Example usage for java.io File getParent

List of usage examples for java.io File getParent

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Introduction

In this page you can find the example usage for java.io File getParent.

Prototype

public String getParent()

Source Link

Document

Returns the pathname string of this abstract pathname's parent, or null if this pathname does not name a parent directory.

Usage

From source file:apps.quantification.LearnQuantificationSVMPerf.java

public static void main(String[] args) throws IOException {
    String cmdLineSyntax = LearnQuantificationSVMPerf.class.getName()
            + " [OPTIONS] <path to svm_perf_learn> <path to svm_perf_classify> <trainingIndexDirectory> <outputDirectory>";

    Options options = new Options();

    OptionBuilder.withArgName("f");
    OptionBuilder.withDescription("Number of folds");
    OptionBuilder.withLongOpt("f");
    OptionBuilder.isRequired(true);/*from w  w w .j av a 2s.  com*/
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("c");
    OptionBuilder.withDescription("The c value for svm_perf (default 0.01)");
    OptionBuilder.withLongOpt("c");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("t");
    OptionBuilder.withDescription("Path for temporary files");
    OptionBuilder.withLongOpt("t");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("l");
    OptionBuilder.withDescription("The loss function to optimize (default 2):\n"
            + "               0  Zero/one loss: 1 if vector of predictions contains error, 0 otherwise.\n"
            + "               1  F1: 100 minus the F1-score in percent.\n"
            + "               2  Errorrate: Percentage of errors in prediction vector.\n"
            + "               3  Prec/Rec Breakeven: 100 minus PRBEP in percent.\n"
            + "               4  Prec@p: 100 minus precision at p in percent.\n"
            + "               5  Rec@p: 100 minus recall at p in percent.\n"
            + "               10  ROCArea: Percentage of swapped pos/neg pairs (i.e. 100 - ROCArea).");
    OptionBuilder.withLongOpt("l");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("w");
    OptionBuilder.withDescription("Choice of structural learning algorithm (default 9):\n"
            + "               0: n-slack algorithm described in [2]\n"
            + "               1: n-slack algorithm with shrinking heuristic\n"
            + "               2: 1-slack algorithm (primal) described in [5]\n"
            + "               3: 1-slack algorithm (dual) described in [5]\n"
            + "               4: 1-slack algorithm (dual) with constraint cache [5]\n"
            + "               9: custom algorithm in svm_struct_learn_custom.c");
    OptionBuilder.withLongOpt("w");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("p");
    OptionBuilder.withDescription("The value of p used by the prec@p and rec@p loss functions (default 0)");
    OptionBuilder.withLongOpt("p");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg();
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("v");
    OptionBuilder.withDescription("Verbose output");
    OptionBuilder.withLongOpt("v");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    OptionBuilder.withArgName("s");
    OptionBuilder.withDescription("Don't delete temporary training file in svm_perf format (default: delete)");
    OptionBuilder.withLongOpt("s");
    OptionBuilder.isRequired(false);
    OptionBuilder.hasArg(false);
    options.addOption(OptionBuilder.create());

    SvmPerfLearnerCustomizer classificationLearnerCustomizer = null;
    SvmPerfClassifierCustomizer classificationCustomizer = null;

    int folds = -1;

    GnuParser parser = new GnuParser();
    String[] remainingArgs = null;
    try {
        CommandLine line = parser.parse(options, args);

        remainingArgs = line.getArgs();

        classificationLearnerCustomizer = new SvmPerfLearnerCustomizer(remainingArgs[0]);
        classificationCustomizer = new SvmPerfClassifierCustomizer(remainingArgs[1]);

        folds = Integer.parseInt(line.getOptionValue("f"));

        if (line.hasOption("c"))
            classificationLearnerCustomizer.setC(Float.parseFloat(line.getOptionValue("c")));

        if (line.hasOption("w"))
            classificationLearnerCustomizer.setW(Integer.parseInt(line.getOptionValue("w")));

        if (line.hasOption("p"))
            classificationLearnerCustomizer.setP(Integer.parseInt(line.getOptionValue("p")));

        if (line.hasOption("l"))
            classificationLearnerCustomizer.setL(Integer.parseInt(line.getOptionValue("l")));

        if (line.hasOption("v"))
            classificationLearnerCustomizer.printSvmPerfOutput(true);

        if (line.hasOption("s"))
            classificationLearnerCustomizer.setDeleteTrainingFiles(false);

        if (line.hasOption("t")) {
            classificationLearnerCustomizer.setTempPath(line.getOptionValue("t"));
            classificationCustomizer.setTempPath(line.getOptionValue("t"));
        }

    } catch (Exception exp) {
        System.err.println("Parsing failed.  Reason: " + exp.getMessage());
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    assert (classificationLearnerCustomizer != null);

    if (remainingArgs.length != 4) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(cmdLineSyntax, options);
        System.exit(-1);
    }

    String indexFile = remainingArgs[2];

    File file = new File(indexFile);

    String indexName = file.getName();
    String indexPath = file.getParent();

    String outputPath = remainingArgs[3];

