ubic.gemma.persistence.persister.RelationshipPersister.java Source code

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Here is the source code for ubic.gemma.persistence.persister.RelationshipPersister.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2006 University of British Columbia
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
package ubic.gemma.persistence.persister;

import org.apache.commons.lang3.reflect.FieldUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import ubic.gemma.model.analysis.expression.ExpressionExperimentSet;
import ubic.gemma.model.analysis.expression.coexpression.CoexpressionAnalysis;
import ubic.gemma.model.association.Gene2GOAssociation;
import ubic.gemma.model.association.Gene2GeneProteinAssociation;
import ubic.gemma.model.association.TfGeneAssociation;
import ubic.gemma.model.expression.experiment.BioAssaySet;
import ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDao;
import ubic.gemma.persistence.service.analysis.expression.coexpression.CoexpressionAnalysisDao;
import ubic.gemma.persistence.service.association.Gene2GOAssociationDao;
import ubic.gemma.persistence.service.association.Gene2GeneProteinAssociationDao;
import ubic.gemma.persistence.service.association.TfGeneAssociationDao;

import java.util.Collection;
import java.util.HashSet;

/**
 * Persist objects like Gene2GOAssociation.
 *
 * @author pavlidis
 */
public abstract class RelationshipPersister extends ExpressionPersister {

    @Autowired
    private Gene2GOAssociationDao gene2GoAssociationDao;

    @Autowired
    private CoexpressionAnalysisDao coexpressionAnalysisDao;

    @Autowired
    private TfGeneAssociationDao tfGeneAssociationDao;

    @Autowired
    private ExpressionExperimentSetDao expressionExperimentSetDao;

    @Autowired
    private Gene2GeneProteinAssociationDao gene2GeneProteinAssociationDao;

    @Override
    @Transactional
    public Object persist(Object entity) {
        if (entity == null)
            return null;

        if (entity instanceof Gene2GOAssociation) {
            return this.persistGene2GOAssociation((Gene2GOAssociation) entity);
        } else if (entity instanceof CoexpressionAnalysis) {
            return this.persistCoexpressionAnalysis((CoexpressionAnalysis) entity);
        } else if (entity instanceof ExpressionExperimentSet) {
            return this.persistExpressionExperimentSet((ExpressionExperimentSet) entity);
        } else if (entity instanceof Gene2GeneProteinAssociation) {
            return this.persistGene2GeneProteinAssociation((Gene2GeneProteinAssociation) entity);
        } else if (entity instanceof TfGeneAssociation) {
            return this.persistTfGeneAssociation((TfGeneAssociation) entity);
        }
        return super.persist(entity);

    }

    @Override
    @Transactional
    public Object persistOrUpdate(Object entity) {
        if (entity == null)
            return null;
        return super.persistOrUpdate(entity);
    }

    private ExpressionExperimentSet persistExpressionExperimentSet(ExpressionExperimentSet entity) {
        if (!this.isTransient(entity))
            return entity;

        Collection<BioAssaySet> setMembers = new HashSet<>();

        for (BioAssaySet baSet : entity.getExperiments()) {
            if (this.isTransient(baSet)) {
                baSet = (BioAssaySet) this.persist(baSet);
            }
            setMembers.add(baSet);
        }
        entity.getExperiments().clear();
        entity.getExperiments().addAll(setMembers);

        return expressionExperimentSetDao.create(entity);
    }

    private Gene2GOAssociation persistGene2GOAssociation(Gene2GOAssociation association) {
        if (association == null)
            return null;
        if (!this.isTransient(association))
            return association;
        try {
            FieldUtils.writeField(association, "gene", this.persistGene(association.getGene()), true);
        } catch (IllegalAccessException e) {
            e.printStackTrace();
        }
        return gene2GoAssociationDao.create(association);
    }

    private TfGeneAssociation persistTfGeneAssociation(TfGeneAssociation entity) {
        if (entity == null)
            return null;
        if (!this.isTransient(entity))
            return entity;

        if (this.isTransient(entity.getFirstGene()) || this.isTransient(entity.getSecondGene())) {
            throw new IllegalArgumentException(
                    "Associations can only be made between genes that already exist in the system");
        }

        return tfGeneAssociationDao.create(entity);

    }

    private CoexpressionAnalysis persistCoexpressionAnalysis(CoexpressionAnalysis entity) {
        if (entity == null)
            return null;
        if (!this.isTransient(entity))
            return entity;
        entity.setProtocol(this.persistProtocol(entity.getProtocol()));
        if (this.isTransient(entity.getExperimentAnalyzed())) {
            throw new IllegalArgumentException("Persist the experiment before running analyses on it");
        }

        return coexpressionAnalysisDao.create(entity);
    }

    /**
     * The persisting method for Gene2GeneProteinAssociation which validates the the Gene2GeneProteinAssociation does
     * not already exist in the system. If it does then the persisted object is returned
     *
     * @param gene2GeneProteinAssociation the object to persist
     * @return the persisted object
     */
    private Gene2GeneProteinAssociation persistGene2GeneProteinAssociation(
            Gene2GeneProteinAssociation gene2GeneProteinAssociation) {
        if (gene2GeneProteinAssociation == null)
            return null;
        if (!this.isTransient(gene2GeneProteinAssociation))
            return gene2GeneProteinAssociation;

        // Deletes any old existing one.
        return gene2GeneProteinAssociationDao.create(gene2GeneProteinAssociation);
    }

}