-/* Copyright (c) 2013 Alexander Sherstnev\r
- * Copyright (c) 2011 Peter Troshin\r
+/* Copyright (c) 2014 Alexander Sherstnev\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.1\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
import compbio.engine.client.SkeletalExecutable;\r
\r
/**\r
- * Class assumptions: 1. Number of runs of each WS = number of folders with name\r
- * 2. Number of successful runs = all runs with no result file 3. Per period of\r
- * time = limit per file creating time 4. Runtime (avg/max) = finish time -\r
- * start time 5. Task & result size = result.size\r
- * \r
- * Abandoned runs - not collected runs\r
- * \r
- * Cancelled runs - cancelled\r
- * \r
- * Cluster vs local runs\r
- * \r
- * Reasons for failure = look in the err out?\r
- * \r
- * \r
* Metadata required:\r
* \r
* work directory for local and cluster tasks = from Helper or cmd parameter. WS\r
* names - enumeration. Status file names and content.\r
* \r
- * @author Peter Troshin\r
* @author Alexander Sherstnev\r
* \r
*/\r
@Parameter\r
private List<String> parameters = new ArrayList<String>();\r
\r
- @Parameter(names = { "-log", "-verbose" }, description = "Level of verbosity")\r
- public Integer verbose = 1;\r
+ @Parameter(names = { "-h", "-help", "--help" }, help = true, description = "Print help")\r
+ public boolean help;\r
\r
@Parameter(names = "-start", description = "Start time")\r
public String starttime;\r
}\r
\r
public class ExecutionStatUpdater {\r
- static SimpleDateFormat DF = new SimpleDateFormat("dd/MM/yyyy hh:mm:ss");\r
- static SimpleDateFormat shortDF = new SimpleDateFormat("dd/MM/yyyy");\r
+ static SimpleDateFormat DF = new SimpleDateFormat("dd/MM/yyyy");\r
private static final Logger log = Logger.getLogger(ExecutionStatUpdater.class);\r
-\r
final private File workingDirectory;\r
final private List<JobStat> stats;\r
- /**\r
- * Consider the job that has been working for longer than timeOutInHours\r
- * completed, whatever the outcome\r
- */\r
- final private int timeOutInHours;\r
\r
- /**\r
- * List subdirectories in the job directory\r
- * \r
- * @param workingDirectory\r
- * @param timeOutInHours\r
- */\r
- public ExecutionStatUpdater(String workingDirectory, int timeOutInHours) {\r
- log.info("Starting stat collector for directory: " + workingDirectory);\r
- log.info("Maximum allowed runtime(h): " + timeOutInHours);\r
+ public ExecutionStatUpdater(String workingDirectory) {\r
+ log.info("Starting stat updater for directory: " + workingDirectory);\r
if (!PathValidator.isValidDirectory(workingDirectory)) {\r
throw new IllegalArgumentException("workingDirectory '" + workingDirectory + "' does not exist!");\r
}\r
this.workingDirectory = new File(workingDirectory);\r
stats = new ArrayList<JobStat>();\r
- if (timeOutInHours <= 0) {\r
- throw new IllegalArgumentException("Timeout value must be greater than 0! Given value: " + timeOutInHours);\r
- }\r
- this.timeOutInHours = timeOutInHours;\r
}\r
\r
boolean hasCompleted(JobDirectory jd) {\r
JobStat jstat = jd.getJobStat();\r
- if (jstat.hasResult() || jstat.getIsCancelled() || jstat.getIsFinished() || hasTimedOut(jd)) {\r
+ if (jstat.hasResult() || jstat.getIsCancelled() || jstat.getIsFinished()) {\r
return true;\r
}\r
return false;\r
}\r
\r
- boolean hasTimedOut(JobDirectory jd) {\r
- return ((System.currentTimeMillis() - jd.jobdir.lastModified()) / (1000 * 60 * 60)) > timeOutInHours;\r
- }\r
-\r
- /*\r
- * Make sure that collectStatistics methods was called prior to calling\r
- * this! TODO consider running collectStatistics from here on the first call\r
- */\r
- StatProcessor getStats() {\r
- if (stats.isEmpty()) {\r
- log.info("Please make sure collectStatistics method was called prior to calling getStats()!");\r
- }\r
- return new StatProcessor(stats);\r
- }\r
-\r
void writeStatToDB(String dbname) throws SQLException {\r
Set<JobStat> rjobs = new HashSet<JobStat>(stats);\r
StatDB statdb = new StatDB(dbname);\r
- log.debug("Removing records that has already been recorded");\r
+ log.debug("Filtering out records that has already been recorded. init Njobs = " + rjobs.size());\r
statdb.removeRecordedJobs(rjobs);\r
- log.debug("New records left: " + rjobs.size());\r
+ log.debug("Njobs left: " + rjobs.size());\r
statdb.insertData(rjobs);\r
}\r
\r
- /**\r
- * main function\r
- * @throws ParseException \r
- */\r
- public static void main(String[] args) throws IOException, SQLException, ParseException {\r
- mainJCommander jct = new mainJCommander();\r
- new JCommander(jct, args);\r
- String WorkingDir = "jobsout";\r
- String DBname = "ExecutionStatistic";\r
+ public static void printHelp() {\r
