/*
 * CDDL HEADER START
 *
 * The contents of this file are subject to the terms of the
 * Common Development and Distribution License (the "License").
 * You may not use this file except in compliance with the License.
 *
 * See LICENSE.txt included in this distribution for the specific
 * language governing permissions and limitations under the License.
 *
 * When distributing Covered Code, include this CDDL HEADER in each
 * file and include the License file at LICENSE.txt.
 * If applicable, add the following below this CDDL HEADER, with the
 * fields enclosed by brackets "[]" replaced with your own identifying
 * information: Portions Copyright [yyyy] [name of copyright owner]
 *
 * CDDL HEADER END
 */

/*
 * Copyright (c) 2005, 2012, Oracle and/or its affiliates. All rights reserved.
 *
 * Portions Copyright 2011 Jens Elkner.
 */
package org.opensolaris.opengrok.index;

import java.io.File;
import java.io.IOException;
import java.lang.reflect.Field;
import java.net.InetAddress;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
import java.util.logging.Level;
import java.util.logging.LogManager;
import java.util.logging.Logger;

import org.opensolaris.opengrok.Info;
import org.opensolaris.opengrok.OpenGrokLogger;
import org.opensolaris.opengrok.analysis.AnalyzerGuru;
import org.opensolaris.opengrok.configuration.Configuration;
import org.opensolaris.opengrok.configuration.Project;
import org.opensolaris.opengrok.configuration.RuntimeEnvironment;
import org.opensolaris.opengrok.history.HistoryException;
import org.opensolaris.opengrok.history.HistoryGuru;
import org.opensolaris.opengrok.history.Repository;
import org.opensolaris.opengrok.history.RepositoryFactory;
import org.opensolaris.opengrok.history.RepositoryInfo;
import org.opensolaris.opengrok.util.Executor;
import org.opensolaris.opengrok.util.Getopt;
import org.opensolaris.opengrok.web.Prefix;

/**
 * Creates and updates an inverted source index
 * as well as generates Xref, file stats etc., if specified
 * in the options
 */
@SuppressWarnings({"PMD.AvoidPrintStackTrace", "PMD.SystemPrintln"})
public final class Indexer {
    private static final String ON = "on";
    private static final String OFF = "off";
    private static Indexer index = new Indexer();
    static final Logger log = Logger.getLogger(Indexer.class.getName());

    private static final String DERBY_EMBEDDED_DRIVER =
        "org.apache.derby.jdbc.EmbeddedDriver";

    private static final String DERBY_CLIENT_DRIVER =
        "org.apache.derby.jdbc.ClientDriver";

    /**
     * Get the indexer instance.
     * @return a singleton
     */
    public static Indexer getInstance() {
        return index;
    }

    /**
     * Program entry point
     * @param argv argument vector
     */
    @SuppressWarnings("PMD.UseStringBufferForStringAppends")
    public static void main(String argv[]) {
        boolean runIndex = true;
        boolean update = true;
        boolean optimizedChanged = false;
        ArrayList<String> zapCache = new ArrayList<String>();
        CommandLineOptions cmdOptions = new CommandLineOptions();

        if (argv.length == 0) {
            System.err.println(cmdOptions.getUsage());
            System.exit(1);
        } else {
            Executor.registerErrorHandler();
            boolean searchRepositories = false;
            ArrayList<String> subFiles = new ArrayList<String>();
            ArrayList<String> repositories = new ArrayList<String>();
            HashSet<String> allowedSymlinks = new HashSet<String>();
            String configFilename = null;
            String configHost = null;
            boolean addProjects = false;
            boolean refreshHistory = false;
            String defaultProject = null;
            boolean listFiles = false;
            boolean listRepos = false;
            boolean listTokens = false;
            int noThreads = 2 + (2 * Runtime.getRuntime().availableProcessors());

            // Parse command line options:
            Getopt getopt = new Getopt(argv, cmdOptions.getCommandString());

            try {
                getopt.parse();
            } catch (ParseException ex) {
System.err.println(ex.getMessage());
System.err.println(cmdOptions.getUsage());
                System.exit(1);
            }

            try {
                Configuration cfg = null;
                int cmd;

                // We need to read the configuration file first, since we
                // will try to overwrite options..
                while ((cmd = getopt.getOpt()) != -1) {
                    if (cmd == 'R') {
                        cfg = Configuration.read(new File(getopt.getOptarg()));
                        break;
                    }
                }

                if (cfg == null) {
                    cfg = new Configuration();
                }

