/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* MISO is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.sqlstore;
import net.sf.ehcache.Cache;
import net.sf.ehcache.CacheManager;
import net.sf.ehcache.Element;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import uk.ac.bbsrc.tgac.miso.core.data.type.QcType;
import uk.ac.bbsrc.tgac.miso.core.store.SampleQcStore;
import uk.ac.bbsrc.tgac.miso.core.store.SampleStore;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.core.RowMapper;
import org.springframework.jdbc.core.namedparam.MapSqlParameterSource;
import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
import org.springframework.jdbc.core.simple.SimpleJdbcInsert;
import org.springframework.transaction.annotation.Transactional;
import uk.ac.bbsrc.tgac.miso.core.data.AbstractSampleQC;
import uk.ac.bbsrc.tgac.miso.core.data.Sample;
import uk.ac.bbsrc.tgac.miso.core.data.SampleQC;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedSampleException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory;
import uk.ac.bbsrc.tgac.miso.sqlstore.cache.CacheAwareRowMapper;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
import javax.persistence.CascadeType;
import java.io.IOException;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
/**
* uk.ac.bbsrc.tgac.miso.sqlstore
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
public class SQLSampleQCDAO implements SampleQcStore {
private static final String TABLE_NAME = "SampleQC";
public static final String SAMPLE_QC =
"SELECT qcId, sample_sampleId, qcUserName, qcDate, qcMethod, results " +
"FROM "+TABLE_NAME;
public static final String SAMPLE_QC_SELECT_BY_ID =
SAMPLE_QC + " WHERE qcId=?";
public static final String SAMPLE_QC_SELECT_BY_SAMPLE_ID =
SAMPLE_QC + " WHERE sample_sampleId=? " +
"ORDER BY qcDate ASC";
public static final String SAMPLE_QC_UPDATE =
"UPDATE "+TABLE_NAME+" " +
"SET sample_sampleId=:sample_sampleId, qcUserName=:qcUserName, qcDate=:qcDate, qcMethod=:qcMethod, results=:results " +
"WHERE qcId=:qcId";
public static final String SAMPLE_QC_TYPE_SELECT =
"SELECT qcTypeId, name, description, qcTarget, units " +
"FROM QCType WHERE qcTarget = 'Sample'";
public static final String SAMPLE_QC_TYPE_SELECT_BY_ID =
SAMPLE_QC_TYPE_SELECT + " AND qcTypeId = ?";
public static final String SAMPLE_QC_TYPE_SELECT_BY_NAME =
SAMPLE_QC_TYPE_SELECT + " AND name = ?";
public static final String SAMPLE_QC_DELETE =
"DELETE FROM "+TABLE_NAME+" WHERE qcId=:qcId";
protected static final Logger log = LoggerFactory.getLogger(SQLSampleQCDAO.class);
private JdbcTemplate template;
private SampleStore sampleDAO;
private CascadeType cascadeType;
@Autowired
private CacheManager cacheManager;
public void setCacheManager(CacheManager cacheManager) {
this.cacheManager = cacheManager;
}
@Autowired
private DataObjectFactory dataObjectFactory;
public void setDataObjectFactory(DataObjectFactory dataObjectFactory) {
this.dataObjectFactory = dataObjectFactory;
}
public void setSampleDAO(SampleStore sampleDAO) {
this.sampleDAO = sampleDAO;
}
public JdbcTemplate getJdbcTemplate() {
return template;
}
public void setJdbcTemplate(JdbcTemplate template) {
this.template = template;
}
public void setCascadeType(CascadeType cascadeType) {
this.cascadeType = cascadeType;
}
@Transactional(readOnly = false, rollbackFor = IOException.class)
public long save(SampleQC sampleQC) throws IOException {
MapSqlParameterSource params = new MapSqlParameterSource();
params.addValue("sample_sampleId", sampleQC.getSample().getId())
.addValue("qcUserName", sampleQC.getQcCreator())
.addValue("qcDate", sampleQC.getQcDate())
.addValue("qcMethod", sampleQC.getQcType().getQcTypeId())
.addValue("results", sampleQC.getResults());
if (sampleQC.getId() == AbstractSampleQC.UNSAVED_ID) {
SimpleJdbcInsert insert = new SimpleJdbcInsert(template)
.withTableName(TABLE_NAME)
.usingGeneratedKeyColumns("qcId");
Number newId = insert.executeAndReturnKey(params);
sampleQC.setId(newId.longValue());
}
else {
params.addValue("qcId", sampleQC.getId());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(SAMPLE_QC_UPDATE, params);
}
if (this.cascadeType != null) {
Sample s = sampleQC.getSample();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (s!=null) sampleDAO.save(s);
}
