/*
* 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.Cacheable;
import com.googlecode.ehcache.annotations.KeyGenerator;
import com.googlecode.ehcache.annotations.Property;
import com.googlecode.ehcache.annotations.TriggersRemove;
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 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.AbstractPartition;
import uk.ac.bbsrc.tgac.miso.core.data.SequencerPoolPartition;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.store.PartitionStore;
import uk.ac.bbsrc.tgac.miso.core.store.PoolStore;
import uk.ac.bbsrc.tgac.miso.core.store.SequencerPartitionContainerStore;
import uk.ac.bbsrc.tgac.miso.core.store.Store;
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 0.1.6
*/
public class SQLSequencerPoolPartitionDAO implements PartitionStore {
private static final String TABLE_NAME = "_Partition";
public static final String PARTITIONS_SELECT =
"SELECT partitionId, partitionNumber, pool_poolId, securityProfile_profileId " +
"FROM "+TABLE_NAME;
public static final String PARTITION_SELECT_BY_ID =
PARTITIONS_SELECT + " " + "WHERE partitionId = ?";
public static final String PARTITION_UPDATE =
"UPDATE "+TABLE_NAME+" " +
"SET partitionNumber=:partitionNumber, pool_poolId=:pool_poolId, securityProfile_profileId=:securityProfile_profileId " +
"WHERE partitionId=:partitionId";
public static final String PARTITIONS_BY_RELATED_RUN =
"SELECT l.partitionId, l.partitionNumber, l.pool_poolId, l.securityProfile_profileId " +
"FROM "+TABLE_NAME+" l, Run_SequencerPartitionContainer rf, Run r " +
"WHERE l.container_containerId=rf.containers_containerId " +
"AND rf.Run_runId=r.runId " +
"AND r.runId=?";
public static final String PARTITIONS_BY_RELATED_SEQUENCER_PARTITION_CONTAINER =
"SELECT l.partitionId, l.partitionNumber, l.pool_poolId, l.securityProfile_profileId " +
"FROM "+TABLE_NAME+" l " +
"INNER JOIN SequencerPartitionContainer_Partition fl ON l.partitionId = fl.partitions_partitionId " +
"AND fl.container_containerId=?";
public static final String PARTITIONS_BY_RELATED_POOL =
PARTITIONS_SELECT + " WHERE pool_poolId = ?";
public static String PARTITIONS_BY_RELATED_PROJECT =
"SELECT l.* " +
"FROM Project p, "+TABLE_NAME+" l " +
"INNER JOIN Study st ON st.project_projectId = p.projectId " +
"LEFT JOIN Experiment ex ON st.studyId = ex.study_studyId " +
"INNER JOIN Pool_Experiment pex ON ex.experimentId = pex.experiments_experimentId " +
"LEFT JOIN Pool pool ON pool.poolId = pex.pool_poolId " +
"LEFT JOIN "+TABLE_NAME+" l ON pool.poolId = l.pool_poolId " +
"LEFT JOIN SequencerPartitionContainer_Partition fl ON l.partitionId = fl.partitions_partitionId " +
"LEFT JOIN SequencerPartitionContainer fa ON fl.container_containerId = fa.containerId " +
"INNER JOIN Run_SequencerPartitionContainer rf ON fa.containerId = rf.containers_containerId " +
"LEFT JOIN Run ra ON rf.Run_runId = ra.runId " +
"WHERE p.projectId=?";
//just changed this bit to see if it fixes the missing partition problem...
public static final String PARTITIONS_BY_RELATED_SUBMISSION =
"SELECT l.partitionId, l.partitionNumber, l.pool_poolId, l.securityProfile_profileId " +
"FROM "+TABLE_NAME+" l, Submission_Partition_Dilution sl " +
"WHERE l.partitionId=sl.partition_partitionId " +
"AND sl.submission_submissionId=?";
protected static final Logger log = LoggerFactory.getLogger(SQLSequencerPoolPartitionDAO.class);
private JdbcTemplate template;
private SequencerPartitionContainerStore sequencerPartitionContainerDAO;
private PoolStore poolDAO;
private Store<SecurityProfile> securityProfileDAO;
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 setPoolDAO(PoolStore poolDAO) {
this.poolDAO = poolDAO;
}
public void setSequencerPartitionContainerDAO(SequencerPartitionContainerStore sequencerPartitionContainerDAO) {
this.sequencerPartitionContainerDAO = sequencerPartitionContainerDAO;
}
public Store<SecurityProfile> getSecurityProfileDAO() {
return securityProfileDAO;
}
public void setSecurityProfileDAO(Store<SecurityProfile> securityProfileDAO) {
this.securityProfileDAO = securityProfileDAO;
}
public JdbcTemplate getJdbcTemplate() {
return template;
}
public void setJdbcTemplate(JdbcTemplate template) {
this.template = template;
}
public void setCascadeType(CascadeType cascadeType) {
this.cascadeType = cascadeType;
}
private void purgeListCache(SequencerPoolPartition s, boolean replace) {
Cache cache = cacheManager.getCache("partitionListCache");
DbUtils.updateListCache(cache, replace, s, SequencerPoolPartition.class);
}
private void purgeListCache(SequencerPoolPartition s) {
purgeListCache(s, true);
}
@Override
@Transactional(readOnly = false, rollbackFor = IOException.class)
@TriggersRemove(cacheName = {"sequencerPoolPartitionCache", "lazySequencerPoolPartitionCache"},
keyGenerator = @KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name = "includeMethod", value = "false"),
@Property(name = "includeParameterTypes", value = "false")
