/*
 * Copyright 2015-2017 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.app.cli.admin;

import com.beust.jcommander.ParameterException;
import org.opencb.opencga.app.cli.CommandExecutor;
import org.opencb.opencga.app.cli.admin.executors.*;
import org.opencb.opencga.core.common.ArrayUtils;
import org.opencb.opencga.core.common.GitRepositoryState;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Created by imedina on 03/02/15.
 */
public class AdminMain {

    public static final String VERSION = GitRepositoryState.get().getBuildVersion();

    public static void main(String[] args) {

        // Add password parameter
        List<String> argsList = new ArrayList<>();
        argsList.addAll(Arrays.asList(args));
        argsList.add("--password");
        args = ArrayUtils.toStringArray(argsList);

        AdminCliOptionsParser cliOptionsParser = new AdminCliOptionsParser();
        try {
            cliOptionsParser.parse(args);
        } catch (ParameterException e) {
            System.err.println(e.getMessage());
            cliOptionsParser.printUsage();
            System.exit(1);
        }

        String parsedCommand = cliOptionsParser.getCommand();
        if (parsedCommand == null || parsedCommand.isEmpty()) {
            if (cliOptionsParser.getGeneralOptions().version) {
                System.out.println("Version " + GitRepositoryState.get().getBuildVersion());
                System.out.println("Git version: " + GitRepositoryState.get().getBranch() + " " + GitRepositoryState.get().getCommitId());
                System.exit(0);
            } else if (cliOptionsParser.getGeneralOptions().help) {
                cliOptionsParser.printUsage();
                System.exit(0);
            } else {
                cliOptionsParser.printUsage();
                System.exit(1);
            }
        } else {
            CommandExecutor commandExecutor = null;
            // Check if any command -h option is present
            if (cliOptionsParser.isHelp()) {
                cliOptionsParser.printUsage();
                System.exit(0);
            } else {
                String parsedSubCommand = cliOptionsParser.getSubCommand();
                if (parsedSubCommand == null || parsedSubCommand.isEmpty()) {
                    cliOptionsParser.printUsage();
                } else {
                    switch (parsedCommand) {
                        case "catalog":
                            commandExecutor = new CatalogCommandExecutor(cliOptionsParser.getCatalogCommandOptions());
                            break;
                        case "users":
                            commandExecutor = new UsersCommandExecutor(cliOptionsParser.getUsersCommandOptions());
                            break;
                        case "audit":
                            commandExecutor = new AuditCommandExecutor(cliOptionsParser.getAuditCommandOptions());
                            break;
                        case "server":
                            commandExecutor = new ServerCommandExecutor(cliOptionsParser.getServerCommandOptions());
                            break;
                        case "meta":
                            commandExecutor = new MetaCommandExecutor(cliOptionsParser.getMetaCommandOptions());
                            break;
                        case "migration":
                            commandExecutor = new MigrationCommandExecutor(cliOptionsParser.getMigrationCommandOptions());
                            break;
                        default:
                            System.out.printf(String.format("ERROR: not valid command passed: '%s'", parsedCommand));
                            break;
                    }

                    if (commandExecutor != null) {
                        try {
                            commandExecutor.loadConfiguration();
                            commandExecutor.loadStorageConfiguration();
                        } catch (IOException ex) {
                            if (commandExecutor.getLogger() == null) {
                                ex.printStackTrace();
                            } else {
                                commandExecutor.getLogger().error("Error reading OpenCGA Storage configuration: " + ex.getMessage());
                            }
                        }
                        try {
                            commandExecutor.execute();
                        } catch (Exception e) {
                            e.printStackTrace();
                            System.exit(1);
                        }
                    } else {
                        cliOptionsParser.printUsage();
                        System.exit(1);
                    }
                }

            }
        }
    }

}

@@ -826,181 +826,55 @@
 mon.
-ArrayUtils;%0Aimport org.opencb.opencga.core.common.GitRepositoryState;%0A%0Aimport java.io.IOException;%0Aimport java.util.ArrayList;%0Aimport java.util.Arrays;%0Aimport java.util.List
+GitRepositoryState;%0A%0Aimport java.io.IOException
 ;%0A%0A/
@@ -1119,181 +1119,76 @@
     
-List%3CString%3E argsList = new ArrayList%3C%3E();%0A        argsList.addAll(Arrays.asList(args));%0A        argsList.add(%22--password%22);%0A        args = ArrayUtils.toStringArray(argsList
+args = org.apache.commons.lang3.ArrayUtils.addAll(args, %22--password%22
 );%0A%0A

use java commons lang to add parameter to args. Clean unused imports