uni.bielefeld.cmg.sparkhit.util.ParameterForReporter.java Source code

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Here is the source code for uni.bielefeld.cmg.sparkhit.util.ParameterForReporter.java

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package uni.bielefeld.cmg.sparkhit.util;

/**
 * Created by Liren Huang on 13/01/16.
 *
 *      SparkHit
 * Copyright (c) 2015-2015:
 * Liren Huang     <huanglr at cebitec.uni-bielefeld.de>
 *
 * SparkHit is free software: you can redistribute it and/or modify it
 * under the terms of the GNU General Public License as published by the Free
 * Software Foundation, either version 3 of the License, or (at your option)
 * any later version.
 *
 * This program is distributed in the hope that it will be useful, but WITHOU
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
 * more details.
 *
 * You should have received a copy of the GNU General Public License along
 * with this program. If not, see <http://www.gnu.org/licenses/>.
 */

import org.apache.commons.cli.*;

import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

public class ParameterForReporter {
    private String[] arguments;
    private InfoDumper info = new InfoDumper();

    public ParameterForReporter(String[] arguments) throws IOException, ParseException {
        this.arguments = arguments;
    }

    private static final Options parameter = new Options();

    DefaultParam param = new DefaultParam();

    /* parameter IDs */
    private static final String INPUT_HIT = "input", INPUT_KEY = "word", INPUT_VALUE = "count",
            OUTPUT_REPORT = "outfile", PARTITIONS = "partition", VERSION = "version", HELP2 = "h", HELP = "help";

    private static final Map<String, Integer> parameterMap = new HashMap<String, Integer>();

    public void putParameterID() {
        int o = 0;

        parameterMap.put(INPUT_HIT, o++);
        parameterMap.put(INPUT_KEY, o++);
        parameterMap.put(INPUT_VALUE, o++);
        parameterMap.put(OUTPUT_REPORT, o++);
        parameterMap.put(PARTITIONS, o++);
        parameterMap.put(VERSION, o++);
        parameterMap.put(HELP, o++);
        parameterMap.put(HELP2, o++);
    }

    public void addParameterInfo() {

        /* use Object parameter of Options class to store parameter information */

        parameter.addOption(OptionBuilder.withArgName("input sparkhit result file").hasArg()
                .withDescription(
                        "Input spark hit result file in tabular format. Accept wild card, s3n schema, hdfs schema")
                .create(INPUT_HIT));

        parameter.addOption(OptionBuilder.withArgName("columns for identifier").hasArg().withDescription(
                "a list of column number used to represent a category you want to summarize. eg, 1,3,8 means counting column 1 (chr), column 3 (strain), column 8 (identity)")
                .create(INPUT_KEY));

        parameter.addOption(OptionBuilder.withArgName("column for count number").hasArg().withDescription(
                "the number of column value which will be used to aggregate for the report. set to 0 the value will be 1 for every identifier")
                .create(INPUT_VALUE));

        parameter.addOption(OptionBuilder.withArgName("output report file").hasArg()
                .withDescription("Output report file in text format").create(OUTPUT_REPORT));

        parameter.addOption(OptionBuilder.withArgName("re-partition number").hasArg().withDescription(
                "re generate number of partitions for .gz data, as .gz data only have one partition (spark parallelization)")
                .create(PARTITIONS));

        parameter
                .addOption(OptionBuilder.hasArg(false).withDescription("show version information").create(VERSION));

        parameter.addOption(
                OptionBuilder.hasArg(false).withDescription("print and show this information").create(HELP));

        parameter.addOption(OptionBuilder.hasArg(false).withDescription("").create(HELP2));

    }

    /* main method */
    public DefaultParam importCommandLine() {

        /* Assigning Parameter ID to an ascending number */
        putParameterID();

        /* Assigning parameter descriptions to each parameter ID */
        addParameterInfo();

        /* need a Object parser of PosixParser class for the function parse of CommandLine class */
        PosixParser parser = new PosixParser();

        /* print out help information */
        HelpParam help = new HelpParam(parameter, parameterMap);

        /* check each parameter for assignment */
        try {
            long input_limit = -1;
            int threads = Runtime.getRuntime().availableProcessors();

            /* Set Object cl of CommandLine class for Parameter storage */
            CommandLine cl = parser.parse(parameter, arguments, true);
            if (cl.hasOption(HELP)) {
                help.printReporterHelp();
                System.exit(0);
            }

            if (cl.hasOption(HELP2)) {
                help.printReporterHelp();
                System.exit(0);
            }

            if (cl.hasOption(VERSION)) {
                System.exit(0);
            }

            /* Checking all parameters */

            String value;

            if ((value = cl.getOptionValue(PARTITIONS)) != null) {
                param.partitions = Integer.decode(value);
            }

            if ((value = cl.getOptionValue(INPUT_KEY)) != null) {
                param.word = value;
            }

            if ((value = cl.getOptionValue(INPUT_VALUE)) != null) {
                param.count = Integer.decode(value);
            }

            if ((value = cl.getOptionValue(INPUT_HIT)) != null) {
                param.inputResultPath = value;
            } else {
                help.printReporterHelp();
                System.exit(0);
                // throw new IOException("Input file not specified.\nUse -help for list of options");
            }

            /* not applicable for HDFS and S3 */
            /* using TextFileBufferInput for such purpose */
            //         File inputFastq = new File(param.inputFqPath).getAbsoluteFile();
            //         if (!inputFastq.exists()){
            //            err.println("Input query file not found.");
            //            return;
            //i         }

            if ((value = cl.getOptionValue(OUTPUT_REPORT)) != null) {
                param.outputPath = value;
            } else {
                info.readMessage("Output file not set of -outfile options");
                info.screenDump();
            }

            File outfile = new File(param.outputPath).getAbsoluteFile();
            if (outfile.exists()) {
                info.readParagraphedMessages(
                        "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite.");
                info.screenDump();
                Runtime.getRuntime().exec("rm -rf " + param.outputPath);
            }

            // param.bestNas = (param.alignLength * param.readIdentity) / 100;
            // param.bestKmers = param.alignLength - (param.alignLength - param.bestNas) * 4 - 3;

        } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this.
            info.readMessage("Parameter settings incorrect.");
            info.screenDump();
            e.printStackTrace();
            System.exit(0);
        } catch (RuntimeException e) {
            info.readMessage("Parameter settings incorrect.");
            info.screenDump();
            e.printStackTrace();
            System.exit(0);
        } catch (ParseException e) {
            info.readMessage("Parameter settings incorrect.");
            info.screenDump();
            e.printStackTrace();
            System.exit(0);
        }

        return param;
    }
}