayInfo); } System.out.println("Creating VPN routes"); for (String destCIDR : CIDRblocks) { CreateVpnConnectionRouteRequest routeReq = new CreateVpnConnectionRouteRequest(); CreateVpnConnectionRouteResult routeRes = new CreateVpnConnectionRouteResult(); routeReq.setDestinationCidrBlock(destCIDR); routeReq.setVpnConnectionId(vpnConnId); routeRes = ec2.createVpnConnectionRoute(routeReq); } // Parse XML file File file = new File(customerGatewayInfoPath); DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); Document document = db.parse(customerGatewayInfoPath); XPathFactory xPathfactory = XPathFactory.newInstance(); XPath xpath = xPathfactory.newXPath(); XPathExpression exprGetipAddress = xpath .compile("/vpn_connection/ipsec_tunnel/vpn_gateway/tunnel_outside_address/ip_address"); NodeList vpnGateway = (NodeList) exprGetipAddress.evaluate(document, XPathConstants.NODESET); if (vpnGateway != null) { for (int i = 0; i < vpnGateway.getLength(); i++) { String vpnGatewayIP = vpnGateway.item(i).getTextContent(); System.out .println("AWS vpnGatewayIP for tunnel " + Integer.toString(i) + " " + vpnGatewayIP); } } System.out.println("=============================================="); XPathExpression exprGetKey = xpath.compile("/vpn_connection/ipsec_tunnel/ike/pre_shared_key"); NodeList presharedKeyList = (NodeList) exprGetKey.evaluate(document, XPathConstants.NODESET); if (presharedKeyList != null) { for (int i = 0; i < presharedKeyList.getLength(); i++) { String pre_shared_key = presharedKeyList.item(i).getTextContent(); System.out.println( "AWS pre_shared_key for tunnel " + Integer.toString(i) + " " + pre_shared_key); } } System.out.println("Creating VPN creation completed!"); } else { boolean yn; Scanner scan = new Scanner(System.in); System.out.println("Enter yes or no to delete VPN connection: "); String input = scan.next(); String answer = input.trim().toLowerCase(); while (true) { if (answer.equals("yes")) { yn = true; break; } else if (answer.equals("no")) { yn = false; System.exit(0); } else { System.out.println("Sorry, I didn't catch that. Please answer yes/no"); } } // Delete all existing VPN connections System.out.println("Deleting AWS VPN connection(s)"); for (String vpnConID : connectionIdList) { DeleteVpnConnectionResult delVPNres = new DeleteVpnConnectionResult(); DeleteVpnConnectionRequest delVPNreq = new DeleteVpnConnectionRequest(); delVPNreq.setVpnConnectionId(vpnConID); delVPNres = ec2.deleteVpnConnection(delVPNreq); System.out.println("Successfully deleted AWS VPN conntion: " + vpnConID); } } } catch (AmazonServiceException ase) { System.out.println("Caught Exception: " + ase.getMessage()); System.out.println("Reponse Status Code: " + ase.getStatusCode()); System.out.println("Error Code: " + ase.getErrorCode()); System.out.println("Request ID: " + ase.getRequestId()); } }
From source file:com.hp.test.framework.Reporting.Utlis.java
public static void main(String ar[]) throws IOException { ArrayList<String> runs_list = new ArrayList<String>(); String basepath = replacelogs(); String path = basepath + "ATU Reports\\Results"; File directory = new File(path); File[] subdirs = directory.listFiles((FileFilter) DirectoryFileFilter.DIRECTORY); String htmlReport = basepath + "HTML_Design_Files\\CSS\\HtmlReport.html"; for (File dir : subdirs) { runs_list.add(dir.getName());// w ww . j a v a 2s . c o m } String Reports_path = basepath + "ATU Reports\\"; int LatestRun = Utlis.getLastRun(Reports_path); String Last_run_path = Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "\\"; HtmlParse.replaceMainTable(false, new File(Last_run_path + "/CurrentRun.html")); HtmlParse.replaceCountsinJSFile(new File("HTML_Design_Files/JS/3dChart.js"), Last_run_path); UpdateTestCaseDesciption.basepath = Last_run_path; UpdateTestCaseDesciption.getTestCaseHtmlPath(Last_run_path + "/CurrentRun.html"); UpdateTestCaseDesciption.replaceDetailsTable(Last_run_path + "/CurrentRun.html"); // GenerateFailReport.genarateFailureReport(new File(htmlReport), Reports_path + "Results\\Run_" + String.valueOf(LatestRun)); genarateFailureReport(new File(htmlReport), Reports_path + "Results\\"); Map<String, List<String>> runCounts = GetCountsrunsWise(runs_list, path); int success = replaceCounts(runCounts, path); if (success == 0) { File SourceFile = new File(path + "\\lineChart_temp.js"); File RenameFile = new File(path + "\\lineChart.js"); renameOriginalFile(SourceFile, RenameFile); File SourceFile1 = new File(path + "\\barChart_temp.js"); File RenameFile1 = new File(path + "\\barChart.js"); renameOriginalFile(SourceFile1, RenameFile1); Utlis.getpaths(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun)); try { Utlis.replaceMainTable(false, new File(Reports_path + "index.html")); Utlis.replaceMainTable(true, new File(Reports_path + "results\\" + "ConsolidatedPage.html")); Utlis.replaceMainTable(true, new File(Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); fileList.add( new File(Reports_path + "\\Results\\Run_" + String.valueOf(LatestRun) + "CurrentRun.html")); for (File f : fileList) { Utlis.replaceMainTable(true, f); } } catch (Exception ex) { log.info("Error in updating Report format" + ex.getMessage()); } Last_run_path = Reports_path + "Results\\Run_" + String.valueOf(LatestRun) + "\\"; // HtmlParse.replaceMainTable(false, new File(Last_run_path + "/CurrentRun.html")); // HtmlParse.replaceCountsinJSFile(new File("../HTML_Design_Files/JS/3dChart.js"), Last_run_path); ArrayList<String> to_list = new ArrayList<String>(); ReportingProperties reportingproperties = new ReportingProperties(); String temp_eml = reportingproperties.getProperty("TOLIST"); String JenkinsURL = reportingproperties.getProperty("JENKINSURL"); String ScreenShotsDir = reportingproperties.getProperty("ScreenShotsDirectory"); Boolean cleanScreenshotsDir = Boolean.valueOf(reportingproperties.getProperty("CleanPreScreenShots")); Boolean generatescreenshots = Boolean.valueOf(reportingproperties.getProperty("GenerateScreenShots")); String HtmlreportFilePrefix = reportingproperties.getProperty("HtmlreportFilePrefix"); if (cleanScreenshotsDir) { if (!CleanFilesinDir(ScreenShotsDir)) { log.error("Not able to Clean the Previous Run Details in the paht" + ScreenShotsDir); } else { log.info("Cleaning Previous Run Details in the paht" + ScreenShotsDir + "Sucess"); } } List<String> scr_fileList; List<String> html_fileList; if (generatescreenshots) { scr_fileList = GetFileListinDir(ScreenShotsDir, "png"); int len = scr_fileList.size(); len = len + 1; screenshot.generatescreenshot(Last_run_path + "CurrentRun.html", ScreenShotsDir + "screenshot_" + len + ".png"); File source = new File(Reports_path + "Results\\HtmlReport.html"); File dest = new File(ScreenShotsDir + HtmlreportFilePrefix + "_HtmlReport.html"); // Files.copy(f.toPath(), (new File((ScreenShotsDir+HtmlreportFilePrefix+"_HtmlReport.html").toPath(),StandardCopyOption.REPLACE_EXISTING); FileUtils.copyFile(source, dest); scr_fileList.clear(); } scr_fileList = GetFileListinDir(ScreenShotsDir, "png"); html_fileList = GetFileListinDir(ScreenShotsDir, "html"); if (temp_eml.length() > 1) { String[] to_list_temp = temp_eml.split(","); if (to_list_temp.length > 0) { for (String to_list_temp1 : to_list_temp) { to_list.add(to_list_temp1); } } if (to_list.size() > 0) { screenshot.generatescreenshot(Last_run_path + "CurrentRun.html", Last_run_path + "screenshot.png"); // cleanTempDir.cleanandCreate(Reports_path, LatestRun); // ZipUtils.ZipFolder(Reports_path + "temp", Reports_path + "ISTF_Reports.zip"); if (generatescreenshots) { SendingEmail.sendmail(to_list, JenkinsURL, scr_fileList, html_fileList); } else { SendingEmail.sendmail(to_list, JenkinsURL, Reports_path + "/Results/HtmlReport.html", Last_run_path + "screenshot.png"); } // FileUtils.deleteQuietly(new File(Reports_path + "ISTF_Reports.zip")); // FileUtils.deleteDirectory(new File(Reports_path + "temp")); } } } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {//from w w w . j a va 2s. co m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:net.sf.extjwnl.cli.ewn.java
public static void main(String[] args) throws IOException, JWNLException { if (args.length < 1) { System.out.println(USAGE); System.exit(0);/*from w ww . j a v a 2 s .c o m*/ } //find dictionary Dictionary d = null; File config = new File(defaultConfig); if (!config.exists()) { if (System.getenv().containsKey("WNHOME")) { String wnHomePath = System.getenv().get("WNHOME"); File wnHome = new File(wnHomePath); if (wnHome.exists()) { d = Dictionary.getFileBackedInstance(wnHomePath); } else { log.error("Cannot find dictionary. Make sure " + defaultConfig + " is available or WNHOME variable is set."); } } } else { d = Dictionary.getInstance(new FileInputStream(config)); } if (null != d) { //parse and execute command line if ((-1 < args[0].indexOf('%') && -1 < args[0].indexOf(':')) || "-script".equals(args[0]) || (-1 < args[0].indexOf('#'))) { d.edit(); //edit if ("-script".equals(args[0])) { if (args.length < 2) { log.error("Filename missing for -script command"); System.exit(1); } else { File script = new File(args[1]); if (script.exists()) { //load into args ArrayList<String> newArgs = new ArrayList<String>(); BufferedReader in = new BufferedReader( new InputStreamReader(new FileInputStream(script), "UTF-8")); try { String str; while ((str = in.readLine()) != null) { String[] bits = str.split(" "); StringBuilder tempArg = null; for (String bit : bits) { int quoteCnt = 0; for (int j = 0; j < bit.length(); j++) { if ('"' == bit.charAt(j)) { quoteCnt++; } } if (null != tempArg) { if (0 == quoteCnt) { tempArg.append(" ").append(bit); } else { tempArg.append(" ").append(bit.replaceAll("\"\"", "\"")); if (1 == (quoteCnt % 2)) { newArgs.add( tempArg.toString().substring(1, tempArg.length() - 1)); tempArg = null; } } } else { if (0 == quoteCnt) { newArgs.add(bit); } else { if (1 == (quoteCnt % 2)) { tempArg = new StringBuilder(bit.replaceAll("\"\"", "\"")); } else { newArgs.add(bit.replaceAll("\"\"", "\"")); } } } } if (null != tempArg) { newArgs.add(tempArg.toString()); } } } finally { try { in.close(); } catch (IOException e) { //nop } } args = newArgs.toArray(args); } } } Word workWord = null; String key = null; String lemma = null; int lexFileNum = -1; int lexId = -1; // String headLemma = null; // int headLexId = -1; POS pos = null; String derivation = null; for (int i = 0; i < args.length; i++) { if (null == key && '-' != args[i].charAt(0) && ((-1 < args[i].indexOf('%') && -1 < args[i].indexOf(':')))) { key = args[i]; log.info("Searching " + key + "..."); if (null != key) { workWord = d.getWordBySenseKey(key); } if (null == workWord) { //parse sensekey lemma = key.substring(0, key.indexOf('%')).replace('_', ' '); String posId = key.substring(key.indexOf('%') + 1, key.indexOf(':')); if ("1".equals(posId) || "2".equals(posId) || "3".equals(posId) || "4".equals(posId) || "5".equals(posId)) { pos = POS.getPOSForId(Integer.parseInt(posId)); String lexFileString = key.substring(key.indexOf(':') + 1); if (-1 < lexFileString.indexOf(':')) { lexFileNum = Integer .parseInt(lexFileString.substring(0, lexFileString.indexOf(':'))); if (lexFileString.indexOf(':') + 1 < lexFileString.length()) { String lexIdString = lexFileString .substring(lexFileString.indexOf(':') + 1); if (-1 < lexIdString.indexOf(':')) { lexId = Integer .parseInt(lexIdString.substring(0, lexIdString.indexOf(':'))); // if (lexIdString.indexOf(':') + 1 < lexIdString.length()) { // headLemma = lexIdString.substring(lexIdString.indexOf(':') + 1); // if (-1 < headLemma.indexOf(':')) { // headLemma = headLemma.substring(0, headLemma.indexOf(':')); // if (null != headLemma && !"".equals(headLemma) && lexIdString.lastIndexOf(':') + 1 < lexIdString.length()) { // headLexId = Integer.parseInt(lexIdString.substring(lexIdString.lastIndexOf(':') + 1)); // } // } else { // log.error("Malformed sensekey " + key); // System.exit(1); // } // } } else { log.error("Malformed sensekey " + key); System.exit(1); } } else { log.error("Malformed sensekey " + key); System.exit(1); } } else { log.error("Malformed sensekey " + key); System.exit(1); } } else { log.error("Malformed sensekey " + key); System.exit(1); } } } else if (-1 < args[i].indexOf('#')) { if (2 < args[i].length()) { derivation = args[i].substring(2); if (null == derivation) { log.error("Missing derivation"); System.exit(1); } else { pos = POS.getPOSForKey(args[i].substring(0, 1)); if (null == pos) { log.error("POS " + args[i] + " is not recognized for derivation " + derivation); System.exit(1); } } } } if ("-add".equals(args[i])) { if (null == key) { log.error("Missing sensekey"); System.exit(1); } if (null != workWord) { log.error("Duplicate sensekey " + workWord.getSenseKey()); System.exit(1); } log.info("Creating " + pos.getLabel() + " synset..."); Synset tempSynset = d.createSynset(pos); log.info("Creating word " + lemma + "..."); workWord = new Word(d, tempSynset, 1, lemma); workWord.setLexId(lexId); tempSynset.getWords().add(workWord); tempSynset.setLexFileNum(lexFileNum); key = null; } if ("-remove".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { d.removeSynset(workWord.getSynset()); workWord = null; key = null; } } if ("-addword".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { Word tempWord = new Word(d, workWord.getSynset(), workWord.getSynset().getWords().size() + 1, args[i]); workWord.getSynset().getWords().add(tempWord); key = null; } else { log.error( "Missing word for addword command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-removeword".