List of usage examples for org.hibernate SQLQuery setFlushMode
@Override
NativeQuery<T> setFlushMode(FlushMode flushMode);
From source file:ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl.java
License:Apache License
@Override public Map<Long, Map<Long, DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets( Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds) { Map<Long, Map<Long, DiffExprGeneSearchResult>> results = new HashMap<>(); Session session = this.getSessionFactory().getCurrentSession(); Map<Long, DiffExResultSetSummaryValueObject> resultSetIdsMap = EntityUtils.getIdMap(resultSets, "getResultSetId"); Map<Long, Collection<Long>> foundInCache = this.fillFromCache(results, resultSetIdsMap.keySet(), geneIds); if (!foundInCache.isEmpty()) { AbstractDao.log.info("Results for " + foundInCache.size() + " resultsets found in cache"); } else {/*from ww w .jav a 2s .c o m*/ AbstractDao.log.info("No results were in the cache"); } Collection<Long> resultSetsNeeded = this.stripUnneededResultSets(foundInCache, resultSetIdsMap.keySet(), geneIds); // Are we finished? if (resultSetsNeeded.isEmpty()) { AbstractDao.log.info("All results were in the cache."); return results; } AbstractDao.log.info(foundInCache.size() + "/" + resultSetIdsMap.size() + " resultsSets had at least some cached results; still need to query " + resultSetsNeeded.size()); assert !resultSetsNeeded.isEmpty(); org.hibernate.SQLQuery queryObject = session.createSQLQuery( DifferentialExpressionResultDaoImpl.fetchBatchDifferentialExpressionAnalysisResultsByResultSetsAndGeneQuery); /* * These values have been tweaked to probe for performance issues. */ int resultSetBatchSize = 50; int geneBatchSize = 100; if (resultSetsNeeded.size() > geneIds.size()) { resultSetBatchSize = Math.min(500, resultSetsNeeded.size()); AbstractDao.log.info("Batching by result sets (" + resultSetsNeeded.size() + " resultSets); " + geneIds.size() + " genes; batch size=" + resultSetBatchSize); } else { geneBatchSize = Math.min(200, geneIds.size()); AbstractDao.log.info("Batching by genes (" + geneIds.size() + " genes); " + resultSetsNeeded.size() + " resultSets; batch size=" + geneBatchSize); } final int numResultSetBatches = (int) Math.ceil(resultSetsNeeded.size() / resultSetBatchSize); queryObject.setFlushMode(FlushMode.MANUAL); StopWatch timer = new StopWatch(); timer.start(); int numResults = 0; long timeForFillingNonSig = 0; Map<Long, Map<Long, DiffExprGeneSearchResult>> resultsFromDb = new HashMap<>(); int numResultSetBatchesDone = 0; // Iterate over batches of resultSets for (Collection<Long> resultSetIdBatch : new BatchIterator<>(resultSetsNeeded, resultSetBatchSize)) { if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Starting batch of resultsets: " + StringUtils.abbreviate(StringUtils.join(resultSetIdBatch, ","), 100)); /* * Get the probes using the CommonQueries gene2cs. Otherwise we (in effect) end up doing this over and over * again. */ Map<Long, Collection<Long>> cs2GeneIdMap = this.getProbesForGenesInResultSetBatch(session, geneIds, resultSetIdsMap, resultSetIdBatch); queryObject.setParameterList("rs_ids", resultSetIdBatch); int numGeneBatchesDone = 0; final int numGeneBatches = (int) Math.ceil(cs2GeneIdMap.size() / geneBatchSize); StopWatch innerQt = new StopWatch(); // iterate over batches of probes (genes) for (Collection<Long> probeBatch : new BatchIterator<>(cs2GeneIdMap.keySet(), geneBatchSize)) { if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Starting batch of probes: " + StringUtils.abbreviate(StringUtils.join(probeBatch, ","), 100)); // would it help to sort the probeBatch/ List<Long> pbL = new Vector<>(probeBatch); Collections.sort(pbL); queryObject.setParameterList("probe_ids", pbL); innerQt.start(); List<?