webservices/compbio/stat/collector/ExecutionStatCollector.java

   1 package compbio.stat.collector;\r
   2 \r
   3 import java.io.File;\r
   4 import java.io.FileFilter;\r
   5 import java.io.IOException;\r
   6 import java.sql.SQLException;\r
   7 import java.text.SimpleDateFormat;\r
   8 import java.util.ArrayList;\r
   9 import java.util.Date;\r
  10 import java.util.HashMap;\r
  11 import java.util.HashSet;\r
  12 import java.util.List;\r
  13 import java.util.Map;\r
  14 import java.util.Set;\r
  15 \r
  16 import org.apache.log4j.Logger;\r
  17 \r
  18 import compbio.engine.client.Executable;\r
  19 import compbio.engine.client.PathValidator;\r
  20 import compbio.metadata.JobStatus;\r
  21 import compbio.util.FileUtil;\r
  22 import compbio.ws.client.Services;\r
  23 \r
  24 /**\r
  25  * Number of runs of each WS = number of folders with name\r
  26  * \r
  27  * Number of successful runs = all runs with no result file\r
  28  * \r
  29  * Per period of time = limit per file creating time Runtime (avg/max) =\r
  30  * \r
  31  * started time - finished time\r
  32  * \r
  33  * Task & result size = result.size\r
  34  * \r
  35  * Abandoned runs - not collected runs\r
  36  * \r
  37  * Cancelled runs - cancelled\r
  38  * \r
  39  * Cluster vs local runs\r
  40  * \r
  41  * Reasons for failure = look in the err out?\r
  42  * \r
  43  * \r
  44  * Metadata required:\r
  45  * \r
  46  * work directory for local and cluster tasks = from Helper or cmd parameter. WS\r
  47  * names - enumeration. Status file names and content.\r
  48  * \r
  49  * @author pvtroshin\r
  50  * \r
  51  */\r
  52 public class ExecutionStatCollector implements Runnable {\r
  53 \r
  54         static final int UNDEFINED = -1;\r
  55 \r
  56         private static final Logger log = Logger\r
  57                         .getLogger(ExecutionStatCollector.class);\r
  58 \r
  59         static SimpleDateFormat DF = new SimpleDateFormat("dd/MM/yyyy hh:mm:ss");\r
  60 \r
  61         final private File workDirectory;\r
  62         final private List<JobStat> stats;\r
  63         /**\r
  64          * Consider the job that has been working for longer than timeOutInHours\r
  65          * completed, whatever the outcome\r
  66          */\r
  67         final private int timeOutInHours;\r
  68 \r
  69         /**\r
  70          * List subdirectories in the job directory\r
  71          * \r
  72          * @param workDirectory\r
  73          * @param timeOutInHours\r
  74          */\r
  75         public ExecutionStatCollector(String workDirectory, int timeOutInHours) {\r
  76                 log.info("Starting stat collector for directory: " + workDirectory);\r
  77                 log.info("Maximum allowed runtime(h): " + timeOutInHours);\r
  78                 if (!PathValidator.isValidDirectory(workDirectory)) {\r
  79                         throw new IllegalArgumentException("workDirectory '"\r
  80                                         + workDirectory + "' does not exist!");\r
  81                 }\r
  82                 this.workDirectory = new File(workDirectory);\r
  83                 stats = new ArrayList<JobStat>();\r
  84                 if (timeOutInHours <= 0) {\r
  85                         throw new IllegalArgumentException(\r
  86                                         "Timeout value must be greater than 0! Given value: "\r
  87                                                         + timeOutInHours);\r
  88                 }\r
  89                 this.timeOutInHours = timeOutInHours;\r
  90         }\r
  91 \r
  92         boolean hasCompleted(JobDirectory jd) {\r
  93                 JobStat jstat = jd.getJobStat();\r
  94                 if (jstat.hasResult() || jstat.getIsCancelled()\r
  95                                 || jstat.getIsFinished() || hasTimedOut(jd)) {\r
  96                         return true;\r
  97                 }\r
  98                 return false;\r
  99         }\r
 100 \r
 101         boolean hasTimedOut(JobDirectory jd) {\r
 102                 return ((System.currentTimeMillis() - jd.jobdir.lastModified()) / (1000 * 60 * 60)) > timeOutInHours;\r
 103         }\r
 104 \r
 105         StatProcessor getStats() {\r
 106                 return new StatProcessor(stats);\r
 107         }\r
 108 \r
 109         void writeStatToDB() throws SQLException {\r
 110                 Set<JobStat> rjobs = new HashSet<JobStat>(stats);\r
 111                 StatDB statdb = new StatDB();\r
 112                 log.debug("Removing records that has already been recorded");\r
 113 \r
 114                 statdb.removeRecordedJobs(rjobs);\r
 115                 log.debug("New records left: " + rjobs.size());\r
 116                 statdb.insertData(rjobs);\r
 117         }\r
 118 \r
 119         /*\r
 120          * static void updateTime(File statFile) throws IOException { long lastMod =\r
 121          * statFile.lastModified(); FileWriter fw = new FileWriter(statFile);\r
 122          * fw.write(new Long(lastMod).toString()); fw.close(); }\r
 123          */\r
 124 \r
 125         /**\r
 126          * Not in use\r
 127          */\r
 128         public static void main(String[] args) throws IOException, SQLException {\r
 129 \r
 130                 // updateTime(new File(\r
 131                 // "D:\\workspace\\JABA2\\jobsout\\AACon#170462904473672\\STARTED"));\r
 132 \r
 133                 File[] files = FileUtil.getFiles("Y:\\fc\\www-jws2\\jaba\\jobsout",\r