                String databaseDriver = cfg.getDatabaseDriver();
                String databaseURL = cfg.getDatabaseUrl();

                // Now we can handle all the other options..
                getopt.reset();
                while ((cmd = getopt.getOpt()) != -1) {
                    switch (cmd) {
                        case 'q':
                            cfg.setVerbose(false);
                            OpenGrokLogger.setOGConsoleLogLevel(Level.WARNING);
                            break;
                        case 'e':
                            cfg.setGenerateHtml(false);
                            break;
                        case 'P':
                            addProjects = true;
                            break;
                        case 'p':
                            defaultProject = getopt.getOptarg();
                            break;
                        case 'c':
                            cfg.setCtags(getopt.getOptarg());
                            break;
                        case 'w':
                             {
                                String webapp = getopt.getOptarg();
                                if (webapp.charAt(0) != '/' && !webapp.startsWith("http")) {
                                    webapp = "/" + webapp;
                                }
                                if (webapp.endsWith("/")) {
                                    webapp = webapp.substring(0, webapp.length()-1);
                                }
                                cfg.setUrlPrefix(webapp + Prefix.SEARCH_R + '?');
                            }
                            break;
                        case 'W':
                            configFilename = getopt.getOptarg();
                            break;
                        case 'U':
                            configHost = getopt.getOptarg();
                            break;
                        case 'R':
                            // already handled
                            break;
                        case 'N':
                            allowedSymlinks.add(getopt.getOptarg());
                            break;
                        case 'n':
                            runIndex = false;
                            break;
                        case 'H':
                            refreshHistory = true;
                            break;
                        case 'h':
                            repositories.add(getopt.getOptarg());
                            break;
                        case 'D':
                            cfg.setHistoryCacheInDB(true);
                            break;
                        case 'j':
                            databaseDriver = getopt.getOptarg();
                            // Should be a full class name, but we also accept
                            // the shorthands "client" and "embedded". Expand
                            // the shorthands here.
                            if ("client".equals(databaseDriver)) {
                                databaseDriver = DERBY_CLIENT_DRIVER;
                            } else if ("embedded".equals(databaseDriver)) {
                                databaseDriver = DERBY_EMBEDDED_DRIVER;
                            }
                            break;
                        case 'u':
                            databaseURL = getopt.getOptarg();
                            break;
                        case 'r':
                             {
                                if (getopt.getOptarg().equalsIgnoreCase(ON)) {
                                    cfg.setRemoteScmSupported(true);
                                } else if (getopt.getOptarg().equalsIgnoreCase(OFF)) {
                                    cfg.setRemoteScmSupported(false);
                                } else {
System.err.println("ERROR: You should pass either \"on\" or \"off\" as argument to -r");
System.err.println("       Ex: \"-r on\" will allow retrival for remote SCM systems");
System.err.println("           \"-r off\" will ignore SCM for remote systems");
                                }
                            }
                            break;
                        case 'o':
                            File ctagsOptions = new File(getopt.getOptarg());
                            if (!(ctagsOptions.isFile() && ctagsOptions.canRead())) 
                            {
System.err.println("ERROR: File '" + ctagsOptions + "' not found for the -o option");
                                System.exit(1);
                            }
                            cfg.setCtagsOptionsFile(ctagsOptions.getPath());
                            break;
                        case 'O':
                             {
                                boolean oldval = cfg.isOptimizeDatabase();
                                if (getopt.getOptarg().equalsIgnoreCase(ON)) {
                                    cfg.setOptimizeDatabase(true);
                                } else if (getopt.getOptarg().equalsIgnoreCase(OFF)) {
                                    cfg.setOptimizeDatabase(false);
                                } else {
System.err.println("ERROR: You should pass either \"on\" or \"off\" as argument to -O");
System.err.println("       Ex: \"-O on\" will optimize the database as part of the index generation");
System.err.println("           \"-O off\" disable optimization of the index database");
                                }
                                if (oldval != cfg.isOptimizeDatabase()) {
                                    optimizedChanged = true;
                                }
                            }
                            break;
                        case 'v':
                            cfg.setVerbose(true);
                            OpenGrokLogger.setOGConsoleLogLevel(Level.INFO);
                            break;
                        case 'C':
                            cfg.setPrintProgress(true);
                            break;

