webservices/compbio/stat/collector/StatDB.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.stat.collector;\r
  19 \r
  20 import java.sql.Connection;\r
  21 import java.sql.DriverManager;\r
  22 import java.sql.PreparedStatement;\r
  23 import java.sql.ResultSet;\r
  24 import java.sql.SQLException;\r
  25 import java.sql.Statement;\r
  26 import java.sql.Timestamp;\r
  27 import java.util.ArrayList;\r
  28 import java.util.Date;\r
  29 import java.util.List;\r
  30 import java.util.Set;\r
  31 \r
  32 import org.apache.log4j.Logger;\r
  33 \r
  34 import compbio.engine.conf.PropertyHelperManager;\r
  35 import compbio.util.Util;\r
  36 import compbio.ws.client.Services;\r
  37 \r
  38 /**\r
  39  * The database must be stored in the application root directory and called\r
  40  * "ExecutionStatistic"\r
  41  * \r
  42  * @author pvtroshin\r
  43  * \r
  44  */\r
  45 public class StatDB {\r
  46 \r
  47         private static final String driver = "org.apache.derby.jdbc.EmbeddedDriver";\r
  48         private static final String protocol = "jdbc:derby:";\r
  49         private static final String statDBName = "ExecutionStatistic";\r
  50 \r
  51         private static final Logger log = Logger.getLogger(StatDB.class);\r
  52 \r
  53         static Connection conn;\r
  54 \r
  55         private synchronized static Connection getDBConnection() throws SQLException {\r
  56 \r
  57                 if (conn != null && !conn.isClosed()) {\r
  58                         return conn;\r
  59                 } else {\r
  60                         try {\r
  61                                 String dbpath = PropertyHelperManager.getLocalPath();\r
  62                                 log.info("Looking for JABAWS access statistics database at: " + dbpath);\r
  63                                 System.setProperty("derby.system.home", dbpath);\r
  64                                 // Apparently under Tomcat webapp you cannot rely on Java\r
  65                                 // auto discovery and have to register the driver explicitly\r
  66                                 Class.forName(driver);\r
  67                                 conn = DriverManager.getConnection(protocol + statDBName + ";create=false");\r
  68 \r
  69                                 conn.setAutoCommit(true);\r
  70                                 /*\r
  71                                  * Runtime.getRuntime().addShutdownHook(new Thread() {\r
  72                                  * \r
  73                                  * @Override public void run() { shutdownDBServer(); } });\r
  74                                  */\r
  75                         } catch (ClassNotFoundException e) {\r
  76                                 log.error(e.getMessage(), e);\r
  77                         }\r
  78                 }\r
  79                 return conn;\r
  80         }\r
  81 \r
  82         public StatDB() throws SQLException {\r
  83                 this.conn = getDBConnection();\r
  84         }\r
  85 \r
  86         /**\r
  87          * Connect to test database\r
  88          * \r
  89          * @param ignored\r
  90          * @throws SQLException\r
  91          */\r
  92         StatDB(boolean ignored) throws SQLException {\r
  93                 this.conn = getTestDBConnection();\r
  94         }\r
  95 \r
  96         private static Connection getTestDBConnection() throws SQLException {\r
  97                 System.setProperty("derby.system.home", "testsrc/testdata");\r
  98                 Connection conn = DriverManager.getConnection(protocol + statDBName\r
  99                                 + ";create=false");\r
 100                 conn.setAutoCommit(true);\r
 101                 log.debug("Connecting to the TEST database!");\r
 102                 return conn;\r
 103         }\r
 104 \r
 105         // ServiceName,jobname,start,finish,inputSize,resultSize,isCancelled,isCollected\r
 106         /**\r
 107          * \r
 108          * rs.getBoolean(i) will return true for any non-zero value and false for 0\r
 109          * on SMALLINT data column.\r
 110          * \r
 111          * @throws SQLException\r
 112          */\r
 113         private void createStatTable() throws SQLException {\r
 114 \r
 115                 /*\r
 116                  * Creating a statement object that we can use for running various SQL\r
