uk.ac.ebi.ep.data.repositories.UniprotXrefRepositoryImpl.java Source code

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Here is the source code for uk.ac.ebi.ep.data.repositories.UniprotXrefRepositoryImpl.java

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package uk.ac.ebi.ep.data.repositories;

import com.mysema.query.jpa.impl.JPAQuery;
import com.mysema.query.types.expr.BooleanExpression;
import java.util.List;
import java.util.stream.Collectors;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import org.springframework.transaction.annotation.Transactional;
import uk.ac.ebi.ep.data.domain.QUniprotXref;
import uk.ac.ebi.ep.data.domain.UniprotXref;

/**
 *
 * @author joseph
 */
public class UniprotXrefRepositoryImpl implements UniprotXrefRepositoryCustom {

    @PersistenceContext
    private EntityManager entityManager;
    private static final QUniprotXref $ = QUniprotXref.uniprotXref;
    private static final String PDB = "PDB";

    @Override
    public List<UniprotXref> findPDBcodesByAccession(String accession) {
        JPAQuery query = new JPAQuery(entityManager);

        BooleanExpression isAccession = $.accession.accession.equalsIgnoreCase(accession);
        List<UniprotXref> pdb = query.from($).where($.source.equalsIgnoreCase(PDB)
                .and($.sourceName.isNotNull().or($.sourceName.isNotEmpty())).and(isAccession)).list($);

        return pdb.stream().distinct().collect(Collectors.toList());
    }

    @Transactional(readOnly = true)
    @Override
    public List<String> findPdbCodesWithNoNames() {
        JPAQuery query = new JPAQuery(entityManager);
        List<String> result = query.from($).where($.source.equalsIgnoreCase(PDB)).list($.sourceId);
        return result;
    }

    @Transactional(readOnly = true)
    @Override
    public UniprotXref findPdbById(String pdbId) {
        JPAQuery query = new JPAQuery(entityManager);

        UniprotXref pdb = query.from($)
                .where($.source.equalsIgnoreCase(PDB).and($.sourceId.equalsIgnoreCase(pdbId))).singleResult($);

        return pdb;
    }

    @Override
    public List<UniprotXref> findPDBcodes() {
        JPAQuery query = new JPAQuery(entityManager);
        List<UniprotXref> result = query.from($).where($.source.equalsIgnoreCase(PDB)).list($);
        return result;
    }

}