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { workWord.getSynset().getWords().remove(workWord); key = null; } } if ("-setgloss".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { workWord.getSynset().setGloss(args[i]); key = null; } else { log.error("Missing gloss for setgloss command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setadjclus".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { workWord.getSynset().setIsAdjectiveCluster(Boolean.parseBoolean(args[i])); key = null; } else { log.error("Missing flag for setadjclus command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setverbframe".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length) { if (workWord instanceof Verb) { Verb verb = (Verb) workWord; if ('-' == args[i].charAt(0)) { verb.getVerbFrameFlags().clear(Integer.parseInt(args[i].substring(1))); } else { verb.getVerbFrameFlags().set(Integer.parseInt(args[i])); } } else { log.error("Word at " + workWord.getSenseKey() + " should be verb"); System.exit(1); } key = null; } else { log.error("Missing index for setverbframe command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setverbframeall".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length) { if (workWord.getSynset() instanceof VerbSynset) { if ('-' == args[i].charAt(0)) { workWord.getSynset().getVerbFrameFlags() .clear(Integer.parseInt(args[i].substring(1))); } else { workWord.getSynset().getVerbFrameFlags().set(Integer.parseInt(args[i])); } } else { log.error("Synset at " + workWord.getSenseKey() + " should be verb"); System.exit(1); } key = null; } else { log.error("Missing index for setverbframeall command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setlexfile".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { if (-1 < args[i].indexOf('.')) { workWord.getSynset() .setLexFileNum(LexFileNameLexFileIdMap.getMap().get(args[i])); } else { workWord.getSynset().setLexFileNum(Integer.parseInt(args[i])); } } else { log.error("Missing file number or name for setlexfile command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-addptr".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length) { Word targetWord = d.getWordBySenseKey(args[i]); if (null != targetWord) { i++; if (i < args.length) { PointerType pt = PointerType.getPointerTypeForKey(args[i]); if (null != pt) { Pointer p; if (pt.isLexical()) { p = new Pointer(pt, workWord, targetWord); } else { p = new Pointer(pt, workWord.getSynset(), targetWord.getSynset()); } if (!workWord.getSynset().getPointers().contains(p)) { workWord.getSynset().getPointers().add(p); } else { log.error("Duplicate pointer of type " + pt + " to " + targetWord.getSenseKey() + " in addptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Invalid pointer type at " + args[i] + " in addptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Missing pointer type at " + args[i] + " in addptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Missing target at " + args[i] + " in addptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } key = null; } else { log.error("Missing sensekey for addptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-removeptr".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length) { Word targetWord = d.getWordBySenseKey(args[i]); if (null != targetWord) { i++; if (i < args.length) { PointerType pt = PointerType.getPointerTypeForKey(args[i]); if (null != pt) { Pointer p; if (pt.isLexical()) { p = new Pointer(pt, workWord, targetWord); } else { p = new Pointer(pt, workWord.getSynset(), targetWord.getSynset()); } if (workWord.getSynset().getPointers().contains(p)) { workWord.getSynset().getPointers().remove(p); } else { log.error("Missing pointer of type " + pt + " to " + targetWord.getSenseKey() + " in removeptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Invalid pointer type at " + args[i] + " in removeptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Missing pointer type at " + args[i] + " in removeptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } else { log.error("Missing target at " + args[i] + " in removeptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } key = null; } else { log.error("Missing sensekey for removeptr command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setlexid".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { workWord.setLexId(Integer.parseInt(args[i])); key = null; } else { log.error("Missing lexid for setlexid command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-setusecount".equals(args[i])) { if (null == workWord) { log.error("Missing sensekey"); System.exit(1); } else { i++; if (i < args.length && '-' != args[i].charAt(0)) { workWord.setUseCount(Integer.parseInt(args[i])); key = null; } else { log.error("Missing count for setusecount command for sensekey " + workWord.getSenseKey()); System.exit(1); } } } if ("-addexc".equals(args[i])) { i++; if (i < args.length && '-' != args[i].charAt(0)) { String baseform = args[i]; Exc e = d.getException(pos, derivation); if (null != e) { if (null != e.getExceptions()) { if (!e.getExceptions().contains(baseform)) { e.getExceptions().add(baseform); } } } else { ArrayList<String> list = new ArrayList<String>(1); list.add(baseform); d.createException(pos, derivation, list); } derivation = null; } else { log.error("Missing baseform for addexc command for derivation " + derivation); System.exit(1); } } if ("-removeexc".equals(args[i])) { Exc e = d.getException(pos, derivation); if (null != e) { i++; if (i < args.length && '-' != args[i].charAt(0)) { String baseform = args[i]; if (null != e.getExceptions()) { if (e.getExceptions().contains(baseform)) { e.getExceptions().remove(baseform); } if (0 == e.getExceptions().size()) { d.removeException(e); } } } else { d.removeException(e); } } else { log.error("Missing derivation " + derivation); System.exit(1); } derivation = null; } } d.save(); } else { //browse String key = args[0]; if (1 == args.length) { for (POS pos : POS.getAllPOS()) { IndexWord iw = d.getIndexWord(pos, key); if (null == iw) { System.out.println("\nNo information available for " + pos.getLabel() + " " + key); } else { System.out.println( "\nInformation available for " + iw.getPOS().getLabel() + " " + iw.getLemma()); printAvailableInfo(iw); } if (null != d.getMorphologicalProcessor()) { List<String> forms = d.getMorphologicalProcessor().lookupAllBaseForms(pos, key); if (null != forms) { for (String form : forms) { if (!key.equals(form)) { iw = d.getIndexWord(pos, form); if (null != iw) { System.out.println("\nInformation available for " + iw.getPOS().getLabel() + " " + iw.getLemma()); printAvailableInfo(iw); } } } } } } } else { boolean needHelp = false; boolean needGloss = false; boolean needLex = false; boolean needOffset = false; boolean needSenseNum = false; boolean needSenseKeys = false; int needSense = 0; for (String arg : args) { if ("-h".equals(arg)) { needHelp = true; } if ("-g".equals(arg)) { needGloss = true; } if ("-a".equals(arg)) { needLex = true; } if ("-o".equals(arg)) { needOffset = true; } if ("-s".equals(arg)) { needSenseNum = true; } if ("-k".equals(arg)) { needSenseKeys = true; } if (arg.startsWith("-n") && 2 < arg.length()) { needSense = Integer.parseInt(arg.substring(2)); } } for (String arg : args) { if (arg.startsWith("-ants") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display synsets containing direct antonyms of the search string.