 117                  * statements commands against the database.\r
 118                  */\r
 119                 Statement s = conn.createStatement();\r
 120                 String create = "create table exec_stat("\r
 121                                 + "number INT GENERATED ALWAYS AS IDENTITY,"\r
 122                                 + "service_name VARCHAR(15) NOT NULL, "\r
 123                                 + "cluster_job_id VARCHAR(30), "\r
 124                                 + "job_id VARCHAR(35) NOT NULL PRIMARY KEY, "\r
 125                                 + "start TIMESTAMP," + "finish TIMESTAMP,"\r
 126                                 + "inputsize BIGINT," + "resultsize BIGINT,"\r
 127                                 + "isCancelled SMALLINT NOT NULL,"\r
 128                                 + "isCollected SMALLINT NOT NULL, "\r
 129                                 + "isClusterJob SMALLINT NOT NULL)";\r
 130                 // We create a table...\r
 131                 log.debug(create);\r
 132                 s.execute(create);\r
 133                 s.close();\r
 134                 conn.close();\r
 135         }\r
 136 \r
 137         static void clearStatTable() throws SQLException {\r
 138                 Connection conn = getDBConnection();\r
 139                 String query = "delete from exec_stat";\r
 140                 Statement st = conn.createStatement();\r
 141                 st.executeUpdate(query);\r
 142                 st.close();\r
 143                 conn.commit();\r
 144                 conn.close();\r
 145         }\r
 146 \r
 147         void insertData(Set<JobStat> jobstatus) throws SQLException {\r
 148                 log.info("Inserting " + jobstatus.size()\r
 149                                 + " new records into the statistics database");\r
 150 \r
 151                 conn.setAutoCommit(false);\r
 152                 String insert = "insert into exec_stat (service_name, cluster_job_id, job_id, start, finish, "\r
 153                                 + "inputsize, resultsize, isCancelled, isCollected, isClusterJob) "\r
 154                                 + "VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)";\r
 155                 PreparedStatement pstm = conn.prepareStatement(insert);\r
 156                 for (JobStat js : jobstatus) {\r
 157                         // Has to present\r
 158                         pstm.setString(1, js.webService.toString());\r
 159 \r
 160                         if (!Util.isEmpty(js.clusterJobId)) {\r
 161                                 pstm.setString(2, js.clusterJobId);\r
 162                         } else {\r
 163                                 pstm.setString(2, null);\r
 164                         }\r
 165                         // Has to present\r
 166                         pstm.setString(3, js.jobname);\r
 167 \r
 168                         if (js.start != ExecutionStatCollector.UNDEFINED) {\r
 169                                 pstm.setTimestamp(4, new Timestamp(js.start));\r
 170                         } else {\r
 171                                 pstm.setTimestamp(4, null);\r
 172                         }\r
 173                         if (js.finish != ExecutionStatCollector.UNDEFINED) {\r
 174                                 pstm.setTimestamp(5, new Timestamp(js.finish));\r
 175                         } else {\r
 176                                 pstm.setTimestamp(5, null);\r
 177                         }\r
 178                         // -1 if UNDEFINED\r
 179                         pstm.setLong(6, js.inputSize);\r
 180                         // -1 if UNDEFINED\r
 181                         pstm.setLong(7, js.resultSize);\r
 182 \r
 183                         pstm.setBoolean(8, js.isCancelled);\r
 184                         pstm.setBoolean(9, js.isCollected);\r
 185                         pstm.setBoolean(10, js.isClusterJob());\r
 186                         pstm.executeUpdate();\r
 187                 }\r
 188                 conn.commit();\r
 189                 conn.setAutoCommit(true);\r
 190                 pstm.close();\r
 191         }\r
 192 \r
 193         public Date getEarliestRecord() throws SQLException {\r
 194                 String query = "select min(start) from exec_stat";\r
 195                 Statement st = conn.createStatement();\r
 196                 ResultSet res = st.executeQuery(query);\r
