/*
* 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 com.eaglegenomics.simlims.core.SecurityProfile;
import com.googlecode.ehcache.annotations.KeyGenerator;
import com.googlecode.ehcache.annotations.Property;
import net.sf.ehcache.Cache;
import net.sf.ehcache.CacheManager;
import net.sf.ehcache.Element;
import org.springframework.beans.factory.annotation.Autowired;
import uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryDilution;
import uk.ac.bbsrc.tgac.miso.core.exception.MisoNamingException;
import uk.ac.bbsrc.tgac.miso.core.service.naming.MisoNamingScheme;
import uk.ac.bbsrc.tgac.miso.core.store.EmPCRDilutionStore;
import uk.ac.bbsrc.tgac.miso.core.store.LibraryDilutionStore;
import uk.ac.bbsrc.tgac.miso.core.store.EmPCRStore;
import uk.ac.bbsrc.tgac.miso.core.store.Store;
import com.googlecode.ehcache.annotations.Cacheable;
import com.googlecode.ehcache.annotations.TriggersRemove;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
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.sqlstore.cache.CacheAwareRowMapper;
import uk.ac.bbsrc.tgac.miso.sqlstore.util.DbUtils;
import uk.ac.bbsrc.tgac.miso.core.data.impl.emPCR;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
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 SQLEmPCRDAO implements EmPCRStore {
private static final String TABLE_NAME="emPCR";
public static String EMPCR_SELECT =
"SELECT pcrId, concentration, pcrUserName, creationDate, name, dilution_dilutionId, securityProfile_profileId " +
"FROM " + TABLE_NAME;
public static final String EMPCR_SELECT_BY_PCR_ID =
EMPCR_SELECT + " WHERE pcrId=?";
public static final String EMPCR_SELECT_BY_RELATED_DILUTION =
EMPCR_SELECT + " WHERE dilution_dilutionId=?";
public static String EMPCR_SELECT_BY_PROJECT =
"SELECT e.* FROM Project p " +
"INNER JOIN Sample sa ON sa.project_projectId = p.projectId " +
"INNER JOIN Library li ON li.sample_sampleId = sa.sampleId " +
"INNER JOIN LibraryDilution ld ON ld.library_libraryId = li.libraryId " +
"INNER JOIN "+TABLE_NAME+" e ON e.dilution_dilutionId = ld.dilutionId " +
"WHERE p.projectId=?";
public static final String EMPCR_UPDATE =
"UPDATE " + TABLE_NAME +
" SET concentration=:concentration, pcrUserName=:pcrUserName, creationDate=:creationDate, name=:name, dilution_dilutionId=:dilution_dilutionId, securityProfile_profileId=:securityProfile_profileId " +
"WHERE pcrId=:pcrId";
public static final String EMPCR_DELETE =
"DELETE FROM "+TABLE_NAME+" WHERE pcrId=:pcrId";
protected static final Logger log = LoggerFactory.getLogger(SQLEmPCRDAO.class);
private JdbcTemplate template;
private LibraryDilutionStore libraryDilutionDAO;
private EmPCRDilutionStore emPCRDilutionDAO;
private CascadeType cascadeType;
private Store<SecurityProfile> securityProfileDAO;
@Autowired
private MisoNamingScheme<emPCR> namingScheme;
@Override
public MisoNamingScheme<emPCR> getNamingScheme() {
return namingScheme;
}
@Override
public void setNamingScheme(MisoNamingScheme<emPCR> namingScheme) {
this.namingScheme = namingScheme;
}
@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 JdbcTemplate getJdbcTemplate() {
return template;
}
public void setJdbcTemplate(JdbcTemplate template) {
this.template = template;
}
public void setLibraryDilutionDAO(LibraryDilutionStore libraryDilutionDAO) {
this.libraryDilutionDAO = libraryDilutionDAO;
}
public void setEmPCRDilutionDAO(EmPCRDilutionStore emPCRDilutionDAO) {
this.emPCRDilutionDAO = emPCRDilutionDAO;
}
public void setCascadeType(CascadeType cascadeType) {
