Java tutorial
/** The ISAconverter, ISAvalidator & BII Management Tool are components of the ISA software suite (http://www.isa-tools.org) Exhibit A The ISAconverter, ISAvalidator & BII Management Tool are licensed under the Mozilla Public License (MPL) version 1.1/GPL version 2.0/LGPL version 2.1 "The contents of this file are subject to the Mozilla Public License Version 1.1 (the "License"). You may not use this file except in compliance with the License. You may obtain copies of the Licenses at http://www.mozilla.org/MPL/MPL-1.1.html. Software distributed under the License is distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for the specific language governing rights and limitations under the License. The Original Code is the ISAconverter, ISAvalidator & BII Management Tool. The Initial Developer of the Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com; Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com; http://www.isa-tools.org). All portions of the code written by the ISA Team are Copyright (c) 2007-2011 ISA Team. All Rights Reserved. Contributor(s): Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics 2010;26(18):2354-6. Alternatively, the contents of this file may be used under the terms of either the GNU General Public License Version 2 or later (the "GPL") - http://www.gnu.org/licenses/gpl-2.0.html, or the GNU Lesser General Public License Version 2.1 or later (the "LGPL") - http://www.gnu.org/licenses/lgpl-2.1.html, in which case the provisions of the GPL or the LGPL are applicable instead of those above. If you wish to allow use of your version of this file only under the terms of either the GPL or the LGPL, and not to allow others to use your version of this file under the terms of the MPL, indicate your decision by deleting the provisions above and replace them with the notice and other provisions required by the GPL or the LGPL. If you do not delete the provisions above, a recipient may use your version of this file under the terms of any one of the MPL, the GPL or the LGPL. Sponsors: The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone). */ package org.isatools.isatab.commandline; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Options; import org.apache.log4j.Logger; import org.isatools.isatab.ISATABUnloader; import uk.ac.ebi.bioinvindex.dao.ejb3.DaoFactory; import uk.ac.ebi.bioinvindex.utils.i18n; import javax.persistence.EntityManager; import javax.persistence.EntityManagerFactory; import javax.persistence.Persistence; import java.io.PrintWriter; import java.util.Properties; import java.util.Set; import static java.lang.System.out; /** * Performs the unloading of ISATAB studies from the BII database * <p/> * date: Jun 6, 2008 * * @author brandizi */ public class UnloadShellCommand extends AbstractImportLayerShellCommand { public static void main(String[] args) { try { Options clopts = createCommonOptions(); CommandLine cmdl = AbstractImportLayerShellCommand.parseCommandLine(clopts, args, UnloadShellCommand.class); args = cmdl.getArgs(); if (args == null || args.length == 0) { printUsage(clopts); System.exit(1); } setup(args); setupLog4JPath(cmdl, null); // Need to initialize this here, otherwise above config will fail log = Logger.getLogger(UnloadShellCommand.class); Properties hibProps = AbstractImportLayerShellCommand.getHibernateProperties(); hibProps.setProperty("hibernate.search.indexing_strategy", "event"); hibProps.setProperty("hibernate.hbm2ddl.auto", "update"); hibProps.setProperty("hbm2ddl.drop", "false"); EntityManagerFactory entityManagerFactory = Persistence.createEntityManagerFactory("BIIEntityManager", hibProps); EntityManager entityManager = entityManagerFactory.createEntityManager(); ISATABUnloader unloader = null; for (String studyAcc : args) { unloader = new ISATABUnloader(DaoFactory.getInstance(entityManager), studyAcc); log.info("\n\n " + i18n.msg("unloader_unloading_study", studyAcc)); unloader.unload(); Set<String> messages = unloader.getMessages(); log.info("\n\n Unloading of " + studyAcc + ", messages: "); for (String message : messages) { log.info(message); } log.info("\n\n"); } log.info("\n"); System.exit(0); } catch (Exception ex) { String msg = "ERROR: problem while running the ISATAB unloader: " + ex.getMessage(); if (log == null) { out.println(msg + "\n"); ex.printStackTrace(); } else { log.fatal(msg, ex); } System.exit(1); } } public static void printUsage(Options opts) { out.println(); HelpFormatter helpFormatter = new HelpFormatter(); PrintWriter pw = new PrintWriter(out, true); helpFormatter.printHelp(pw, 80, "unload [options] <study-acc> ...", "\nUnloads from the BII database an ISA-TAB study which was previously submitted.\n\nOptions:", opts, 2, 4, "\n", false); printUsageCommonNotes(); out.println("PLEASE NOTE: "); out.println( " the unloading feature has been designed mainly having in mind the use case where a submission with"); out.println( " problems is unloaded from the database just after it has been uploaded. In other cases, entities which have"); out.println( " been reused with later submissions won't be removed. For instance, if an ontology term is reused in a study different"); out.println(" than the one being removed, that term is kept in the database."); out.println(); } }