Workflow.java

/**
 * 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);
      }
    }
  }
}