 134                                 directories);\r
 135                 List<JobStat> stats = new ArrayList<JobStat>();\r
 136                 for (File file : files) {\r
 137                         JobDirectory jd = new JobDirectory(file);\r
 138                         stats.add(jd.getJobStat());\r
 139                         // System.out.println(jd.getJobStat().getJobReportTabulated());\r
 140                 }\r
 141                 StatProcessor sp = new StatProcessor(stats);\r
 142                 System.out.println(sp.reportStat());\r
 143                 System.out.println();\r
 144                 System.out.println("!!!!!!!!!!!!!!!!!!");\r
 145                 System.out.println();\r
 146 \r
 147                 Set<JobStat> rjobs = new HashSet<JobStat>(sp.stats);\r
 148                 StatDB statdb = new StatDB();\r
 149                 statdb.removeRecordedJobs(rjobs);\r
 150                 statdb.insertData(rjobs);\r
 151         }\r
 152 \r
 153         static FileFilter directories = new FileFilter() {\r
 154                 @Override\r
 155                 public boolean accept(File pathname) {\r
 156                         return pathname.isDirectory()\r
 157                                         && !pathname.getName().startsWith(".");\r
 158                 }\r
 159         };\r
 160 \r
 161         static class JobDirectory {\r
 162 \r
 163                 File jobdir;\r
 164                 Map<String, File> files = new HashMap<String, File>();\r
 165 \r
 166                 JobDirectory(File directory) {\r
 167                         this.jobdir = directory;\r
 168                         for (File f : jobdir.listFiles()) {\r
 169                                 files.put(f.getName(), f);\r
 170                         }\r
 171                 }\r
 172 \r
 173                 boolean hasStatus(JobStatus status) {\r
 174                         return files.containsKey(status.toString());\r
 175                 }\r
 176 \r
 177                 boolean isCollected() {\r
 178                         return hasStatus(JobStatus.COLLECTED);\r
 179                 }\r
 180 \r
 181                 boolean isCancelled() {\r
 182                         return hasStatus(JobStatus.CANCELLED);\r
 183                 }\r
 184 \r
 185                 long getStartTime() {\r
 186                         long starttime = UNDEFINED;\r
 187                         File startfile = files.get(JobStatus.STARTED.toString());\r
 188                         if (startfile == null) {\r
 189                                 startfile = files.get(JobStatus.SUBMITTED.toString());\r
 190                         }\r
 191                         if (startfile != null) {\r
 192                                 starttime = startfile.lastModified();\r
 193                                 /*\r
 194                                  * String start = FileUtil.readFileToString(startfile);\r
 195                                  * starttime = Long.parseLong(start.trim());\r
 196                                  */\r
 197                         }\r
 198                         return starttime;\r
 199                 }\r
 200 \r
 201                 String getClusterJobID() {\r
 202                         String clustjobId = "";\r
 203                         File jobid = files.get("JOBID");\r
 204                         try {\r
 205                                 if (jobid != null) {\r
 206                                         clustjobId = FileUtil.readFileToString(jobid);\r
 207                                 }\r
 208                         } catch (IOException ioe) {\r
 209                                 log.error(\r
 210                                                 "IO Exception while reading the content of JOBID file for job "\r
 211                                                                 + jobid, ioe);\r
 212                         }\r
 213                         return clustjobId.trim();\r
 214                 }\r
 215 \r
 216                 long getFinishedTime() {\r
 217                         long ftime = UNDEFINED;\r
 218                         File finished = files.get(JobStatus.FINISHED.toString());\r
 219                         if (finished != null) {\r
 220                                 ftime = finished.lastModified();\r
 221                                 /*\r
 222                                  * String start = FileUtil.readFileToString(finished); ftime =\r
 223                                  * Long.parseLong(start.trim());\r
 224                                  */\r
 225                                 // System.out.println("f " + ftime);\r
 226                         }\r
 227                         /*\r
 228                          * } catch (IOException e) { log.log(Level.WARN,\r
 229                          * "Cannot parse finished time: " + e.getMessage(), e); } catch\r
 230                          * (NumberFormatException e) { log.log(Level.WARN,\r
 231                          * "Cannot parse finished time: " + e.getMessage(), e); }\r
 232                          */\r
 233                         return ftime;\r
 234                 }\r
 235 \r
 236                 private Services getService() {\r
 237                         return Services.getServiceByJobDirectory(jobdir);\r
 238                 }\r
 239 \r
 240                 // Mafft, Muscle, Tcoffee, Clustal task:fasta.in result:fasta.out\r