    SvmPerfLearner classificationLearner = new SvmPerfLearner();

    classificationLearner.setRuntimeCustomizer(classificationLearnerCustomizer);

    FileSystemStorageManager fssm = new FileSystemStorageManager(indexPath, false);
    fssm.open();

    IIndex training = TroveReadWriteHelper.readIndex(fssm, indexName, TroveContentDBType.Full,
            TroveClassificationDBType.Full);

    final TextualProgressBar progressBar = new TextualProgressBar("Learning the quantifiers");

    IOperationStatusListener status = new IOperationStatusListener() {

        @Override
        public void operationStatus(double percentage) {
            progressBar.signal((int) percentage);
        }
    };

    QuantificationLearner quantificationLearner = new QuantificationLearner(folds, classificationLearner,
            classificationLearnerCustomizer, classificationCustomizer, ClassificationMode.PER_CATEGORY,
            new LogisticFunction(), status);

    IQuantifier[] quantifiers = quantificationLearner.learn(training);

    File executableFile = new File(classificationLearnerCustomizer.getSvmPerfLearnPath());
    IDataManager classifierDataManager = new SvmPerfDataManager(new SvmPerfClassifierCustomizer(
            executableFile.getParentFile().getAbsolutePath() + Os.pathSeparator() + "svm_perf_classify"));
    String description = "_SVMPerf_C-" + classificationLearnerCustomizer.getC() + "_W-"
            + classificationLearnerCustomizer.getW() + "_L-" + classificationLearnerCustomizer.getL();
    if (classificationLearnerCustomizer.getL() == 4 || classificationLearnerCustomizer.getL() == 5)
        description += "_P-" + classificationLearnerCustomizer.getP();
    if (classificationLearnerCustomizer.getAdditionalParameters().length() > 0)
        description += "_" + classificationLearnerCustomizer.getAdditionalParameters();
    String quantifierPrefix = indexName + "_Quantifier-" + folds + description;

    FileSystemStorageManager fssmo = new FileSystemStorageManager(
            outputPath + File.separatorChar + quantifierPrefix, true);
    fssmo.open();
    QuantificationLearner.write(quantifiers, fssmo, classifierDataManager);
    fssmo.close();

    BufferedWriter bfs = new BufferedWriter(
            new FileWriter(outputPath + File.separatorChar + quantifierPrefix + "_rates.txt"));
    TShortDoubleHashMap simpleTPRs = quantificationLearner.getSimpleTPRs();
    TShortDoubleHashMap simpleFPRs = quantificationLearner.getSimpleFPRs();
    TShortDoubleHashMap scaledTPRs = quantificationLearner.getScaledTPRs();
    TShortDoubleHashMap scaledFPRs = quantificationLearner.getScaledFPRs();

    ContingencyTableSet contingencyTableSet = quantificationLearner.getContingencyTableSet();

    short[] cats = simpleTPRs.keys();
    for (int i = 0; i < cats.length; ++i) {
        short cat = cats[i];
        String catName = training.getCategoryDB().getCategoryName(cat);
        ContingencyTable contingencyTable = contingencyTableSet.getCategoryContingencyTable(cat);
        double simpleTPR = simpleTPRs.get(cat);
        double simpleFPR = simpleFPRs.get(cat);
        double scaledTPR = scaledTPRs.get(cat);
        double scaledFPR = scaledFPRs.get(cat);
        String line = quantifierPrefix + "\ttrain\tsimple\t" + catName + "\t" + cat + "\t"
                + contingencyTable.tp() + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t"
                + contingencyTable.tn() + "\t" + simpleTPR + "\t" + simpleFPR + "\n";
        bfs.write(line);
        line = quantifierPrefix + "\ttrain\tscaled\t" + catName + "\t" + cat + "\t" + contingencyTable.tp()
                + "\t" + contingencyTable.fp() + "\t" + contingencyTable.fn() + "\t" + contingencyTable.tn()
                + "\t" + scaledTPR + "\t" + scaledFPR + "\n";
        bfs.write(line);
    }
    bfs.close();
}

From source file:org.ala.spatial.web.services.DownloadController.java

public static void main(String[] args) {

    // maxent - 1323641423144
    // aloc   - 1323844048457

    String pid = "1323844048457";

    try {//w w w.ja  v a 2  s  .  c o  m
        File dir = sfindFile(pid);

        if (dir != null) {
            //System.out.println("Found session data: " + dir.getAbsolutePath());
            //return "Found session data: " + dir.getAbsolutePath();

            String parentName = "ALA_";
            String parentPath = dir.getParent().substring(dir.getParent().lastIndexOf("/") + 1);

            String zipfile = dir.getParent() + "/" + pid + ".zip";

            if ("maxent".equals(parentPath)) {
                fixMaxentFiles(pid, dir);
                Zipper.zipDirectory(dir.getParent() + "/temp/" + pid, zipfile);
            } else if ("layers".equals(parentPath) || "aloc".equals(parentPath)) {
                fixAlocFiles(pid, dir);
                Zipper.zipDirectory(dir.getParent() + "/temp/" + pid, zipfile);
            } else {
                Zipper.zipDirectory(dir.getAbsolutePath(), zipfile);
            }

