uk.ac.ebi.bioinvindex.persistence.OntologyEntryPersister.java Source code

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Here is the source code for uk.ac.ebi.bioinvindex.persistence.OntologyEntryPersister.java

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package uk.ac.ebi.bioinvindex.persistence;

/*
 * __________
 * 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:
 * __________
 *
 * This work is licenced under the Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License. To view a copy of this licence, visit http://creativecommons.org/licenses/by-sa/2.0/uk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California 94105, USA.
 *
 * __________
 * 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.
 */

import java.sql.Timestamp;

import javax.persistence.PersistenceException;

import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.bioinvindex.dao.OntologyEntryDAO;
import uk.ac.ebi.bioinvindex.dao.ejb3.DaoFactory;
import uk.ac.ebi.bioinvindex.model.term.OntologyEntry;
import uk.ac.ebi.bioinvindex.model.xref.ReferenceSource;

/**
 * Persists an {@link OntologyEntry}. This class is abstract in order to make {@link #getPersistedClass()} correctly working.
 * 
 * You can do something like: 
 *   <p><code>oePersister = new OntologyEntryPersister<OntologyTerm> ( daoFactory ) {};</code></p>
 * in order to use this persister directly.<p> 
 * 
 * date: Apr 15, 2008
 * @author brandizi
 *
 * @param <OE>
 */
public abstract class OntologyEntryPersister<OE extends OntologyEntry> extends AnnotatablePersister<OE> {
    private final ReferenceSourcePersister sourcePersister;

    public OntologyEntryPersister(DaoFactory daoFactory, Timestamp submissionTs) {
        super(daoFactory, submissionTs);
        dao = daoFactory.getOntologyEntryDAO(getPersistedClass());
        sourcePersister = new ReferenceSourcePersister(daoFactory, submissionTs);
    }

    /**
     * If the OE doesn't already exist, forward the source to the source persister (set the existing source in case it already
     * exists), and then saves the OE. Does not fix the accession (as done by {@link AccessiblePersister#preProcess(uk.ac.ebi.bioinvindex.model.impl.Accessible)}),  
     * since the accession must be always provided. 
     *  
     */
    @Override
    public void preProcess(OE oe) {
        super.preProcess(oe);

        if (StringUtils.trimToNull(oe.getAcc()) == null)
            throw new BIIPersistenceException(
                    "We never auto-generate the accession for Ontology Entries, term is:" + oe);

        // First check your source and save it if doesn't exist
        ReferenceSource source = oe.getSource();
        ReferenceSource sourceDB = sourcePersister.persist(source);
        if (sourceDB != source)
            oe.setSource(sourceDB);
    }

    /** Not supported, you MUST always provide an accession */
    protected String getAccessionPrefix() {
        throw new BIIPersistenceException("We never auto-generate the accession for Ontology Entries");
    }

    /**
     * Searches by accession and source's accession. 
     * 
     */
    @SuppressWarnings("unchecked")
    @Override
    protected OE lookup(OE object) {
        String acc = StringUtils.trimToNull(object.getAcc());

        if (acc == null || acc.contains("NULL-ACCESSION"))
            // Assume it's a new term
            return null;

        ReferenceSource source = object.getSource();

        if (source == null) {
            throw new PersistenceException("Source is null for term " + object + "!!!");
        }

        return ((OntologyEntryDAO<OE>) dao).getOntologyEntryByAccAndRefSource(acc, object.getSource().getAcc());
    }

    @Override
    protected String getCacheKey(OE object) {
        return object.getAcc() + object.getName() + object.getClass().getName() + object.getSource().getName();
    }

}