uk.ac.sanger.cgp.wwdocker.interfaces.Workflow.java Source code

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Here is the source code for uk.ac.sanger.cgp.wwdocker.interfaces.Workflow.java

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/**
 * Copyright (c) 2015 Genome Research Ltd.
 * 
 * Author: Cancer Genome Project cgpit@sanger.ac.uk
 * 
 * This file is part of WwDocker.
 * 
 * WwDocker is free software: you can redistribute it and/or modify it under
 * the terms of the GNU Affero 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 Affero General Public License for more
 * details.
 * 
 * You should have received a copy of the GNU Affero General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 * 
 * 1. The usage of a range of years within a copyright statement contained within
 * this distribution should be interpreted as being equivalent to a list of years
 * including the first and last year specified and all consecutive years between
 * them. For example, a copyright statement that reads 'Copyright (c) 2005, 2007-
 * 2009, 2011-2012' should be interpreted as being identical to a statement that
 * reads 'Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012' and a copyright
 * statement that reads "Copyright (c) 2005-2012' should be interpreted as being
 * identical to a statement that reads 'Copyright (c) 2005, 2006, 2007, 2008,
 * 2009, 2010, 2011, 2012'."
 */

package uk.ac.sanger.cgp.wwdocker.interfaces;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.StandardCopyOption;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.apache.commons.configuration.BaseConfiguration;
import org.apache.commons.io.IOUtils;
import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import uk.ac.sanger.cgp.wwdocker.Config;
import uk.ac.sanger.cgp.wwdocker.actions.Utils;
import uk.ac.sanger.cgp.wwdocker.enums.HostStatus;

/**
 *
 * @author kr2
 */
public interface Workflow {

    static final Logger logger = LogManager.getLogger();

    List filesToPush(File iniFile);

    List filesToPull(File iniFile);

    String[] getFindLogsCmds();

    String baseDockerCommand(BaseConfiguration config, String extras);

    int runDocker(BaseConfiguration config, File iniFile);

    boolean provisionHost(String host, BaseConfiguration config, File thisJar, File tmpConf, String mode,
            Map<String, String> envs) throws InterruptedException;

    default String seqwareWhiteStarImage(BaseConfiguration config) {
        String[] pullImages = config.getStringArray("pullDockerImages");
        String whitestar = null;
        for (String i : pullImages) {
            if (i.contains("seqware_whitestar_pancancer")) {
                whitestar = i;
                break;
            }
        }
        return whitestar;
    }

    default int cleanDockerPath(BaseConfiguration config) {
        String command = baseDockerCommand(config, null);
        List<String> args = new ArrayList(Arrays.asList(command.split(" ")));
        args.add("/bin/bash");
        args.add("-c");
        args.add("rm -rf /datastore/oozie-* /datastore/*.ini /datastore/logs.tar.gz /datastore/toInclude.lst");

        ProcessBuilder pb = new ProcessBuilder(args);

        Map<String, String> pEnv = pb.environment();
        pEnv.putAll(Config.getEnvs(config));
        logger.info("Executing: " + String.join(" ", args));
        int exitCode = -1;
        Process p = null;
        try {
            p = pb.start();
            String progErr = IOUtils.toString(p.getErrorStream());
            String progOut = IOUtils.toString(p.getInputStream());
            exitCode = p.waitFor();
            Utils.logOutput(progErr, Level.ERROR);
            Utils.logOutput(progOut, Level.TRACE);
        } catch (InterruptedException | IOException e) {
            logger.error(e.getMessage(), e);
        } finally {
            if (p != null) {
                p.destroy();
                exitCode = p.exitValue();
            }
        }
        return exitCode;
    }

    default String iniPathByState(BaseConfiguration config, String iniFile, HostStatus hs) {
        File tmp = new File(iniFile);
        String statePath = config.getString("wfl_inis");
        if (!statePath.endsWith("/")) {
            statePath = statePath.concat("/");
        }
        return statePath.concat(hs.name()).concat("/").concat(tmp.getName());
    }

    default void iniUpdate(File iniFrom, BaseConfiguration config, HostStatus hs) {
        List<File> iniFiles = new ArrayList(1);
        iniFiles.add(iniFrom);
        iniUpdate(iniFiles, config, hs);
    }

    default void iniUpdate(List<File> inisFrom, BaseConfiguration config, HostStatus hs) {
        String iniBaseTo = config.getString("wfl_inis");
        if (!iniBaseTo.endsWith("/")) {
            iniBaseTo = iniBaseTo.concat("/");
        }
        iniBaseTo = iniBaseTo.concat(hs.name()).concat("/");
        File dirCreate = new File(iniBaseTo);
        if (!dirCreate.exists()) {
            if (!dirCreate.mkdirs()) {
                throw new RuntimeException("Failed to create full path: " + dirCreate.getAbsolutePath());
            }
        }
        for (File iniFrom : inisFrom) {
            File iniTo = new File(iniBaseTo.concat(iniFrom.getName()));
            try {
                Files.move(iniFrom.toPath(), iniTo.toPath(), StandardCopyOption.REPLACE_EXISTING);
            } catch (IOException e) {
                throw new RuntimeException(e.getMessage(), e);
            }
        }
    }
}