\n" + "\n" + "Direct antonyms are a pair of words between which there is an\n" + "associative bond built up by co-occurrences.\n" + "\n" + "Antonym synsets are preceded by \"=>\"."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nAntonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.ANTONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //ants if (arg.startsWith("-hype") && 6 == arg.length()) { if (needHelp) { System.out.println( "Recursively display hypernym (superordinate) tree for the search\n" + "string.\n" + "\n" + "Hypernym is the generic term used to designate a whole class of\n" + "specific instances. Y is a hypernym of X if X is a (kind of) Y.\n" + "\n" + "Hypernym synsets are preceded by \"=>\", and are indented from\n" + "the left according to their level in the hierarchy."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nHypernyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.HYPERNYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //hype if (arg.startsWith("-hypo") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display immediate hyponyms (subordinates) for the search string.\n" + "\n" + "Hyponym is the generic term used to designate a member of a class.\n" + "X is a hyponym of Y if X is a (kind of) Y.\n" + "\n" + "Hyponym synsets are preceded by \"=>\"."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nHyponyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.HYPONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //hypo if (arg.startsWith("-tree") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display hyponym (subordinate) tree for the search string. This is\n" + "a recursive search that finds the hyponyms of each hyponym. \n" + "\n" + "Hyponym is the generic term used to designate a member of a class.\n" + "X is a hyponym of Y if X is a (kind of) Y. \n" + "\n" + "Hyponym synsets are preceded by \"=>\", and are indented from the left\n" + "according to their level in the hierarchy."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nHyponyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.HYPONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //tree if (arg.startsWith("-enta") && 6 == arg.length()) { if (needHelp) { System.out.println( "Recursively display entailment relations of the search string.\n" + "\n" + "The action represented by the verb X entails Y if X cannot be done\n" + "unless Y is, or has been, done.\n" + "\n" + "Entailment synsets are preceded by \"=>\", and are indented from the left\n" + "according to their level in the hierarchy."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nEntailment of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.ENTAILMENT, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //enta if (arg.startsWith("-syns") && 6 == arg.length()) { POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nSynonyms of " + p.getLabel() + " " + iw.getLemma()); if (POS.ADJECTIVE == p) { if (needHelp) { System.out.println( "Display synonyms and synsets related to synsets containing\n" + "the search string. If the search string is in a head synset\n" + "the 'cluster's' satellite synsets are displayed. If the search\n" + "string is in a satellite synset, its head synset is displayed.\n" + "If the search string is a pertainym the word or synset that it\n" + "pertains to is displayed.\n" + "\n" + "A cluster is a group of adjective synsets that are organized around\n" + "antonymous pairs or triplets. An adjective cluster contains two or more\n" + "head synsets that contan antonyms. Each head synset has one or more\n" + "satellite synsets.\n" + "\n" + "A head synset contains at least one word that has a direct antonym\n" + "in another head synset of the same cluster.\n" + "\n" + "A satellite synset represents a concept that is similar in meaning to\n" + "the concept represented by its head synset.\n" + "\n" + "Direct antonyms are a pair of words between which there is an\n" + "associative bond built up by co-occurrences.\n" + "\n" + "Direct antonyms are printed in parentheses following the adjective.\n" + "The position of an adjective in relation to the noun may be restricted\n" + "to the prenominal, postnominal or predicative position. Where present\n" + "these restrictions are noted in parentheses.\n" + "\n" + "A pertainym is a relational adjective, usually defined by such phrases\n" + "as \"of or pertaining to\" and that does not have an antonym. It pertains\n" + "to a noun or another pertainym.\n" + "\n" + "Senses contained in head synsets are displayed above the satellites,\n" + "which are indented and preceded by \"=>\". Senses contained in\n" + "satellite synsets are displayed with the head synset below. The head\n" + "synset is preceded by \"=>\".\n" + "\n" + "Pertainym senses display the word or synsets that the search string\n" + "pertains to."); } tracePointers(iw, PointerType.SIMILAR_TO, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PARTICIPLE_OF, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } if (POS.ADVERB == p) { if (needHelp) { System.out.println( "Display synonyms and synsets related to synsets containing\n" + "the search string. If the search string is a pertainym the word\n" + "or synset that it pertains to is displayed.\n" + "\n" + "A pertainym is a relational adverb that is derived from an adjective.\n" + "\n" + "Pertainym senses display the word that the search string is derived from\n" + "and the adjective synset that contains the word. If the adjective synset\n" + "is a satellite synset, its head synset is also displayed."); } tracePointers(iw, PointerType.PERTAINYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } if (POS.NOUN == p || POS.VERB == p) { if (needHelp) { System.out.println( "Recursively display hypernym (superordinate) tree for the search\n" + "string.\n" + "\n" + "Hypernym is the generic term used to designate a whole class of\n" + "specific instances. Y is a hypernym of X if X is a (kind of) Y.