org.ut.biolab.medsavant.shared.util.DirectorySettings.java Source code

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Here is the source code for org.ut.biolab.medsavant.shared.util.DirectorySettings.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 org.ut.biolab.medsavant.shared.util;

import java.io.File;
import java.io.IOException;
import java.util.Calendar;
import java.util.GregorianCalendar;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

/**
 *
 * @author AndrewBrook, tarkvara, mfiume
 */
public class DirectorySettings {

    private static File medSavantDir;
    private static File tmpDir;
    private static Log LOG = LogFactory.getLog(DirectorySettings.class);

    //Should this be configurable in the properties file?    
    private static final String CHMOD = "/bin/chmod";

    /**
     * Retrieve the directory where MedSavant stores supporting files.
     *
     * @return
     */
    public static File getMedSavantDirectory() {

        return medSavantDir;
    }

    public static File getDatabaseWorkingDir() throws IOException {
        File f = new File(getTmpDirectory(), "database_work");
        if (!f.exists()) {
            f.mkdirs();
        }
        Runtime rt = Runtime.getRuntime();
        Process proc = rt.exec(CHMOD + " -R 777 " + f.getAbsolutePath());
        try {
            proc.waitFor();
        } catch (Exception ex) {
            LOG.error("Can't chmod on database working dir ", ex);
        }
        return f;

    }

    private static File getDirectory(String parent, String dirName) {
        File result = new File(parent, dirName);
        if (!result.exists()) {
            result.mkdirs();
        }
        return result;
    }

    public static File getAnnotatedTSVDirectory() {
        return new File(getMedSavantDirectory().getAbsolutePath() + File.separator + "annotatedTSV");
    }

    public static File getAnnotatedTSVDirectory(String database, int projectId, int refId) {
        return new File(getAnnotatedTSVDirectory(), database + "_" + projectId + "_" + refId);
    }

    public static File getGenoTypeDirectory() {
        return new File(getMedSavantDirectory().getAbsolutePath() + File.separator + "genotypes");
    }

    public static File getGenoTypeDirectory(String database, int projectId) {
        File f = new File(getGenoTypeDirectory(), database + "_" + projectId);
        if (!f.exists()) {
            f.mkdirs();
        }
        return f;
        //return new File(getMedSavantDirectory().getAbsolutePath()+File.pathSeparator+"genotypes"+File.pathSeparator+"project_"+projectId);
    }

    public static File getAnnotatedTSVDirectory(String database, int projectId) {
        File f = new File(getGenoTypeDirectory(database, projectId), "annotatedTSV");
        if (!f.exists()) {
            f.mkdirs();
        }
        return f;
    }

    public static File getTmpDirectory() {
        return tmpDir;
    }

    public static File getCacheDirectory() {
        return getDirectory(getMedSavantDirectory().getAbsolutePath(), "cache");
    }

    /**
     * Create a directory whose name includes a date-stamp.
     *
     * @param parent the parent directory, typically <code>new File(".")</code>
     */
    public static File generateDateStampDirectory(File parent) throws IOException {
        File dir;
        do {
            Calendar today = new GregorianCalendar();
            String dateStamp = today.get(Calendar.YEAR) + "_" + (today.get(Calendar.MONTH) + 1) + "_"
                    + today.get(Calendar.DAY_OF_MONTH) + "_" + today.get(Calendar.HOUR_OF_DAY) + "_"
                    + today.get(Calendar.MINUTE) + "_" + today.get(Calendar.SECOND) + "_"
                    + today.get(Calendar.MILLISECOND);
            dir = new File(parent.getCanonicalFile(), dateStamp);
            try {
                Thread.sleep(50);
            } catch (InterruptedException iex) {
            }
        } while (dir.exists());

        dir.mkdirs();
        return dir;
    }

    public static void setTmpDirectory(String path) {
        tmpDir = new File(path);
        tmpDir.mkdirs();
    }

    public static void setMedSavantDirectory(String path) {
        File f = new File(path);
        if (!f.exists()) {
            f.mkdirs();
        }
        medSavantDir = f;
    }
}