engine/compbio/engine/cluster/drmaa/ClusterUtil.java

   1 /* Copyright (c) 2009 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     \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.engine.cluster.drmaa;\r
  19 \r
  20 import java.io.IOException;\r
  21 import java.text.NumberFormat;\r
  22 \r
  23 import org.apache.log4j.Logger;\r
  24 import org.ggf.drmaa.DrmaaException;\r
  25 import org.ggf.drmaa.JobInfo;\r
  26 import org.ggf.drmaa.Session;\r
  27 \r
  28 import compbio.engine.Configurator;\r
  29 import compbio.engine.client.Util;\r
  30 import compbio.metadata.JobExecutionException;\r
  31 import compbio.metadata.JobStatus;\r
  32 \r
  33 public class ClusterUtil {\r
  34 \r
  35         private static final Logger log = Logger.getLogger(ClusterUtil.class);\r
  36 \r
  37         public static final NumberFormat CLUSTER_STAT_IN_SEC = NumberFormat\r
  38                         .getInstance();\r
  39 \r
  40         static {\r
  41                 CLUSTER_STAT_IN_SEC.setMinimumFractionDigits(4);\r
  42         }\r
  43 \r
  44         public static final boolean cancelJob(final String jobId,\r
  45                         ClusterSession csession) {\r
  46                 assert Util.isValidJobId(jobId);\r
  47                 boolean cancelled = true;\r
  48                 Session session = csession.getSession();\r
  49                 try {\r
  50                         log.info("Job " + jobId + " is successfully cancelled");\r
  51                         compbio.engine.client.Util.writeMarker(Configurator.getWorkDirectory(jobId),\r
  52                                         JobStatus.CANCELLED);\r
  53                         session.control(ClusterSession.getClusterJobId(jobId).getJobId(),\r
  54                                         Session.TERMINATE);\r
  55                 } catch (DrmaaException e) {\r
  56                         // Log silently\r
  57                         log.error("Job " + jobId + " cancellation failed!");\r
  58                         log.error("Cause: " + e.getLocalizedMessage(), e.getCause());\r
  59                         cancelled = false;\r
  60                 } catch (IOException e) {\r
  61                         log.error(\r
  62                                         "Could not read JOBID file to determine cluster jobid for taskid: "\r
  63                                                         + jobId + " Message: " + e.getLocalizedMessage(), e\r
  64                                                         .getCause());\r
  65                 } finally {\r
  66                         log\r
  67                                         .trace("Job "\r
  68                                                         + jobId\r
  69                                                         + " has been successfully removed from the cluster engine job list");\r
  70                         csession.removeJob(jobId);\r
  71                 }\r
  72                 return cancelled;\r
  73         }\r
  74 \r
  75         public static final JobInfo waitForResult(ClusterSession csession,\r
  76                         String jobId) throws JobExecutionException {\r
  77                 JobInfo jinfo = null;\r
  78                 assert Util.isValidJobId(jobId);\r
  79                 try {\r
  80                         jinfo = csession.waitForJob(jobId);\r
  81                 } catch (DrmaaException e) {\r
  82                         log.error(e.getLocalizedMessage(), e.getCause());\r
  83                         throw new JobExecutionException(e);\r
  84                 } catch (IOException e) {\r
  85                         log.error("Could not read JOBID file for job " + jobId\r
  86                                         + " Message " + e.getMessage(), e.getCause());\r
  87                         throw new JobExecutionException(e);\r
  88                 } finally {\r
  89                         // at this point the job has finished\r
  90                         csession.removeJob(jobId);\r
  91                 }\r
  92                 return jinfo;\r
  93         }\r
  94 \r
  95 }\r