com.act.biointerpretation.l2expansion.L2RenderingDriver.java Source code

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Here is the source code for com.act.biointerpretation.l2expansion.L2RenderingDriver.java

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/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program 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 WITHOUT 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/>. *
*                                                                        *
*************************************************************************/

package com.act.biointerpretation.l2expansion;

import com.act.biointerpretation.mechanisminspection.ReactionRenderer;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import java.io.File;
import java.util.ArrayList;
import java.util.List;

/**
 * Used to render an already-genderated prediction corpus for manual curation.
 */
public class L2RenderingDriver {

    private static final Logger LOGGER = LogManager.getFormatterLogger(L2RenderingDriver.class);

    private static final String OPTION_CORPUS_PATH = "c";
    private static final String OPTION_OUTPUT_DIRECTORY = "r";
    private static final String OPTION_IMAGE_FORMAT = "f";
    private static final String OPTION_IMAGE_WIDTH = "w";
    private static final String OPTION_IMAGE_HEIGHT = "h";
    private static final String OPTION_HELP = "h";

    private static final String DEFAULT_IMAGE_FORMAT = "png";
    private static final String DEFAULT_IMAGE_WIDTH = "1000";
    private static final String DEFAULT_IMAGE_HEIGHT = "1000";

    public static final String HELP_MESSAGE = "This class is used to render an already-generated prediction corpus.  The corpus is read in from "
            + "file, and basic statistics about it are generated. Without -r, nothing more is done.  With "
            + "-r, the corpus is also rendered into a specified directory. This entails printing one image of "
            + "each prediction, and one image of each ro that occurs in any prediction. The corpus itself is "
            + "also printed to the same directory, as well as a file containing the product inchis from the corpus, "
            + "which contains one inchi per line, and can be used as input to the BingSearchRanker.";

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_CORPUS_PATH).argName("corpus file path")
                    .desc("The path to the prediction corpus file.").hasArg().longOpt("corpus-path").required());
            add(Option.builder(OPTION_OUTPUT_DIRECTORY).argName("output directory")
                    .desc("The path to the directory in which to render the corpus.").hasArg()
                    .longOpt("output-directory").required());
            add(Option.builder(OPTION_IMAGE_FORMAT).argName("image format")
                    .desc("The format in which to print the images, i.e 'png'").hasArg().longOpt("image-format"));
            add(Option.builder(OPTION_IMAGE_WIDTH).argName("image width").desc("The width of the images to print")
                    .hasArg().longOpt("image-width"));
            add(Option.builder(OPTION_IMAGE_HEIGHT).argName("image height")
                    .desc("The height of the images to print").hasArg().longOpt("image-height"));
            add(Option.builder(OPTION_HELP).argName("help").desc("Prints this help message.").longOpt("help"));
        }
    };

    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();

    static {
        HELP_FORMATTER.setWidth(100);
    }

    public static void main(String[] args) throws Exception {

        // Build command line parser.
        Options opts = new Options();
        for (Option.Builder b : OPTION_BUILDERS) {
            opts.addOption(b.build());
        }

        CommandLine cl = null;
        try {
            CommandLineParser parser = new DefaultParser();
            cl = parser.parse(opts, args);
        } catch (ParseException e) {
            LOGGER.error("Argument parsing failed: %s", e.getMessage());
            HELP_FORMATTER.printHelp(L2RenderingDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            System.exit(1);
        }

        // Print help.
        if (cl.hasOption(OPTION_HELP)) {
            HELP_FORMATTER.printHelp(L2RenderingDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            return;
        }

        // Set up input corpus file.
        File corpusFile = new File(cl.getOptionValue(OPTION_CORPUS_PATH));
        if (!corpusFile.exists()) {
            LOGGER.error("Input corpus file does not exist");
            return;
        }
        //Set up output directory.
        File outputDirectory = new File(cl.getOptionValue(OPTION_OUTPUT_DIRECTORY));
        if (outputDirectory.exists() && !outputDirectory.isDirectory()) {
            LOGGER.error("Can't render corpus: supplied image directory is an existing non-directory file.");
            return;
        }
        outputDirectory.mkdir();

        LOGGER.info("Reading in corpus from file.");
        L2PredictionCorpus predictionCorpus = L2PredictionCorpus.readPredictionsFromJsonFile(corpusFile);
        LOGGER.info("Finished reading in corpus with %d predictions", predictionCorpus.getCorpus().size());

        // Set image format options
        String format = cl.getOptionValue(OPTION_IMAGE_FORMAT, DEFAULT_IMAGE_FORMAT);
        Integer width = Integer.parseInt(cl.getOptionValue(OPTION_IMAGE_WIDTH, DEFAULT_IMAGE_WIDTH));
        Integer height = Integer.parseInt(cl.getOptionValue(OPTION_IMAGE_HEIGHT, DEFAULT_IMAGE_HEIGHT));

        // Render the corpus.
        LOGGER.info("Drawing images for each prediction in corpus.");
        ReactionRenderer reactionRenderer = new ReactionRenderer(format, width, height);
        PredictionCorpusRenderer renderer = new PredictionCorpusRenderer(reactionRenderer);
        renderer.renderCorpus(predictionCorpus, outputDirectory);

        LOGGER.info("L2RenderingDriver complete!");
    }

}