\n" + "\n" + "Hypernym synsets are preceded by \"=>\", and are indented from\n" + "the left according to their level in the hierarchy."); } tracePointers(iw, PointerType.HYPERNYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } } //syns if (arg.startsWith("-smem") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all holonyms of the search string.\n" + "\n" + "A holonym is the name of the whole of which the 'meronym' names a part.\n" + "Y is a holonym of X if X is a part of Y.\n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nMember Holonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //smem if (arg.startsWith("-ssub") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all holonyms of the search string.\n" + "\n" + "A holonym is the name of the whole of which the 'meronym' names a part.\n" + "Y is a holonym of X if X is a part of Y.\n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nSubstance Holonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.SUBSTANCE_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //ssub if (arg.startsWith("-sprt") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all holonyms of the search string.\n" + "\n" + "A holonym is the name of the whole of which the 'meronym' names a part.\n" + "Y is a holonym of X if X is a part of Y.\n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nPart Holonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.PART_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //sprt if (arg.startsWith("-memb") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all meronyms of the search string. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nMember Meronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //memb if (arg.startsWith("-subs") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all meronyms of the search string. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nSubstance Meronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.SUBSTANCE_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //subs if (arg.startsWith("-part") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all meronyms of the search string. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nPart Meronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.PART_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //part if (arg.startsWith("-mero") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all meronyms of the search string. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nMeronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.SUBSTANCE_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PART_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //mero if (arg.startsWith("-holo") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all holonyms of the search string.\n" + "\n" + "A holonym is the name of the whole of which the 'meronym' names a part.\n" + "Y is a holonym of X if X is a part of Y.\n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nHolonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.SUBSTANCE_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PART_HOLONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //holo if (arg.startsWith("-caus") && 6 == arg.length()) { if (needHelp) { System.out.println("Recursively display CAUSE TO relations of the search string.\n" + "\n" + "The action represented by the verb X causes the action represented by\n" + "the verb Y.\n" + "\n" + "CAUSE TO synsets are preceded by \"=>\", and are indented from the left\n" + "according to their level in the hierarchy."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\n'Cause to' of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.CAUSE, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //caus if (arg.startsWith("-pert") && 6 == arg.length()) { POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nPertainyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.PERTAINYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //pert if (arg.startsWith("-attr") && 6 == arg.length()) { POS p = POS.getPOSForKey(arg.substring(5)); if (needHelp) { if (POS.NOUN == p) { System.out .println("Display adjectives for which search string is an attribute."); } if (POS.ADJECTIVE == p) { System.out.println("Display nouns that are attributes of search string."); } } IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nAttributes of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.ATTRIBUTE, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //attr if (arg.startsWith("-deri") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display derived forms - nouns and verbs that are related morphologically.\n" + "Each related synset is preceeded by its part of speech. Each word in the\n" + "synset is followed by its sense number."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nDerived forms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.NOMINALIZATION, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //deri if (arg.startsWith("-domn") && 6 == arg.length()) { if (needHelp) { System.out.println("Display domain to which this synset belongs."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nDomain of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.CATEGORY, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.USAGE, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.REGION, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //domn if (arg.startsWith("-domt") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all synsets belonging to the domain."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nDomain of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.CATEGORY_MEMBER, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.USAGE_MEMBER, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.REGION_MEMBER, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //domt if (arg.startsWith("-faml") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display familiarity and polysemy information for the search string.\n" + "The polysemy count is the number of senses in WordNet."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { String[] freqs = { "extremely rare", "very rare", "rare", "uncommon", "common", "familiar", "very familiar", "extremely familiar" }; String[] pos = { "a noun", "a verb", "an adjective", "an adverb" }; int cnt = iw.getSenses().size(); int familiar = 0; if (cnt == 0) { familiar = 0; } if (cnt == 1) { familiar = 1; } if (cnt == 2) { familiar = 2; } if (cnt >= 3 && cnt <= 4) { familiar = 3; } if (cnt >= 5 && cnt <= 8) { familiar = 4; } if (cnt >= 9 && cnt <= 16) { familiar = 5; } if (cnt >= 17 && cnt <= 32) { familiar = 6; } if (cnt > 32) { familiar = 7; } System.out.println("\n" + iw.getLemma() + " used as " + pos[p.getId() - 1] + " is " + freqs[familiar] + " (polysemy count = " + cnt + ")"); } } //faml if (arg.startsWith("-fram") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display applicable verb sentence frames for the search string.