List of usage examples for org.hibernate SQLQuery setParameterList
@Override
NativeQuery<T> setParameterList(String name, Object[] values);
From source file:service.ProblemService.java
public static List<ProblemInfo> getProblems(List<Integer> platforms, List<String> tags) { Session session = HibernateUtil.getSessionFactory().openSession(); String sql = "SELECT id, title, platform, problem_url from problem "; boolean emptyPlatform = true; boolean emptyTags = true; if (platforms != null && platforms.size() > 0) { emptyPlatform = false;// w w w.j a v a 2 s . c o m sql += "where platform in(:platforms)"; } if (tags != null && tags.size() > 0) { emptyTags = false; if (emptyPlatform) { sql += "where "; } else { sql += "and "; } sql += "id in(select id from tags where tag_name in (:tags))"; } SQLQuery query = session.createSQLQuery(sql); if (!emptyPlatform) { query.setParameterList("platforms", platforms); } if (!emptyTags) { query.setParameterList("tags", tags); } List result = query.list(); List<ProblemInfo> problems = new ArrayList<>(); for (Iterator iterator = result.iterator(); iterator.hasNext();) { Object[] objects = (Object[]) iterator.next(); int id = (Integer) objects[0]; String title = (String) objects[1]; Platform platform = Platform.fromOrdinal((Integer) objects[2]); String problemUrl = (String) objects[3]; ProblemInfo problemInfo = new ProblemInfo(id, title, platform, problemUrl); problems.add(problemInfo); } session.close(); return problems; }
From source file:ubic.gemma.persistence.service.analysis.expression.diff.DifferentialExpressionAnalysisDaoImpl.java
License:Apache License
private void fetchExperimentsTestingGeneNativeQuery(Collection<CompositeSequence> probes, Collection<BioAssaySet> result, final String nativeQuery, Taxon taxon) { if (probes.isEmpty()) return;//from ww w. j a v a2 s.co m SQLQuery nativeQ = this.getSessionFactory().getCurrentSession().createSQLQuery(nativeQuery); nativeQ.setParameterList("probes", EntityUtils.getIds(probes)); nativeQ.setParameter("taxon", taxon); List<?> list = nativeQ.list(); Set<Long> ids = new HashSet<>(); for (Object o : list) { ids.add(((BigInteger) o).longValue()); } if (!ids.isEmpty()) { //noinspection unchecked result.addAll(this.getHibernateTemplate() .findByNamedParam("from ExpressionExperiment e where e.id in (:ids)", "ids", ids)); } }
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 . j a v a 2s .c om 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.service.analysis.expression.diff.DifferentialExpressionResultDaoImpl.java
License:Apache License
/** * Key method for getting contrasts associated with results. *///from www. j a va 2 s. c o m @Override public Map<Long, ContrastsValueObject> loadContrastDetailsForResults(Collection<Long> ids) { //language=SQL final String queryString = "SELECT DISTINCT c.ID, c.LOG_FOLD_CHANGE, c.FACTOR_VALUE_FK," + " c.DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_FK, c.PVALUE FROM CONTRAST_RESULT c" + " WHERE c.DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_FK IN (:ids) "; Map<Long, ContrastsValueObject> probeResults = new HashMap<>(); if (ids.isEmpty()) { return probeResults; } SQLQuery query = this.getSessionFactory().getCurrentSession().createSQLQuery(queryString); int BATCH_SIZE = 2000; // previously: 500, then 1000. New optimized query is plenty fast. StopWatch timer = new StopWatch(); for (Collection<Long> batch : new BatchIterator<>(ids, BATCH_SIZE)) { timer.reset(); timer.start(); query.setParameterList("ids", batch); List<?> batchR = query.list(); for (Object o : batchR) { Object[] ol = (Object[]) o; Long resultId = ((BigInteger) ol[3]).longValue(); if (!probeResults.containsKey(resultId)) { probeResults.put(resultId, new ContrastsValueObject(resultId)); } ContrastsValueObject cvo = probeResults.get(resultId); Long contrastId = ((BigInteger) ol[0]).longValue(); Double logFoldChange = ol[1] == null ? null : (Double) ol[1]; Long factorValueId = ol[2] == null ? null : ((BigInteger) ol[2]).longValue(); Double pvalue = ol[4] == null ? null : (Double) ol[4]; cvo.addContrast(contrastId, factorValueId, logFoldChange, pvalue, null); } if (timer.getTime() > 2000) { AbstractDao.log.info("Fetch " + batch.size() + " results with contrasts: " + timer.getTime() + "ms; query was\n " + queryString.replace(":ids", StringUtils.join(batch, ","))); } } return probeResults; }
From source file:ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl.java
License:Apache License
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public List<Object[]> getRawCoexpressionFromDbViaGenes(Collection<Long> geneIds, Taxon t, int stringency) {
String sqlQuery1 = "select ID, POSITIVE, SUPPORT, FIRST_GENE_FK, SECOND_GENE_FK, SUPPORT_DETAILS_FK from "
+ CoexpressionQueryUtils.getGeneLinkTableName(t)
+ " where FIRST_GENE_FK in (:genes) and SUPPORT>=:s";
Session sess = this.getSessionFactory().getCurrentSession();
SQLQuery query1 = sess.createSQLQuery(sqlQuery1);
query1.setParameterList("genes", geneIds.toArray());
query1.setParameter("s", Math.max(1, stringency));
// This is actually pretty fast.
