List of usage examples for java.sql ResultSet isLast
boolean isLast() throws SQLException;
ResultSet object. From source file:unikn.dbis.univis.visualization.graph.VGraph.java
/** * @param result The given resultset from the sql action. * @throws SQLException/*from www.j ava 2 s .co m*/ */ public void fillChartData(VDimension dimension, ResultSet result, ResultSet testResult) throws SQLException { layout.setAlignment(SwingConstants.CENTER); ResultSetMetaData data = result.getMetaData(); int idPos = data.getColumnCount(); int namePos = idPos - 1; int bufferPos = namePos - 1; List<String> testList = new ArrayList<String>(); while (testResult.next()) { testList.add(testResult.getString(1)); } List<String> helpList = new ArrayList<String>(testList); if (root == null) { cellHistory.historize(); if (ChartType.BAR_CHART_VERTICAL.equals(chartType) || ChartType.BAR_CHART_HORIZONTAL.equals(chartType) || ChartType.AREA_CHART.equals(chartType)) { dataset = new DefaultCategoryDataset(); while (result.next()) { ((DefaultCategoryDataset) dataset).addValue(result.getInt(1), result.getString(namePos + 1), ""); } } else { dataset = new DefaultPieDataset(); while (result.next()) { ((DefaultPieDataset) dataset).setValue(result.getString(namePos + 1), result.getInt(1)); } } root = createVertex(rootHeadLine, ""); root.setCellId("root"); cache.insert(root); cellHistory.add(root); } else { cellHistory.historize(); String buffer = ""; if (ChartType.BAR_CHART_VERTICAL.equals(chartType) || ChartType.BAR_CHART_HORIZONTAL.equals(chartType) || ChartType.AREA_CHART.equals(chartType)) { while (result.next()) { String currentValue = result.getString(idPos); if (!buffer.equals(currentValue)) { if (!result.isFirst()) { if (!helpList.isEmpty()) { for (String missing : helpList) { ((DefaultCategoryDataset) dataset).addValue(0, missing, ""); } } } dataset = new DefaultCategoryDataset(); VGraphCell nextCell = createVertex( MessageResolver.getMessage("data_reference." + dimension.getI18nKey()) + " (" + result.getString(bufferPos) + ")", result.getString(idPos)); createEdges(nextCell, result.getString(idPos)); cache.insert(nextCell); cellHistory.add(nextCell); helpList = new ArrayList<String>(testList); } for (String available : testList) { if (result.getString(namePos).equals(available)) { helpList.remove(available); } } ((DefaultCategoryDataset) dataset).addValue(result.getInt(1), result.getString(namePos), ""); buffer = currentValue; if (result.isLast()) { if (!helpList.isEmpty()) { for (String missing : helpList) { ((DefaultCategoryDataset) dataset).addValue(0, missing, ""); } } } } } else { while (result.next()) { String currentValue = result.getString(idPos); LOG.info(result.getString(2)); if (!buffer.equals(currentValue)) { dataset = new DefaultPieDataset(); VGraphCell nextCell = createVertex( MessageResolver.getMessage("data_reference." + dimension.getI18nKey()) + " (" + result.getString(bufferPos) + ")", result.getString(idPos)); createEdges(nextCell, result.getString(idPos)); cache.insert(nextCell); cellHistory.add(nextCell); } ((DefaultPieDataset) dataset).setValue(result.getString(namePos), result.getInt(1)); buffer = currentValue; } } } layout.run(facade); facade.setOrdered(true); Map nested = facade.createNestedMap(true, true); cache.edit(nested); }
From source file:org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor.java
/** * ==========================/*from w ww . ja v a2 s.com*/ * EXPERIMENTAL FACTORS * ========================== */ private void processEFactor(Connection connection) throws SQLException, ObjectStoreException { long bT = System.currentTimeMillis(); // to monitor time spent in the process ResultSet res = getEFactors(connection); int count = 0; int prevRank = -1; int prevSub = -1; ExperimentalFactor ef = null; String name = null; while (res.next()) { Integer submissionId = new Integer(res.getInt("experiment_id")); if (deletedSubMap.containsKey(submissionId)) { continue; } Integer rank = new Integer(res.getInt("rank")); String value = res.getString("value"); // the data is alternating between EF types and names, in order. if (submissionId != prevSub) { // except for the first record, this is a new EF object if (!res.isFirst()) { submissionEFMap.put(prevSub, ef); LOG.info("EF