this.cascadeType = cascadeType;
}
public Store<SecurityProfile> getSecurityProfileDAO() {
return securityProfileDAO;
}
public void setSecurityProfileDAO(Store<SecurityProfile> securityProfileDAO) {
this.securityProfileDAO = securityProfileDAO;
}
@Transactional(readOnly = false, rollbackFor = IOException.class)
@TriggersRemove(cacheName={"emPCRCache", "lazyEmPCRCache"},
keyGenerator = @KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name = "includeMethod", value = "false"),
@Property(name = "includeParameterTypes", value = "false")
}
)
)
public long save(emPCR pcr) throws IOException {
Long securityProfileId = pcr.getSecurityProfile().getProfileId();
if (securityProfileId == null || (this.cascadeType != null)) { // && this.cascadeType.equals(CascadeType.PERSIST))) {
securityProfileId = securityProfileDAO.save(pcr.getSecurityProfile());
}
MapSqlParameterSource params = new MapSqlParameterSource();
params.addValue("concentration", pcr.getConcentration())
.addValue("creationDate", pcr.getCreationDate())
.addValue("pcrUserName", pcr.getPcrCreator())
.addValue("dilution_dilutionId", pcr.getLibraryDilution().getId())
.addValue("securityProfile_profileId", securityProfileId);
if (pcr.getId() == emPCR.UNSAVED_ID) {
SimpleJdbcInsert insert = new SimpleJdbcInsert(template)
.withTableName(TABLE_NAME)
.usingGeneratedKeyColumns("pcrId");
try {
pcr.setId(DbUtils.getAutoIncrement(template, TABLE_NAME));
String name = namingScheme.generateNameFor("name", pcr);
pcr.setName(name);
if (namingScheme.validateField("name", pcr.getName())) {
params.addValue("name", name);
Number newId = insert.executeAndReturnKey(params);
if (newId.longValue() != pcr.getId()) {
log.error("Expected emPCR ID doesn't match returned value from database insert: rolling back...");
new NamedParameterJdbcTemplate(template).update(EMPCR_DELETE, new MapSqlParameterSource().addValue("pcrId", newId.longValue()));
throw new IOException("Something bad happened. Expected emPCR ID doesn't match returned value from DB insert");
}
}
else {
throw new IOException("Cannot save emPCR - invalid field:" + pcr.toString());
}
}
catch (MisoNamingException e) {
throw new IOException("Cannot save emPCR - issue with naming scheme", e);
}
/*
String name = "EMP"+ DbUtils.getAutoIncrement(template, TABLE_NAME);
params.addValue("name", name);
Number newId = insert.executeAndReturnKey(params);
pcr.setPcrId(newId.longValue());
pcr.setName(name);
*/
}
else {
try {
if (namingScheme.validateField("name", pcr.getName())) {
params.addValue("pcrId", pcr.getId())
.addValue("name", pcr.getName());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(EMPCR_UPDATE, params);
}
else {
throw new IOException("Cannot save emPCR - invalid field:" + pcr.toString());
}
}
catch (MisoNamingException e) {
throw new IOException("Cannot save emPCR - issue with naming scheme", e);
}
/*
params.addValue("pcrId", pcr.getPcrId())
.addValue("name", pcr.getName());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(EMPCR_UPDATE, params);
*/
}
if (this.cascadeType != null) {
LibraryDilution ld = pcr.getLibraryDilution();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (ld != null) libraryDilutionDAO.save(ld);
}
else if (this.cascadeType.equals(CascadeType.REMOVE)) {
if (ld != null) {
//Cache pc = cacheManager.getCache("libraryDilutionCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(ld.getId()));
DbUtils.updateCaches(cacheManager, ld, LibraryDilution.class);
}
}
}
