Java tutorial
/* * Copyright 2008-2013 Microarray Informatics Team, EMBL-European Bioinformatics Institute * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * * * For further details of the Gene Expression Atlas project, including source code, * downloads and documentation, please see: * * http://gxa.github.com/gxa */ package uk.ac.ebi.atlas.search.diffanalytics; import com.google.common.base.Optional; import com.google.common.base.Stopwatch; import com.google.common.collect.ImmutableSet; import org.apache.commons.lang.mutable.MutableInt; import org.apache.commons.lang3.StringUtils; import org.apache.log4j.Logger; import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.context.annotation.Scope; import org.springframework.dao.DataAccessException; import org.springframework.jdbc.core.JdbcTemplate; import org.springframework.jdbc.core.RowCallbackHandler; import uk.ac.ebi.atlas.search.DatabaseQuery; import uk.ac.ebi.atlas.search.OracleObjectFactory; import uk.ac.ebi.atlas.solr.query.conditions.IndexedAssayGroup; import uk.ac.ebi.atlas.utils.Visitor; import uk.ac.ebi.atlas.utils.VisitorException; import javax.inject.Inject; import javax.inject.Named; import javax.sql.DataSource; import java.sql.ResultSet; import java.sql.SQLException; import java.util.Collection; import java.util.List; import java.util.concurrent.TimeUnit; @Named @Scope("prototype") public class DiffAnalyticsDao { private static final Logger LOGGER = Logger.getLogger(DiffAnalyticsDao.class); static final int RESULT_SIZE = 50; private final DataSource dataSource; private final JdbcTemplate jdbcTemplate; private DiffAnalyticsRowMapper dbeRowMapper; private OracleObjectFactory oracleObjectFactory; @Inject public DiffAnalyticsDao(@Qualifier("dataSourceOracle") DataSource dataSource, DiffAnalyticsRowMapper dbeRowMapper, OracleObjectFactory oracleObjectFactory) { this.dbeRowMapper = dbeRowMapper; this.dataSource = dataSource; this.jdbcTemplate = new JdbcTemplate(dataSource); this.oracleObjectFactory = oracleObjectFactory; } public List<DiffAnalytics> fetchTopExpressions(Optional<Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, String species) { Optional<ImmutableSet<IndexedAssayGroup>> uniqueIndexedContrasts = uniqueIndexedContrasts(indexedContrasts); log("fetchTopExpressions", uniqueIndexedContrasts, geneIds); Stopwatch stopwatch = Stopwatch.createStarted(); DatabaseQuery<Object> indexedContrastQuery = buildSelect(uniqueIndexedContrasts, geneIds, species); jdbcTemplate.setMaxRows(RESULT_SIZE); List<DiffAnalytics> results; try { results = jdbcTemplate.query(indexedContrastQuery.getQuery(), dbeRowMapper, indexedContrastQuery.getParameters().toArray()); stopwatch.stop(); LOGGER.debug(String.format("fetchTopExpressions returned %s expressions in %.2f seconds", results.size(), stopwatch.elapsed(TimeUnit.MILLISECONDS) / 1000D)); } catch (Exception e) { LOGGER.error(e.getMessage(), e); throw e; } return results; } // get uniques, as we get contrasts multiple times for each assay group in the contrast private Optional<ImmutableSet<IndexedAssayGroup>> uniqueIndexedContrasts( Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts) { if (!indexedContrasts.isPresent()) { return Optional.absent(); } return Optional.of(ImmutableSet.copyOf(indexedContrasts.get())); } public void visitEachExpression(Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, final Visitor<DiffAnalytics> visitor, String specie) { Optional<ImmutableSet<IndexedAssayGroup>> uniqueIndexedContrasts = uniqueIndexedContrasts(indexedContrasts); log("visitEachExpression", uniqueIndexedContrasts, geneIds); Stopwatch stopwatch = Stopwatch.createStarted(); String species = ""; if (StringUtils.isNotBlank(specie)) { species = specie; } DatabaseQuery<Object> indexedContrastQuery = buildSelect(uniqueIndexedContrasts, geneIds, species); final MutableInt count = new MutableInt(0); JdbcTemplate template = new JdbcTemplate(dataSource); template.setFetchSize(5000); try { template.query(indexedContrastQuery.getQuery(), new RowCallbackHandler() { @Override public void processRow(ResultSet resultSet) throws SQLException { count.increment(); DiffAnalytics dbe = dbeRowMapper.mapRow(resultSet, count.intValue()); try { visitor.visit(dbe); } catch (VisitorException e) { // throw SQLException so result set is closed throw new SQLException(e); } } }, indexedContrastQuery.getParameters().toArray()); } catch (DataAccessException e) { if (e.getCause() != null && e.getCause().getCause() != null && e.getCause().getCause() instanceof VisitorException) { throw (VisitorException) (e.getCause().getCause()); } else { throw e; } } stopwatch.stop(); LOGGER.debug(String.format("visitEachExpression processed %s expressions in %s seconds", count.intValue(), stopwatch.elapsed(TimeUnit.SECONDS))); } public int fetchResultCount(Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, String specie) { Optional<ImmutableSet<IndexedAssayGroup>> uniqueIndexedContrasts = uniqueIndexedContrasts(indexedContrasts); log("fetchResultCount", uniqueIndexedContrasts, geneIds); Stopwatch stopwatch = Stopwatch.createStarted(); DatabaseQuery databaseQuery = buildCount(uniqueIndexedContrasts, geneIds, specie); int count = jdbcTemplate.queryForObject(databaseQuery.getQuery(), Integer.class, databaseQuery.getParameters().toArray()); LOGGER.debug(String.format("fetchResultCount returned %s in %.2f seconds", count, stopwatch.elapsed(TimeUnit.MILLISECONDS) / 1000D)); return count; } DatabaseQuery<Object> buildCount(Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, String species) { DiffAnalyticsQueryBuilder builder = createDifferentialGeneQueryBuilder(indexedContrasts, geneIds, species); return builder.buildCount(); } DatabaseQuery<Object> buildSelect(Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, String species) { DiffAnalyticsQueryBuilder builder = createDifferentialGeneQueryBuilder(indexedContrasts, geneIds, species); return builder.buildSelect(); } DiffAnalyticsQueryBuilder createDifferentialGeneQueryBuilder( Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds, String species) { DiffAnalyticsQueryBuilder builder = new DiffAnalyticsQueryBuilder(); if (indexedContrasts.isPresent() && !indexedContrasts.get().isEmpty()) { builder.withExperimentContrasts( oracleObjectFactory.createOracleArrayForIndexedAssayGroup(indexedContrasts.get())) .withSpecies(species); } if (geneIds.isPresent() && !geneIds.get().isEmpty()) { builder.withGeneIds(oracleObjectFactory.createOracleArrayForIdentifiers(geneIds.get())) .withSpecies(species); } return builder; } private void log(final String methodName, Optional<? extends Collection<IndexedAssayGroup>> indexedContrasts, Optional<? extends Collection<String>> geneIds) { LOGGER.debug(String.format(methodName + " for %s unique contrasts and %s genes", (indexedContrasts.isPresent()) ? indexedContrasts.get().size() : 0, (geneIds.isPresent()) ? geneIds.get().size() : 0)); } }