webservices/compbio/stat/collector/JobDirectory.java

   1 /* Copyright (c) 2013 Alexander Sherstnev\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.io.File;\r
  21 import java.io.IOException;\r
  22 import java.util.HashMap;\r
  23 import java.util.Map;\r
  24 \r
  25 import org.apache.log4j.Logger;\r
  26 \r
  27 import compbio.engine.client.Executable;\r
  28 import compbio.engine.client.SkeletalExecutable;\r
  29 import compbio.metadata.JobStatus;\r
  30 import compbio.util.FileUtil;\r
  31 import compbio.ws.client.Services;\r
  32 import compbio.ws.client.ServicesUtil;\r
  33 \r
  34 /**\r
  35  * \r
  36  * @author Alexander Sherstnev\r
  37  * \r
  38  */\r
  39 public class JobDirectory {\r
  40 \r
  41         static final int UNDEFINED = -1;\r
  42 \r
  43         private static final Logger log = Logger.getLogger(JobDirectory.class);\r
  44         \r
  45         File jobdir;\r
  46         Map<String, File> files = new HashMap<String, File>();\r
  47 \r
  48         JobDirectory(File directory) {\r
  49                 this.jobdir = directory;\r
  50                 for (File f : jobdir.listFiles()) {\r
  51                 files.put(f.getName(), f);\r
  52                 }\r
  53         }\r
  54 \r
  55         boolean hasStatus(JobStatus status) {\r
  56                 return files.containsKey(status.toString());\r
  57         }\r
  58 \r
  59         boolean isCollected() {\r
  60                 return hasStatus(JobStatus.COLLECTED);\r
  61         }\r
  62 \r
  63         boolean isCancelled() {\r
  64                 return hasStatus(JobStatus.CANCELLED);\r
  65         }\r
  66 \r
  67         long getStartTime() {\r
  68                 long starttime = UNDEFINED;\r
  69                 File startfile = files.get(JobStatus.STARTED.toString());\r
  70                 if (startfile == null) {\r
  71                         startfile = files.get(JobStatus.SUBMITTED.toString());\r
  72                 }\r
  73                 try {\r
  74                         if (startfile != null) {\r
  75                                 String start = FileUtil.readFileToString(startfile);\r
  76                                 starttime = Long.parseLong(start.trim());\r
  77                         }\r
  78                 } catch (IOException ignore) {\r
  79                         log.warn("IOException while reading STARTED status file! Ignoring...", ignore);\r
  80                         // fall back\r
  81                         starttime = startfile.lastModified();\r
  82                 } catch (NumberFormatException ignore) {\r
  83                         log.warn("NumberFormatException while reading STARTED status file! Ignoring...", ignore);\r
  84                         // fall back\r
  85                         starttime = startfile.lastModified();\r
  86                 }\r
  87                 return starttime;\r
  88         }\r
  89 \r
  90         String getClusterJobID() {\r
  91                 String clustjobId = "";\r
  92                 File jobid = files.get("JOBID");\r
  93                 try {\r
  94                 if (jobid != null) {\r
  95                         clustjobId = FileUtil.readFileToString(jobid);\r
  96                 }\r
  97                 } catch (IOException ioe) {\r
  98                 log.error(\r
  99                         "IO Exception while reading the content of JOBID file for job "\r
 100                                 + jobid, ioe);\r
 101                 }\r
 102                 return clustjobId.trim();\r
 103         }\r
 104 \r
 105         long getFinishedTime() {\r
 106                 long ftime = UNDEFINED;\r
 107                 File finished = files.get(JobStatus.FINISHED.toString());\r
 108                 if (finished != null) {\r
 109                 try {\r
 110                         if (finished != null) {\r
 111                         String start = FileUtil.readFileToString(finished);\r
 112                         ftime = Long.parseLong(start.trim());\r
 113                         }\r
 114                 } catch (IOException ignore) {\r
 115                         log.warn(\r
 116                                 "IOException while reading FINISHED status file! Ignoring...",\r
 117                                 ignore);\r
 118                         // fall back\r
 119                         ftime = finished.lastModified();\r
 120                 } catch (NumberFormatException ignore) {\r
 121                         log.warn(\r
 122                                 "NumberFormatException while reading FINISHED status file! Ignoring...",\r
 123                                 ignore);\r
 124                         // fall back\r
 125                         ftime = finished.lastModified();\r
 126                 }\r
 127                 }\r
 128                 return ftime;\r
 129         }\r
 130 \r
 131         private Services getService() {\r
 132                 return ServicesUtil.getServiceByJobDirectory(jobdir);\r
 133         }\r
 134 \r
 135         long getResultSize() {\r
 136                 Class<? extends Executable<?>> name = ServicesUtil\r
 137                         .getRunnerByJobDirectory(jobdir);\r
 138 \r
 139                 File f = null;\r
 140                 if (name.getSimpleName().equalsIgnoreCase("IUPred")) {\r
 141                 f = files.get("out.glob");\r
 142                 if (f == null)\r
 143                         f = files.get("out.short");\r
 144                 if (f == null)\r
 145                         f = files.get("out.long");\r
 146                 } else {\r
 147                 f = files.get(SkeletalExecutable.OUTPUT);\r
 148                 }\r
 149                 if (f != null) {\r
 150                 return f.length();\r
 151                 }\r
 152                 return UNDEFINED;\r
 153         }\r
 154 \r
 155         long getInputSize() {\r
 156                 Class<? extends Executable<?>> name = ServicesUtil\r
 157                         .getRunnerByJobDirectory(jobdir);\r
 158 \r
 159                 File input = files.get(SkeletalExecutable.INPUT);\r
 160                 if (input != null) {\r
 161                 return input.length();\r
 162                 }\r
 163                 return UNDEFINED;\r
 164         }\r
 165 \r
 166         JobStat getJobStat() {\r
 167                 return JobStat.newInstance(getService(), getClusterJobID(),\r
 168                         jobdir.getName(), getStartTime(), getFinishedTime(),\r
 169                         getInputSize(), getResultSize(), isCancelled(),\r
 170                         isCollected());\r
 171         }\r
 172 \r
 173         public int hashCode() {\r
 174                 final int prime = 31;\r
 175                 int result = 1;\r
 176                 result = prime * result\r
 177                         + ((jobdir == null) ? 0 : jobdir.hashCode());\r
 178                 return result;\r
 179         }\r
 180 \r
 181         public boolean equals(Object obj) {\r
 182                 if (this == obj)\r
 183                 return true;\r
 184                 if (obj == null)\r
 185                 return false;\r
 186                 if (getClass() != obj.getClass())\r
 187                 return false;\r
 188                 JobDirectory other = (JobDirectory) obj;\r
 189                 if (jobdir == null) {\r
 190                 if (other.jobdir != null)\r
 191                         return false;\r
 192                 } else if (!jobdir.equals(other.jobdir))\r
 193                 return false;\r
 194                 return true;\r
 195         }\r
 196 }\r
 197 \r