\n" + "\n" + "A frame is a sentence template illustrating the usage of a verb.\n" + "\n" + "Verb sentence frames are preceded with the string \"*>\" if a sentence\n" + "frame is acceptable for all of the words in the synset, and with \"=>\"\n" + "if a sentence frame is acceptable for the search string only."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nVerb frames of " + p.getLabel() + " " + iw.getLemma()); for (int i = 0; i < iw.getSenses().size(); i++) { Synset synset = iw.getSenses().get(i); for (String vf : synset.getVerbFrames()) { System.out.println("\t*> " + vf); } for (Word word : synset.getWords()) { if (iw.getLemma().equalsIgnoreCase(word.getLemma())) { if (word instanceof Verb) { Verb verb = (Verb) word; for (String vf : verb.getVerbFrames()) { System.out.println("\t=> " + vf); } } } } } } } //fram if (arg.startsWith("-hmer") && 6 == arg.length()) { if (needHelp) { System.out.println( "Display meronyms for search string tree. This is a recursive search\n" + "the prints all the meronyms of the search string and all of its\n" + "hypernyms. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nMeronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_MERONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.SUBSTANCE_MERONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PART_MERONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //hmer if (arg.startsWith("-hhol") && 6 == arg.length()) { if (needHelp) { System.out.println( "\"Display holonyms for search string tree. This is a recursive search\n" + "that prints all the holonyms of the search string and all of the\n" + "holonym's holonyms.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nHolonyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_HOLONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.SUBSTANCE_HOLONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PART_HOLONYM, PointerUtils.INFINITY, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //hhol if (arg.startsWith("-mero") && 6 == arg.length()) { if (needHelp) { System.out.println("Display all meronyms of the search string. \n" + "\n" + "A meronym is the name of a constituent part, the substance of, or a\n" + "member of something. X is a meronym of Y if X is a part of Y.\n" + "\n" + "A holonym is the name of the whole of which the meronym names a part.\n" + "Y is a holonym of X if X is a part of Y."); } POS p = POS.getPOSForKey(arg.substring(5)); IndexWord iw = d.lookupIndexWord(p, key); if (null != iw) { System.out.println("\nMeronyms of " + p.getLabel() + " " + iw.getLemma()); tracePointers(iw, PointerType.MEMBER_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.SUBSTANCE_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); tracePointers(iw, PointerType.PART_MERONYM, 1, needSense, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } //mero if (arg.startsWith("-grep") && 6 == arg.length()) { if (needHelp) { System.out .println("Print all strings in the database containing the search string\n" + "as an individual word, or as the first or last string in a word or\n" + "collocation."); } POS p = POS.getPOSForKey(arg.substring(5)); System.out.println("\nGrep of " + p.getLabel() + " " + key); Iterator<IndexWord> ii = d.getIndexWordIterator(p, key); while (ii.hasNext()) { System.out.println(ii.next().getLemma()); } } //grep if ("-over".equals(arg)) { for (POS pos : POS.getAllPOS()) { if (null != d.getMorphologicalProcessor()) { IndexWord iw = d.getIndexWord(pos, key); //for plurals like species, glasses if (null != iw && key.equals(iw.getLemma())) { printOverview(pos, iw, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } List<String> forms = d.getMorphologicalProcessor().lookupAllBaseForms(pos, key); if (null != forms) { for (String form : forms) { if (!form.equals(key)) { iw = d.getIndexWord(pos, form); if (null != iw) { printOverview(pos, iw, needGloss, needLex, needOffset, needSenseNum, needSenseKeys); } } } } } } } //over } } } } }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments */// w w w . j a v a 2 s. c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); try { File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:com.interflora.ftp.SampleFTPS.java
public static final void main(String[] args) { boolean storeFile = true, binaryTransfer = false, error = false, listFiles = false, listNames = false, hidden = false;//ww w . ja v a 2 s . co m boolean localActive = false, useEpsvWithIPv4 = false, feat = false, printHash = false; boolean mlst = false, mlsd = false; boolean lenient = false; long keepAliveTimeout = -1; int controlKeepAliveReplyTimeout = -1; int minParams = 5; // listings require 3 params String protocol = "TLS,false"; // SSL protocol String doCommand = null; String trustmgr = "all"; String proxyHost = null; int proxyPort = 80; String proxyUser = null; String proxyPassword = null; //sample : rose-misc01.hyd.ftd.untd.com rosedev test123 /TestSftp C:/Users/skarin/Desktop/RosePaths.txt //172.16.160.70 demand quevfoc5 /TestSftp C:/Users/skarin/Desktop/RosePaths.txt int base = 0; for (base = 0; base < args.length; base++) { if (args[base].equals("-s")) { storeFile = true; } else if (args[base].equals("-a")) { localActive = true; } else if (args[base].equals("-b")) { binaryTransfer = true; } else if (args[base].equals("-c")) { doCommand = args[++base]; minParams = 3; } else if (args[base].equals("-d")) { mlsd = true; minParams = 3; } else if (args[base].equals("-e")) { useEpsvWithIPv4 = true; } else if (args[base].equals("-f")) { feat = true; minParams = 3; } else if (args[base].equals("-h")) { hidden = true; } else if (args[base].equals("-k")) { keepAliveTimeout = Long.parseLong(args[++base]); } else if (args[base].equals("-l")) { listFiles = true; minParams = 3; } else if (args[base].equals("-L")) { lenient = true; } else if (args[base].equals("-n")) { listNames = true; minParams = 3; } else if (args[base].equals("-p")) { protocol = args[++base]; } else if (args[base].equals("-t")) { mlst = true; minParams = 3; } else if (args[base].equals("-w")) { controlKeepAliveReplyTimeout = Integer.parseInt(args[++base]); } else if (args[base].equals("-T")) { trustmgr = args[++base]; } else if (args[base].equals("-PrH")) { proxyHost = args[++base]; String parts[] = proxyHost.split(":"); if (parts.length == 2) { proxyHost = parts[0]; proxyPort = Integer.parseInt(parts[1]); } } else if (args[base].equals("-PrU")) { proxyUser = args[++base]; } else if (args[base].equals("-PrP")) { proxyPassword = args[++base]; } else if (args[base].equals("-#")) { printHash = true; } else { break; } } int