GeneralCliOptions.java

/*
 * Copyright 2015-2016 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.storage.app.cli;

import com.beust.jcommander.DynamicParameter;
import com.beust.jcommander.JCommander;
import com.beust.jcommander.Parameter;
import com.beust.jcommander.ParameterException;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Created on 26/01/16
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class GeneralCliOptions {

    protected final JCommander jcommander;

    protected final GeneralOptions generalOptions;
    protected final CommonOptions commonOptions;



    public GeneralCliOptions() {
        generalOptions = new GeneralOptions();
        jcommander = new JCommander(generalOptions);
        commonOptions = new CommonOptions();
    }

    public void parse(String[] args) throws ParameterException {
        jcommander.parse(args);
    }

    public String getCommand() {
        return (jcommander.getParsedCommand() != null) ? jcommander.getParsedCommand() : "";
    }

    public String getSubCommand() {
        String parsedCommand = jcommander.getParsedCommand();
        if (jcommander.getCommands().containsKey(parsedCommand)) {
            String subCommand = jcommander.getCommands().get(parsedCommand).getParsedCommand();
            return subCommand != null ? subCommand: "";
        } else {
            return null;
        }
    }

    public boolean isHelp() {
        String parsedCommand = jcommander.getParsedCommand();
        if (parsedCommand != null) {
            JCommander jCommander = jcommander.getCommands().get(parsedCommand);
            List<Object> objects = jCommander.getObjects();
            if (!objects.isEmpty() && objects.get(0) instanceof CommonOptions) {
                return ((CommonOptions) objects.get(0)).help;
            }
        }
        return commonOptions.help;
    }


    /**
     * This class contains all those parameters available for all 'commands'
     */
    public class CommandOptions {

        @Parameter(names = {"-h", "--help"},  description = "This parameter prints this help", help = true)
        public boolean help;

        public JCommander getSubCommand() {
            return jcommander.getCommands().get(getCommand()).getCommands().get(getSubCommand());
        }

        public String getParsedSubCommand() {
            String parsedCommand = jcommander.getParsedCommand();
            if (jcommander.getCommands().containsKey(parsedCommand)) {
                String subCommand = jcommander.getCommands().get(parsedCommand).getParsedCommand();
                return subCommand != null ? subCommand: "";
            } else {
                return "";
            }
        }
    }


    public class GeneralOptions {

        @Parameter(names = {"-h", "--help"}, help = true)
        public boolean help;

        @Parameter(names = {"--version"})
        public boolean version;

    }


    /**
     * This class contains all those common parameters available for all 'subcommands'
     */
    public class CommonOptions {

        @Parameter(names = {"-h", "--help"}, description = "Print this help", help = true)
        public boolean help;

        @Parameter(names = {"-L", "--log-level"}, description = "One of the following: 'error', 'warn', 'info', 'debug', 'trace'")
        public String logLevel = "info";

        @Parameter(names = {"--log-file"}, description = "One of the following: 'error', 'warn', 'info', 'debug', 'trace'")
        public String logFile;

        @Parameter(names = {"-v", "--verbose"}, description = "Increase the verbosity of logs")
        public boolean verbose = false;

        @Parameter(names = {"-C", "--conf"}, description = "Configuration file path.")
        public String configFile;

        @Parameter(names = {"--storage-engine"}, arity = 1, description = "One of the listed in storage-configuration.yml")
        public String storageEngine;

        @DynamicParameter(names = "-D", description = "Storage engine specific parameters go here comma separated, ie. -Dmongodb" +
                ".compression=snappy", hidden = false)
        public Map<String, String> params = new HashMap<>(); //Dynamic parameters must be initialized

    }

    public class IndexCommandOptions {

        @Parameter(names = {"-d", "--database"}, description = "DataBase name to load the data", required = false, arity = 1)
        public String dbName;

        @Parameter(names = {"-i", "--input"}, description = "File to index in the selected backend", required = true, variableArity = true)
        public String input;

        @Parameter(names = {"-o", "--outdir"}, description = "Directory where output files will be saved (optional)", arity = 1, required = false)
        public String outdir;

    }

    public class QueryCommandOptions {

        @Parameter(names = {"-o", "--output"}, description = "Output file. [STDOUT]", required = false, arity = 1)
        public String output;

        @Parameter(names = {"-d", "--database"}, description = "DataBase name", required = false, arity = 1)
        public String dbName;

        @Parameter(names = {"-i", "--include"}, description = "", required = false, arity = 1)
        public String include;

        @Parameter(names = {"-e", "--exclude"}, description = "", required = false, arity = 1)
        public String exclude;

        @Parameter(names = {"--skip"}, description = "Skip some number of elements.", required = false, arity = 1)
        public int skip;

        @Parameter(names = {"--limit"}, description = "Limit the number of returned elements.", required = false, arity = 1)
        public int limit;

        @Parameter(names = {"--count"}, description = "Count results. Do not return elements.", required = false, arity = 0)
        public boolean count;

    }

}