/*
* 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.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.LibraryQcStore;
import uk.ac.bbsrc.tgac.miso.core.store.LibraryStore;
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.AbstractLibraryQC;
import uk.ac.bbsrc.tgac.miso.core.data.Library;
import uk.ac.bbsrc.tgac.miso.core.data.LibraryQC;
import uk.ac.bbsrc.tgac.miso.core.exception.MalformedLibraryException;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
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.List;
/**
* uk.ac.bbsrc.tgac.miso.sqlstore
* <p/>
* Info
*
* @author Rob Davey
* @since 0.0.2
*/
public class SQLLibraryQCDAO implements LibraryQcStore {
private static final String TABLE_NAME = "LibraryQC";
public static final String LIBRARY_QC =
"SELECT qcId, library_libraryId, qcUserName, qcDate, qcMethod, results, insertSize " +
"FROM "+TABLE_NAME;
public static final String LIBRARY_QC_SELECT_BY_ID =
LIBRARY_QC + " WHERE qcId=?";
public static final String LIBRARY_QC_SELECT_BY_LIBRARY_ID =
LIBRARY_QC + " WHERE library_libraryId=? " +
"ORDER BY qcDate ASC";
public static final String LIBRARY_QC_UPDATE =
"UPDATE "+TABLE_NAME+
" SET library_libraryId=:library_libraryId, qcUserName=:qcUserName, qcDate=:qcDate, qcMethod=:qcMethod, results=:results, insertSize=:insertSize " +
"WHERE qcId=:qcId";
public static final String LIBRARY_QC_TYPE_SELECT =
"SELECT qcTypeId, name, description, qcTarget, units " +
"FROM QCType WHERE qcTarget = 'Library'";
public static final String LIBRARY_QC_TYPE_SELECT_BY_ID =
LIBRARY_QC_TYPE_SELECT + " AND qcTypeId = ?";
public static final String LIBRARY_QC_TYPE_SELECT_BY_NAME =
LIBRARY_QC_TYPE_SELECT + " AND name = ?";
public static final String LIBRARY_QC_DELETE =
"DELETE FROM "+TABLE_NAME+" WHERE qcId=:qcId";
protected static final Logger log = LoggerFactory.getLogger(SQLLibraryQCDAO.class);
private JdbcTemplate template;
private LibraryStore libraryDAO;
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 setLibraryDAO(LibraryStore libraryDAO) {
this.libraryDAO = libraryDAO;
}
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(LibraryQC libraryQC) throws IOException {
MapSqlParameterSource params = new MapSqlParameterSource();
params.addValue("library_libraryId", libraryQC.getLibrary().getId())
//.addValue("qcUserName", SecurityContextHolder.getContext().getAuthentication().getName())
.addValue("qcUserName", libraryQC.getQcCreator())
.addValue("qcDate", libraryQC.getQcDate())
.addValue("qcMethod", libraryQC.getQcType().getQcTypeId())
.addValue("results", libraryQC.getResults())
.addValue("insertSize", libraryQC.getInsertSize());
if (libraryQC.getId() == AbstractLibraryQC.UNSAVED_ID) {
SimpleJdbcInsert insert = new SimpleJdbcInsert(template)
.withTableName(TABLE_NAME)
.usingGeneratedKeyColumns("qcId");
Number newId = insert.executeAndReturnKey(params);
libraryQC.setId(newId.longValue());
}
else {
params.addValue("qcId", libraryQC.getId());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(LIBRARY_QC_UPDATE, params);
}
if (this.cascadeType != null) {
Library l = libraryQC.getLibrary();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (l != null) libraryDAO.save(l);
}
else if (this.cascadeType.equals(CascadeType.REMOVE)) {
if (l != null) {
//Cache pc = cacheManager.getCache("libraryCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(l.getId()));
DbUtils.updateCaches(cacheManager, l, Library.class);
}
}
else if (this.cascadeType.equals(CascadeType.ALL)) {
if (l != null) {
libraryDAO.save(l);
