org.isatools.isatab_v1.DublinTestSet.java Source code

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Here is the source code for org.isatools.isatab_v1.DublinTestSet.java

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/*
 * __________
 * CREDITS
 * __________
 *
 * Team page: http://isatab.sf.net/
 * - Marco Brandizi (software engineer: ISAvalidator, ISAconverter, BII data management utility, BII model)
 * - Eamonn Maguire (software engineer: ISAcreator, ISAcreator configurator, ISAvalidator, ISAconverter,  BII data management utility, BII web)
 * - Nataliya Sklyar (software engineer: BII web application, BII model,  BII data management utility)
 * - Philippe Rocca-Serra (technical coordinator: user requirements and standards compliance for ISA software, ISA-tab format specification, BII model, ISAcreator wizard, ontology)
 * - Susanna-Assunta Sansone (coordinator: ISA infrastructure design, standards compliance, ISA-tab format specification, BII model, funds raising)
 *
 * Contributors:
 * - Manon Delahaye (ISA team trainee: BII web services)
 * - Richard Evans (ISA team trainee: rISAtab)
 *
 *
 * ______________________
 * Contacts and Feedback:
 * ______________________
 *
 * Project overview: http://isatab.sourceforge.net/
 *
 * To follow general discussion: isatab-devel@list.sourceforge.net
 * To contact the developers: isatools@googlegroups.com
 *
 * To report bugs: http://sourceforge.net/tracker/?group_id=215183&atid=1032649
 * To request enhancements: http://sourceforge.net/tracker/?group_id=215183&atid=1032652
 *
 *
 * __________
 * License:
 * __________
 *
 * Reciprocal Public License 1.5 (RPL1.5)
 * [OSI Approved License]
 *
 * Reciprocal Public License (RPL)
 * Version 1.5, July 15, 2007
 * Copyright (C) 2001-2007
 * Technical Pursuit Inc.,
 * All Rights Reserved.
 *
 * http://www.opensource.org/licenses/rpl1.5.txt
 *
 * __________
 * Sponsors
 * __________
 * This work has been funded mainly by the EU Carcinogenomics (http://www.carcinogenomics.eu) [PL 037712] and in part by the
 * EU NuGO [NoE 503630](http://www.nugo.org/everyone) projects and in part by EMBL-EBI.
 */

package org.isatools.isatab_v1;

import org.apache.commons.io.FileUtils;
import org.dbunit.operation.DatabaseOperation;
import org.isatools.isatab.ISATABPersister;
import org.isatools.isatab_v1.mapping.ISATABMapper;
import org.isatools.tablib.schema.FormatSetInstance;
import org.isatools.tablib.utils.BIIObjectStore;
import org.junit.Test;
import uk.ac.ebi.bioinvindex.dao.ejb3.DaoFactory;
import uk.ac.ebi.bioinvindex.model.Study;
import uk.ac.ebi.bioinvindex.utils.datasourceload.DataLocationManager;
import uk.ac.ebi.bioinvindex.utils.test.TransactionalDBUnitEJB3DAOTest;

import java.io.File;
import java.io.IOException;
import java.sql.Timestamp;

import static java.lang.System.out;
import static org.junit.Assert.assertTrue;

public class DublinTestSet extends TransactionalDBUnitEJB3DAOTest {

    public DublinTestSet() throws Exception {
        super();
    }

    protected void prepareSettings() {
        //beforeTestOperations.clear ();
        beforeTestOperations.add(DatabaseOperation.CLEAN_INSERT);
        dataSetLocation = "test-data/isatab/db_datasets/empty.xml";
    }

    @SuppressWarnings("static-access")
    @Test
    public void testPersistence() throws Exception {

        out.println("\n\n_______________________ Dublin Test Set Persistence _______________________\n\n");

        persist("/target/test-classes/test-data/isatab/isatab_v1_200810/iconix_20081107red");
        persist("/target/test-classes/test-data/isatab/isatab_creator_200811/griffin-gauguier");
        persist("/target/test-classes/test-data/isatab/isatab_creator_200811/gg_proteomics");

        out.println("\n\n___________________ /end: Dublin Test Set Persistence ___________________\n\n");
    }

    @SuppressWarnings("static-access")
    private void persist(String path) throws IOException {
        out.println("\n\n_________ Loading and mapping: " + path + " _______\n\n");

        String baseDir = System.getProperty("basedir");
        String filesPath = baseDir + path;
        ISATABLoader loader = new ISATABLoader(filesPath);

        FormatSetInstance isatabInstance = loader.load();

        out.println("\n\n_____ Loaded, now mapping");
        BIIObjectStore store = new BIIObjectStore();
        ISATABMapper isatabMapper = new ISATABMapper(store, isatabInstance);

        isatabMapper.map();
        assertTrue("Oh no! No mapped object! ", store.size() > 0);

        out.println("\n_____________ Persisting");

        // Test the repository too
        String repoPath = baseDir + "/target/bii_test_repo/meta_data";
        File repoDir = new File(repoPath);
        if (!repoDir.exists()) {
            FileUtils.forceMkdir(repoDir);
        }

        if (!transaction.isActive()) {
            transaction.begin();
        }
        ISATABPersister persister = new ISATABPersister(store, DaoFactory.getInstance(entityManager));
        Timestamp ts = persister.persist(filesPath);
        transaction.commit();

        for (Study study : store.valuesOfType(Study.class)) {
            assertTrue("Oh no! Submission didn't go to the repository!",
                    new File(repoPath + "/" + DataLocationManager.getObfuscatedStudyFileName(study)).exists());
        }

        out.println("\n\n\n\n_______________ Done, Submission TS: " + ts.getTime() + " (" + ts + " + "
                + ts.getNanos() + "ns)");
    }

}