 197                 boolean exist = res.next();\r
 198                 Date date = new Date();\r
 199                 if (exist) {\r
 200                         date = res.getDate(1);\r
 201                 }\r
 202 \r
 203                 res.close();\r
 204                 st.close();\r
 205                 return date;\r
 206         }\r
 207 \r
 208         public int getTotalJobsCount(Timestamp from, Timestamp to)\r
 209                         throws SQLException {\r
 210                 String allQuery = "select count(*) from exec_stat where start BETWEEN ? and ? ";\r
 211                 return getIntResult(from, to, allQuery);\r
 212         }\r
 213 \r
 214         public int getCancelledCount(Timestamp from, Timestamp to)\r
 215                         throws SQLException {\r
 216                 // js.isCancelled\r
 217                 String cancelledQuery = "select count(*) from exec_stat where start BETWEEN ? and ?  and  isCancelled=1 ";\r
 218                 return getIntResult(from, to, cancelledQuery);\r
 219         }\r
 220 \r
 221         public int getAbandonedCount(Timestamp from, Timestamp to)\r
 222                         throws SQLException {\r
 223                 // !js.isCollected && !js.isCancelled && js.hasResult()\r
 224                 String abandonedQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and isCollected=0 and isCancelled=0 and resultsize>0 ";\r
 225                 return getIntResult(from, to, abandonedQuery);\r
 226         }\r
 227 \r
 228         public int getIncompleteCount(Timestamp from, Timestamp to)\r
 229                         throws SQLException {\r
 230                 // !js.hasResult()\r
 231                 String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 and isCancelled=0";\r
 232                 return getIntResult(from, to, incompleteQuery);\r
 233         }\r
 234 \r
 235         private int getIntResult(Timestamp from, Timestamp to, String query)\r
 236                         throws SQLException {\r
 237 \r
 238                 log.debug("getIntRes: QUERY: " + query);\r
 239                 log.debug("getIntRes: FROM: " + from);\r
 240                 log.debug("getIntRes: TO: " + to);\r
 241 \r
 242                 PreparedStatement pstm = conn.prepareStatement(query);\r
 243                 pstm.setTimestamp(1, from);\r
 244                 pstm.setTimestamp(2, to);\r
 245                 pstm.execute();\r
 246                 ResultSet res = pstm.getResultSet();\r
 247                 boolean exist = res.next();\r
 248                 int count = 0;\r
 249                 if (exist) {\r
 250                         count = res.getInt(1);\r
 251                 }\r
 252                 log.debug("getIntRes: RES: " + count);\r
 253                 res.close();\r
 254                 pstm.close();\r
 255                 return count;\r
 256         }\r
 257 \r
 258         public List<JobStat> readData(Timestamp from, Timestamp to,\r
 259                         Services wservice, Boolean clusterOnly) throws SQLException {\r
 260 \r
 261                 String query = "select service_name, cluster_job_id, job_id, start, finish, inputsize, "\r
 262                                 + "resultsize, isCancelled, isCollected from exec_stat where start BETWEEN ? and ? ";\r
 263 \r
 264                 if (wservice != null) {\r
 265                         query += " and service_name=? ";\r
 266                 }\r
 267 \r
 268                 if (clusterOnly != null) {\r
 269                         if (clusterOnly) {\r
 270                                 query += " and isClusterJob!=0 ";\r
 271                         } else {\r
 272                                 query += " and isClusterJob=0 ";\r
 273                         }\r
 274                 }\r
 275 \r
 276                 log.debug("QUERY: " + query);\r
 277                 log.debug("FROM: " + from);\r
 278                 log.debug("TO: " + to);\r
 279                 log.debug("WS: " + wservice);\r
 280 \r
 281                 PreparedStatement pstm = conn.prepareStatement(query);\r
 282                 pstm.setTimestamp(1, from);\r
 283                 pstm.setTimestamp(2, to);\r
 284                 if (wservice != null) {\r
 285                         pstm.setString(3, wservice.toString());\r
 286                 }\r
 287                 pstm.execute();\r