            System.out.println(
                    "Found " + dir.getName() + " in " + dir.getParent() + " and zipped at: " + zipfile);
            //return "Found " + dir.getName() + " in " + dir.getParent() + " and zipped at: " + zipfile;

            if ("maxent".equals(parentPath)) {
                parentName = "ALA_Prediction_";
            } else if ("sampling".equals(parentPath)) {
                parentName = "ALA_Species_Samples_";
            } else if ("layers".equals(parentPath) || "aloc".equals(parentPath)) {
                parentName = "ALA_Classification_";
            } else if ("gdm".equals(parentPath)) {
                parentName = "ALA_GDM_";
            } else if ("filtering".equals(parentPath)) {
                parentName = "ALA_EnvFilter_";
            } else if ("sitesbyspecies".equals(parentPath)) {
                parentName = "ALA_SitesBySpecies_";
            }

            File file = new File(zipfile);

            System.out.println("File generated: " + file.getAbsolutePath());

        } else {
            System.out.println("Could not find session data");
            //return "Could not find session data";
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

From source file:com.clustercontrol.agent.Agent.java

/**
 * ?/*from   w ww. j av  a 2s . c o m*/
 * 
 * @param args ??
 */
public static void main(String[] args) throws Exception {

    // ?
    if (args.length != 1) {
        System.out.println("Usage : java Agent [Agent.properties File Path]");
        System.exit(1);
    }

    try {
        // System
        m_log.info("starting Hinemos Agent...");
        m_log.info("java.vm.version = " + System.getProperty("java.vm.version"));
        m_log.info("java.vm.vendor = " + System.getProperty("java.vm.vendor"));
        m_log.info("java.home = " + System.getProperty("java.home"));
        m_log.info("os.name = " + System.getProperty("os.name"));
        m_log.info("os.arch = " + System.getProperty("os.arch"));
        m_log.info("os.version = " + System.getProperty("os.version"));
        m_log.info("user.name = " + System.getProperty("user.name"));
        m_log.info("user.dir = " + System.getProperty("user.dir"));
        m_log.info("user.country = " + System.getProperty("user.country"));
        m_log.info("user.language = " + System.getProperty("user.language"));
        m_log.info("file.encoding = " + System.getProperty("file.encoding"));

        // System(SET)
        String limitKey = "jdk.xml.entityExpansionLimit"; // TODO JRE???????????????????
        System.setProperty(limitKey, "0");
        m_log.info(limitKey + " = " + System.getProperty(limitKey));

        // TODO ???agentHome
        // ??????????
        File file = new File(args[0]);
        agentHome = file.getParentFile().getParent() + "/";
        m_log.info("agentHome=" + agentHome);

        // 
        long startDate = HinemosTime.currentTimeMillis();
        m_log.info("start date = " + new Date(startDate) + "(" + startDate + ")");
        agentInfo.setStartupTime(startDate);

        // Agent??
        m_log.info("Agent.properties = " + args[0]);

        // ?
        File scriptDir = new File(agentHome + "script/");
        if (scriptDir.exists()) {
            File[] listFiles = scriptDir.listFiles();
            if (listFiles != null) {
                for (File f : listFiles) {
                    boolean ret = f.delete();
                    if (ret) {
                        m_log.debug("delete script : " + f.getName());
                    } else {
                        m_log.warn("delete script error : " + f.getName());
                    }
                }
            } else {
                m_log.warn("listFiles is null");
            }
        } else {
            //????????
            boolean ret = scriptDir.mkdir();
            if (!ret) {
                m_log.warn("mkdir error " + scriptDir.getPath());
            }
        }

        // queue?
        m_sendQueue = new SendQueue();

        // Agent?
        Agent agent = new Agent(args[0]);

        //-----------------
        //-- 
        //-----------------
        m_log.debug("exec() : create topic ");

        m_receiveTopic = new ReceiveTopic(m_sendQueue);
        m_receiveTopic.setName("ReceiveTopicThread");
        m_log.info("receiveTopic start 1");
        m_receiveTopic.start();
        m_log.info("receiveTopic start 2");

        // ?
        agent.exec();

        m_log.info("Hinemos Agent started");

        // ?
        agent.waitAwakeAgent();
    } catch (Throwable e) {
        m_log.error("Agent.java: Runtime Exception Occurred. " + e.getClass().getName() + ", " + e.getMessage(),
                e);
    }
}