MAP: " + dccIdMap.get(prevSub) + "|" + ef.efNames); LOG.info("EF MAP types: " + rank + "|" + ef.efTypes); } ef = new ExperimentalFactor(); } if (rank != prevRank || submissionId != prevSub) { // this is a name if (getPreferredSynonym(value) != null) { value = getPreferredSynonym(value); } ef.efNames.add(value); name = value; count++; } else { // this is a type ef.efTypes.put(name, value); name = null; if (res.isLast()) { submissionEFMap.put(submissionId, ef); LOG.debug("EF MAP last: " + submissionId + "|" + rank + "|" + ef.efNames); } } prevRank = rank; prevSub = submissionId; } res.close(); LOG.info("created " + count + " experimental factors"); LOG.info("PROCESS TIME experimental factors: " + (System.currentTimeMillis() - bT) + " ms"); }
From source file:org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor.java
/** * =====================/*from w w w.jav a2 s . c o m*/ * DATA ATTRIBUTES * ===================== */ private void processAppliedDataAttributesNEW(Connection connection) throws SQLException, ObjectStoreException { // attempts to collate attributes // TODO check! long bT = System.currentTimeMillis(); // to monitor time spent in the process ResultSet res = getAppliedDataAttributes(connection); int count = 0; Integer previousDataId = 0; String previousName = null; String value = null; String type = null; while (res.next()) { Integer dataId = new Integer(res.getInt("data_id")); // check if not belonging to a deleted sub // better way? Integer submissionId = dataSubmissionMap.get(dataId); if (submissionId == null || deletedSubMap.containsKey(submissionId)) { continue; } String name = res.getString("heading"); // LOG.info("DA " + dataId + ": " + name); if (previousDataId == 0) { //first pass value = res.getString("value"); type = res.getString("name"); previousDataId = dataId; previousName = name; LOG.info("DA0 " + dataId + ": " + name + "|" + value); continue; } if (dataId > previousDataId) { Item dataAttribute = storeDataAttribute(value, type, previousDataId, previousName); value = res.getString("value"); type = res.getString("name"); count++; previousDataId = dataId; previousName = name; LOG.info("DA1 new: " + previousDataId + ": " + previousName + "|" + value); continue; } if (!name.equalsIgnoreCase(previousName)) { Item dataAttribute = storeDataAttribute(value, type, dataId, previousName); // LOG.info("DA2 store: " + dataId + ": " + previousName + "|" + value); count++; value = res.getString("value"); previousName = name; LOG.info("DA2 new: " + dataId + ": " + previousName + "|" + value); } else { value = value + ", " + res.getString("value"); } type = res.getString("name"); previousDataId = dataId; if (res.isLast()) { Item dataAttribute = storeDataAttribute(value, type, dataId, name); count++; } } LOG.info("created " + count + " data attributes"); res.close(); LOG.info("PROCESS TIME data attributes: " + (System.currentTimeMillis() - bT) + " ms"); }
From source file:org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor.java
/** * * ====================/* ww w. j av a 2s. co m*/ * DAG * ==================== * * In chado, Applied protocols in a submission are linked to each other via * the flow of data (output of a parent AP are input to a child AP). * The method process the data from chado to build the objects * (SubmissionDetails, AppliedProtocol, AppliedData) and their * respective maps to chado identifiers needed to traverse the DAG. * It then traverse the DAG, assigning the experiment_id to all data. * * @param connection * @throws SQLException * @throws ObjectStoreException */ private void processDag(Connection connection) throws SQLException, ObjectStoreException { long bT = System.currentTimeMillis(); // to monitor time spent in the process ResultSet res = getDAG(connection); AppliedProtocol node = new AppliedProtocol(); AppliedData branch = null; Integer count = new Integer(0); Integer actualSubmissionId = new Integer(0); // to store the experiment id (see below) Integer previousAppliedProtocolId = new Integer(0); boolean isADeletedSub = false; while (res.next()) { Integer submissionId = new Integer(res.getInt("experiment_id")); Integer protocolId = new Integer(res.getInt("protocol_id")); Integer