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.Load.MetaData_Loader; import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl; import org.LexGrid.LexBIG.LexBIGService.LexBIGService; import org.LexGrid.LexBIG.LexBIGService.LexBIGServiceManager; import org.LexGrid.LexBIG.Utility.Constructors; 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; /** * Loads optional XML-based metadata to be associated with an existing coding * scheme. * * <pre> * Example: java org.LexGrid.LexBIG.admin.LoadMetadata * -u,--urn <name> URN uniquely identifying the code system. * -v,--version <id> Version identifier. * -in,--input <uri> URI or path specifying location of the XML file. * -v, --validate <int> Perform validation of the input file * without loading data. If specified, the '-f', and '-o' * options are ignored. Supported levels of validation include: * 0 = Verify document is valid * -o, --overwrite If specified, existing metadata for the code system * will be erased. Otherwise, new metadata will be appended to * existing metadata (if present). * -f,--force Force overwrite (no confirmation). * * 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.LoadMetadata -in "file:///path/to/file.xml" -o * -or- * org.LexGrid.LexBIG.admin.LoadMetadata -in "file:///path/to/file.xml" * </pre> * * @author <A HREF="mailto:johnson.thomas@mayo.edu">Thomas Johnson</A> */ @LgAdminFunction public class LoadMetadata { public static void main(String[] args) { try { new LoadMetadata().run(args); } catch (LBResourceUnavailableException e) { Util.displayTaggedMessage(e.getMessage()); } catch (Exception e) { Util.displayAndLogError("REQUEST FAILED !!!", e); } } public LoadMetadata() { 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("LoadMetadata", options, "\n LoadMetadata -in \"file:///path/to/file.obo\" -o" + "\n LoadMetadata -in \"file:///path/to/file.obo\"" + Util.getURIHelp(), e); return; } // Interpret provided values ... URI source = Util.string2FileURI(cl.getOptionValue("in")); String urn = cl.getOptionValue("u"); String ver = cl.getOptionValue("v"); boolean force = cl.hasOption("f"); boolean overwrite = cl.hasOption("o"); CodingSchemeSummary css = null; // Find in list of registered vocabularies ... LexBIGService lbs = LexBIGServiceImpl.defaultInstance(); 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; } } // 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; } // Continue and confirm the action (if not bypassed by force option) // ... Util.displayTaggedMessage("A matching coding scheme was found ..."); if (vl >= 0) { Util.displayTaggedMessage("VALIDATING SOURCE URI: " + source.toString()); } else { Util.displayTaggedMessage("LOADING FROM URI: " + source.toString()); Util.displayTaggedMessage( overwrite ? "OVERWRITE EXISTING METADATA" : "APPEND TO EXISTING METADATA"); } // Find the registered extension handling this type of load ... LexBIGServiceManager lbsm = lbs.getServiceManager(null); MetaData_Loader loader = (MetaData_Loader) lbsm.getLoader("MetaDataLoader"); // Perform the requested load or validate action ... if (vl >= 0) { loader.validateAuxiliaryData(source, null, vl); Util.displayTaggedMessage("VALIDATION SUCCESSFUL"); } else { boolean confirmed = true; if (overwrite && !force) { Util.displayMessage("OVERWRITE EXISTING METADATA? ('Y' to confirm, any other key to cancel)"); char choice = Util.getConsoleCharacter(); confirmed = choice == 'Y' || choice == 'y'; } if (confirmed) { loader.loadAuxiliaryData(source, Constructors.createAbsoluteCodingSchemeVersionReference(css), overwrite, false, true); Util.displayLoaderStatus(loader); } } } } /** * Return supported command options. * * @return org.apache.commons.cli.Options */ private Options getCommandOptions() { Options options = new Options(); Option o; o = new Option("u", "urn", true, "URN uniquely identifying the code system."); o.setArgName("name"); o.setRequired(false); options.addOption(o); o = new Option("v", "version", true, "Version identifier."); o.setArgName("id"); o.setRequired(false); options.addOption(o); o = new Option("in", "input", true, "URI or path specifying location of the XML file."); o.setArgName("uri"); o.setRequired(true); options.addOption(o); o = new Option("v", "validate", true, "Validation only; no load. If specified, 'o' and 'f' " + "are ignored. 0 to verify the document is well-formed."); o.setArgName("int"); o.setRequired(false); options.addOption(o); o = new Option("o", "overwrite", false, "If specified, existing metadata for the code system " + "will be erased. Otherwise, new metadata will be appended " + "to existing metadata (if present). "); o.setRequired(false); options.addOption(o); o = new Option("f", "force", false, "Force overwrite (no confirmation)."); o.setRequired(false); options.addOption(o); return options; } }