From source file:main.RankerOCR.java

/**
 * Command line interface for RankerOCR.
 * <p>//from  w w w.  j a va2s  .  c om
 * <b>Command line input:</b>
 * <ul>
 * usage: java -jar Ranker-OCR [options]
 * </ul>
 * <b>Options list:</b>
 * <ul>
 * <li>-gui Launch a graphical user interface</li>
 * <li>-help Show the help</li>
 * <li>-indoc1 [arg] Set the file name of the original document</li>
 * <li>-indoc2 [arg] Set the file name of the document to compare</li>
 * <li>-ranker [arg] Set the ranker used for the comparison</li>
 * <li>-outdoc [arg] Set the document where write the results</li>
 * <li>-separator [arg] Set the delimiter char use in the CSV out file</li>
 * </ul>
 * <b>Return values are if error:</b>
 * <ul>
 * <li>(-1) The precision parameter is not a number.</li>
 * <li>(-2) The precision parameter is lower than 0.</li>
 * <li>(-3) The precision parameter is greater than 10.</li>
 * <li>(-11) The ranker name is wrong</li>
 * <li>(-21) The separator char is empty</li>
 * <li>(-22) The separator is not a char</li>
 * <li>(-31) File name doesn't exist</li>
 * <li>(-32) File name is not a file</li>
 * <li>(-33) Error when access to documents files</li>
 * <li>(-34) Output file can not be write</li>
 * <li>(-35) Output file can not be created</li>
 * <li>(-41) Error when parsing parameters</li>
 * <li>(-100) Internal error when creating the ranker. Please report a
 * bug</li>
 * <li>(-101) Internal error when get the ranker list. Please report a
 * bug.</li>
 * <li>(-102) Error when access to help file. Please report a bug.</li>
 * </ul>
 * <p>
 * @param args Argument array which can have the values from options list
 */
public static void main(String[] args) {
    //Parse command line
    CommandLineParser parser = new GnuParser();
    try {
        CommandLine cmd = parser.parse(options, args);
        if (cmd.hasOption("help")) {
            showHelp(hf, options);
        } else if (cmd.hasOption("gui")) {
            display.DispalyRankerOCR.main(new String[] {});
        } else if (cmd.hasOption("indoc1") && cmd.hasOption("indoc2") && cmd.hasOption("outdoc")) {
            //<editor-fold defaultstate="collapsed" desc="Rank documents">
            //Prepare parameter
            Class ranker = evalRanker(cmd.getOptionValue("ranker", "SimpleRanker"));
            char separator = evalSeparator(cmd.getOptionValue("separator", "\t"));
            File f1 = evalInputFile(cmd.getOptionValue("indoc1", ""));
            File f2 = evalInputFile(cmd.getOptionValue("indoc2", ""));
            File f3 = evalOutputFile(cmd.getOptionValue("outdoc", ""), separator);
            //Read file
            String s1 = readInputDocText(f1);
            String s2 = readInputDocText(f2);
            //Compare file
            double percent = rankDocuments(s1, s2, ranker);
            //Write result
            String[] s = { Double.toString(percent), ranker.getSimpleName(), f1.getName(), f2.getName(),
                    f1.getParent(), f2.getParent(), new Date().toString() };
            writeOutpuDocCsv(f3, separator, s);
            //</editor-fold>
        } else {
            printFormated("java -jar Ranker-OCR [options]  please type " + "-help for more info");
        }
    } catch (ParseException ex) {
        printFormated(ex.getLocalizedMessage());
        System.exit(-41);
    }
}

From source file:com.cws.esolutions.security.main.PasswordUtility.java

public static void main(final String[] args) {
    final String methodName = PasswordUtility.CNAME + "#main(final String[] args)";

    if (DEBUG) {/*from  w w w  .j  a v a2 s .co m*/
        DEBUGGER.debug("Value: {}", methodName);
    }

    if (args.length == 0) {
        HelpFormatter usage = new HelpFormatter();
        usage.printHelp(PasswordUtility.CNAME, options, true);

        System.exit(1);
    }

    BufferedReader bReader = null;
    BufferedWriter bWriter = null;

    try {
        // load service config first !!
        SecurityServiceInitializer.initializeService(PasswordUtility.SEC_CONFIG, PasswordUtility.LOG_CONFIG,
                false);

        if (DEBUG) {
            DEBUGGER.debug("Options options: {}", options);

            for (String arg : args) {
                DEBUGGER.debug("Value: {}", arg);
            }
        }

        CommandLineParser parser = new PosixParser();
        CommandLine commandLine = parser.parse(options, args);

        if (DEBUG) {
            DEBUGGER.debug("CommandLineParser parser: {}", parser);
            DEBUGGER.debug("CommandLine commandLine: {}", commandLine);
            DEBUGGER.debug("CommandLine commandLine.getOptions(): {}", (Object[]) commandLine.getOptions());
            DEBUGGER.debug("CommandLine commandLine.getArgList(): {}", commandLine.getArgList());
        }

        final SecurityConfigurationData secConfigData = PasswordUtility.svcBean.getConfigData();
        final SecurityConfig secConfig = secConfigData.getSecurityConfig();
        final PasswordRepositoryConfig repoConfig = secConfigData.getPasswordRepo();
        final SystemConfig systemConfig = secConfigData.getSystemConfig();

        if (DEBUG) {
            DEBUGGER.debug("SecurityConfigurationData secConfig: {}", secConfigData);
            DEBUGGER.debug("SecurityConfig secConfig: {}", secConfig);
            DEBUGGER.debug("RepositoryConfig secConfig: {}", repoConfig);
            DEBUGGER.debug("SystemConfig systemConfig: {}", systemConfig);
        }

        if (commandLine.hasOption("encrypt")) {
            if ((StringUtils.isBlank(repoConfig.getPasswordFile()))
                    || (StringUtils.isBlank(repoConfig.getSaltFile()))) {
                System.err.println("The password/salt files are not configured. Entries will not be stored!");
            }

