1 package compbio.stat.collector;
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3 import java.sql.Connection;
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4 import java.sql.DriverManager;
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5 import java.sql.PreparedStatement;
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6 import java.sql.ResultSet;
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7 import java.sql.SQLException;
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8 import java.sql.Statement;
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9 import java.sql.Timestamp;
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10 import java.util.ArrayList;
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11 import java.util.Date;
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12 import java.util.List;
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13 import java.util.Set;
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15 import org.apache.log4j.Logger;
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17 import compbio.engine.conf.PropertyHelperManager;
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18 import compbio.util.Util;
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19 import compbio.ws.client.Services;
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22 * The database must be stored in the application root directory and called
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23 * "ExecutionStatistic"
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28 public class StatDB {
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30 private static final String driver = "org.apache.derby.jdbc.EmbeddedDriver";
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31 private static final String protocol = "jdbc:derby:";
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32 private static final String statDBName = "ExecutionStatistic";
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34 private static final Logger log = Logger.getLogger(StatDB.class);
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36 static Connection conn;
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38 private synchronized static Connection getDBConnection()
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39 throws SQLException {
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41 if (conn != null && !conn.isClosed()) {
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44 String dbpath = PropertyHelperManager.getLocalPath();
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45 log.info("Looking for JABAWS access statistics database at: "
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47 System.setProperty("derby.system.home", dbpath);
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48 conn = DriverManager.getConnection(protocol + statDBName
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51 conn.setAutoCommit(true);
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53 Runtime.getRuntime().addShutdownHook(new Thread() {
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62 public StatDB() throws SQLException {
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63 this.conn = getDBConnection();
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67 * Connect to test database
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70 * @throws SQLException
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72 StatDB(boolean ignored) throws SQLException {
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73 this.conn = getTestDBConnection();
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76 private static Connection getTestDBConnection() throws SQLException {
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77 System.setProperty("derby.system.home", "testsrc/testdata");
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78 Connection conn = DriverManager.getConnection(protocol + statDBName
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80 conn.setAutoCommit(true);
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84 // ServiceName,jobname,start,finish,inputSize,resultSize,isCancelled,isCollected
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87 * rs.getBoolean(i) will return true for any non-zero value and false for 0
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88 * on SMALLINT data column.
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90 * @throws SQLException
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92 private void createStatTable() throws SQLException {
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95 * Creating a statement object that we can use for running various SQL
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96 * statements commands against the database.
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98 Statement s = conn.createStatement();
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99 String create = "create table exec_stat("
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100 + "number INT GENERATED ALWAYS AS IDENTITY,"
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101 + "service_name VARCHAR(15) NOT NULL, "
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102 + "cluster_job_id VARCHAR(30), "
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103 + "job_id VARCHAR(35) NOT NULL PRIMARY KEY, "
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104 + "start TIMESTAMP," + "finish TIMESTAMP,"
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105 + "inputsize BIGINT," + "resultsize BIGINT,"
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106 + "isCancelled SMALLINT NOT NULL,"
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107 + "isCollected SMALLINT NOT NULL, "
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108 + "isClusterJob SMALLINT NOT NULL)";
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109 // We create a table...
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110 System.out.println(create);
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116 void insertData(Set<JobStat> jobstatus) throws SQLException {
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117 System.out.println("Inserting " + jobstatus.size());
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119 conn.setAutoCommit(false);
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120 String insert = "insert into exec_stat (service_name, cluster_job_id, job_id, start, finish, "
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121 + "inputsize, resultsize, isCancelled, isCollected, isClusterJob) "
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122 + "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)";
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123 PreparedStatement pstm = conn.prepareStatement(insert);
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124 for (JobStat js : jobstatus) {
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126 pstm.setString(1, js.webService.toString());
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128 if (!Util.isEmpty(js.clusterJobId)) {
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129 pstm.setString(2, js.clusterJobId);
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131 pstm.setString(2, null);
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134 pstm.setString(3, js.jobname);
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136 if (js.start != ExecutionStatCollector.UNDEFINED) {
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137 pstm.setTimestamp(4, new Timestamp(js.start));
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139 pstm.setTimestamp(4, null);
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141 if (js.finish != ExecutionStatCollector.UNDEFINED) {
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142 pstm.setTimestamp(5, new Timestamp(js.finish));
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144 pstm.setTimestamp(5, null);
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147 pstm.setLong(6, js.inputSize);
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149 pstm.setLong(7, js.resultSize);
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151 pstm.setBoolean(8, js.isCancelled);
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152 pstm.setBoolean(9, js.isCollected);
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153 pstm.setBoolean(10, js.isClusterJob());
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154 pstm.executeUpdate();
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160 public Date getEarliestRecord() throws SQLException {
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161 String query = "select min(start) from exec_stat";
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162 Statement st = conn.createStatement();
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163 ResultSet res = st.executeQuery(query);
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164 boolean exist = res.next();
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165 Date date = new Date();
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167 date = res.getDate(1);