appliedProtocolId = new Integer(res.getInt("applied_protocol_id")); Integer dataId = new Integer(res.getInt("data_id")); String direction = res.getString("direction"); LOG.debug("DAG: " + submissionId + " p:" + protocolId + " ap:" + appliedProtocolId + " d:" + dataId + " | " + direction); // the results are ordered, first ap have a subId // if we find a deleted sub, we know that subsequent records with null // subId belongs to the deleted sub // note that while the subId is null in the database, it is = 0 here if (submissionId == 0) { if (isADeletedSub) { LOG.debug("DEL: skipping" + isADeletedSub); continue; } } else { if (deletedSubMap.containsKey(submissionId)) { isADeletedSub = true; LOG.debug("DEL: " + submissionId + " ->" + isADeletedSub); continue; } else { isADeletedSub = false; LOG.debug("DEL: " + submissionId + " ->" + isADeletedSub); } } // build a data node for each iteration if (appliedDataMap.containsKey(dataId)) { branch = appliedDataMap.get(dataId); } else { branch = new AppliedData(); } // could use > (order by apid, apdataid, direction) // NB: using isLast() is expensive if (!appliedProtocolId.equals(previousAppliedProtocolId) || res.isLast()) { // the submissionId != null for the first applied protocol if (submissionId > 0) { firstAppliedProtocols.add(appliedProtocolId); LOG.debug("DAG fap subId:" + submissionId + " apID: " + appliedProtocolId); // set actual submission id // we can either be at a first applied protocol (submissionId > 0).. actualSubmissionId = submissionId; } else { // ..or already down the dag, and we use the stored id. submissionId = actualSubmissionId; } // last one: fill the list of outputs // and add to the general list of data ids for the submission, // used to fetch features if (res.isLast()) { if ("output".equalsIgnoreCase(direction)) { node.outputs.add(dataId); mapSubmissionAndData(submissionId, dataId); } } // if it is not the first iteration, let's store it if (previousAppliedProtocolId > 0) { appliedProtocolMap.put(previousAppliedProtocolId, node); } // new node AppliedProtocol newNode = new AppliedProtocol(); newNode.protocolId = protocolId; newNode.submissionId = submissionId; if (direction.startsWith("in")) { // add this applied protocol to the list of nextAppliedProtocols branch.nextAppliedProtocols.add(appliedProtocolId); // ..and update the map updateAppliedDataMap(branch, dataId); // .. and add the dataId to the list of input Data for this applied protocol newNode.inputs.add(dataId); mapSubmissionAndData(submissionId, dataId); //*** } else if (direction.startsWith("out")) { // add the dataId to the list of output Data for this applied protocol: // it will be used to link to the next set of applied protocols newNode.outputs.add(dataId); if (previousAppliedProtocolId > 0) { branch.previousAppliedProtocols.add(previousAppliedProtocolId); updateAppliedDataMap(branch, dataId); //*** mapSubmissionAndData(submissionId, dataId); //**** } } else { // there is some problem with the strings 'input' or 'output' throw new IllegalArgumentException( "Data direction not valid for dataId: " + dataId + "|" + direction + "|"); } // for the new round.. node = newNode; previousAppliedProtocolId = appliedProtocolId; } else { // keep feeding IN et OUT if (direction.startsWith("in")) { node.inputs.add(dataId); if (submissionId > 0) { // initial data mapSubmissionAndData(submissionId, dataId); } // as above branch.nextAppliedProtocols.add(appliedProtocolId); updateAppliedDataMap(branch, dataId); } else if (direction.startsWith("out")) { node.outputs.add(dataId); branch.previousAppliedProtocols.add(appliedProtocolId); updateAppliedDataMap(branch, dataId); //*** } else { throw new IllegalArgumentException( "Data direction not valid for dataId: " + dataId + "|" + direction + "|"); } } count++; } LOG.info("created " + appliedProtocolMap.size() + "(" + count + " applied data points) DAG nodes (= applied protocols) in map"); res.close(); // now traverse the DAG, and associate submission with all the applied protocols traverseDag(); // set the dag level as an attribute to applied protocol setAppliedProtocolSteps(connection); LOG.info("PROCESS TIME DAG: " + (System.currentTimeMillis() - bT) + " ms"); }