            File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile());
            File saltFile = FileUtils.getFile(repoConfig.getSaltFile());

            if (DEBUG) {
                DEBUGGER.debug("File passwordFile: {}", passwordFile);
                DEBUGGER.debug("File saltFile: {}", saltFile);
            }

            final String entryName = commandLine.getOptionValue("entry");
            final String username = commandLine.getOptionValue("username");
            final String password = commandLine.getOptionValue("password");
            final String salt = RandomStringUtils.randomAlphanumeric(secConfig.getSaltLength());

            if (DEBUG) {
                DEBUGGER.debug("String entryName: {}", entryName);
                DEBUGGER.debug("String username: {}", username);
                DEBUGGER.debug("String password: {}", password);
                DEBUGGER.debug("String salt: {}", salt);
            }

            final String encodedSalt = PasswordUtils.base64Encode(salt);
            final String encodedUserName = PasswordUtils.base64Encode(username);
            final String encryptedPassword = PasswordUtils.encryptText(password, salt,
                    secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(),
                    secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(),
                    systemConfig.getEncoding());
            final String encodedPassword = PasswordUtils.base64Encode(encryptedPassword);

            if (DEBUG) {
                DEBUGGER.debug("String encodedSalt: {}", encodedSalt);
                DEBUGGER.debug("String encodedUserName: {}", encodedUserName);
                DEBUGGER.debug("String encodedPassword: {}", encodedPassword);
            }

            if (commandLine.hasOption("store")) {
                try {
                    new File(passwordFile.getParent()).mkdirs();
                    new File(saltFile.getParent()).mkdirs();

                    boolean saltFileExists = (saltFile.exists()) ? true : saltFile.createNewFile();

                    if (DEBUG) {
                        DEBUGGER.debug("saltFileExists: {}", saltFileExists);
                    }

                    // write the salt out first
                    if (!(saltFileExists)) {
                        throw new IOException("Unable to create salt file");
                    }

                    boolean passwordFileExists = (passwordFile.exists()) ? true : passwordFile.createNewFile();

                    if (!(passwordFileExists)) {
                        throw new IOException("Unable to create password file");
                    }

                    if (commandLine.hasOption("replace")) {
                        File[] files = new File[] { saltFile, passwordFile };

                        if (DEBUG) {
                            DEBUGGER.debug("File[] files: {}", (Object) files);
                        }

                        for (File file : files) {
                            if (DEBUG) {
                                DEBUGGER.debug("File: {}", file);
                            }

                            String currentLine = null;
                            File tmpFile = new File(FileUtils.getTempDirectory() + "/" + "tmpFile");

                            if (DEBUG) {
                                DEBUGGER.debug("File tmpFile: {}", tmpFile);
                            }

                            bReader = new BufferedReader(new FileReader(file));
                            bWriter = new BufferedWriter(new FileWriter(tmpFile));

                            while ((currentLine = bReader.readLine()) != null) {
                                if (!(StringUtils.equals(currentLine.trim().split(",")[0], entryName))) {
                                    bWriter.write(currentLine + System.getProperty("line.separator"));
                                    bWriter.flush();
                                }
                            }

                            bWriter.close();

                            FileUtils.deleteQuietly(file);
                            FileUtils.copyFile(tmpFile, file);
                            FileUtils.deleteQuietly(tmpFile);
                        }
                    }

                    FileUtils.writeStringToFile(saltFile, entryName + "," + encodedUserName + "," + encodedSalt
                            + System.getProperty("line.separator"), true);
                    FileUtils.writeStringToFile(passwordFile, entryName + "," + encodedUserName + ","
                            + encodedPassword + System.getProperty("line.separator"), true);
                } catch (IOException iox) {
                    ERROR_RECORDER.error(iox.getMessage(), iox);
                }
            }

            System.out.println("Entry Name " + entryName + " stored.");
        }

        if (commandLine.hasOption("decrypt")) {
            String saltEntryName = null;
            String saltEntryValue = null;
            String decryptedPassword = null;
            String passwordEntryName = null;

            if ((StringUtils.isEmpty(commandLine.getOptionValue("entry"))
                    && (StringUtils.isEmpty(commandLine.getOptionValue("username"))))) {
                throw new ParseException("No entry or username was provided to decrypt.");
            }

            if (StringUtils.isEmpty(commandLine.getOptionValue("username"))) {
                throw new ParseException("no entry provided to decrypt");
            }

            String entryName = commandLine.getOptionValue("entry");
            String username = commandLine.getOptionValue("username");

            if (DEBUG) {
                DEBUGGER.debug("String entryName: {}", entryName);
                DEBUGGER.debug("String username: {}", username);
            }