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175 public int getTotalJobsCount(Timestamp from, Timestamp to)
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176 throws SQLException {
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177 String allQuery = "select count(*) from exec_stat where start BETWEEN ? and ? ";
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178 return getIntResult(from, to, allQuery);
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181 public int getCancelledCount(Timestamp from, Timestamp to)
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182 throws SQLException {
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184 String cancelledQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and isCancelled=1 ";
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185 return getIntResult(from, to, cancelledQuery);
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188 public int getAbandonedCount(Timestamp from, Timestamp to)
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189 throws SQLException {
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190 // !js.isCollected && !js.isCancelled && js.hasResult()
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191 String abandonedQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and isCollected=0 and isCancelled=0 and resultsize>0 ";
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192 return getIntResult(from, to, abandonedQuery);
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195 public int getIncompleteCount(Timestamp from, Timestamp to)
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196 throws SQLException {
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198 String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 ";
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199 return getIntResult(from, to, incompleteQuery);
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202 private int getIntResult(Timestamp from, Timestamp to, String query)
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203 throws SQLException {
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205 log.debug("getIntRes: QUERY: " + query);
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206 log.debug("getIntRes: FROM: " + from);
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207 log.debug("getIntRes: TO: " + to);
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209 PreparedStatement pstm = conn.prepareStatement(query);
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210 pstm.setTimestamp(1, from);
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211 pstm.setTimestamp(2, to);
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213 ResultSet res = pstm.getResultSet();
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214 boolean exist = res.next();
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217 count = res.getInt(1);
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219 log.debug("getIntRes: RES: " + count);
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225 public List<JobStat> readData(Timestamp from, Timestamp to,
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226 Services wservice, Boolean clusterOnly) throws SQLException {
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228 String query = "select service_name, cluster_job_id, job_id, start, finish, inputsize, "
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229 + "resultsize, isCancelled, isCollected from exec_stat where start BETWEEN ? and ? ";
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231 if (wservice != null) {
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232 query += " and service_name=? ";
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235 if (clusterOnly != null) {
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237 query += " and isClusterJob!=0 ";
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239 query += " and isClusterJob=0 ";
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243 log.debug("QUERY: " + query);
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244 log.debug("FROM: " + from);
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245 log.debug("TO: " + to);
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246 log.debug("WS: " + wservice);
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248 PreparedStatement pstm = conn.prepareStatement(query);
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249 pstm.setTimestamp(1, from);
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250 pstm.setTimestamp(2, to);
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251 if (wservice != null) {
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252 pstm.setString(3, wservice.toString());
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255 List<JobStat> stats = new ArrayList<JobStat>();
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256 ResultSet rs = pstm.getResultSet();
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259 while (rs.next()) {
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261 stats.add(JobStat.newInstance(Services.getService(rs.getString(1)),
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262 rs.getString(2), rs.getString(3), rs.getTimestamp(4),
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263 rs.getTimestamp(5), rs.getLong(6), rs.getLong(7),
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264 rs.getBoolean(8), rs.getBoolean(9)));
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267 log.debug("QUERY result len: " + rcount);
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275 * Removes the job if
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277 * 1) It has already been recorded
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279 * 2) It has not completed and did not timeout - this is to prevent
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280 * recording the information on the incomplete jobs.
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283 * @throws SQLException
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285 public void removeRecordedJobs(Set<JobStat> fsJobs) throws SQLException {
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287 String query = "select job_id from exec_stat";
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289 Statement st = conn.createStatement();
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290 ResultSet result = st.executeQuery(query);
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292 while (result.next()) {
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293 String recordedJob = result.getString(1);
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294 JobStat recStat = JobStat.newIncompleteStat(recordedJob);
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295 if (fsJobs.contains(recStat)) {
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296 fsJobs.remove(recStat);
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303 public static synchronized final void shutdownDBServer() {
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304 // ## DATABASE SHUTDOWN SECTION ##
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306 * In embedded mode, an application should shut down Derby. Shutdown
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307 * throws the XJ015 exception to confirm success.
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310 if (conn != null) {
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313 } catch (SQLException e) {
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314 System.err.println("Database commit failed with "
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315 + e.getLocalizedMessage());
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317 boolean gotSQLExc = false;
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319 DriverManager.getConnection("jdbc:derby:;shutdown=true");
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320 } catch (SQLException se) {
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321 if (se.getSQLState().equals("XJ015")) {
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326 System.err.println("Database did not shut down normally");
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328 System.out.println("Database shut down normally");
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331 public static void main(String[] args) throws SQLException {
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332 // new StatDB().createStatTable();
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333 // insertData(null);
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335 * StatDB statdb = new StatDB(); Date from = new Date();
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336 * from.setMonth(1); System.out.println(new
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337 * StatProcessor(statdb.readData( new Timestamp(from.getTime()), new
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338 * Timestamp(new Date().getTime()), null, null)).reportStat());
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