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