                        case 's':
                        {
                            File sourceRoot = new File(getopt.getOptarg());
                            if (!sourceRoot.isDirectory()) {
System.err.println("ERROR: Source root must be a directory");
                                System.exit(1);
                            }
                            cfg.setSourceRoot(sourceRoot.getCanonicalPath());
                            break;
                        }
                        case 'd':
                        {
                            File dataRoot = new File(getopt.getOptarg());
                            if (!dataRoot.exists() && !dataRoot.mkdirs()) {
System.err.println("ERROR: Cannot create data root");
                                System.exit(1);
                            }
                            if (!dataRoot.isDirectory()) {
System.err.println("ERROR: Data root must be a directory");
                                System.exit(1);
                            }
                            cfg.setDataRoot(dataRoot.getCanonicalPath());
                            break;
                        }
                        case 'i':
                            cfg.getIgnoredNames().add(getopt.getOptarg());
                            break;
                        case 'I':
                            cfg.getIncludedNames().add(getopt.getOptarg());
                            break;
                        case 'S':
                            searchRepositories = true;
                            break;
                        case 'Q':
                            if (getopt.getOptarg().equalsIgnoreCase(ON)) {
                                cfg.setQuickContextScan(true);
                            } else if (getopt.getOptarg().equalsIgnoreCase(OFF)) {
                                cfg.setQuickContextScan(false);
                            } else {
System.err.println("ERROR: You should pass either \"on\" or \"off\" as argument to -Q");
System.err.println("       Ex: \"-Q on\" will just scan a \"chunk\" of the file and insert \"[..all..]\"");
System.err.println("           \"-Q off\" will try to build a more accurate list by reading the complete file.");
                            }

                            break;
                        case 'm': {
                            try {
                                cfg.setIndexWordLimit(Integer.parseInt(getopt.getOptarg()));
                            } catch (NumberFormatException exp) {
System.err.println("ERROR: Failed to parse argument to \"-m\": " + exp.getMessage());
                                System.exit(1);
                            }
                            break;
                        }
                        case 'a':
                            if (getopt.getOptarg().equalsIgnoreCase(ON)) {
                                cfg.setAllowLeadingWildcard(true);
                            } else if (getopt.getOptarg().equalsIgnoreCase(OFF)) {
                                cfg.setAllowLeadingWildcard(false);
                            } else {
System.err.println("ERROR: You should pass either \"on\" or \"off\" as argument to -a");
System.err.println("       Ex: \"-a on\" will allow a search to start with a wildcard");
System.err.println("           \"-a off\" will disallow a search to start with a wildcard");
                                System.exit(1);
                            }

                            break;

                        case 'A':
                             {
                                String[] arg = getopt.getOptarg().split(":");
                                if (arg.length != 2) {
System.err.println("ERROR: You must specify: -A extension:class");
System.err.println("       Ex: -A foo:org.opensolaris.opengrok.analysis.c.CAnalyzer");
System.err.println("           will use the C analyzer for all files ending with .foo");
System.err.println("       Ex: -A c:-");
System.err.println("           will disable the c-analyzer for for all files ending with .c");
                                    System.exit(1);
                                }

                                arg[0] = arg[0].substring(arg[0].lastIndexOf('.') + 1).toUpperCase();
                                if (arg[1].equals("-")) {
                                    AnalyzerGuru.addExtension(arg[0], null);
                                    break;
                                }