            File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile());
            File saltFile = FileUtils.getFile(repoConfig.getSaltFile());

            if (DEBUG) {
                DEBUGGER.debug("File passwordFile: {}", passwordFile);
                DEBUGGER.debug("File saltFile: {}", saltFile);
            }

            if ((!(saltFile.canRead())) || (!(passwordFile.canRead()))) {
                throw new IOException(
                        "Unable to read configured password/salt file. Please check configuration and/or permissions.");
            }

            for (String lineEntry : FileUtils.readLines(saltFile, systemConfig.getEncoding())) {
                saltEntryName = lineEntry.split(",")[0];

                if (DEBUG) {
                    DEBUGGER.debug("String saltEntryName: {}", saltEntryName);
                }

                if (StringUtils.equals(saltEntryName, entryName)) {
                    saltEntryValue = PasswordUtils.base64Decode(lineEntry.split(",")[2]);

                    break;
                }
            }

            if (StringUtils.isEmpty(saltEntryValue)) {
                throw new SecurityException("No entries were found that matched the provided information");
            }

            for (String lineEntry : FileUtils.readLines(passwordFile, systemConfig.getEncoding())) {
                passwordEntryName = lineEntry.split(",")[0];

                if (DEBUG) {
                    DEBUGGER.debug("String passwordEntryName: {}", passwordEntryName);
                }

                if (StringUtils.equals(passwordEntryName, saltEntryName)) {
                    String decodedPassword = PasswordUtils.base64Decode(lineEntry.split(",")[2]);

                    decryptedPassword = PasswordUtils.decryptText(decodedPassword, saltEntryValue,
                            secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(),
                            secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(),
                            systemConfig.getEncoding());

                    break;
                }
            }

            if (StringUtils.isEmpty(decryptedPassword)) {
                throw new SecurityException("No entries were found that matched the provided information");
            }

            System.out.println(decryptedPassword);
        } else if (commandLine.hasOption("encode")) {
            System.out.println(PasswordUtils.base64Encode((String) commandLine.getArgList().get(0)));
        } else if (commandLine.hasOption("decode")) {
            System.out.println(PasswordUtils.base64Decode((String) commandLine.getArgList().get(0)));
        }
    } catch (IOException iox) {
        ERROR_RECORDER.error(iox.getMessage(), iox);

        System.err.println("An error occurred during processing: " + iox.getMessage());
        System.exit(1);
    } catch (ParseException px) {
        ERROR_RECORDER.error(px.getMessage(), px);

        System.err.println("An error occurred during processing: " + px.getMessage());
        System.exit(1);
    } catch (SecurityException sx) {
        ERROR_RECORDER.error(sx.getMessage(), sx);

        System.err.println("An error occurred during processing: " + sx.getMessage());
        System.exit(1);
    } catch (SecurityServiceException ssx) {
        ERROR_RECORDER.error(ssx.getMessage(), ssx);
        System.exit(1);
    } finally {
        try {
            if (bReader != null) {
                bReader.close();
            }

            if (bWriter != null) {
                bReader.close();
            }
        } catch (IOException iox) {
        }
    }

    System.exit(0);
}

From source file:com.mvdb.etl.actions.ExtractDBChanges.java

public static void main(String[] args) throws JSONException {

    ActionUtils.setUpInitFileProperty();
    //        boolean success = ActionUtils.markActionChainBroken("Just Testing");        
    //        System.exit(success ? 0 : 1);
    ActionUtils.assertActionChainNotBroken();
    ActionUtils.assertEnvironmentSetupOk();
    ActionUtils.assertFileExists("~/.mvdb", "~/.mvdb missing. Existing.");
    ActionUtils.assertFileExists("~/.mvdb/status.InitCustomerData.complete",
            "300init-customer-data.sh not executed yet. Exiting");
    //This check is not required as data can be modified any number of times
    //ActionUtils.assertFileDoesNotExist("~/.mvdb/status.ModifyCustomerData.complete", "ModifyCustomerData already done. Start with 100init.sh if required. Exiting");

    ActionUtils.createMarkerFile("~/.mvdb/status.ExtractDBChanges.start", true);

    //String schemaDescription = "{ 'root' : [{'table' : 'orders', 'keyColumn' : 'order_id', 'updateTimeColumn' : 'update_time'}]}";

    String customerName = null;/*  w  ww.j  a v  a2 s  .c  o  m*/
    final CommandLineParser cmdLinePosixParser = new PosixParser();
    final Options posixOptions = constructPosixOptions();
    CommandLine commandLine;
    try {
        commandLine = cmdLinePosixParser.parse(posixOptions, args);
        if (commandLine.hasOption("customer")) {
            customerName = commandLine.getOptionValue("customer");
        }
    } catch (ParseException parseException) // checked exception
    {
        System.err.println(
                "Encountered exception while parsing using PosixParser:\n" + parseException.getMessage());
    }

    if (customerName == null) {
        System.err.println("Could not find customerName. Aborting...");
        System.exit(1);
    }