}
)
)
public long save(SequencerPoolPartition partition) throws IOException {
Long securityProfileId = partition.getSecurityProfile().getProfileId();
if (securityProfileId == null || this.cascadeType != null) { // && this.cascadeType.equals(CascadeType.PERSIST)) {
securityProfileDAO.save(partition.getSecurityProfile());
}
MapSqlParameterSource params = new MapSqlParameterSource();
params.addValue("partitionNumber", partition.getPartitionNumber())
.addValue("securityProfile_profileId", securityProfileId);
if (partition.getPool() != null) {
params.addValue("pool_poolId", partition.getPool().getId());
// if this pool is marked as ready to run, and is now added to a partition, unmark it
if (partition.getPool().getReadyToRun()) {
partition.getPool().setReadyToRun(false);
}
poolDAO.save(partition.getPool());
}
else {
params.addValue("pool_poolId", null);
}
if (partition.getId() == AbstractPartition.UNSAVED_ID) {
SimpleJdbcInsert insert = new SimpleJdbcInsert(template)
.withTableName(TABLE_NAME)
.usingGeneratedKeyColumns("partitionId");
Number newId = insert.executeAndReturnKey(params);
partition.setId(newId.longValue());
}
else {
params.addValue("partitionId", partition.getId());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(PARTITION_UPDATE, params);
}
if (this.cascadeType != null) {
purgeListCache(partition);
}
return partition.getId();
}
@Override
@Cacheable(cacheName="partitionListCache",
keyGenerator = @KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name="includeMethod", value="false"),
@Property(name="includeParameterTypes", value="false")
}
)
)
public List<SequencerPoolPartition> listAll() throws IOException {
return template.query(PARTITIONS_SELECT, new PartitionMapper(true));
}
@Override
public int count() throws IOException {
return template.queryForInt("SELECT count(*) FROM "+TABLE_NAME);
}
@Cacheable(cacheName="sequencerPoolPartitionCache",
keyGenerator = @KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name = "includeMethod", value = "false"),
@Property(name = "includeParameterTypes", value = "false")
}
)
)
public SequencerPoolPartition get(long partitionId) throws IOException {
List eResults = template.query(PARTITION_SELECT_BY_ID, new Object[]{partitionId}, new PartitionMapper());
return eResults.size() > 0 ? (SequencerPoolPartition) eResults.get(0) : null;
}
public SequencerPoolPartition lazyGet(long partitionId) throws IOException {
List eResults = template.query(PARTITION_SELECT_BY_ID, new Object[]{partitionId}, new PartitionMapper(true));
return eResults.size() > 0 ? (SequencerPoolPartition) eResults.get(0) : null;
}
public Collection<SequencerPoolPartition> listByRunId(long runId) throws IOException {
return template.query(PARTITIONS_BY_RELATED_RUN, new Object[]{runId}, new PartitionMapper());
}
public Collection<SequencerPoolPartition> listBySequencerPartitionContainerId(long sequencerPartitionContainerId) throws IOException {
return template.query(PARTITIONS_BY_RELATED_SEQUENCER_PARTITION_CONTAINER, new Object[]{sequencerPartitionContainerId}, new PartitionMapper(true));
}
public List<SequencerPoolPartition> listByPoolId(long poolId) throws IOException {
return template.query(PARTITIONS_BY_RELATED_POOL, new Object[]{poolId}, new PartitionMapper(true));
}
public List<SequencerPoolPartition> listBySubmissionId(long submissionId) throws IOException {
return template.query(PARTITIONS_BY_RELATED_SUBMISSION, new Object[]{submissionId}, new PartitionMapper());
}
public List<SequencerPoolPartition> listByProjectId(long projectId) throws IOException {
return template.query(PARTITIONS_BY_RELATED_PROJECT, new Object[]{projectId}, new PartitionMapper(true));
}
public class PartitionMapper extends CacheAwareRowMapper<SequencerPoolPartition> {
public PartitionMapper() {
super(SequencerPoolPartition.class);
}
public PartitionMapper(boolean lazy) {
super(SequencerPoolPartition.class, lazy);
}
public SequencerPoolPartition mapRow(ResultSet rs, int rowNum) throws SQLException {
long id = rs.getLong("partitionId");
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
Element element;
if ((element = lookupCache(cacheManager).get(DbUtils.hashCodeCacheKeyFor(id))) != null) {
log.debug("Cache hit on map for SequencerPoolPartition " + id);
return (SequencerPoolPartition)element.getObjectValue();
}
}
SequencerPoolPartition l = dataObjectFactory.getSequencerPoolPartition();
l.setId(id);
l.setPartitionNumber(rs.getInt("partitionNumber"));
try {
l.setSecurityProfile(securityProfileDAO.get(rs.getLong("securityProfile_profileId")));
l.setPool(poolDAO.get(rs.getLong("pool_poolId")));
if (!isLazy()) {
l.setSequencerPartitionContainer(sequencerPartitionContainerDAO.getSequencerPartitionContainerByPartitionId(id));
}
}
catch (IOException e1) {
e1.printStackTrace();
}
if (isCacheEnabled() && lookupCache(cacheManager) != null) {
lookupCache(cacheManager).put(new Element(DbUtils.hashCodeCacheKeyFor(id) ,l));
}
return l;
}
}
}