net.sourceforge.metware.binche.loader.OfficialChEBIOboLoader.java Source code

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Here is the source code for net.sourceforge.metware.binche.loader.OfficialChEBIOboLoader.java

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/**
 * OfficialChEBIOboLoader.java
 *
 * 2013.02.11
 *
 * This file is part of the CheMet library
 * 
 * The CheMet library is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * CheMet is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with CheMet.  If not, see <http://www.gnu.org/licenses/>.
 */

package net.sourceforge.metware.binche.loader;

import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.prefs.BackingStoreException;
import java.util.prefs.Preferences;
import net.sourceforge.metware.binche.BiNChe;
import net.sourceforge.metware.binche.execs.PreProcessOboFile;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;

/**
 * This class downloads and processes the ChEBI OBO file, to maximize its utility for the enrichment analysis. The
 * main processing class is {@link PreProcessOboFile}, which calls the reasoner to infer to assertions.
 *
 * @name    OfficialChEBIOboLoader
 * @date    2013.02.11
 * @author  Pablo Moreno
 * @brief   Handles the download and processing of the official ChEBI ontology OBO file.
 */
public class OfficialChEBIOboLoader {

    private static final Logger LOGGER = Logger.getLogger(OfficialChEBIOboLoader.class);

    private final String oboURL = "ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo";

    /**
     * The constructor loads the OBO file from the ChEBI ftp and executes the reasoning steps.
     *
     * @throws IOException
     * @throws BackingStoreException
     */
    public OfficialChEBIOboLoader() throws IOException, BackingStoreException {
        Preferences binchePrefs = Preferences.userNodeForPackage(BiNChe.class);

        if (binchePrefs.keys().length == 0) {
            binchePrefs = (new DefaultPreferenceSetter()).getDefaultSetPrefs();
        }

        PreProcessOboFile ppof = new PreProcessOboFile();
        File tmpFileObo = File.createTempFile("BiNChE", ".obo");
        FileUtils.copyURLToFile(new URL(oboURL), tmpFileObo);
        ppof.getTransitiveClosure(tmpFileObo.getAbsolutePath(),
                binchePrefs.get(BiNChEOntologyPrefs.RoleOntology.name(), null), false, true,
                BiNChEOntologyPrefs.RoleOntology.getRootChEBIEntries(), Arrays.asList("rdfs:label"),
                new ArrayList<String>());
        File tmpRoleOnt = new File(binchePrefs.get(BiNChEOntologyPrefs.RoleOntology.name(), null) + ".temp");
        tmpRoleOnt.delete();

        ppof.getTransitiveClosure(tmpFileObo.getAbsolutePath(),
                binchePrefs.get(BiNChEOntologyPrefs.StructureOntology.name(), null), false, false,
                BiNChEOntologyPrefs.StructureOntology.getRootChEBIEntries(), Arrays.asList("rdfs:label", "InChI"),
                new ArrayList<String>());
        File tmpStructOnt = new File(binchePrefs.get(BiNChEOntologyPrefs.StructureOntology.name(), null) + ".temp");
        tmpStructOnt.delete();

        ppof.getTransitiveClosure(tmpFileObo.getAbsolutePath(),
                binchePrefs.get(BiNChEOntologyPrefs.RoleAndStructOntology.name(), null), true, true,
                BiNChEOntologyPrefs.RoleAndStructOntology.getRootChEBIEntries(),
                Arrays.asList("rdfs:label", "InChI"), Arrays.asList("http://purl.obolibrary.org/obo/RO_0000087"));
        File tmpStructRoleOnt = new File(
                binchePrefs.get(BiNChEOntologyPrefs.RoleAndStructOntology.name(), null) + ".temp");
        tmpStructRoleOnt.delete();
        File structRoleAnnot = new File(
                binchePrefs.get(BiNChEOntologyPrefs.RoleAndStructOntology.name(), null).replace(".obo", ".txt"));
        String fullPath = binchePrefs.get(BiNChEOntologyPrefs.RoleAndStructOntology.name(), null);
        structRoleAnnot.renameTo(new File(
                fullPath.substring(0, fullPath.lastIndexOf(File.separator)) + File.separator + "chebi_roles.anno"));

        tmpFileObo.delete();
    }

    /**
     * Main method to run the obo file download and process.
     *
     * @param args
     * @throws BackingStoreException
     * @throws IOException
     */
    public static void main(String[] args) throws BackingStoreException, IOException {
        new OfficialChEBIOboLoader();
    }

}