 288                 List<JobStat> stats = new ArrayList<JobStat>();\r
 289                 ResultSet rs = pstm.getResultSet();\r
 290                 int rcount = 0;\r
 291 \r
 292                 while (rs.next()) {\r
 293                         rcount++;\r
 294                         stats.add(JobStat.newInstance(Services.getService(rs.getString(1)),\r
 295                                         rs.getString(2), rs.getString(3), rs.getTimestamp(4),\r
 296                                         rs.getTimestamp(5), rs.getLong(6), rs.getLong(7),\r
 297                                         rs.getBoolean(8), rs.getBoolean(9)));\r
 298                 }\r
 299 \r
 300                 log.debug("QUERY result len: " + rcount);\r
 301                 rs.close();\r
 302                 pstm.close();\r
 303 \r
 304                 return stats;\r
 305         }\r
 306 \r
 307         /**\r
 308          * Removes the job if\r
 309          * \r
 310          * 1) It has already been recorded\r
 311          * \r
 312          * 2) It has not completed and did not timeout - this is to prevent\r
 313          * recording the information on the incomplete jobs.\r
 314          * \r
 315          * @param fsJobs\r
 316          * @throws SQLException\r
 317          */\r
 318         public void removeRecordedJobs(Set<JobStat> fsJobs) throws SQLException {\r
 319 \r
 320                 String query = "select job_id from exec_stat";\r
 321 \r
 322                 Statement st = conn.createStatement();\r
 323                 ResultSet result = st.executeQuery(query);\r
 324 \r
 325                 while (result.next()) {\r
 326                         String recordedJob = result.getString(1);\r
 327                         JobStat recStat = JobStat.newIncompleteStat(recordedJob);\r
 328                         if (fsJobs.contains(recStat)) {\r
 329                                 fsJobs.remove(recStat);\r
 330                         }\r
 331                 }\r
 332                 result.close();\r
 333                 st.close();\r
 334         }\r
 335 \r
 336         public static synchronized final void shutdownDBServer() {\r
 337                 // ## DATABASE SHUTDOWN SECTION ##\r
 338                 /***\r
 339                  * In embedded mode, an application should shut down Derby. Shutdown\r
 340                  * throws the XJ015 exception to confirm success.\r
 341                  ***/\r
 342                 try {\r
 343                         if (conn != null) {\r
 344                                 conn.close();\r
 345                         }\r
 346                 } catch (SQLException e) {\r
 347                         log.warn("Database commit failed with " + e.getLocalizedMessage());\r
 348                 }\r
 349                 boolean gotSQLExc = false;\r
 350                 try {\r
 351                         DriverManager.getConnection("jdbc:derby:;shutdown=true");\r
 352                 } catch (SQLException se) {\r
 353                         if (se.getSQLState().equals("XJ015")) {\r
 354                                 gotSQLExc = true;\r
 355                         }\r
 356                 }\r
 357                 if (!gotSQLExc) {\r
 358                         log.warn("Database did not shut down normally");\r
 359                 } else {\r
 360                         log.info("Database shut down normally");\r
 361                 }\r
 362         }\r
 363         public static void main(String[] args) {\r
 364                 // This is called from Ant cleanStatTable task\r
 365                 try {\r
 366                         clearStatTable();\r
 367                         shutdownDBServer();\r
 368                 } catch (SQLException e) {\r
 369                         System.err.println("Fails to clean up JABAWS stat database!");\r
 370                         e.printStackTrace();\r
 371                 }\r
 372                 // new StatDB().createStatTable();\r
 373                 // insertData(null);\r
 374                 /*\r
 375                  * StatDB statdb = new StatDB(); Date from = new Date();\r
 376                  * from.setMonth(1); System.out.println(new\r
 377                  * StatProcessor(statdb.readData( new Timestamp(from.getTime()), new\r
 378                  * Timestamp(new Date().getTime()), null, null)).reportStat());\r
 379                  */\r
 380         }\r
 381 }\r