remain = args.length - base; if (remain < minParams) // server, user, pass, remote, local [protocol] { System.err.println(USAGE); System.exit(1); } String server = args[base++]; int port = 0; String parts[] = server.split(":"); if (parts.length == 2) { server = parts[0]; port = Integer.parseInt(parts[1]); } String username = args[base++]; String password = args[base++]; String remote = null; if (args.length - base > 0) { remote = args[base++]; } String local = null; if (args.length - base > 0) { local = args[base++]; } final FTPClient ftp; if (protocol == null) { if (proxyHost != null) { System.out.println("Using HTTP proxy server: " + proxyHost); ftp = new FTPHTTPClient(proxyHost, proxyPort, proxyUser, proxyPassword); } else { ftp = new FTPClient(); } } else { FTPSClient ftps; if (protocol.equals("true")) { ftps = new FTPSClient(true); } else if (protocol.equals("false")) { ftps = new FTPSClient(false); } else { String prot[] = protocol.split(","); if (prot.length == 1) { // Just protocol ftps = new FTPSClient(protocol); } else { // protocol,true|false ftps = new FTPSClient(prot[0], Boolean.parseBoolean(prot[1])); } } ftp = ftps; if ("all".equals(trustmgr)) { ftps.setTrustManager(TrustManagerUtils.getAcceptAllTrustManager()); } else if ("valid".equals(trustmgr)) { ftps.setTrustManager(TrustManagerUtils.getValidateServerCertificateTrustManager()); } else if ("none".equals(trustmgr)) { ftps.setTrustManager(null); } /* try{ //ftps.setFileType(FTP.ASCII_FILE_TYPE); ftps.execPBSZ(0); // Set protection buffer size ftps.execPROT("C"); // Set data channel protection to private }catch(IOException ex ){ex.printStackTrace();}; */ } // System.out.println("After I/O Exception"); if (printHash) { ftp.setCopyStreamListener(createListener()); } if (keepAliveTimeout >= 0) { ftp.setControlKeepAliveTimeout(keepAliveTimeout); } if (controlKeepAliveReplyTimeout >= 0) { ftp.setControlKeepAliveReplyTimeout(controlKeepAliveReplyTimeout); } ftp.setListHiddenFiles(hidden); // suppress login details ftp.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out), true)); try { int reply; if (port > 0) { ftp.connect(server, port); } else { System.out.println("Trying to Connect to the server \t" + server); ftp.connect(server); } System.out.println("Connected to " + server + " on " + (port > 0 ? port : ftp.getDefaultPort())); // After connection attempt, you should check the reply code to verify // success. reply = ftp.getReplyCode(); if (!FTPReply.isPositiveCompletion(reply)) { ftp.disconnect(); System.err.println("FTP server refused connection."); System.exit(1); } } catch (IOException e) { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { // do nothing } } System.err.println("Could not connect to server."); e.printStackTrace(); System.exit(1); } __main: try { if (!ftp.login(username, password)) { ftp.logout(); error = true; break __main; } System.out.println("Remote system is " + ftp.getSystemType()); if (binaryTransfer) { ftp.setFileType(FTP.BINARY_FILE_TYPE); } // Use passive mode as default because most of us are // behind firewalls these days. if (localActive) { ftp.enterLocalActiveMode(); } else { ftp.enterLocalPassiveMode(); } ftp.setUseEPSVwithIPv4(useEpsvWithIPv4); if (storeFile) { //InputStream input; File fname = new File(local); FileInputStream input = new FileInputStream(fname); String localfilename = fname.getName(); System.out.println("Local file name " + localfilename); ftp.storeFile(remote + "/test/" + localfilename, input); input.close(); } else if (listFiles) { if (lenient) { FTPClientConfig config = new FTPClientConfig(); config.setLenientFutureDates(true); ftp.configure(config); } for (FTPFile f : ftp.listFiles(remote)) { System.out.println(f.getRawListing()); System.out.println(f.toFormattedString()); } } else if (mlsd) { for (FTPFile f : ftp.mlistDir(remote)) { System.out.println(f.getRawListing()); System.out.println(f.toFormattedString()); } } else if (mlst) { FTPFile f = ftp.mlistFile(remote); if (f != null) { System.out.println(f.toFormattedString()); } } else if (listNames) { for (String s : ftp.listNames(remote)) { System.out.println(s); } } else if (feat) { // boolean feature check if (remote != null) { // See if the command is present if (ftp.hasFeature(remote)) { System.out.println("Has feature: " + remote); } else { if (FTPReply.isPositiveCompletion(ftp.getReplyCode())) { System.out.println("FEAT " + remote + " was not detected"); } else { System.out.println("Command failed: " + ftp.getReplyString()); } } // Strings feature check String[] features = ftp.featureValues(remote); if (features != null) { for (String f : features) { System.out.println("FEAT " + remote + "=" + f + "."); } } else { if (FTPReply.isPositiveCompletion(ftp.getReplyCode())) { System.out.println("FEAT " + remote + " is not present"); } else { System.out.println("Command failed: " + ftp.getReplyString()); } } } else { if (ftp.features()) { // Command listener has already printed the output } else { System.out.println("Failed: " + ftp.getReplyString()); } } } else if (doCommand != null) { if (ftp.doCommand(doCommand, remote)) { // Command listener has already printed the output // for(String s : ftp.getReplyStrings()) { // System.out.println(s); // } } else { System.out.println("Failed: " + ftp.getReplyString()); } } else { OutputStream output; output = new FileOutputStream(local); ftp.retrieveFile(remote, output); output.close(); } ftp.noop(); // check that control connection is working OK ftp.logout(); } catch (FTPConnectionClosedException e) { error = true; System.err.println("Server closed connection."); e.printStackTrace(); } catch (IOException e) { error = true; e.printStackTrace(); } finally { if (ftp.isConnected()) { try { ftp.disconnect(); } catch (IOException f) { // do nothing } } } System.exit(error ? 1 : 0); }
From source file:de.dfki.dmas.owls2wsdl.core.OWLS2WSDL.java