return (List<Object[]>) query1.list();
}
From source file:ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl.java
License:Apache License
/** * Alternative method: query twice, once to get the coexpression basics and then again to get the support details, * instead of using a join./* w w w. j a va 2s .com*/ * * @param populateTestedInDetails populate tested in details * @param stringency stringency * @param geneIds gene IDs * @param t taxon */ private Map<Long, List<CoexpressionValueObject>> getCoexpressionFromDbViaGenes2(Collection<Long> geneIds, Taxon t, int stringency, boolean populateTestedInDetails) { StopWatch timer = new StopWatch(); timer.start(); List<Object[]> q1results = this.getRawCoexpressionFromDbViaGenes(geneIds, t, stringency); CoexpressionDaoImpl.log.debug(q1results.size() + " raw coexpression results for " + geneIds.size() + " genes at support>=" + stringency + " " + timer.getTime() + "ms"); if (q1results.isEmpty()) { return new HashMap<>(); } List<Object[]> supportDetails = new ArrayList<>(); /* * Because we are not trimming the results at all here, this can be a lot of data to iterate over, even at * high stringencies. For example, for 20 genes at a stringency of 5, because the query above does not * constrain to data sets, there can be >500 per gene, or >100k links in total. Fetching the support details * here is rather wasteful if we are not retaining the results, but we don't know that until we know which * data sets are supporting. */ BatchIterator<Object[]> batches = BatchIterator.batches(q1results, CoexpressionDaoImpl.BATCH_SIZE); int n = 1; for (Collection<Object[]> batch : batches) { StopWatch timer2 = new StopWatch(); timer2.start(); List<Long> supportDetailsIds = new ArrayList<>(); for (Object[] oa : batch) { Long supportDetailsId = ((BigInteger) oa[5]).longValue(); supportDetailsIds.add(supportDetailsId); } // Note: should never be empty String sqlQuery2 = "select ID,BYTES from " + CoexpressionQueryUtils.getSupportDetailsTableName(t) + " where ID in (:ids)"; SQLQuery query2 = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery2); query2.setParameterList("ids", supportDetailsIds.toArray()); supportDetails.addAll(query2.list()); if (timer2.getTime() > 1000) { CoexpressionDaoImpl.log .debug("Fetch batch " + n + " of support details: " + timer2.getTime() + "ms"); } n++; } CoexpressionDaoImpl.log .debug("Fetched details for " + supportDetails.size() + " coexpressions, " + n + " batches"); if (timer.getTime() > 5000) { CoexpressionDaoImpl.log.info("Coexpression query: " + geneIds.size() + " genes took " + timer.getTime() + "ms: " + q1results.size() + " results"); } timer.reset(); timer.start(); // it might be better to do this in the loop above, incrementally per batch. Map<Long, List<CoexpressionValueObject>> results = this.convertToValueObjects(q1results, supportDetails, geneIds); if (timer.getTime() > 100) { CoexpressionDaoImpl.log .info("Convert to value objects " + q1results.size() + " results: " + timer.getTime() + "ms"); } timer.reset(); timer.start(); for (Long g : results.keySet()) { List<CoexpressionValueObject> gc = results.get(g); Collections.sort(gc); if (populateTestedInDetails) { this.populateTestedInDetails(gc); } } if (timer.getTime() > 100) { CoexpressionDaoImpl.log .info("Filter, sort and finish " + q1results.size() + " results: " + timer.getTime() + "ms"); } return results; }
From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java
License:Apache License
/** * Key method: find Genes link to a phenotype taking into account private and public evidence Here on the cases : * <ul>// w w w . ja v a2 s .c o m * <li>1- Admin - can see anything * <li>2- user not logged in - only public data * <li>3- user logged in only showing what he has read access - public, shared + owned * <li>4- user logged in only showing what he has write access - owned. * </ul> */ @Override public Collection<GeneEvidenceValueObject> findGenesWithPhenotypes(Set<String> phenotypeUris, Taxon taxon, boolean showOnlyEditable, Collection<Long> externalDatabaseIds) { if (phenotypeUris.isEmpty()) { return new HashSet<>(); } // build query. // base query; 0: gene id 1: ncbi id 2: name 3: symbol 4: taxon id 5: taxon name 6: characteristic value URI String sqlSelectQuery = "select distinct gene.ID as gid, gene.NCBI_GENE_ID, gene.OFFICIAL_NAME, " + "gene.OFFICIAL_SYMBOL, tax.ID as taxonid, tax.COMMON_NAME, charac.VALUE_URI "; String sqlQuery = sqlSelectQuery + this.getPhenotypesGenesAssociationsBeginQuery(false); sqlQuery += this.addValuesUriToQuery(SecurityUtil.isUserAdmin() ? " where " : " and ", phenotypeUris); if (!SecurityUtil.isUserAdmin()) { if (!sqlQuery.trim().endsWith("where")) { sqlQuery += " and "; } sqlQuery += EntityUtils.addGroupAndUserNameRestriction(showOnlyEditable, true); } sqlQuery += this.addTaxonToQuery(taxon, !showOnlyEditable); sqlQuery += this.addExternalDatabaseQuery(externalDatabaseIds); // create query and set parameters. SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery); queryObject.setParameterList("valueUris", phenotypeUris); if (sqlQuery.contains(":taxonId")) { queryObject.setParameter("taxonId", taxon.getId()); } EntityUtils.addUserAndGroupParameters(queryObject, this.getSessionFactory()); return this.populateGenesWithPhenotypes(queryObject); }
From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java
License:Apache License
/** * find all private phenotypes associated with genes on a specific taxon and containing the valuesUri *///from w ww .ja va 2 s.c om @Override public Map<String, Set<Integer>> findPrivatePhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation) { /* * At this level of the application, we can't access acls. The reason for this so we don't get uneven page * numbers. ACESID 4 is anonymous; MASK=1 is read. */ String sqlQuery = "select gene.NCBI_GENE_ID, charac.VALUE_URI "; sqlQuery += this.getPhenotypesGenesAssociationsBeginQuery(true); if (!sqlQuery.trim().endsWith("where")) { sqlQuery += " and "; } sqlQuery += EntityUtils.addGroupAndUserNameRestriction(showOnlyEditable, false); sqlQuery += "and phen.ID not in " + "(select phen.ID from CHARACTERISTIC as charac " + " inner join PHENOTYPE_ASSOCIATION as phen on charac.PHENOTYPE_ASSOCIATION_FK = phen.ID " + "inner join CHROMOSOME_FEATURE as gene on gene.ID = phen.GENE_FK " + "inner join TAXON tax on tax.ID = gene.TAXON_FK " // ACL + "inner join ACLOBJECTIDENTITY aoi on phen.ID = aoi.OBJECT_ID " + "inner join ACLENTRY ace on ace.OBJECTIDENTITY_FK = aoi.ID " + "inner join ACLSID sid on sid.ID = aoi.OWNER_SID_FK where ace.MASK = 1 and ace.SID_FK = 4 " + "and aoi.OBJECT_CLASS IN " + PhenotypeAssociationDaoImpl.DISCRIMINATOR_CLAUSE + ") "; sqlQuery += this.addTaxonToQuery(taxon); sqlQuery += this.addValuesUriToQuery("and", valuesUri); sqlQuery += this.addExternalDatabaseQuery(externalDatabaseIds); if (noElectronicAnnotation) { sqlQuery += PhenotypeAssociationDaoImpl.QUERY_EV_CODE; } SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery); if (sqlQuery.contains(":valueUris")) { queryObject.setParameterList("valueUris", valuesUri); } if (sqlQuery.contains(":taxonId")) { queryObject.setParameter("taxonId", taxon.getId()); } EntityUtils.addUserAndGroupParameters(queryObject, this.getSessionFactory()); return this.populateGenesAssociations(queryObject); }
From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java
License:Apache License
/** * find all public phenotypes associated with genes on a specific taxon and containing the valuesUri *//*from ww w .j ava 2 s . c o m*/ @Override public Map<String, Set<Integer>> findPublicPhenotypesGenesAssociations(Taxon taxon, Set<String> valuesUri, boolean showOnlyEditable, Collection<Long> externalDatabaseIds, boolean noElectronicAnnotation) { String sqlQuery = "select gene.NCBI_GENE_ID, charac.VALUE_URI "; sqlQuery += this.getPhenotypesGenesAssociationsBeginQuery(true); // rule to find public: anonymous, READ. if (!sqlQuery.trim().endsWith("where")) { sqlQuery += " and "; } sqlQuery += " ace.MASK = 1 and ace.SID_FK = 4 "; sqlQuery += this.addTaxonToQuery(taxon); sqlQuery += this.addValuesUriToQuery("and", valuesUri); sqlQuery += this.addExternalDatabaseQuery(externalDatabaseIds); if (noElectronicAnnotation) { sqlQuery += PhenotypeAssociationDaoImpl.QUERY_EV_CODE; } if (showOnlyEditable) { sqlQuery += "and phen.ID in ( select phen.ID "; sqlQuery += this.getPhenotypesGenesAssociationsBeginQuery(false); if (!sqlQuery.trim().endsWith("where")) { sqlQuery += " and "; } sqlQuery += EntityUtils.addGroupAndUserNameRestriction(true, false); sqlQuery += ") "; } SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery); if (sqlQuery.contains(":valueUris")) { queryObject.setParameterList("valueUris", valuesUri); } if (sqlQuery.contains(":taxonId")) { queryObject.setParameter("taxonId", taxon.getId()); } EntityUtils.addUserAndGroupParameters(queryObject, this.getSessionFactory()); return this.populateGenesAssociations(queryObject); }
From source file:ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl.java
License:Apache License
@Override public Map<CompositeSequence, Collection<Gene>> getGenes(Collection<CompositeSequence> compositeSequences) { Map<CompositeSequence, Collection<Gene>> returnVal = new HashMap<>(); int BATCH_SIZE = 2000; if (compositeSequences.size() == 0) return returnVal; /*/* ww w .j av a 2s . c om*/ * Get the cs->gene mapping */ final String nativeQuery = "SELECT CS, GENE FROM GENE2CS WHERE CS IN (:csids) "; for (CompositeSequence cs : compositeSequences) { returnVal.put(cs, new HashSet<Gene>()); } List<Object> csGene = new ArrayList<>(); Session session = this.getSessionFactory().getCurrentSession(); org.hibernate.SQLQuery queryObject = session.createSQLQuery(nativeQuery); queryObject.addScalar("cs", new LongType()); queryObject.addScalar("gene", new LongType()); Collection<Long> csIdBatch = new HashSet<>(); for (CompositeSequence cs : compositeSequences) { csIdBatch.add(cs.getId()); if (csIdBatch.size() == BATCH_SIZE) { queryObject.setParameterList("csids", csIdBatch); csGene.addAll(queryObject.list()); session.clear(); csIdBatch.clear(); } } if (csIdBatch.size() > 0) { queryObject.setParameterList("csids", csIdBatch); csGene.addAll(queryObject.list()); session.clear(); } StopWatch watch = new StopWatch(); watch.start(); int count = 0; Collection<Long> genesToFetch = new HashSet<>(); Map<Long, Collection<Long>> cs2geneIds = new HashMap<>(); for (Object object : csGene) { Object[] ar = (Object[]) object; Long cs = (Long) ar[0]; Long gene = (Long) ar[1]; if (!cs2geneIds.containsKey(cs)) { cs2geneIds.put(cs, new HashSet<Long>()); } cs2geneIds.get(cs).add(gene); genesToFetch.add(gene); } // nothing found? if (genesToFetch.size() == 0) { returnVal.clear(); return returnVal; } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Built cs -> gene map in " + watch.getTime() + " ms; fetching " + genesToFetch.size() + " genes."); // fetch the genes Collection<Long> batch = new HashSet<>(); Collection<Gene> genes = new HashSet<>(); String geneQuery = "from Gene g where g.id in ( :gs )"; org.hibernate.Query geneQueryObject = this.getSessionFactory().getCurrentSession().createQuery(geneQuery) .setFetchSize(1000); for (Long gene : genesToFetch) { batch.add(gene); if (batch.size() == BATCH_SIZE) { AbstractDao.log.debug("Processing batch ... "); geneQueryObject.setParameterList("gs", batch); //noinspection unchecked genes.addAll(geneQueryObject.list()); batch.clear(); } } if (batch.size() > 0) { geneQueryObject.setParameterList("gs", batch); //noinspection unchecked genes.addAll(geneQueryObject.list()); } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Got information on " + genes.size() + " genes in " + watch.getTime() + " ms"); Map<Long, Gene> geneIdMap = new HashMap<>(); for (Gene g : genes) { Hibernate.initialize(g); Long id = g.getId(); geneIdMap.put(id, g); } // fill in the return value. for (CompositeSequence cs : compositeSequences) { Long csId = cs.getId(); assert csId != null; Collection<Long> genesToAttach = cs2geneIds.get(csId); if (genesToAttach == null) { // this means there was no gene for that cs; we should remove it from the result returnVal.remove(cs); continue; } for (Long geneId : genesToAttach) { returnVal.get(cs).add(geneIdMap.get(geneId)); } ++count; } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Done, " + count + " result rows processed, " + returnVal.size() + "/" + compositeSequences.size() + " probes are associated with genes"); return returnVal; }