                                try {
                                    AnalyzerGuru.addExtension(arg[0],
                                        AnalyzerGuru.findFactory(arg[1]));
                                } catch (Exception e) {
                                    log.log(Level.SEVERE, "Unable to use {0} as a FileAnalyzerFactory", arg[1]);
                                    log.log(Level.FINE, "main", e);
                                    System.exit(1);
                                }
                            }
                            break;
                        case 'L':
                            cfg.setWebappLAF(getopt.getOptarg());
                            break;
                        case 'T':
                            try {
                                noThreads = Integer.parseInt(getopt.getOptarg());
                            } catch (NumberFormatException exp) {
System.err.println("ERROR: Failed to parse argument to \"-T\": " + exp.getMessage());
                                System.exit(1);
                            }
                            break;
                        case 'z':
                            try {
                                cfg.setScanningDepth(Integer.parseInt(getopt.getOptarg()));
                            } catch (NumberFormatException exp) {
System.err.println("ERROR: Failed to parse argument to \"-z\": " + exp.getMessage());
                                System.exit(1);
                            }
                            break;
                        case 'l':
                            if (getopt.getOptarg().equalsIgnoreCase(ON)) {
                                cfg.setUsingLuceneLocking(true);
                            } else if (getopt.getOptarg().equalsIgnoreCase(OFF)) {
                                cfg.setUsingLuceneLocking(false);
                            } else {
System.err.println("ERROR: You should pass either \"on\" or \"off\" as argument to -l");
System.err.println("       Ex: \"-l on\" will enable locks in Lucene");
System.err.println("           \"-l off\" will disable locks in Lucene");
                            }
                            break;
                        case 'B':
                            cfg.setUserPage(getopt.getOptarg());
                            break;
                        case 'X':
                            cfg.setUserPageSuffix(getopt.getOptarg());
                            break;
                        case 'V':
                            System.out.println(Info.getFullVersion());
                            System.exit(0);
                            break;
                        case 'k':
                            zapCache.add(getopt.getOptarg());
                            break;
                        case 'K':
                            listRepos = true;
                            break;
                        case '?':
                            System.err.println(cmdOptions.getUsage());
                            System.exit(0);
                            break;
                        case 't':
                            try {
                                int tmp = Integer.parseInt(getopt.getOptarg());
                                cfg.setTabSize(tmp);
                            } catch (NumberFormatException exp) {
System.err.println("ERROR: Failed to parse argument to \"-t\": " + exp.getMessage());
                                System.exit(1);
                            }
                            break;
                        case 'Z':
                            cfg.setChattyStatusPage(true);
                            break;
                        case 'E':
                            cfg.setCompressXref(false);
                            break;
                        default:
System.err.println("Internal Error - Unimplemented cmdline option: " + (char) cmd);
                            System.exit(1);
                    }
                }
                String s = System.getProperty(Configuration.DIRLIST_TODAY_PROPERTY_KEY);
                if (s != null) {
                    cfg.setDirlistUseToday(Boolean.parseBoolean(s));
                }
                s = System.getProperty(Configuration.DIRLIST_DATE_PROPERTY_KEY);
                if (s != null) {
                    cfg.setDirlistDatePattern(s);
                }
                List<Class<? extends Repository>> repositoryClasses =
                    RepositoryFactory.getRepositoryClasses();
                for (Class<? extends Repository> clazz : repositoryClasses) {
                    try {
                        Field f = clazz.getDeclaredField("CMD_PROPERTY_KEY");
                        Object key = f.get(null);
                        if (key != null) {
                            cfg.setRepoCmd(clazz.getCanonicalName(),
                                System.getProperty(key.toString()));
                        }
                    } catch (Exception e) {
                        // don't care
                    }
                }
                int optind = getopt.getOptind();
                if (optind != -1) {
                    while (optind < argv.length) {
                        subFiles.add(argv[optind]);
                        ++optind;
                    }
                }

                //logging starts here
                if (cfg.isVerbose()) {
                  String fn = LogManager.getLogManager()
                      .getProperty("java.util.logging.FileHandler.pattern");
                  if (fn != null) {
                      System.out.println("Logging filehandler pattern: " + fn);
                  }
                }

                if (cfg.isHistoryCacheInDB()) {
                    // The default database driver is Derby's client driver.
                    if (databaseDriver == null) {
                        databaseDriver = DERBY_CLIENT_DRIVER;
                    }

                    // The default URL depends on the database driver.
                    if (databaseURL == null) {
                        StringBuilder defaultURL = new StringBuilder();
                        defaultURL.append("jdbc:derby:");
                        if (databaseDriver.equals(DERBY_EMBEDDED_DRIVER)) {
                            defaultURL.append(cfg.getDataRoot())
                                .append(File.separator);
                        } else {
                            defaultURL.append("//localhost/");
                        }
                        defaultURL.append("cachedb;create=true");
                        databaseURL = defaultURL.toString();
                    }
                }

                cfg.setDatabaseDriver(databaseDriver);
                cfg.setDatabaseUrl(databaseURL);

