edu.toronto.cs.phenotips.obo2solr.Main.java Source code

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Here is the source code for edu.toronto.cs.phenotips.obo2solr.Main.java

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/*
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership.
 *
 * This is free software; you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2.1 of
 * the License, or (at your option) any later version.
 *
 * This software is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this software; if not, write to the Free
 * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
 * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
 */
package edu.toronto.cs.phenotips.obo2solr;

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

import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;

public class Main {
    public static final String OBO_DB_LOCATION_OPTION = "i";

    public static final String OUTPUT_XML_LOCATION_OPTION = "o";

    public static final String INDEX_FILEDS_OPTION = "f";

    public static final String DEFAULT_OUTPUT_XML_LOCATION = "out.xml";

    public static final String HELP_OPTION = "h";

    public static void main(String[] args) {
        Options options = generateOptions();
        try {
            CommandLineParser parser = new PosixParser();
            CommandLine cmd = parser.parse(options, args);
            if (!cmd.hasOption(OBO_DB_LOCATION_OPTION) || cmd.hasOption(HELP_OPTION)) {
                showUsage(options);
                System.exit(cmd.hasOption(HELP_OPTION) ? 0 : 1);
            }
            ParameterPreparer paramPrep = new ParameterPreparer();
            SolrUpdateGenerator generator = new SolrUpdateGenerator();
            File input = paramPrep.getInputFileHandler(cmd.getOptionValue(OBO_DB_LOCATION_OPTION));
            File output = paramPrep.getOutputFileHandler(
                    cmd.getOptionValue(OUTPUT_XML_LOCATION_OPTION, DEFAULT_OUTPUT_XML_LOCATION));
            Map<String, Double> fieldSelection = paramPrep
                    .getFieldSelection(cmd.getOptionValue(INDEX_FILEDS_OPTION, ""));
            generator.transform(input, output, fieldSelection);
        } catch (Exception ex) {
            ex.printStackTrace();
        }

    }

    protected static Options generateOptions() {
        Options options = new Options();
        options.addOption(OBO_DB_LOCATION_OPTION, "obo-db-location", true,
                "Path or URL of the input database (MANDATORY).");
        options.addOption(OUTPUT_XML_LOCATION_OPTION, "output-file", true,
                "Path of the output file. Default: " + DEFAULT_OUTPUT_XML_LOCATION);
        options.addOption(INDEX_FILEDS_OPTION, "fields-to-index", true,
                "Fields to index. By default, all fields are marked for indexing.");
        options.addOption(HELP_OPTION, "help", false, "Displays help and exits.");
        return options;
    }

    protected static void showUsage(Options options) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("java " + Main.class.getName() + " [options]", options);
    }

    protected static void failWithMessage(String message) {
        System.err.println(message);
        System.exit(1);
    }
}