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 org.LexGrid.LexBIG.DataModel.Core.AbsoluteCodingSchemeVersionReference; import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException; import org.LexGrid.LexBIG.Extensions.Load.OBO_Loader; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.annotations.LgAdminFunction; 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; import edu.mayo.informatics.resourcereader.core.StringUtils; /** * Imports a file specified in the Open Biomedical Ontologies (OBO) format to * the LexBIG repository. * * <pre> * Example: java org.LexGrid.LexBIG.admin.LoadOBO * -in,--input <uri> URI or path specifying location of the source file * -v, --validate <int> Perform validation of the candidate * resource without loading data. If specified, the '-a' and '-t' * options are ignored. Supported levels of validation include: * 0 = Verify document is valid * -a, --activate ActivateScheme on successful load; if unspecified the vocabulary is loaded but not activated * -t, --tag <id> An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign. * * Example: java -Xmx512m -cp lgRuntime.jar * org.LexGrid.LexBIG.admin.LoadOBO -in "file:///path/to/file.obo" -a * -or- * org.LexGrid.LexBIG.admin.LoadOBO -in "file:///path/to/file.obo" -v 0 * </pre> * * @author <A HREF="mailto:kanjamala.pradip@mayo.edu">Pradip Kanjamala</A> * @author <A HREF="mailto:johnson.thomas@mayo.edu">Thomas Johnson</A> */ @LgAdminFunction public class LoadOBO { public static void main(String[] args) { try { new LoadOBO().run(args); } catch (LBResourceUnavailableException e) { Util.displayTaggedMessage(e.getMessage()); } catch (Exception e) { Util.displayAndLogError("REQUEST FAILED !!!", e); } } public LoadOBO() { 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(); int vl = -1; try { cl = new BasicParser().parse(options, args); if (cl.hasOption("v")) vl = Integer.parseInt(cl.getOptionValue("v")); } catch (ParseException e) { Util.displayCommandOptions("LoadOBO", options, "\n LoadOBO -in \"file:///path/to/file.obo\" -a" + "\n LoadOBO -in \"file:///path/to/file.obo\" -mf \"file:///path/to/myCodingScheme-manifest.xml\" -a" + "\n LoadOBO -in \"file:///path/to/file.obo\" -v 0" + Util.getURIHelp(), e); return; } // Interpret provided values ... String manUriStr = cl.getOptionValue("mf"); URI manifest = null; if (!StringUtils.isNull(manUriStr)) manifest = Util.string2FileURI(manUriStr); URI source = Util.string2FileURI(cl.getOptionValue("in")); boolean activate = vl < 0 && cl.hasOption("a"); if (vl >= 0) { Util.displayTaggedMessage("VALIDATING SOURCE URI: " + source.toString()); } else { Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); Util.displayTaggedMessage(activate ? "ACTIVATE ON SUCCESS" : "NO ACTIVATION"); } // Find the registered extension handling this type of load ... LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); LexBIGServiceManager lbsm = lbs.getServiceManager(null); OBO_Loader loader = (OBO_Loader) lbsm.getLoader(org.LexGrid.LexBIG.Impl.loaders.OBOLoaderImpl.name); // Perform the requested load or validate action ... if (vl >= 0) { loader.validate(source, null, vl); Util.displayTaggedMessage("VALIDATION SUCCESSFUL"); } else { loader.setCodingSchemeManifestURI(manifest); loader.load(source, null, false, true); Util.displayLoaderStatus(loader); } // If specified, set the associated tag on the newly loaded // scheme(s) ... if (vl < 0 && cl.hasOption("t")) { String tag = cl.getOptionValue("t"); AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.setVersionTag(ref, tag); Util.displayTaggedMessage("Tag assigned>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } // If requested, activate the newly loaded scheme(s) ... if (activate) { AbsoluteCodingSchemeVersionReference[] refs = loader.getCodingSchemeReferences(); for (int i = 0; i < refs.length; i++) { AbsoluteCodingSchemeVersionReference ref = refs[i]; lbsm.activateCodingSchemeVersion(ref); Util.displayTaggedMessage("Scheme activated>> " + ref.getCodingSchemeURN() + " Version>> " + ref.getCodingSchemeVersion()); } } } } /** * Return supported command options. * * @return org.apache.commons.cli.Options */ private Options getCommandOptions() { Options options = new Options(); Option o; o = new Option("in", "input", true, "URI or path specifying location of the source file."); o.setArgName("uri"); o.setRequired(true); options.addOption(o); o = new Option("mf", "manifest", true, "URI or path specifying location of the manifest file."); o.setArgName("uri"); o.setRequired(false); options.addOption(o); o = new Option("v", "validate", true, "Validation only; no load. If specified, 'a' and 't' " + "are ignored. 0 to verify the file conforms to the OBO format."); o.setArgName("int"); o.setRequired(false); options.addOption(o); o = new Option("a", "activate", false, "ActivateScheme on successful load; if unspecified the " + "vocabulary is loaded but not activated."); o.setRequired(false); options.addOption(o); o = new Option("t", "tag", true, "An optional tag ID (e.g. 'PRODUCTION' or 'TEST') to assign."); o.setArgName("id"); o.setRequired(false); options.addOption(o); return options; } }