                // automatically allow symlinks that are directly in source root
                String file = cfg.getSourceRoot();
                if (file != null) {
                    File sourceRootFile = new File(file);
                    File[] projectDirs = sourceRootFile.listFiles();
                    if (projectDirs != null) {
                        for (File projectDir : projectDirs) {
                            if (!projectDir.getCanonicalPath()
                                .equals(projectDir.getAbsolutePath()))
                            {
                                allowedSymlinks.add(projectDir.getAbsolutePath());
                            }
                        }
                    }
                }

                allowedSymlinks.addAll(cfg.getAllowedSymlinks());
                cfg.setAllowedSymlinks(allowedSymlinks);

                //Set updated configuration in RuntimeEnvironment
                RuntimeEnvironment.setConfig(cfg);
                Indexer.prepareIndexer(searchRepositories, addProjects,
                    defaultProject, configFilename, refreshHistory, listFiles,
                    listTokens, subFiles, repositories, zapCache, listRepos);
                if (listRepos || !zapCache.isEmpty()) {
                    return;
                }
                if (runIndex || (optimizedChanged && cfg.isOptimizeDatabase())) {
                    IndexChangedListener progress = new DefaultIndexChangedListener();
                    Indexer.doIndexerExecution(update, noThreads, subFiles,
                        progress);
                }
                Indexer.sendToConfigHost(configHost);
            } catch (IndexerException ex) {
                log.log(Level.SEVERE, "Exception running indexer: " + ex.getMessage());
                log.log(Level.FINE, "main", ex);
                System.err.println(cmdOptions.getUsage());
                System.exit(1);
            } catch (Throwable e) {
                log.log(Level.SEVERE, e.getLocalizedMessage());
                log.log(Level.FINE, "main", e);
                System.exit(1);
            }
        }

    }

    // PMD wants us to use length() > 0 && charAt(0) instead of startsWith()
    // for performance. We prefer clarity over performance here, so silence it.
    /**
     * Prepare the environment to execute indexing. Basically it does some 
     * consistency checks wrt. commadline options sets and executes simple tasks
     * like zapping or refreshing the history cache, list available projects
     * including their path, create spelling index for related projects, 
     * writing the config file.
     * 
     * @param searchRepositories    If {@code true} scan for new repositories in
     *      the source root directory.
     * @param addProjects       If {@code true} add automatically projects found
     * @param defaultProject    The name of the project to use as default. Might
     *      be {@code null}.
     * @param configFilename    The pathname of the configuration file to write.
     *      If {@code null} writing the config file gets skipped.
     * @param refreshHistory    If {@code true}, create/update the history cache
     *      for the given or all projects.
     * @param listFiles         If {@code true}, print a list of all files of 
     *      the index database for given projects to stdout.
     * @param listTokens        If {@code true}, print a list of frequent 
     *      tokens for related projects to stdout.
     * @param subFiles          Determine target projects by the given repo
     *      files when <var>listFiles</var> or <var>createDict</var> is set to
     *      {@code true}. {@code null} implies "all projects".
     * @param repositories      Target repositories.{@code null} implies 
     *      "all projects". 
     * @param zapCache          List of project names, whose history cache should
     *      be zapped. An Asterisk ('*') implies zap all. Ignored if empty. 
     * @param listRepoPathes    If {@code true}, just list available projects
     *      incl. their path, zap projects (if set) and return.
     * @throws IndexerException
     * @throws IOException
     * @throws NullPointerException if <var>env</var> or <var>zapCache</var> is 
     *      {@code null}
     */
    @SuppressWarnings("PMD.SimplifyStartsWith")
    public static void prepareIndexer(boolean searchRepositories,
        boolean addProjects,
        String defaultProject,
        String configFilename,
        boolean refreshHistory,
        boolean listFiles,
        boolean listTokens,
        List<String> subFiles,
        List<String> repositories,
        List<String> zapCache,
        boolean listRepoPathes) throws IndexerException, IOException
    {
        Configuration cfg = RuntimeEnvironment.getConfig();
        if (cfg.getDataRoot() == null) {
            throw new IndexerException("Please specify a DATA ROOT path");
        }

        if (cfg.getSourceRootFile() == null) {
            throw new IndexerException("Please specify a SRC_ROOT with option -s");
        }

        if (!RuntimeEnvironment.validateExuberantCtags()) {
            throw new IndexerException("Didn't find Exuberant Ctags");
        }
        if (zapCache == null) {
            throw new IndexerException("Internal error, zapCache shouldn't be null");
        }