> queryResult = queryObject.list(); innerQt.stop(); if (innerQt.getTime() > 2000) { // show the actual query with params. AbstractDao.log.info("Query time: " + innerQt.getTime() + "ms:\n " + queryObject.getQueryString().replace(":probe_ids", StringUtils.join(probeBatch, ",")) .replace(":rs_ids", StringUtils.join(resultSetIdBatch, ","))); } innerQt.reset(); /* * Each query tuple are the probe, result, resultsSet, qvalue, pvalue. */ for (Object o : queryResult) { // Long resultSetId = ( ( BigInteger )((Object[])o)[2] ).longValue(); // if (!resultSetId.equals) numResults += this.processResultTuple(o, resultsFromDb, cs2GeneIdMap); } if (timer.getTime() > 5000 && AbstractDao.log.isInfoEnabled()) { AbstractDao.log.info("Batch time: " + timer.getTime() + "ms; Fetched DiffEx " + numResults + " results so far. " + numResultSetBatchesDone + "/" + numResultSetBatches + " resultset batches completed. " + numGeneBatchesDone + "/" + numGeneBatches + " gene batches done."); timer.reset(); timer.start(); } // Check if task was cancelled. if (Thread.currentThread().isInterrupted()) { throw new TaskCancelledException("Search was cancelled"); } numGeneBatchesDone++; if (DifferentialExpressionResultDaoImpl.CORRECTED_PVALUE_THRESHOLD_TO_BE_CONSIDERED_DIFF_EX < 1.0) { timeForFillingNonSig += this.fillNonSignificant(pbL, resultSetIdsMap, resultsFromDb, resultSetIdBatch, cs2GeneIdMap, session); } } // over probes. // Check if task was cancelled. if (Thread.currentThread().isInterrupted()) { throw new TaskCancelledException("Search was cancelled"); } numResultSetBatchesDone++; } if (timer.getTime() > 1000 && AbstractDao.log.isInfoEnabled()) { AbstractDao.log.info("Fetching DiffEx from DB took total of " + timer.getTime() + " ms : geneIds=" + StringUtils.abbreviate(StringUtils.join(geneIds, ","), 50) + " result set=" + StringUtils.abbreviate(StringUtils.join(resultSetsNeeded, ","), 50)); if (timeForFillingNonSig > 100) { AbstractDao.log.info("Filling in non-significant values: " + timeForFillingNonSig + "ms in total"); } } // Add the DB results to the cached results. this.addToCache(resultsFromDb, resultSetsNeeded, geneIds); for (Long resultSetId : resultsFromDb.keySet()) { Map<Long, DiffExprGeneSearchResult> geneResults = resultsFromDb.get(resultSetId); if (results.containsKey(resultSetId)) { results.get(resultSetId).putAll(geneResults); } else { results.put(resultSetId, geneResults); } } return results; }
From source file:ubic.gemma.persistence.util.CommonQueries.java
License:Apache License
/** * @param session session/* w w w. j a v a2 s.c om*/ * @param genes genes * @param arrayDesigns array design * @return map of probe IDs to collections of gene IDs. */ public static Map<Long, Collection<Long>> getCs2GeneIdMap(Collection<Long> genes, Collection<Long> arrayDesigns, Session session) { Map<Long, Collection<Long>> cs2genes = new HashMap<>(); String queryString = "SELECT CS AS csid, GENE AS geneId FROM GENE2CS g WHERE g.GENE IN (:geneIds) AND g.AD IN (:ads)"; SQLQuery queryObject = session.createSQLQuery(queryString); queryObject.addScalar("csid", LongType.INSTANCE); queryObject.addScalar("geneId", LongType.INSTANCE); queryObject.setParameterList("ads", arrayDesigns); queryObject.setParameterList("geneIds", genes); queryObject.setReadOnly(true); queryObject.setFlushMode(FlushMode.MANUAL); ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY); CommonQueries.addGeneIds(cs2genes, results); results.close(); return cs2genes; }
From source file:ubic.gemma.persistence.util.CommonQueries.java
License:Apache License
/** * @param session session// w w w. ja va 2s . co m * @param probes probes * @return map of probes to all the genes 'detected' by those probes. Probes that don't map to genes will have an * empty gene collection. */ public static Map<Long, Collection<Long>> getCs2GeneMapForProbes(Collection<Long> probes, Session session) { if (probes.isEmpty()) return new HashMap<>(); Map<Long, Collection<Long>> cs2genes = new HashMap<>(); String queryString = "SELECT CS AS csid, GENE AS geneId FROM GENE2CS g WHERE g.CS IN (:probes) "; org.hibernate.SQLQuery queryObject = session.createSQLQuery(queryString); queryObject.addScalar("csid", LongType.INSTANCE); queryObject.addScalar("geneId", LongType.INSTANCE); queryObject.setParameterList("probes", probes, LongType.INSTANCE); queryObject.setReadOnly(true); queryObject.setFlushMode(FlushMode.MANUAL); ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY); CommonQueries.addGeneIds(cs2genes, results); results.close(); return cs2genes; }