 241                 // Probcons task:fasta.in result:alignment.out\r
 242                 /*\r
 243                  * TODO replace with Universal names for WS!\r
 244                  */\r
 245                 long getResultSize() {\r
 246                         Class<? extends Executable<?>> name = Services\r
 247                                         .getRunnerByJobDirectory(jobdir);\r
 248 \r
 249                         File f = null;\r
 250                         if (name.getSimpleName().equalsIgnoreCase("Probcons")) {\r
 251                                 f = files.get("alignment.out");\r
 252                         } else if (name.getSimpleName().equalsIgnoreCase("ClustalW")) {\r
 253                                 f = files.get("output.txt");\r
 254                         } else {\r
 255                                 f = files.get("fasta.out");\r
 256                         }\r
 257                         if (f != null) {\r
 258                                 return f.length();\r
 259                         }\r
 260                         return UNDEFINED;\r
 261                 }\r
 262 \r
 263                 /*\r
 264                  * TODO unify input!\r
 265                  */\r
 266                 long getInputSize() {\r
 267                         Class<? extends Executable<?>> name = Services\r
 268                                         .getRunnerByJobDirectory(jobdir);\r
 269 \r
 270                         File input = null;\r
 271                         if (name.getSimpleName().equalsIgnoreCase("ClustalW")) {\r
 272                                 input = files.get("input.txt");\r
 273                         } else {\r
 274                                 input = files.get("fasta.in");\r
 275                         }\r
 276 \r
 277                         if (input != null) {\r
 278                                 return input.length();\r
 279                         }\r
 280                         return UNDEFINED;\r
 281                 }\r
 282 \r
 283                 JobStat getJobStat() {\r
 284                         return JobStat.newInstance(getService(), getClusterJobID(),\r
 285                                         jobdir.getName(), getStartTime(), getFinishedTime(),\r
 286                                         getInputSize(), getResultSize(), isCancelled(),\r
 287                                         isCollected());\r
 288                 }\r
 289 \r
 290                 @Override\r
 291                 public int hashCode() {\r
 292                         final int prime = 31;\r
 293                         int result = 1;\r
 294                         result = prime * result\r
 295                                         + ((jobdir == null) ? 0 : jobdir.hashCode());\r
 296                         return result;\r
 297                 }\r
 298 \r
 299                 @Override\r
 300                 public boolean equals(Object obj) {\r
 301                         if (this == obj)\r
 302                                 return true;\r
 303                         if (obj == null)\r
 304                                 return false;\r
 305                         if (getClass() != obj.getClass())\r
 306                                 return false;\r
 307                         JobDirectory other = (JobDirectory) obj;\r
 308                         if (jobdir == null) {\r
 309                                 if (other.jobdir != null)\r
 310                                         return false;\r
 311                         } else if (!jobdir.equals(other.jobdir))\r
 312                                 return false;\r
 313                         return true;\r
 314                 }\r
 315         }\r
 316 \r
 317         private void collectStatistics() {\r
 318                 File[] files = workDirectory.listFiles(directories);\r
 319                 for (File file : files) {\r
 320                         JobDirectory jd = new JobDirectory(file);\r
 321                         JobStat jstat = jd.getJobStat();\r
 322                         // Do not record stats on the job that has not completed yet\r
 323                         if (hasCompleted(jd)) {\r
 324                                 stats.add(jstat);\r
 325                         } else {\r
 326                                 log.debug("Skipping the job: " + jstat);\r
 327                                 log.debug("As it has not completed yet");\r
 328                         }\r
 329                         // System.out.println(jd.getJobStat().getJobReportTabulated());\r
 330                 }\r
 331         }\r
 332 \r
 333         @Override\r
 334         public void run() {\r
 335                 log.info("Started updating statistics at " + new Date());\r
 336                 log.info("For directory: " + workDirectory.getAbsolutePath());\r
 337 \r
 338                 collectStatistics();\r
 339 \r
 340                 StatProcessor local_stats = getStats();\r
 341                 log.info("Found " + local_stats.getJobNumber() + " jobs!");\r
 342                 try {\r
 343                         writeStatToDB();\r
 344                 } catch (SQLException e) {\r
 345                         log.error("Fails to update jobs statistics database!");\r
 346                         log.error(e.getLocalizedMessage(), e);\r
 347                 }\r
 348                 log.info("Finished updating statistics at " + new Date());\r
 349         }\r
 350 }\r