Java tutorial
/* * Copyright (C) 2012 SeqWare * * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU 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 General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. */ package net.sourceforge.seqware.pipeline.workflowV2; import java.io.File; import java.io.IOException; import java.util.HashMap; import java.util.Iterator; import java.util.Map; import joptsimple.OptionSet; import net.sourceforge.seqware.common.model.Workflow; import net.sourceforge.seqware.common.util.Log; import org.apache.commons.io.FileUtils; import org.jdom.Document; import org.jdom.Element; import org.jdom.JDOMException; import org.jdom.input.SAXBuilder; /** * Utility methods that have been refactored out. * These can hopefully be placed eventually in something like Workflow so that they * can be re-used. * * @author dyuen */ public class WorkflowV2Utility { public static final String WORKFLOW_CLASS = "workflow_class"; public static final String WORKFLOW_ENGINE = "workflow_engine"; public static final String WORKFLOW_TYPE = "workflow_type"; /** * Locate and parse metadata information and return a map representation * * @param bundle * @return map if the parse is successful, null if not */ public static Map<String, String> parseMetaInfo(File bundle) { final String bundlePath = bundle.getAbsolutePath(); //parse metadata.xml to Map<String,String> @SuppressWarnings("unchecked") //safe to use <File> Iterator<File> it = FileUtils.iterateFiles(bundle, new String[] { "xml" }, true); if (!it.hasNext()) { return null; } File metadataFile = null; while (it.hasNext()) { File file = it.next(); if (file.getName().equals("metadata.xml")) { metadataFile = file; break; } } if (metadataFile == null) { return null; } return parseMetadataInfo(metadataFile, bundlePath); } /** * Parse the metadata info * * @param file * @param bundleDir * @return */ private static Map<String, String> parseMetadataInfo(File file, String bundleDir) { Map<String, String> ret = new HashMap<String, String>(); //parse metadataFile SAXBuilder builder = new SAXBuilder(); try { Document document = (Document) builder.build(file); Element root = document.getRootElement(); ret.put("bundle_version", root.getAttributeValue("version")); Element wf = root.getChild("workflow"); ret.put("name", wf.getAttributeValue("name")); ret.put("workflow_version", wf.getAttributeValue("version")); ret.put("seqware_version", wf.getAttributeValue("seqware_version")); ret.put("description", wf.getChildText("description")); String basedir = wf.getAttributeValue("basedir"); if (basedir != null) { basedir = wf.getAttributeValue("basedir").replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir); ret.put("basedir", basedir); //parse the workflow_directory_name String[] _arr = basedir.split("/"); if (_arr.length > 2) { String tmp = _arr[1]; String[] _arrtmp = tmp.split("_", 3); if (_arrtmp.length == 3) { ret.put("workflow_directory_name", _arrtmp[2]); } } } Element command = wf.getChild("workflow_command"); if (command != null) { ret.put("workflow_command", command.getAttributeValue("command") .replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); } Element template = wf.getChild("workflow_template"); if (template != null) { ret.put("workflow_template", template.getAttributeValue("path").replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); } Element java_class = wf.getChild(WORKFLOW_CLASS); if (java_class != null) { ret.put(WORKFLOW_CLASS, java_class.getAttributeValue("path") .replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); } Element config = wf.getChild("config"); if (config != null) { ret.put("config", config.getAttributeValue("path").replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); } // Element classes = wf.getChild("classes"); // if (classes != null) { // ret.put("classes", classes.getAttributeValue("path").replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); // } Element build = wf.getChild("build"); if (build != null) { ret.put("build", build.getAttributeValue("command").replaceFirst("\\$\\{workflow_bundle_dir\\}", bundleDir)); } Element requirements = wf.getChild("requirements"); if (requirements != null) { ret.put("compute", requirements.getAttributeValue("compute")); ret.put("memory", requirements.getAttributeValue("memory")); ret.put("network", requirements.getAttributeValue("network")); ret.put(WORKFLOW_ENGINE, requirements.getAttributeValue(WORKFLOW_ENGINE)); ret.put(WORKFLOW_TYPE, requirements.getAttributeValue(WORKFLOW_TYPE)); } } catch (JDOMException e) { Log.error("Error parsing metadata.xml", e); } catch (IOException e) { Log.error("IO Error parsing metadata.xml", e); } return ret; } /** * Determine the bundle path from the provided options * * @return bundlePath */ public static String determineRelativeBundlePath(OptionSet options) { String bundlePath; // get bundle path if (options.has("bundle")) { bundlePath = (String) options.valueOf("bundle"); } else { bundlePath = (String) options.valueOf("provisioned-bundle-dir"); } return bundlePath; } public static boolean requiresNewLauncher(Workflow workflow) { String workflowClass = workflow.getWorkflowClass(); String workflowEngine = workflow.getWorkflowEngine(); String workflowType = workflow.getWorkflowType(); return requiresNewLauncher(workflowClass, workflowEngine, workflowType); } public static boolean requiresNewLauncher(String workflowClass, String workflowEngine, String workflowType) { // if we specify workflow_class, workflow_template_path and the hints in the requirements we should be // able to determine which actual launcher to delegate to // if we need a workflow_class, then we always use the new launcher if (workflowClass != null) { Log.stdout("requiresNewLauncher - byClass " + workflowClass); return true; } // if Oozie is required or a if ftl2 is a requirement, we use the new launcher else if ((workflowEngine != null && workflowEngine.contains("Oozie") && !workflowEngine.contains("Pegasus")) || (workflowType != null && workflowType.contains("ftl2"))) { Log.stdout("requiresNewLauncher - byEngine or Type " + workflowEngine + " " + workflowType); return true; } Log.stdout("requiresNewLauncher - fall-through"); // otherwise, we fall through to the old launcher return false; } public static boolean requiresNewLauncher(OptionSet options) { final String bundlePath = WorkflowV2Utility.determineRelativeBundlePath(options); final File bundle = new File(bundlePath); // determine whether we're really dealing with a new bundle or whether we should delegate to the old launcher final Map<String, String> parseMetaInfo = WorkflowV2Utility.parseMetaInfo(bundle); String workflowClass = parseMetaInfo.get(WorkflowV2Utility.WORKFLOW_CLASS); String workflowEngine = parseMetaInfo.get(WorkflowV2Utility.WORKFLOW_ENGINE); String workflowType = parseMetaInfo.get(WorkflowV2Utility.WORKFLOW_TYPE); return requiresNewLauncher(workflowClass, workflowEngine, workflowType); } }