+ System.out.println("\nUsage: <Class or Jar file name> -dir <JOBDIR> -db <StatDB> -start <DATE1> -end <DATE2> -h");\r
+ System.out.println("\n[OPTIONS]");\r
\r
- long StartTime = 0L;\r
- Date currDate = new Date();\r
- long EndTime = currDate.getTime();\r
- if (null != jct.starttime) {\r
- Date ST = shortDF.parse(jct.starttime);\r
- if (null != ST) {\r
- StartTime = ST.getTime();\r
- }\r
- }\r
- if (null != jct.endtime) {\r
- Date ET = shortDF.parse(jct.endtime);\r
- if (null != ET) {\r
- EndTime = ET.getTime();\r
- }\r
- }\r
- if (null != jct.dbname) {\r
- DBname = jct.dbname;\r
- }\r
- if (null != jct.workingdir) {\r
- WorkingDir = jct.workingdir;\r
- }\r
+ System.out.println("\n-dir <JOBDIR> - a directory with jabaws jobs");\r
\r
- System.out.println("Start time: " + jct.starttime + " = " + StartTime);\r
- System.out.println("End time: " + jct.endtime + " = " + EndTime);\r
+ System.out.println("\n-db <StatDB> - a JABAWS statistics database. If information on");\r
+ System.out.println("jobs from the job directory have been stored in the database,");\r
+ System.out.println("the information is not going to the database [Default:");\r
+ System.out.println("ExecutionStatistic]");\r
\r
- ExecutionStatUpdater esu = new ExecutionStatUpdater(WorkingDir, 1);\r
- esu.collectStatistics(StartTime, EndTime);\r
- esu.writeStatToDB(DBname);\r
+ System.out.println("\n-start <DATE1> - start date for processing jobs. Timestamp of");\r
+ System.out.println("last modification of a job should be later than DATE1. The");\r
+ System.out.println("date format is dd/mm/yy. If the input date format is different");\r
+ System.out.println("the default value is used [Default: 00/00/00]");\r
+\r
+ System.out.println("\n-end <DATE2> - end date for processing jobs. Timestamp of");\r
+ System.out.println("last modification of a job should be earlier than DATE2. The");\r
+ System.out.println("date format is dd/mm/yy. If the input date format is different");\r
+ System.out.println("the default value is used [Default: current date]\n");\r
}\r
\r
static FileFilter directories = new FileFilter() {\r
log.trace("training input: " + dir.getName() + File.separator + SkeletalExecutable.INPUT);\r
}\r
}\r
- log.debug("Statistics collected!");\r
+ log.debug("Statistics prepared...");\r
}\r
\r
+ /**\r
+ * Starts stat DB update program, the only mandatory parameter is a job\r
+ * directory.\r
+ * \r
+ * @param args\r
+ * Usage: java -jar <Jar file name> -dir <JOBDIR> -db <StatDB>\r
+ * -start <DATE1> -end <DATE2> -h\r
+ * \r
+ * ACTION [OPTIONS]\r
+ * \r
+ * -dir <JOBDIR> - a directory with jabaws jobs\r
+ * \r
+ * -db <StatDB> - a JABAWS statistics database. If information on\r
+ * jobs from the job directory have been stored in the database,\r
+ * the information is not going to the database [Default:\r
+ * ExecutionStatistic]\r
+ * \r
+ * -start <DATE1> - start date for processing jobs. Timestamp of\r
+ * last modification of a job should be later than DATE1. The\r
+ * date format is dd/mm/yy. If the input date format is different\r
+ * the default value is used [Default: 00/00/00]\r
+ * \r
+ * -end <DATE2> - end date for processing jobs. Timestamp of last\r
+ * modification of a job should be earlier than DATE2. The date\r
+ * format is dd/mm/yy. If the input date format is different the\r
+ * default value is used [Default: current date]\r
+ * \r
+ * @throws ParseException\r
+ * \r
+ */\r
+ public static void main(String[] args) throws IOException, SQLException, ParseException {\r
+ mainJCommander jct = new mainJCommander();\r
+ new JCommander(jct, args);\r
+ String WorkingDir = "";\r
+ String DBname = "ExecutionStatistic";\r
+\r
+ long StartTime = 0L;\r
+ Date currDate = new Date();\r
+ long EndTime = currDate.getTime();\r
+ if (null != jct.starttime) {\r
+ Date ST = DF.parse(jct.starttime);\r
+ if (null != ST) {\r
+ StartTime = ST.getTime();\r
+ }\r
+ }\r
+ if (null != jct.endtime) {\r
+ Date ET = DF.parse(jct.endtime);\r
+ if (null != ET) {\r
+ EndTime = ET.getTime();\r
+ }\r
+ }\r
+ if (null != jct.dbname) {\r
+ DBname = jct.dbname;\r
+ }\r
+ if (null == jct.workingdir || jct.help) {\r
+ printHelp();\r
+ return;\r
+ }\r
+\r
+ WorkingDir = jct.workingdir;\r
+ log.trace("Collect statistics from jobs at " + WorkingDir);\r
+ log.trace("Start time: " + jct.starttime + " = " + StartTime + " ms");\r
+ log.trace("End time: " + jct.endtime + " = " + EndTime + " ms");\r
+\r
+ ExecutionStatUpdater esu = new ExecutionStatUpdater(WorkingDir);\r
+ esu.collectStatistics(StartTime, EndTime);\r
+ esu.writeStatToDB(DBname);\r
+ return;\r
+ }\r
}\r
git://source.jalview.org / jabaws.git / commitdiff