Java tutorial
/* * Copyright: (c) 2004-2010 Mayo Foundation for Medical Education and * Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the * triple-shield Mayo logo are trademarks and service marks of MFMER. * * Except as contained in the copyright notice above, or as used to identify * MFMER as the author of this software, the trade names, trademarks, service * marks, or product names of the copyright holder shall not be used in * advertising, promotion or otherwise in connection with this software without * prior written authorization of the copyright holder. * * Licensed under the Eclipse Public License, Version 1.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.eclipse.org/legal/epl-v10.html * */ package org.LexGrid.LexBIG.admin; import java.net.URI; import java.util.Enumeration; import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary; import org.LexGrid.LexBIG.DataModel.InterfaceElements.CodingSchemeRendering; import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; import org.LexGrid.LexBIG.Extensions.Export.OBO_Exporter; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.Impl.exporters.OBOExport; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.LexBIG.Utility.Constructors; import org.apache.commons.cli.BasicParser; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.lexevs.system.ResourceManager; /** * Exports content from the repository to a file in the Open Biomedical * Ontologies (OBO) format. * * <pre> * Example: java org.LexGrid.LexBIG.admin.ExportOBO * -out,--output <uri> URI or path of the directory to contain the * resulting OBO file. The file name will be automatically derived * from the coding scheme name. * -u,--urn <name> URN or local name of the coding scheme to export. * -v,--version <id> The assigned tag/label or absolute version * identifier of the coding scheme. * -f,--force If specified, allows the destination file to be * overwritten if present. * * Note: If the URN and version values are unspecified, a * list of available coding schemes will be presented for * user selection. * * Example: java -Xmx512m -cp lgRuntime.jar * org.LexGrid.LexBIG.admin.ExportOBO -out "file:///path/to/dir" * -u "FBbt" -v "PRODUCTION" -f * </pre> * * @author <A HREF="mailto:johnson.thomas@mayo.edu">Thomas Johnson</A> */ public class ExportOBO { public static void main(String[] args) { try { new ExportOBO().run(args); } catch (LBResourceUnavailableException e) { Util.displayTaggedMessage(e.getMessage()); } catch (Exception e) { Util.displayAndLogError("REQUEST FAILED !!!", e); } } public ExportOBO() { super(); } /** * Primary entry point for the program. * * @throws Exception */ public void run(String[] args) throws Exception { synchronized (ResourceManager.instance()) { // Parse the command line ... CommandLine cl = null; Options options = getCommandOptions(); try { cl = new BasicParser().parse(options, args); } catch (ParseException e) { Util.displayCommandOptions("ExportOBO", options, "\n ExportOBO -out \"file:///path/to/dir\" -u \"FBbt\" -v \"PRODUCTION\" -f" + Util.getURIHelp(), e); Util.displayMessage(Util.getPromptForSchemeHelp()); return; } // Interpret provided values ... URI destination = null; try { destination = Util.string2FileURI(cl.getOptionValue("out")); } catch (Exception e) { Util.displayMessage(e.getMessage()); Util.displayMessage("Please make sure the destination is an existing directory."); return; } String urn = cl.getOptionValue("u"); String ver = cl.getOptionValue("v"); boolean overwrite = cl.hasOption("f"); Util.displayTaggedMessage("WRITING TO: " + destination.toString()); LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); // Find in list of registered vocabularies ... CodingSchemeSummary css = null; if (urn != null && ver != null) { urn = urn.trim(); ver = ver.trim(); Enumeration<? extends CodingSchemeRendering> schemes = lbs.getSupportedCodingSchemes() .enumerateCodingSchemeRendering(); while (schemes.hasMoreElements() && css == null) { CodingSchemeSummary summary = schemes.nextElement().getCodingSchemeSummary(); if (urn.equalsIgnoreCase(summary.getCodingSchemeURI()) && ver.equalsIgnoreCase(summary.getRepresentsVersion())) css = summary; } } String csuri = urn; String csver = ver; // Found it? If not, prompt... if (css == null) { if (urn != null || ver != null) { Util.displayMessage("No matching coding scheme was found for the given URN or version."); Util.displayMessage(""); } css = Util.promptForCodeSystem(); if (css == null) return; csuri = css.getCodingSchemeURI(); csver = css.getRepresentsVersion(); } // Find the registered extension handling this type of export ... OBO_Exporter exporter = (OBO_Exporter) lbsm.getExporter(OBOExport.name); // Perform the requested action ... exporter.export(Constructors.createAbsoluteCodingSchemeVersionReference(csuri, csver), destination, overwrite, false, true); Util.displayExporterStatus(exporter); } } /** * Return supported command options. * * @return org.apache.commons.cli.Options */ private Options getCommandOptions() { Options options = new Options(); Option o; o = new Option("out", "output", true, "URI or path of the directory to contain the " + "resulting OBO file. The file name will be automatically " + "derived from the coding scheme name."); o.setArgName("uri"); o.setRequired(true); options.addOption(o); o = new Option("u", "urn", true, "URN or local name of the coding scheme to export."); o.setArgName("name"); o.setRequired(false); options.addOption(o); o = new Option("v", "version", true, "The assigned tag/label or absolute version identifier of the coding scheme."); o.setRequired(false); options.addOption(o); o = new Option("f", "force", false, "If specified, allows the destination file to be overwritten " + "if present."); o.setRequired(false); options.addOption(o); return options; } }