    ApplicationContext context = Top.getContext();

    final OrderDAO orderDAO = (OrderDAO) context.getBean("orderDAO");
    final ConfigurationDAO configurationDAO = (ConfigurationDAO) context.getBean("configurationDAO");
    final GenericDAO genericDAO = (GenericDAO) context.getBean("genericDAO");
    File snapshotDirectory = getSnapshotDirectory(configurationDAO, customerName);
    try {
        FileUtils.writeStringToFile(new File("/tmp/etl.extractdbchanges.directory.txt"),
                snapshotDirectory.getName(), false);
    } catch (IOException e) {
        e.printStackTrace();
        System.exit(1);
        return;
    }
    long currentTime = new Date().getTime();
    Configuration lastRefreshTimeConf = configurationDAO.find(customerName, "last-refresh-time");
    Configuration schemaDescriptionConf = configurationDAO.find(customerName, "schema-description");
    long lastRefreshTime = Long.parseLong(lastRefreshTimeConf.getValue());
    OrderJsonFileConsumer orderJsonFileConsumer = new OrderJsonFileConsumer(snapshotDirectory);
    Map<String, ColumnMetadata> metadataMap = orderDAO.findMetadata();
    //write file schema-orders.dat in snapshotDirectory
    genericDAO.fetchMetadata("orders", snapshotDirectory);
    //writes files: header-orders.dat, data-orders.dat in snapshotDirectory
    JSONObject json = new JSONObject(schemaDescriptionConf.getValue());
    JSONArray rootArray = json.getJSONArray("root");
    int length = rootArray.length();
    for (int i = 0; i < length; i++) {
        JSONObject jsonObject = rootArray.getJSONObject(i);
        String table = jsonObject.getString("table");
        String keyColumnName = jsonObject.getString("keyColumn");
        String updateTimeColumnName = jsonObject.getString("updateTimeColumn");
        System.out.println("table:" + table + ", keyColumn: " + keyColumnName + ", updateTimeColumn: "
                + updateTimeColumnName);
        genericDAO.fetchAll2(snapshotDirectory, new Timestamp(lastRefreshTime), table, keyColumnName,
                updateTimeColumnName);
    }

    //Unlikely failure
    //But Need to factor this into a separate task so that extraction does not have to be repeated. 
    //Extraction is an expensive task. 
    try {
        String sourceDirectoryAbsolutePath = snapshotDirectory.getAbsolutePath();

        File sourceRelativeDirectoryPath = getRelativeSnapShotDirectory(configurationDAO,
                sourceDirectoryAbsolutePath);
        String hdfsRoot = ActionUtils.getConfigurationValue(ConfigurationKeys.GLOBAL_CUSTOMER,
                ConfigurationKeys.GLOBAL_HDFS_ROOT);
        String targetDirectoryFullPath = hdfsRoot + "/data" + sourceRelativeDirectoryPath;

        ActionUtils.copyLocalDirectoryToHdfsDirectory(sourceDirectoryAbsolutePath, targetDirectoryFullPath);
        String dirName = snapshotDirectory.getName();
        ActionUtils.setConfigurationValue(customerName, ConfigurationKeys.LAST_COPY_TO_HDFS_DIRNAME, dirName);
    } catch (Throwable e) {
        e.printStackTrace();
        logger.error("Objects Extracted from database. But copy of snapshot directory<"
                + snapshotDirectory.getAbsolutePath() + "> to hdfs <" + ""
                + ">failed. Fix the problem and redo extract.", e);
        System.exit(1);
    }

    //Unlikely failure
    //But Need to factor this into a separate task so that extraction does not have to be repeated. 
    //Extraction is an expensive task. 
    String targetZip = null;
    try {
        File targetZipDirectory = new File(snapshotDirectory.getParent(), "archives");
        if (!targetZipDirectory.exists()) {
            boolean success = targetZipDirectory.mkdirs();
            if (success == false) {
                logger.error("Objects copied to hdfs. But able to create archive directory <"
                        + targetZipDirectory.getAbsolutePath() + ">. Fix the problem and redo extract.");
                System.exit(1);
            }
        }
        targetZip = new File(targetZipDirectory, snapshotDirectory.getName() + ".zip").getAbsolutePath();
        ActionUtils.zipFullDirectory(snapshotDirectory.getAbsolutePath(), targetZip);
    } catch (Throwable e) {
        e.printStackTrace();
        logger.error("Objects copied to hdfs. But zipping of snapshot directory<"
                + snapshotDirectory.getAbsolutePath() + "> to  <" + targetZip
                + ">failed. Fix the problem and redo extract.", e);
        System.exit(1);
    }

    //orderDAO.findAll(new Timestamp(lastRefreshTime), orderJsonFileConsumer);
    Configuration updateRefreshTimeConf = new Configuration(customerName, "last-refresh-time",
            String.valueOf(currentTime));
    configurationDAO.update(updateRefreshTimeConf, String.valueOf(lastRefreshTimeConf.getValue()));
    ActionUtils.createMarkerFile("~/.mvdb/status.ExtractDBChanges.complete", true);

