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