List of usage examples for java.sql PreparedStatement setFetchSize
void setFetchSize(int rows) throws SQLException;
ResultSet objects generated by this Statement. From source file:org.wso2.carbon.dataservices.core.description.query.SQLQuery.java
private PreparedStatement createProcessedPreparedStatement(int queryType, InternalParamCollection params, Connection conn) throws DataServiceFault { try {//from w ww .j a v a 2 s.c o m /* * lets see first if there's already a batch prepared statement * created */ boolean inTheMiddleOfABatch = false; PreparedStatement stmt = this.getBatchPreparedStatement(); int currentParamCount = this.getParamCount(); /* create a new prepared statement */ if (stmt == null) { /* batch mode is not supported for dynamic queries */ Object[] result = this.processDynamicQuery(this.getQuery(), params); String dynamicSQL = (String) result[0]; currentParamCount = (Integer) result[1]; String processedSQL = this.createProcessedQuery(dynamicSQL, params, currentParamCount); if (queryType == SQLQuery.DS_QUERY_TYPE_NORMAL) { if (this.isReturnGeneratedKeys()) { if (this.getKeyColumns() != null) { stmt = conn.prepareStatement(processedSQL, this.getKeyColumns()); } else { stmt = conn.prepareStatement(processedSQL, Statement.RETURN_GENERATED_KEYS); } } else { stmt = conn.prepareStatement(processedSQL); } } else if (queryType == SQLQuery.DS_QUERY_TYPE_STORED_PROC) { stmt = conn.prepareCall(processedSQL); } else { throw new DataServiceFault("Unsupported query type: " + queryType); } } else { inTheMiddleOfABatch = true; } if (!inTheMiddleOfABatch) { /* set query timeout */ if (this.isHasQueryTimeout()) { stmt.setQueryTimeout(this.getQueryTimeout()); } /* adding the try catch to avoid setting this for jdbc drivers that do not implement this method. */ try { /* set fetch direction */ if (this.isHasFetchDirection()) { stmt.setFetchDirection(this.getFetchDirection()); } /* set fetch size - user's setting */ if (this.isHasFetchSize()) { stmt.setFetchSize(this.getFetchSize()); } else { /* * stream data by sections - avoid the full result set * to be loaded to memory, and only stream if there * aren't any OUT parameters, MySQL fails in the * scenario of streaming and OUT parameters, so the * possibility is there for other DBMSs */ if (!this.hasOutParams() && this.getFetchSizeProperty().isChangeFetchSize()) { stmt.setFetchSize(this.getFetchSizeProperty().getFetchSize()); } } } catch (Throwable e) { log.debug("Exception while setting fetch size: " + e.getMessage(), e); } /* set max field size */ if (this.isHasMaxFieldSize()) { stmt.setMaxFieldSize(this.getMaxFieldSize()); } /* set max rows */ if (this.isHasMaxRows()) { stmt.setMaxRows(this.getMaxRows()); } } int currentOrdinal = 0; InternalParam param; ParamValue value; for (int i = 1; i <= currentParamCount; i++) { param = params.getParam(i); value = param.getValue(); /* * handle array values, if value is null, this param has to be * an OUT param */ if (value != null && value.getValueType() == ParamValue.PARAM_VALUE_ARRAY) { for (ParamValue arrayElement : value.getArrayValue()) { this.setParamInPreparedStatement(stmt, param, arrayElement == null ? null : arrayElement.toString(), queryType, currentOrdinal); currentOrdinal++; } } else { /* scalar value */ this.setParamInPreparedStatement(stmt, param, value != null ? value.getScalarValue() : null, queryType, currentOrdinal); currentOrdinal++; } } /* if we are in JDBC batch processing mode, batch it! */ if (this.isJDBCBatchRequest()) { stmt.addBatch(); } return stmt; } catch (SQLException e) { throw new DataServiceFault(e, "Error in 'createProcessedPreparedStatement'"); } }
From source file:uk.ac.ebi.orchem.search.SimilaritySearch.java
/** * Performs a similarity search between a query molecule and the orchem fingerprint table. * * @param queryFp fingerprint of the query molecule * @param _cutOff tanimoto score below which to stop searching * @param _topN top N results after which to stop searching * @param debugYN Y or N to debug output back * @param idsOnlyYN Y or N to indicate to just return IDs of results (faster) * @param extraWhereClause option to include an extra SQL where clause refering to the base compound table * @return array of {@link uk.ac.ebi.orchem.bean.OrChemCompound compounds} * @throws Exception//from w w w . jav a2 s. com */ private static oracle.sql.ARRAY search(BitSet queryFp, Float _cutOff, Integer _topN, String debugYN, String idsOnlyYN, String extraWhereClause) throws Exception { /* * The comment block below describes the search algorithm. From: "Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time" S.Joshua Swamidass and Pierre Baldi http://dx.doi.org/10.1021/ci600358f Top K Hits ---------- We can search for the top K hits by starting from the maximum (where A=B), and exploring discrete possible values of B right and left of the maximum. More