}

From source file:de.ipbhalle.metfusion.main.SubstructureSearch.java

public static void main(String[] args) {
    String token = "eeca1d0f-4c03-4d81-aa96-328cdccf171a";
    //String token = "a1004d0f-9d37-47e0-acdd-35e58e34f603";
    //test();//from  ww w .j  a v  a2  s.  c  o  m

    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/136m0498_MSMS.mf");
    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/148m0859_MSMS.mf");
    //      File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/164m0445a_MSMS.mf");
    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/192m0757a_MSMS.mf");
    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/MetFusion_ChemSp_mfs/naringenin.mf");

    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/Known_BT_MSMS_ChemSp/1MeBT_MSMS.mf");

    //File file = new File("/home/mgerlich/projects/metfusion_tp/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/150m0655a_MSMS.mf");
    File file = new File(
            "C:/Users/Michael/Dropbox/Eawag_IPB_Shared_MassBank/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/192m0757b_MSMS.mf");

    MetFusionBatchFileHandler mbf = new MetFusionBatchFileHandler(file);
    try {
        mbf.readFile();
    } catch (IOException e) {
        //System.out.println(e.getMessage());
        System.err.println(
                "Error reading from MetFusion settings file [" + file.getAbsolutePath() + "]. Aborting!");
        System.exit(-1);
    }

    MetFusionBatchSettings settings = mbf.getBatchSettings();
    List<String> absent = settings.getSubstrucAbsent();
    List<String> present = settings.getSubstrucPresent();
    for (String s : present) {
        System.out.println("present -> " + s);
    }
    for (String s : absent) {
        System.out.println("absent -> " + s);
    }
    String formula = settings.getMfFormula();
    System.out.println("formula -> " + formula);

    boolean useFormulaAsQuery = true;
    boolean useSDF = false;
    String sdfFile = "";
    if (useSDF) {
        sdfFile = "C:/Users/Michael/Dropbox/Eawag_IPB_Shared_MassBank/BTs/Unknown_BT_MSMS_ChemSp/mf_with_substruct_formula/results_afterFormulaQuery/192m0757b_MSMS.sdf";
        if (sdfFile.isEmpty()) { // TODO alternatively use SDF file from query file?
            System.err.println("SDF file needs to be specified! Exiting.");
            System.exit(-1);
        }
    }

    SubstructureSearch ss = new SubstructureSearch(present, absent, token, formula, mbf, useFormulaAsQuery,
            useSDF, sdfFile);
    ss.run();
    List<ResultSubstructure> remaining = ss.getResultsRemaining();
    List<Result> resultsForSDF = new ArrayList<Result>();

    StringBuilder sb = new StringBuilder();
    String sep = ",";
    for (ResultSubstructure rs : remaining) {
        sb.append(rs.getId()).append(sep);

        Result r = new Result(rs.getPort(), rs.getId(), rs.getName(), rs.getScore());
        r.setMol(rs.getMol());
        r.setSmiles(rs.getSmiles());
        r.setInchi(rs.getInchi());
        r.setInchikey(rs.getInchikey());
        resultsForSDF.add(r);
    }
    String ids = sb.toString();

    String fileSep = System.getProperty("file.separator");
    if (!ids.isEmpty()) {
        ids = ids.substring(0, ids.length() - 1);
        System.out.println("ids -> " + ids);
        settings.setMfDatabaseIDs(ids);
        String filename = file.getName();
        String prefix = filename.substring(0, filename.lastIndexOf("."));
        filename = filename.replace(prefix, prefix + "_ids");
        String dir = file.getParent();
        System.out.println("dir -> " + dir);
        if (!dir.endsWith(fileSep))
            dir += fileSep;

        File output = new File(file.getParent(), filename);
        mbf.writeFile(output, settings);
        SDFOutputHandler so = new SDFOutputHandler(dir + prefix + ".sdf");
        boolean writeOK = so.writeOriginalResults(resultsForSDF, false);
        if (!writeOK)
            System.err.println("Error writing SDF [" + so.getFilename());
    }
}

From source file:Main.java

public static int getDepth(File file) {
    if (file.getParent() == null || new File(file.getParent()).getPath().equals(new File(file.getPath())))
        return 1;
    return 1 + getDepth(new File(file.getParent()));
}

From source file:Main.java

public static void saveFile(final String fileName, final String str) {
    try {/*from   www . ja  v a2 s.c  o m*/
        File f = new File(fileName);
        if (new File(f.getParent()).exists() == false) {
            f.getParentFile().mkdirs();
        }
        f.createNewFile();
        PrintStream p = new PrintStream(new FileOutputStream(f, false));
        p.println(str);
        p.close();

    } catch (Exception e) {
        e.printStackTrace();
        System.err.println(fileName);
    }
}

From source file:Main.java

/**
 * get parent path/*  w  w  w.  jav a2 s.c  om*/
 * @param path current file path
 * @return parent path
 */
public static String getParentPath(String path) {
    File file = new File(path);
    return file.getParent();
}