Java tutorial
/** * 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.workflow; import com.jcraft.jsch.Session; import java.io.File; import java.nio.file.Path; import java.nio.file.Paths; import java.util.ArrayList; import java.util.List; import java.util.Map; import org.apache.commons.configuration.BaseConfiguration; 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.Local; import static uk.ac.sanger.cgp.wwdocker.actions.Local.execCommand; import uk.ac.sanger.cgp.wwdocker.actions.Remote; import uk.ac.sanger.cgp.wwdocker.actions.Utils; import uk.ac.sanger.cgp.wwdocker.interfaces.Workflow; /** * * @author kr2 */ public class TestWorkflow implements Workflow { private static final Logger logger = LogManager.getLogger(); BaseConfiguration config; private static final String[] logSearchCmd = {}; public TestWorkflow(BaseConfiguration config) { this.config = config; } @Override public String[] getFindLogsCmds() { return logSearchCmd; } @Override public List filesToPush(File iniFile) { List files = new ArrayList(); files.add(iniFile); logger.trace(iniFile); BaseConfiguration wkflConf = Config.loadConfig(iniFile.getAbsolutePath(), new Character(':'), false); if (wkflConf.getBoolean("testMode")) { logger.info(iniFile.getAbsolutePath() + " is set as testMode=true, no BAMs to transfer"); } else { // Add construct the paths to the local files List analysisIds = wkflConf.getList("tumourAnalysisIds"); analysisIds.add(wkflConf.getList("controlAnalysisId")); List bamFiles = wkflConf.getList("tumourBams"); bamFiles.add(wkflConf.getList("controlBam")); if (analysisIds.size() != bamFiles.size()) { throw new RuntimeException( "Number of *AnalysisId[s] is not equal to the number of *Bam[s] in workfile: " + iniFile.getAbsolutePath()); } for (int i = 0; i < analysisIds.size(); i++) { String analysisId = (String) analysisIds.get(i); String bamFile = (String) bamFiles.get(i); File bamPath = new File( config.getString("data_root").concat("/").concat(analysisId).concat("/").concat(bamFile)); if (!bamPath.exists()) { throw new RuntimeException("Unable to find BAM file (" + bamPath.getAbsolutePath() + ") expected from worfile: " + iniFile.getAbsolutePath()); } files.add(bamPath); } } return files; } @Override public List filesToPull(File iniFile) { List files = new ArrayList(); //@TODO return files; } @Override public String baseDockerCommand(BaseConfiguration config, String extras) { File workflow = Paths.get(config.getString("workflowDir"), config.getString("workflow").replaceAll(".*/", "").replaceAll("\\.zip$", "")).toFile(); // probably want to clean the data store before we write the ini file //docker run --rm -h master -v /cgp/datastore:/datastore -v /cgp/workflows/Workflow_Bundle_SangerPancancerCgpCnIndelSnvStr_1.0.5.1_SeqWare_1.1.0-alpha.5:/workflow -i seqware/seqware_whitestar_pancancer rm -rf /datastore/ String command = "docker run --rm -h master"; command = command.concat(" -v ").concat(config.getString("datastoreDir")).concat(":/datastore"); // command = command.concat(" -v ").concat(workflow.getAbsolutePath()).concat(":/workflow"); command = command.concat(" ").concat(seqwareWhiteStarImage(config)); return command; } @Override public int runDocker(BaseConfiguration config, File iniFile) { String command = baseDockerCommand(config, null); command = command.concat(" perl /datastore/run.pl ").concat(iniFile.getName().replace(".ini", "")); // this changes the amount of output return execCommand(command, Config.getEnvs(config), false); } @Override public boolean provisionHost(String host, BaseConfiguration config, File thisJar, File tmpConf, String mode, Map<String, String> envs) throws InterruptedException { boolean provisioned = false; String remoteWorkflowDir = config.getString("workflowDir"); String localSeqwareJar = config.getString("seqware"); File jreDist = Utils.expandUserFile(config, "jreDist", true); String[] pullDockerImages = config.getStringArray("pullDockerImages"); String optDir = "/opt/wwdocker"; String workerLog = config.getString("log4-worker"); File localTmp = Utils.expandUserDirPath(config, "primaryLargeTmp", true); List<String> createPaths = new ArrayList(); createPaths.add("/opt/wwdocker"); createPaths.add("/opt/wwdocker/jre"); createPaths.add(remoteWorkflowDir); createPaths.add(config.getString("datastoreDir")); Session ssh = Remote.getSession(config, host); Remote.createPaths(ssh, createPaths); Remote.chmodPaths(ssh, "a+wrx", createPaths, true); Remote.cleanFiles(ssh, new String[] { config.getString("log4-delete") }); if (Remote.dockerPull(ssh, pullDockerImages) != 0) { return provisioned; } if (Remote.curl(ssh, localSeqwareJar, remoteWorkflowDir) == null) { return provisioned; } Local.pushToHost(jreDist.getAbsolutePath(), host, optDir, envs, ssh, localTmp); if (Remote.expandJre(ssh, jreDist) != 0) { return provisioned; } Local.pushToHost("testData/run.pl", host, config.getString("datastoreDir"), envs, ssh, localTmp); if (Local.pushToHost(thisJar.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // this jar file || Local.pushToHost(workerLog, host, optDir, envs, ssh, localTmp) != 0 // worker log config || Local.pushToHost(tmpConf.getAbsolutePath(), host, optDir, envs, ssh, localTmp) != 0 // config file || Remote.chmodPath(ssh, "go-wrx", optDir.concat("/*"), true) != 0 // file will have passwords || Remote.startWorkerDaemon(ssh, thisJar.getName(), tmpConf.getName(), mode) != 0) { return provisioned; } provisioned = true; return provisioned; } }