precisely, for binary fingerprints, we first index the molecules in the database by their fingerprint "bit count" to enable efficient referencing of a particular bit count bin. Next, with respect to a particular query, we calculate the bound on the similarity for every bit count in the database. Then we sort these bit counts by their associated bound and iterate over the molecules in the database, in order of decreasing bound. As we iterate, we calculate the similarity between the query and the database molecule and use a heap to efficiently track the top hits. The algorithm terminates when "the lowest similarity value in the heap is greater than the bound associated with the current database bin" Algorithm 1 Top K Search Require: database of fingerprints binned by bit count Bs Ensure: hits contains top K hits which satisfy SIMILARITY( ) > T 1: hits <- MINHEAP() 2: bounds <- LIST() 3: for all B in database do //iterate over bins 4: tuple <- TUPLE(BOUND(A,B),B) 5: LISTAPPEND(bounds, tuple) 6: end for 7: QUICKSORT(bounds) //NOTE: the length of bounds is constant 8: for all bound, B in bounds do //iterate in order of decreasing bound 9: if bound < T then 10: break //threshold stopping condition 11: end if 12: if K HEAPSIZE(hits) and bound < MINSIMILARITY(hits) then 13: break //top-K stopping condition 14: end if 15: for all in database[B] do 16: S=SIMILARITY( ) 17: tuple <- TUPLE(S, ) 18: if S T then 19: continue //ignore this and continue to next 20: else if LENGTH(hits)< K then 21: HEAPPUSH(hits, tuple) 22: else if S > MINSIMILARITY(hits) then 23: HEAPPOPMIN(hits) 24: HEAPPUSH(hits,tuple) 25: end if 26: end for 27: end for 28: return hits */ boolean debugging = false; if (debugYN.toLowerCase().equals("y")) debugging = true; debug("started", debugging); /********************************************************************** * Similarity search algorithm section * * * **********************************************************************/ Comparator heapComparator = new SimHeapElementTanimComparator(); PriorityBuffer heap = null; OracleConnection conn = null; PreparedStatement pstmtFp = null; PreparedStatement pstmLookup = null; String query = " select bit_count, id, fp from orchem_fingprint_simsearch s where bit_count = ? "; float cutOff = _cutOff.floatValue(); int topN = -1; if (_topN == null) { debug("No topN breakout specified.. searching until lower bound reached", debugging); } else { topN = _topN.intValue(); debug("topN is " + topN + ", result set size limited.", debugging); } try { conn = (OracleConnection) new OracleDriver().defaultConnection(); String compoundTableName = OrChemParameters.getParameterValue(OrChemParameters.COMPOUND_TABLE, conn); String compoundTablePkColumn = OrChemParameters.getParameterValue(OrChemParameters.COMPOUND_PK, conn); String compoundTableMolfileColumn = OrChemParameters.getParameterValue(OrChemParameters.COMPOUND_MOL, conn); if (extraWhereClause != null) { query = " select s.bit_count, s.id, s.fp from " + " orchem_fingprint_simsearch s , " + compoundTableName + " c " + " where s.bit_count = ? " + " and s.id = c." + compoundTablePkColumn + " " + " and " + extraWhereClause; debug("QUERY is " + query, debugging); } float queryBitCount = queryFp.cardinality(); byte[] queryBytes = Utils.toByteArray(queryFp, extFpSize); int queryByteArrLen = queryBytes.length; float lowBucketNum = queryBitCount - 1; float highBucketNum = queryBitCount + 1; float currBucketNum = queryBitCount; pstmtFp = conn.prepareStatement(query); pstmtFp.setFetchSize(250); ResultSet resFp = null; boolean done = false; byte[] dbByteArray = null; float tanimotoCoeff = 0f; heap = new PriorityBuffer(true, heapComparator); int bucksSearched = 0; int loopCount = 0; while (!done) { debug("bucket is " + currBucketNum, debugging); loopCount++; pstmtFp.setFloat(1, currBucketNum); bucksSearched++; resFp = pstmtFp.executeQuery(); float bound = 0f; if (currBucketNum < queryBitCount) bound = currBucketNum / queryBitCount; else bound = queryBitCount / currBucketNum; /* Algorithm step 9..11 Here we can break out because the tanimoto score is becoming to low */ if (bound < cutOff) { debug("bound < cutOff, done", debugging); done = true; } if (!done) { //Algorithm 15-26 while (resFp.next()) { dbByteArray = resFp.getBytes("fp"); tanimotoCoeff = calcTanimoto(queryBytes, queryByteArrLen, dbByteArray, queryBitCount, currBucketNum); if (tanimotoCoeff >= cutOff) { SimHeapElement elm = new SimHeapElement(); elm.setID(resFp.getString("id")); elm.setTanimotoCoeff(new Float(tanimotoCoeff)); if (heap.size() < topN || topN == -1) { heap.add(elm); debug("add elem " + elm.getID(), debugging); } else if (tanimotoCoeff > ((SimHeapElement) (heap.get())).getTanimotoCoeff() .floatValue()) { heap.remove(); heap.add(elm); debug("remove + add elem " + elm.getID(), debugging); } } } resFp.close(); /* Algorithm 