com.epam.catgenome.dao.gene.GeneFileDao.java Source code

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Here is the source code for com.epam.catgenome.dao.gene.GeneFileDao.java

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/*
 * MIT License
 *
 * Copyright (c) 2016 EPAM Systems
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

package com.epam.catgenome.dao.gene;

import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;

import org.apache.commons.collections4.CollectionUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.jdbc.core.namedparam.NamedParameterJdbcDaoSupport;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;

import com.epam.catgenome.dao.BiologicalDataItemDao;
import com.epam.catgenome.dao.DaoHelper;
import com.epam.catgenome.entity.BiologicalDataItem;
import com.epam.catgenome.entity.gene.GeneFile;

/**
 * Source:      GeneFileDao
 * Created:     04.12.15, 18:52
 * Project:     CATGenome Browser
 * Make:        IntelliJ IDEA 14.1.4, JDK 1.8
 *
 * <p>
 * A DAO class for managing {@code GeneFile} entities in the database.
 * </p>
 *
 * @author Mikhail Miroliubov
 */
public class GeneFileDao extends NamedParameterJdbcDaoSupport {
    @Autowired
    private DaoHelper daoHelper;

    private String geneFileSequenceName;

    // New queries
    private String createGeneFileQuery;
    private String loadGeneFileQuery;
    private String loadGeneFilesQuery;
    private String loadGeneFilesByReferenceIdQuery;
    private String deleteGeneFileQuery;

    /**
     * Persists {@code GeneFile} record to the database
     * @param geneFile a {@code GeneFile} instance to be persisted
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public void createGeneFile(GeneFile geneFile, final Long realId) {
        geneFile.setBioDataItemId(geneFile.getId());
        geneFile.setId(realId);

        getNamedParameterJdbcTemplate().update(createGeneFileQuery, BiologicalDataItemDao.FeatureFileParameters
                .getLinkedTableParameters(GeneParameters.GENE_ITEM_ID.name(), geneFile));
    }

    /**
     * Persists {@code GeneFile} record to the database
     * @param geneFile a {@code GeneFile} instance to be persisted
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public void createGeneFile(GeneFile geneFile) {
        getNamedParameterJdbcTemplate().update(createGeneFileQuery, BiologicalDataItemDao.FeatureFileParameters
                .getLinkedTableParameters(GeneParameters.GENE_ITEM_ID.name(), geneFile));
    }

    /**
     * Loads a persisted {@code GeneFile} record by it's ID
     * @param id {@code long} a GeneFile ID
     * @return {@code GeneFile} instance
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public GeneFile loadGeneFile(long id) {
        List<BiologicalDataItem> files = getJdbcTemplate().query(loadGeneFileQuery,
                BiologicalDataItemDao.BiologicalDataItemParameters.getRowMapper(), id);

        return !files.isEmpty() ? (GeneFile) files.get(0) : null;
    }

    @Transactional(propagation = Propagation.MANDATORY)
    public List<GeneFile> loadGeneFiles(Collection<Long> ids) {
        if (CollectionUtils.isEmpty(ids)) {
            return Collections.emptyList();
        }

        long listId = daoHelper.createTempLongList(ids);
        List<BiologicalDataItem> files = getJdbcTemplate().query(loadGeneFilesQuery,
                BiologicalDataItemDao.BiologicalDataItemParameters.getRowMapper(), listId);

        daoHelper.clearTempList(listId);
        return files.stream().map(f -> (GeneFile) f).collect(Collectors.toList());
    }

    /**
     * Loads {@code GeneFile} records, saved for a specific reference ID
     * @param referenceId {@code long} a reference ID in the system
     * @return {@code List&lt;GeneFile&gt;} instance
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public List<GeneFile> loadGeneFilesByReferenceId(long referenceId) {
        return getJdbcTemplate()
                .query(loadGeneFilesByReferenceIdQuery,
                        BiologicalDataItemDao.BiologicalDataItemParameters.getRowMapper(), referenceId)
                .stream().map(f -> (GeneFile) f).collect(Collectors.toList());
    }

    /**
     * Deletes {@code GeneFile} record from the database
     *
     * @param geneFileId ID of a {@code GeneFile} record to delete
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public void deleteGeneFile(final long geneFileId) {
        getJdbcTemplate().update(deleteGeneFileQuery, geneFileId);
    }

    /**
     * Creates a new ID for a {@code GeneFile} instance
     * @return {@code Long} new {@code GeneFile} ID
     */
    @Transactional(propagation = Propagation.MANDATORY)
    public Long createGeneFileId() {
        return daoHelper.createId(geneFileSequenceName);
    }

    @Required
    public void setGeneFileSequenceName(String geneFileSequenceName) {
        this.geneFileSequenceName = geneFileSequenceName;
    }

    @Required
    public void setCreateGeneFileQuery(String createGeneFileQuery) {
        this.createGeneFileQuery = createGeneFileQuery;
    }

    @Required
    public void setLoadGeneFileQuery(String loadGeneFileQuery) {
        this.loadGeneFileQuery = loadGeneFileQuery;
    }

    @Required
    public void setLoadGeneFilesByReferenceIdQuery(String loadGeneFilesByReferenceIdQuery) {
        this.loadGeneFilesByReferenceIdQuery = loadGeneFilesByReferenceIdQuery;
    }

    @Required
    public void setDeleteGeneFileQuery(String deleteGeneFileQuery) {
        this.deleteGeneFileQuery = deleteGeneFileQuery;
    }

    @Required
    public void setLoadGeneFilesQuery(String loadGeneFilesQuery) {
        this.loadGeneFilesQuery = loadGeneFilesQuery;
    }

    enum GeneParameters {
        GENE_ITEM_ID, REFERENCE_GENOME_ID, ORIGINAL_NAME, CREATED_BY, CREATED_DATE, FILE_PATH, INDEX_PATH, BOUNDS_PATH, COMPRESSED, ONLINE, EXTERNAL_DB_TYPE_ID, EXTERNAL_DB_ID, EXTERNAL_DB_ORGANISM
    }
}