        if (searchRepositories || listRepoPathes || !zapCache.isEmpty()) {
            log.log(Level.INFO,"Scanning for repositories...");
            long start = System.currentTimeMillis();
            HistoryGuru.getInstance().addRepositories(cfg.getSourceRoot());
            long time = (System.currentTimeMillis() - start) / 1000;
            log.log(Level.INFO, "Done ({0}s)", Long.valueOf(time));
            if (listRepoPathes || !zapCache.isEmpty()) {
                List<RepositoryInfo> repos = cfg.getRepositories();
                String prefix =  cfg.getSourceRoot();
                if (listRepoPathes) {
                    if (repos.isEmpty()) {
                        System.out.println("No repositories found.");
                        return;
                    }
                    System.out.println("Repositories in " + prefix + ":");
                    for (RepositoryInfo info : cfg.getRepositories()) {
                        String dir = info.getDirectoryName();
                        System.out.println(dir.substring(prefix.length()));
                    }
                }
                if (!zapCache.isEmpty()) {
                    HashSet<String> toZap = new HashSet<String>(zapCache.size() << 1);
                    boolean all = false;
                    for (String repo : zapCache) {
                        if ("*".equals(repo)) {
                            all = true;
                            break;
                        }
                        if (repo.startsWith(prefix)) {
                            repo = repo.substring(prefix.length());
                        }
                        toZap.add(repo);
                    }
                    if (all) {
                        toZap.clear();
                        for (RepositoryInfo info : cfg.getRepositories()) {
                            toZap.add(info.getDirectoryName()
                                .substring(prefix.length()));
                        }
                    }
                    try {
                        HistoryGuru.getInstance().removeCache(toZap);
                    } catch (HistoryException e) {
                        log.warning("Clearing history cache faild: "
                            + e.getLocalizedMessage());
                    }
                }
                return;
            }
        }

        if (addProjects) {
            File files[] = cfg.getSourceRootFile().listFiles();
            List<Project> projects = cfg.getProjects();

            // Keep a copy of the old project list so that we can preserve
            // the customization of existing projects.
            Map<String, Project> oldProjects = new HashMap<String, Project>();
            for (Project p : projects) {
                oldProjects.put(p.getPath(), p);
            }

            projects.clear();

            // Add a project for each top-level directory in source root.
            for (File file : files) {
                String name = file.getName();
                String path = "/" + name;
                if (oldProjects.containsKey(path)) {
                    // This is an existing object. Reuse the old project,
                    // possibly with customizations, instead of creating a
                    // new with default values.
                    projects.add(oldProjects.get(path));
                } else if (!name.startsWith(".") && file.isDirectory()) {
                    // Found a new directory with no matching project, so
                    // create a new project with default properties.
                    Project p = new Project();
                    p.setDescription(name);
                    p.setPath(path);
                    p.setTabSize(cfg.getTabSize());
                    projects.add(p);
                }
            }

            // The projects should be sorted...
            Collections.sort(projects, new Comparator<Project>() {

                @Override
                public int compare(Project p1, Project p2) {
                    String s1 = p1.getDescription();
                    String s2 = p2.getDescription();

                    int ret;
                    if (s1 == null) {
                        ret = (s2 == null) ? 0 : 1;
                    } else {
                        ret = s1.compareTo(s2);
                    }
                    return ret;
                }
            });
        }

        if (defaultProject != null) {
            for (Project p : cfg.getProjects()) {
                if (p.getPath().equals(defaultProject)) {
                    cfg.setDefaultProject(p);
                    break;
                }
            }
        }

        if (configFilename != null) {
            log.log(Level.INFO, "Writing configuration to ''{0}''", configFilename);
            RuntimeEnvironment.writeConfig(new File(configFilename));
            log.info("Done.");
        }

        if (refreshHistory) {
            log.log(Level.INFO, "Generating history cache for all repositories ...");
            HistoryGuru.getInstance().createCache();
            log.info("Done.");
        } else if (repositories != null && !repositories.isEmpty()) {
            log.log(Level.INFO, "Generating history cache for specified repositories ...");
            HistoryGuru.getInstance().createCache(repositories);
            log.info("Done.");
        }

        if (listFiles) {
            IndexDatabase.listAllFiles(subFiles);
        }

        if (listTokens) {
            IndexDatabase.listFrequentTokens(subFiles);
        }
    }