//Cache pc = cacheManager.getCache("libraryCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(l.getId()));
DbUtils.updateCaches(cacheManager, l, Library.class);
}
}
}
return libraryQC.getId();
}
public LibraryQC get(long qcId) throws IOException {
List eResults = template.query(LIBRARY_QC_SELECT_BY_ID, new Object[]{qcId}, new LibraryQcMapper());
LibraryQC e = eResults.size() > 0 ? (LibraryQC) eResults.get(0) : null;
return e;
}
public LibraryQC lazyGet(long qcId) throws IOException {
List eResults = template.query(LIBRARY_QC_SELECT_BY_ID, new Object[]{qcId}, new LibraryQcMapper(true));
LibraryQC e = eResults.size() > 0 ? (LibraryQC) eResults.get(0) : null;
return e;
}
public Collection<LibraryQC> listByLibraryId(long libraryId) throws IOException {
return template.query(LIBRARY_QC_SELECT_BY_LIBRARY_ID, new Object[]{libraryId}, new LibraryQcMapper(true));
}
public Collection<LibraryQC> listAll() throws IOException {
return template.query(LIBRARY_QC, new LibraryQcMapper(true));
}
@Override
public int count() throws IOException {
return template.queryForInt("SELECT count(*) FROM "+TABLE_NAME);
}
public boolean remove(LibraryQC qc) throws IOException {
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
if (qc.isDeletable() &&
(namedTemplate.update(LIBRARY_QC_DELETE,
new MapSqlParameterSource().addValue("qcId", qc.getId())) == 1)) {
Library l = qc.getLibrary();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (l != null) libraryDAO.save(l);
}
else if (this.cascadeType.equals(CascadeType.REMOVE) || this.cascadeType.equals(CascadeType.ALL)) {
if (l != null) {
DbUtils.updateCaches(cacheManager, l, Library.class);
}
}
return true;
}
return false;
}
public class LibraryQcMapper extends CacheAwareRowMapper<LibraryQC> {
public LibraryQcMapper() {
//library qcs aren't cached at present
super(LibraryQC.class, false, false);
}
public LibraryQcMapper(boolean lazy) {
//library qcs aren't cached at present
super(LibraryQC.class, lazy, false);
}
@Override
public LibraryQC 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 LibraryQC " + id);
return (LibraryQC)element.getObjectValue();
}
}
LibraryQC s = dataObjectFactory.getLibraryQC();
s.setId(rs.getLong("qcId"));
s.setQcCreator(rs.getString("qcUserName"));
s.setQcDate(rs.getDate("qcDate"));
s.setResults(rs.getDouble("results"));
s.setInsertSize(rs.getInt("insertSize"));
try {
s.setQcType(getLibraryQcTypeById(rs.getLong("qcMethod")));
if (!isLazy()) {
s.setLibrary(libraryDAO.get(rs.getLong("library_libraryId")));
}
}
catch (IOException e) {
e.printStackTrace();
}
catch (MalformedLibraryException e) {
e.printStackTrace();
}
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
lookupCache(cacheManager).put(new Element(DbUtils.hashCodeCacheKeyFor(id) ,s));
}
return s;
}
}
public Collection<QcType> listAllLibraryQcTypes() throws IOException {
return template.query(LIBRARY_QC_TYPE_SELECT, new LibraryQcTypeMapper());
}
public QcType getLibraryQcTypeById(long qcTypeId) throws IOException {
List eResults = template.query(LIBRARY_QC_TYPE_SELECT_BY_ID, new Object[]{qcTypeId}, new LibraryQcTypeMapper());
QcType e = eResults.size() > 0 ? (QcType) eResults.get(0) : null;
return e;
}
public QcType getLibraryQcTypeByName(String qcName) throws IOException {
List eResults = template.query(LIBRARY_QC_TYPE_SELECT_BY_NAME, new Object[]{qcName}, new LibraryQcTypeMapper());
QcType e = eResults.size() > 0 ? (QcType) eResults.get(0) : null;
return e;
}
public class LibraryQcTypeMapper 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;
}
}
}