12-14: * When top N hits is reached, and the lowest score of the * hits is greater than the current bucket bound, stop. * If not, the next bucket may contain a better score, so go on. */ if (topN != -1 && heap.size() >= topN && ((SimHeapElement) (heap.get())).getTanimotoCoeff().floatValue() > bound) { done = true; debug("topN reached, done", debugging); } else { // calculate new currBucket float up = queryBitCount / highBucketNum; float down = lowBucketNum / queryBitCount; if (up > down) { currBucketNum = highBucketNum; highBucketNum++; } else { currBucketNum = lowBucketNum; lowBucketNum--; } if (lowBucketNum < 1 && highBucketNum > extFpSize) done = true; } } } debug("searched bit_count buckets: " + loopCount, debugging); /******************************************************************** * Search completed. * * * * Next section is just looking up the compounds by ID and * * returning the results, sorted by Tanimoto coefficient * * * *******************************************************************/ String lookupCompoundQuery = " select " + compoundTableMolfileColumn + " from " + " " + compoundTableName + " where " + " " + compoundTablePkColumn + " =?"; pstmLookup = conn.prepareStatement(lookupCompoundQuery); List compounds = new ArrayList(); while (heap.size() != 0) { SimHeapElement bElm = (SimHeapElement) heap.remove(); if (idsOnlyYN.equals("N")) { // return structure to user pstmLookup.setString(1, bElm.getID()); ResultSet resLookup = pstmLookup.executeQuery(); if (resLookup.next()) { OrChemCompound c = new OrChemCompound(); c.setId(bElm.getID()); c.setScore(bElm.getTanimotoCoeff().floatValue()); c.setMolFileClob(resLookup.getClob(compoundTableMolfileColumn)); compounds.add(c); } resLookup.close(); } else { // only return ID and score to user OrChemCompound c = new OrChemCompound(); c.setId(bElm.getID()); c.setScore(bElm.getTanimotoCoeff().floatValue()); compounds.add(c); } } pstmLookup.close(); long befSort = System.currentTimeMillis(); Collections.sort(compounds, new OrChemCompoundTanimComparator()); debug("sorting time (ms) " + (System.currentTimeMillis() - befSort), debugging); OrChemCompound[] output = new OrChemCompound[compounds.size()]; for (int i = 0; i < compounds.size(); i++) { output[i] = (OrChemCompound) (compounds.get(i)); } ArrayDescriptor arrayDescriptor = ArrayDescriptor.createDescriptor("ORCHEM_COMPOUND_LIST", conn); debug("#compounds in result list : " + compounds.size(), debugging); debug("ended", debugging); return new ARRAY(arrayDescriptor, conn, output); } catch (Exception ex) { ex.printStackTrace(); throw (ex); } finally { if (pstmLookup != null) pstmLookup.close(); if (pstmtFp != null) pstmtFp.close(); if (conn != null) conn.close(); } }
From source file:uk.ac.ebi.orchem.search.SimilaritySearch.java
/** * Similarity score calculation between one database compound and a user's query compound. * @param userQuery query structure in SMILES or MOL * @param queryType MOL or SMILES//from ww w . ja v a2s. c o m * @param compoundId ID of database compound to calculate similarity with * @return tanimoto similarity score * @throws Exception */ public static float singleCompoundSimilarity(Clob userQuery, String queryType, String compoundId) throws Exception { OracleConnection conn = null; PreparedStatement pstmtFp = null; ResultSet resFp = null; float tanimotoCoeff = 0; try { //User query int clobLen = new Long(userQuery.length()).intValue(); String query = (userQuery.getSubString(1, clobLen)); IAtomContainer molecule = null; if (queryType.equals(Utils.QUERY_TYPE_MOL)) { molecule = MoleculeCreator.getMoleculeFromMolfile(query); } else if (queryType.equals(Utils.QUERY_TYPE_SMILES)) { SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); molecule = sp.parseSmiles(query); } else throw new RuntimeException("Query type not recognized"); BitSet queryFp = FingerPrinterAgent.FP.getExtendedFingerPrinter().getFingerprint(molecule); float queryBitCount = queryFp.cardinality(); byte[] queryBytes = Utils.toByteArray(queryFp, extFpSize); //Database comound conn = (OracleConnection) new OracleDriver().defaultConnection(); String compoundQuery = "select bit_count, fp from orchem_fingprint_simsearch s where id=?"; pstmtFp = conn.prepareStatement(compoundQuery); pstmtFp.setFetchSize(1); pstmtFp.setString(1, compoundId); resFp = pstmtFp.executeQuery(); if (resFp.next()) { byte[] dbByteArray = resFp.getBytes("fp"); float compoundBitCount = resFp.getFloat("bit_count"); tanimotoCoeff = calcTanimoto(queryBytes, queryBytes.length, dbByteArray, queryBitCount, compoundBitCount); } else throw new RuntimeException("Compound " + compoundId + " not found in similarity table"); } catch (Exception e) { e.printStackTrace(); throw e; } finally { if (resFp != null) resFp.close(); if (pstmtFp != null) pstmtFp.close(); if (conn != null) conn.close(); } return tanimotoCoeff; }