+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
package compbio.stat.collector;\r
\r
import java.sql.Connection;\r
if (conn != null && !conn.isClosed()) {\r
return conn;\r
} else {\r
- String dbpath = PropertyHelperManager.getLocalPath();\r
- log.info("Looking for JABAWS access statistics database at: "\r
- + dbpath);\r
- System.setProperty("derby.system.home", dbpath);\r
- conn = DriverManager.getConnection(protocol + statDBName\r
- + ";create=false");\r
-\r
- conn.setAutoCommit(true);\r
+ try {\r
+ String dbpath = PropertyHelperManager.getLocalPath();\r
+ log.info("Looking for JABAWS access statistics database at: "\r
+ + dbpath);\r
+ System.setProperty("derby.system.home", dbpath);\r
+ // Apparently under Tomcat webapp you cannot rely on Java\r
+ // auto discovery and have to register the driver explicitly\r
+ Class.forName(driver);\r
+ conn = DriverManager.getConnection(protocol + statDBName\r
+ + ";create=false");\r
+\r
+ conn.setAutoCommit(true);\r
+ /*\r
+ * Runtime.getRuntime().addShutdownHook(new Thread() {\r
+ * \r
+ * @Override public void run() { shutdownDBServer(); } });\r
+ */\r
+ } catch (ClassNotFoundException e) {\r
+ log.error(e.getMessage(), e);\r
+ }\r
}\r
return conn;\r
}\r
-\r
public StatDB() throws SQLException {\r
this.conn = getDBConnection();\r
}\r
Connection conn = DriverManager.getConnection(protocol + statDBName\r
+ ";create=false");\r
conn.setAutoCommit(true);\r
+ log.debug("Connecting to the TEST database!");\r
return conn;\r
}\r
\r
+ "isCollected SMALLINT NOT NULL, "\r
+ "isClusterJob SMALLINT NOT NULL)";\r
// We create a table...\r
- System.out.println(create);\r
+ log.debug(create);\r
s.execute(create);\r
s.close();\r
conn.close();\r
}\r
\r
+ static void clearStatTable() throws SQLException {\r
+ Connection conn = getDBConnection();\r
+ String query = "delete from exec_stat";\r
+ Statement st = conn.createStatement();\r
+ st.executeUpdate(query);\r
+ st.close();\r
+ conn.commit();\r
+ conn.close();\r
+ }\r
+\r
void insertData(Set<JobStat> jobstatus) throws SQLException {\r
- System.out.println("Inserting " + jobstatus.size());\r
+ log.info("Inserting " + jobstatus.size()\r
+ + " new records into the statistics database");\r
\r
conn.setAutoCommit(false);\r
String insert = "insert into exec_stat (service_name, cluster_job_id, job_id, start, finish, "\r
pstm.executeUpdate();\r
}\r
conn.commit();\r
+ conn.setAutoCommit(true);\r
pstm.close();\r
}\r
\r
public int getIncompleteCount(Timestamp from, Timestamp to)\r
throws SQLException {\r
// !js.hasResult()\r
- String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 ";\r
+ String incompleteQuery = "select count(*) from exec_stat where start BETWEEN ? and ? and resultsize<=0 and isCancelled=0";\r
return getIntResult(from, to, incompleteQuery);\r
}\r
\r
\r
return stats;\r
}\r
+\r
+ /**\r
+ * Removes the job if\r
+ * \r
+ * 1) It has already been recorded\r
+ * \r
+ * 2) It has not completed and did not timeout - this is to prevent\r
+ * recording the information on the incomplete jobs.\r
+ * \r
+ * @param fsJobs\r
+ * @throws SQLException\r
+ */\r
public void removeRecordedJobs(Set<JobStat> fsJobs) throws SQLException {\r
\r
String query = "select job_id from exec_stat";\r
st.close();\r
}\r
\r
- public void shutdownDBServer() {\r
+ public static synchronized final void shutdownDBServer() {\r
// ## DATABASE SHUTDOWN SECTION ##\r
/***\r
* In embedded mode, an application should shut down Derby. Shutdown\r
conn.close();\r
}\r
} catch (SQLException e) {\r
- System.err.println("Database commit failed with "\r
- + e.getLocalizedMessage());\r
+ log.warn("Database commit failed with " + e.getLocalizedMessage());\r
}\r
boolean gotSQLExc = false;\r
try {\r
}\r
}\r
if (!gotSQLExc) {\r
- System.err.println("Database did not shut down normally");\r
+ log.warn("Database did not shut down normally");\r
} else {\r
- System.out.println("Database shut down normally");\r
+ log.info("Database shut down normally");\r
}\r
}\r
- public static void main(String[] args) throws SQLException {\r
+ public static void main(String[] args) {\r
+ // This is called from Ant cleanStatTable task\r
+ try {\r
+ clearStatTable();\r
+ shutdownDBServer();\r
+ } catch (SQLException e) {\r
+ System.err.println("Fails to clean up JABAWS stat database!");\r
+ e.printStackTrace();\r
+ }\r
// new StatDB().createStatTable();\r
// insertData(null);\r
/*\r
git://source.jalview.org / jabaws.git / blobdiff