    /**
     * Index and optionally optimize related databases. Obtains an 
     * {@link RuntimeEnvironment} instance and registers with it, so that 
     * required infos are obtained from there.
     * 
     * @param update        If {@code true} update the index for related projects.
     * @param noThreads     Number of threads to use for indexing.
     * @param subFiles      Use the giben repo files to determine the projects,
     *      which should be indexed or index db optimized.
     * @param progress      If {@code true} show progress when indexing. Wrt.
     *      to logging and terminal flooding a really bad idea.
     * @throws IOException
     * @see IndexDatabase#update(ExecutorService, IndexChangedListener, List)
     */
    public static void doIndexerExecution(final boolean update, int noThreads, 
        List<String> subFiles, IndexChangedListener progress)
        throws IOException 
    {
        RuntimeEnvironment.register();
        Configuration cfg = RuntimeEnvironment.getConfig();
        log.info("Start indexing ...");

        ExecutorService executor = Executors.newFixedThreadPool(noThreads);

        if (subFiles == null || subFiles.isEmpty()) {
            if (update) {
                IndexDatabase.updateAll(executor, progress);
            } else if (cfg.isOptimizeDatabase()) {
                IndexDatabase.optimizeAll(executor);
            }
        } else {
            List<IndexDatabase> dbs = new ArrayList<IndexDatabase>();

            for (String path : subFiles) {
                Project project = Project.getProject(path);
                if (project == null && cfg.hasProjects()) {
                    log.warning("Could not find a project for '" + path + "'");
                } else {
                    IndexDatabase db;
                    if (project == null) {
                        db = new IndexDatabase();
                    } else {
                        db = new IndexDatabase(project);
                    }
                    int idx = dbs.indexOf(db);
                    if (idx != -1) {
                        db = dbs.get(idx);
                    }

                    if (db.addDirectory(path)) {
                        if (idx == -1) {
                            dbs.add(db);
                        }
                    } else {
                        log.warning("Directory does not exist '" + path + "'");
                    }
                }
            }

            for (final IndexDatabase db : dbs) {
                final boolean optimize = cfg.isOptimizeDatabase();
                db.addIndexChangedListener(progress);
                executor.submit(new Runnable() {

                    @Override
                    public void run() {
                        try {
                            if (update) {
                                db.update();
                            } else if (optimize) {
                                db.optimize();
                            }
                        } catch (Throwable e) {
                            log.warning("An error occured while "
                                + (update ? "updating " : "optimizing ")
                                + db + ": " + e.getMessage());
                            log.log(Level.FINE, "run", e);
                        }
                    }
                });
            }
        }

        executor.shutdown();
        while (!executor.isTerminated()) {
            try {
                // Wait forever
                executor.awaitTermination(999,TimeUnit.DAYS);
            } catch (InterruptedException exp) {
                log.warning("Received interrupt while waiting for executor to finish: "
                    + exp.getMessage());
                log.log(Level.FINE, "doIndexerExecution", exp);
            }
       }
       log.info("Done.");
    }

    /**
     * Send the configuration of the current thread's runtime environment to
     * the given host.
     * @param configHost    where to send the configuration. Format: host:port .
     */
    public static void sendToConfigHost(String configHost) {
        if (configHost != null) {
            String[] cfg = configHost.split(":");
            log.log(Level.INFO, "Sending configuration to {0}", configHost);
            if (cfg.length == 2) {
                try {
                    InetAddress host = InetAddress.getByName(cfg[0]);
                    RuntimeEnvironment.writeConfig(host, Integer.parseInt(cfg[1]));
                } catch (Exception ex) {
                    log.log(Level.WARNING, "Failed to send configuration to " 
                        + configHost 
                        + " (is web application server running with opengrok deployed?): "
                        + ex.getMessage());
                    log.log(Level.FINE, "sendToConfigHost", ex);
                }
            } else if ( cfg.length > 0 ) {
                StringBuilder sb = new StringBuilder("Syntax errors = ");
                for (String s : cfg) {
                    sb.append('[').append(s).append(']').append(", ");
                }
                sb.setLength(sb.length()-2);
                log.warning(sb.toString());
            }
            log.info("Done.");
        }
    }

    private Indexer() {
    }
}