uk.ac.ebi.interpro.scan.jms.main.AbstractI5Runner.java Source code

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Here is the source code for uk.ac.ebi.interpro.scan.jms.main.AbstractI5Runner.java

Source

package uk.ac.ebi.interpro.scan.jms.main;

import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.log4j.Logger;

import java.io.File;
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.nio.file.Path;

/**
 * Abstract class containing common code used by I5 when running in all it's various modes.
 *
 * @author Matthew Fraser, EMBL-EBI, InterPro
 * @version $Id$
 * @since 1.0-SNAPSHOT
 */
public class AbstractI5Runner {

    private static final Logger LOGGER = Logger.getLogger(AbstractI5Runner.class.getName());

    private static final HelpFormatter HELP_FORMATTER = new HelpFormatter();
    private static final String HELP_MESSAGE_TITLE = "java -XX:+UseParallelGC -XX:ParallelGCThreads=2 -XX:+AggressiveOpts "
            + "-XX:+UseFastAccessorMethods -Xms128M -Xmx2048M -jar interproscan-5.jar";
    private static final String HEADER = "\n\nPlease give us your feedback by sending an email to\n\ninterhelp@ebi.ac.uk\n\n";
    private static final String FOOTER = "Copyright \u00a9 EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK. (http://www.ebi.ac.uk) "
            + "The InterProScan software itself is "
            + "provided under the Apache License, Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0.html). "
            + "Third party components (e.g. member database binaries and models) are subject to separate licensing - "
            + "please see the individual member database websites for details.\n\n";

    protected static final Mode DEFAULT_MODE = Mode.STANDALONE;

    protected static void printHelp(final Options commandLineOptionsForHelp) {
        HELP_FORMATTER.printHelp(HELP_MESSAGE_TITLE, HEADER, commandLineOptionsForHelp, FOOTER);
    }

    /**
     * Create any directory/directories required in the supplied path
     * @param path The path
     * @return True if all succeeded
     */
    protected static boolean createDirectory(final String path) {
        File dir = new File(path);
        try {
            boolean dirCreated = dir.mkdirs();
            return dirCreated;
        } catch (SecurityException e) {
            LOGGER.error("Directory creation . Cannot create the specified directory !\n"
                    + "Specified directory path (absolute): " + dir.getAbsolutePath(), e);
            throw new IllegalStateException("The directory (-" + path + ")  you specified cannot be written to:",
                    e);
        }
    }

    /**
     * Check if a specified path exists and is readable.
     * @param path The full file or directory path under review (e.g. "/tmp/test_proteins.fasta")
     * @param checkParent Do we just check the parent path? (e.g. "/tmp")
     * @param checkWriteable Should we also check that the path or parent path can be written to?
     * @param option The user input {@link I5Option} this path relates to (or null if not applicable)
     * @return True if the checks succeed, otherwise false (although the system will exit if a {@link I5Option} check fails)
     */
    protected static boolean checkPathExistence(final String path, final boolean checkParent,
            final boolean checkWriteable, final I5Option option) {
        String pathToCheck = path;
        if (checkParent) {
            pathToCheck = path.substring(0, path.lastIndexOf(File.separator));
        }
        Path p = FileSystems.getDefault().getPath(pathToCheck);
        boolean exists = Files.isReadable(p);
        if (option != null && !exists) {
            System.out.println("For the (-" + option.getShortOpt()
                    + ") option you specified a location which doesn't exist or is not readable:");
            System.out.println(path);
            System.exit(2);
        }
        if (exists && checkWriteable) {
            boolean writable = Files.isWritable(p);
            if (option != null && !writable) {
                System.out.println("For the (-" + option.getShortOpt()
                        + ") option you specified a location which is not writable:");
                System.out.println(path);
                System.exit(2);
            }
            return writable;
        }
        return exists;
    }

    /**
     * Checks if a specified path exists.
     * @param path The path to check (e.g. file path, directory path etc)
     * @return True if the path exists, otherwise false
     */
    protected static boolean checkPathExistence(final String path) {
        return checkPathExistence(path, false, false, null);
    }

}