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

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

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

import com.mysema.query.jpa.impl.JPAQuery;
import com.mysema.query.types.Projections;
import java.util.ArrayList;
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.EnzymePortalPathways;
import uk.ac.ebi.ep.data.domain.QEnzymePortalPathways;
import uk.ac.ebi.ep.data.enzyme.model.Pathway;

/**
 *
 * @author joseph
 */
public class EnzymePortalPathwaysRepositoryImpl implements EnzymePortalPathwaysRepositoryCustom {

    @PersistenceContext
    private EntityManager entityManager;
    private static final QEnzymePortalPathways $ = QEnzymePortalPathways.enzymePortalPathways;

    @Transactional(readOnly = true)
    // @Override
    public List<Pathway> findPathwaysByAccession(String accession) {

        JPAQuery query = new JPAQuery(entityManager);

        List<Pathway> pathways = query.from($).where($.uniprotAccession.accession.equalsIgnoreCase(accession))
                .list(Projections.constructor(Pathway.class, $.pathwayId, $.pathwayName));

        return pathways;
    }

    @Transactional(readOnly = true)
    @Override
    public List<String> findAccessionsByPathwayId(String pathwayId) {

        List<String> enzymes = new ArrayList<>();
        JPAQuery query = new JPAQuery(entityManager);

        List<EnzymePortalPathways> entries = query.from($).where($.pathwayId.equalsIgnoreCase(pathwayId)).distinct()
                .list($).stream().distinct().collect(Collectors.toList());

        entries.stream().forEach(e -> {
            enzymes.add(e.getUniprotAccession().getAccession());
        });

        return enzymes;

    }

    @Transactional(readOnly = true)
    @Override
    public List<Pathway> findPathwaysByName(String name) {
        JPAQuery query = new JPAQuery(entityManager);

        String pathwayName = String.format("%%%s%%", name).toLowerCase();
        List<Pathway> entries = query.from($).where($.pathwayName.toLowerCase().like(pathwayName))
                .list(Projections.constructor(Pathway.class, $.pathwayId, $.pathwayName));

        return entries.stream().distinct().collect(Collectors.toList());

    }
}