public static void main(String[] args) { // http://jakarta.apache.org/commons/cli/usage.html System.out.println("ARG COUNT: " + args.length); OWLS2WSDLSettings.getInstance();//from w ww . j av a2s . co m Options options = new Options(); Option help = new Option("help", "print help message"); options.addOption(help); // create the parser CommandLineParser parser = new GnuParser(); CommandLine cmdLine = null; for (int i = 0; i < args.length; i++) { System.out.println("ARG: " + args[i].toString()); } if (args.length > 0) { if (args[args.length - 1].toString().endsWith(".owl")) { // -kbdir d:\tmp\KB http://127.0.0.1/ontology/ActorDefault.owl Option test = new Option("test", "parse only, don't save"); @SuppressWarnings("static-access") Option kbdir = OptionBuilder.withArgName("dir").hasArg() .withDescription("knowledgebase directory; necessary").create("kbdir"); options.addOption(test); options.addOption(kbdir); try { cmdLine = parser.parse(options, args); if (cmdLine.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl [options] FILE.owl", options); System.exit(0); } } catch (ParseException exp) { // oops, something went wrong System.out.println("Error: Parsing failed, reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl", options, true); } if (args.length == 1) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl [options] FILE.owl", options); System.out.println("Error: Option -kbdir is missing."); System.exit(0); } else { String ontURI = args[args.length - 1].toString(); String persistentName = "KB_" + ontURI.substring(ontURI.lastIndexOf("/") + 1, ontURI.lastIndexOf(".")) + "-MAP.xml"; try { if (cmdLine.hasOption("kbdir")) { String kbdirValue = cmdLine.getOptionValue("kbdir"); if (new File(kbdirValue).isDirectory()) { DatatypeParser p = new DatatypeParser(); p.parse(args[args.length - 1].toString()); p.getAbstractDatatypeKBData(); if (!cmdLine.hasOption("test")) { System.out.println("AUSGABE: " + kbdirValue + File.separator + persistentName); FileOutputStream ausgabeStream = new FileOutputStream( kbdirValue + File.separator + persistentName); AbstractDatatypeKB.getInstance().marshallAsXML(ausgabeStream, true); // System.out); } } } } catch (java.net.MalformedURLException murle) { System.err.println("MalformedURLException: " + murle.getMessage()); System.err.println("Try something like: http://127.0.0.1/ontology/my_ontology.owl"); } catch (Exception e) { System.err.println("Exception: " + e.toString()); } } } else if (args[args.length - 1].toString().endsWith(".xml")) { // -owlclass http://127.0.0.1/ontology/Student.owl#HTWStudent // -xsd -d 1 -h D:\tmp\KB\KB_Student-MAP.xml Option xsd = new Option("xsd", "generate XML Schema"); Option info = new Option("info", "print datatype information"); @SuppressWarnings("static-access") Option owlclass = OptionBuilder.withArgName("class").hasArg() .withDescription("owl class to translate; necessary").create("owlclass"); Option keys = new Option("keys", "list all owlclass keys"); options.addOption(keys); options.addOption(owlclass); options.addOption(info); options.addOption(xsd); options.addOption("h", "hierarchy", false, "use hierarchy pattern"); options.addOption("d", "depth", true, "set recursion depth"); options.addOption("b", "behavior", true, "set inheritance bevavior"); options.addOption("p", "primitive", true, "set default primitive type"); try { cmdLine = parser.parse(options, args); if (cmdLine.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl [options] FILE.xml", options); System.exit(0); } } catch (ParseException exp) { // oops, something went wrong System.out.println("Error: Parsing failed, reason: " + exp.getMessage()); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl", options, true); } if (args.length == 1) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl [options] FILE.xml", options); System.exit(0); } else if (cmdLine.hasOption("keys")) { File f = new File(args[args.length - 1].toString()); try { AbstractDatatypeMapper.getInstance().loadAbstractDatatypeKB(f); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); System.exit(1); } AbstractDatatypeKB.getInstance().getAbstractDatatypeKBData().printRegisteredDatatypes(); System.exit(0); } else if (!cmdLine.hasOption("owlclass")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("owls2wsdl [options] FILE.xml", "", options, "Info: owl class not set.\n e.g. -owlclass http://127.0.0.1/ontology/Student.owl#Student"); System.exit(0); } else { File f = new File(args[args.length - 1].toString()); try { AbstractDatatypeMapper.getInstance().loadAbstractDatatypeKB(f); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); System.exit(1); } String owlclassString = cmdLine.getOptionValue("owlclass"); if (!AbstractDatatypeKB.getInstance().getAbstractDatatypeKBData().containsKey(owlclassString)) { System.err.println("Error: Key " + owlclassString + " not in knowledgebase."); System.exit(1); } if (cmdLine.hasOption("info")) { AbstractDatatypeKB.getInstance().getAbstractDatatypeKBData().get(owlclassString) .printDatatype(); } if (cmdLine.hasOption("xsd")) { boolean hierachy = false; int depth = 0; String inheritanceBehavior = AbstractDatatype.InheritanceByNone; String defaultPrimitiveType = "http://www.w3.org/2001/XMLSchema#string"; if (cmdLine.hasOption("h")) { hierachy = true; } if (cmdLine.hasOption("d")) { depth = Integer.parseInt(cmdLine.getOptionValue("d")); } if (cmdLine.hasOption("b")) { System.out.print("Set inheritance behaviour to: "); if (cmdLine.getOptionValue("b") .equals(AbstractDatatype.InheritanceByParentsFirstRDFTypeSecond)) { System.out.println(AbstractDatatype.InheritanceByParentsFirstRDFTypeSecond); inheritanceBehavior = AbstractDatatype.InheritanceByNone; } else if (cmdLine.getOptionValue("b") .equals(AbstractDatatype.InheritanceByRDFTypeFirstParentsSecond)) { System.out.println(AbstractDatatype.InheritanceByRDFTypeFirstParentsSecond); inheritanceBehavior = AbstractDatatype.InheritanceByRDFTypeFirstParentsSecond; } else if (cmdLine.getOptionValue("b") .equals(AbstractDatatype.InheritanceByRDFTypeOnly)) { System.out.println(AbstractDatatype.InheritanceByRDFTypeOnly); inheritanceBehavior = AbstractDatatype.InheritanceByRDFTypeOnly; } else if (cmdLine.getOptionValue("b") .equals(AbstractDatatype.InheritanceBySuperClassOnly)) { System.out.println(AbstractDatatype.InheritanceBySuperClassOnly); inheritanceBehavior = AbstractDatatype.InheritanceBySuperClassOnly; } else { System.out.println(AbstractDatatype.InheritanceByNone); inheritanceBehavior = AbstractDatatype.InheritanceByNone; } } if (cmdLine.hasOption("p")) { defaultPrimitiveType = cmdLine.getOptionValue("p"); if (defaultPrimitiveType.split("#")[0].equals("http://www.w3.org/2001/XMLSchema")) { System.err.println("Error: Primitive Type not valid: " + defaultPrimitiveType); System.exit(1); } } XsdSchemaGenerator xsdgen = new XsdSchemaGenerator("SCHEMATYPE", hierachy, depth, inheritanceBehavior, defaultPrimitiveType); try { AbstractDatatypeKB.getInstance().toXSD(owlclassString, xsdgen, System.out); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); } } } } else { try { cmdLine = parser.parse(options, args); if (cmdLine.hasOption("help")) { printDefaultHelpMessage(); } } catch (ParseException exp) { // oops, something went wrong System.out.println("Error: Parsing failed, reason: " + exp.getMessage()); printDefaultHelpMessage(); } } } else { OWLS2WSDLGui.createAndShowGUI(); } // for(Iterator it=options.getOptions().iterator(); it.hasNext(); ) { // String optString = ((Option)it.next()).getOpt(); // if(cmdLine.hasOption(optString)) { // System.out.println("Option set: "+optString); // } // } }