else if (this.cascadeType.equals(CascadeType.REMOVE)) {
if (s != null) {
//Cache pc = cacheManager.getCache("sampleCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(s.getId()));
DbUtils.updateCaches(cacheManager, s, Sample.class);
}
}
else if (this.cascadeType.equals(CascadeType.ALL)) {
if (s!=null) {
sampleDAO.save(s);
//Cache pc = cacheManager.getCache("sampleCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(s.getId()));
DbUtils.updateCaches(cacheManager, s, Sample.class);
}
}
}
return sampleQC.getId();
}
public SampleQC get(long qcId) throws IOException {
List eResults = template.query(SAMPLE_QC_SELECT_BY_ID, new Object[]{qcId}, new SampleQcMapper());
SampleQC e = eResults.size() > 0 ? (SampleQC) eResults.get(0) : null;
return e;
}
public SampleQC lazyGet(long qcId) throws IOException {
List eResults = template.query(SAMPLE_QC_SELECT_BY_ID, new Object[]{qcId}, new SampleQcMapper(true));
SampleQC e = eResults.size() > 0 ? (SampleQC) eResults.get(0) : null;
return e;
}
public Collection<SampleQC> listBySampleId(long sampleId) throws IOException {
return new LinkedList(template.query(SAMPLE_QC_SELECT_BY_SAMPLE_ID, new Object[]{sampleId}, new SampleQcMapper(true)));
}
public Collection<SampleQC> listAll() throws IOException {
return template.query(SAMPLE_QC, new SampleQcMapper(true));
}
@Override
public int count() throws IOException {
return template.queryForInt("SELECT count(*) FROM "+TABLE_NAME);
}
public boolean remove(SampleQC qc) throws IOException {
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
if (qc.isDeletable() &&
(namedTemplate.update(SAMPLE_QC_DELETE,
new MapSqlParameterSource().addValue("qcId", qc.getId())) == 1)) {
Sample s = qc.getSample();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (s!=null) sampleDAO.save(s);
}
else if (this.cascadeType.equals(CascadeType.REMOVE)) {
if (s != null) {
//Cache pc = cacheManager.getCache("sampleCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(s.getId()));
DbUtils.updateCaches(cacheManager, s, Sample.class);
}
}
return true;
}
return false;
}
public class SampleQcMapper extends CacheAwareRowMapper<SampleQC> {
public SampleQcMapper() {
//sample qcs aren't cached at present
super(SampleQC.class, false, false);
}
public SampleQcMapper(boolean lazy) {
//sample qcs aren't cached at present
super(SampleQC.class, lazy, false);
}
public SampleQC mapRow(ResultSet rs, int rowNum) throws SQLException {
long id = rs.getLong("qcId");
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
Element element;
if ((element = lookupCache(cacheManager).get(DbUtils.hashCodeCacheKeyFor(id))) != null) {
log.debug("Cache hit on map for SampleQC " + id);
return (SampleQC)element.getObjectValue();
}
}
SampleQC s = dataObjectFactory.getSampleQC();
s.setId(id);
s.setQcCreator(rs.getString("qcUserName"));
s.setQcDate(rs.getDate("qcDate"));
s.setResults(rs.getDouble("results"));
try {
s.setQcType(getSampleQcTypeById(rs.getLong("qcMethod")));
if (!isLazy()) {
s.setSample(sampleDAO.get(rs.getLong("sample_sampleId")));
}
}
catch (IOException e) {
e.printStackTrace();
}
catch (MalformedSampleException e) {
e.printStackTrace();
}
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
lookupCache(cacheManager).put(new Element(DbUtils.hashCodeCacheKeyFor(id) ,s));
}
return s;
}
}
public Collection<QcType> listAllSampleQcTypes() throws IOException {
return template.query(SAMPLE_QC_TYPE_SELECT, new SampleQcTypeMapper());
}
public QcType getSampleQcTypeById(long qcTypeId) throws IOException {
List eResults = template.query(SAMPLE_QC_TYPE_SELECT_BY_ID, new Object[]{qcTypeId}, new SampleQcTypeMapper());
QcType e = eResults.size() > 0 ? (QcType) eResults.get(0) : null;
return e;
}
public QcType getSampleQcTypeByName(String qcName) throws IOException {
List eResults = template.query(SAMPLE_QC_TYPE_SELECT_BY_NAME, new Object[]{qcName}, new SampleQcTypeMapper());
QcType e = eResults.size() > 0 ? (QcType) eResults.get(0) : null;
return e;
}
public class SampleQcTypeMapper implements RowMapper<QcType> {
public QcType mapRow(ResultSet rs, int rowNum) throws SQLException {
QcType qt = new QcType();
qt.setQcTypeId(rs.getLong("qcTypeId"));
qt.setName(rs.getString("name"));
qt.setDescription(rs.getString("description"));
qt.setUnits(rs.getString("units"));
return qt;
}
}
}