return pcr.getId();
}
@Cacheable(cacheName="emPCRCache",
keyGenerator = @KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name = "includeMethod", value = "false"),
@Property(name = "includeParameterTypes", value = "false")
}
)
)
public emPCR get(long pcrId) throws IOException {
List eResults = template.query(EMPCR_SELECT_BY_PCR_ID, new Object[]{pcrId}, new EmPCRMapper());
emPCR e = eResults.size() > 0 ? (emPCR) eResults.get(0) : null;
return e;
}
public emPCR lazyGet(long pcrId) throws IOException {
List eResults = template.query(EMPCR_SELECT_BY_PCR_ID, new Object[]{pcrId}, new EmPCRMapper(true));
emPCR e = eResults.size() > 0 ? (emPCR) eResults.get(0) : null;
return e;
}
public Collection<emPCR> listAllByProjectId(long projectId) throws IOException {
return template.query(EMPCR_SELECT_BY_PROJECT, new Object[]{projectId}, new EmPCRMapper());
}
public Collection<emPCR> listAll() throws IOException {
return template.query(EMPCR_SELECT, new EmPCRMapper(true));
}
@Override
public int count() throws IOException {
return template.queryForInt("SELECT count(*) FROM "+TABLE_NAME);
}
public Collection<emPCR> listAllByDilutionId(long dilutionId) throws IOException {
return template.query(EMPCR_SELECT_BY_RELATED_DILUTION, new Object[]{dilutionId}, new EmPCRMapper());
}
@Transactional(readOnly = false, rollbackFor = IOException.class)
@TriggersRemove(
cacheName={"emPCRCache", "lazyEmPCRCache"},
keyGenerator = @KeyGenerator (
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name="includeMethod", value="false"),
@Property(name="includeParameterTypes", value="false")
}
)
)
public boolean remove(emPCR e) throws IOException {
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
if (e.isDeletable() &&
(namedTemplate.update(EMPCR_DELETE,
new MapSqlParameterSource().addValue("pcrId", e.getId())) == 1)) {
LibraryDilution ld = e.getLibraryDilution();
if (this.cascadeType.equals(CascadeType.PERSIST)) {
if (ld != null) libraryDilutionDAO.save(ld);
}
else if (this.cascadeType.equals(CascadeType.REMOVE)) {
if (ld != null) {
//Cache pc = cacheManager.getCache("emPCRDilutionCache");
//pc.remove(DbUtils.hashCodeCacheKeyFor(ld.getId()));
DbUtils.updateCaches(cacheManager, ld, LibraryDilution.class);
}
}
return true;
}
return false;
}
public class EmPCRMapper extends CacheAwareRowMapper<emPCR> {
public EmPCRMapper() {
super(emPCR.class);
}
public EmPCRMapper(boolean lazy) {
super(emPCR.class, lazy);
}
public emPCR mapRow(ResultSet rs, int rowNum) throws SQLException {
long id = rs.getLong("pcrId");
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
Element element;
if ((element = lookupCache(cacheManager).get(DbUtils.hashCodeCacheKeyFor(id))) != null) {
log.debug("Cache hit on map for emPCR " + id);
return (emPCR)element.getObjectValue();
}
}
emPCR pcr = dataObjectFactory.getEmPCR();
pcr.setId(id);
pcr.setConcentration(rs.getDouble("concentration"));
pcr.setName(rs.getString("name"));
pcr.setCreationDate(rs.getDate("creationDate"));
pcr.setPcrCreator(rs.getString("pcrUserName"));
try {
pcr.setSecurityProfile(securityProfileDAO.get(rs.getLong("securityProfile_profileId")));
pcr.setLibraryDilution(libraryDilutionDAO.get(rs.getLong("dilution_dilutionId")));
if (!isLazy()) {
pcr.setEmPcrDilutions(emPCRDilutionDAO.listAllByEmPCRId(id));
}
}
catch (IOException e1) {
e1.printStackTrace();
}
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
lookupCache(cacheManager).put(new Element(DbUtils.hashCodeCacheKeyFor(id), pcr));
}
return pcr;
}
}
}