htsworkflow/automation/runner.py

   1 #!/usr/bin/env python
   2 from glob import glob
   3 import logging
   4 import os
   5 import re
   6 import sys
   7 import time
   8 import threading
   9
  10 from benderjab import rpc
  11
  12 from htsworkflow.pipelines.configure_run import *
  13
  14 #s_fc = re.compile('FC[0-9]+')
  15 s_fc = re.compile('_[0-9a-zA-Z]*$')
  16
  17
  18 def _get_flowcell_from_rundir(run_dir):
  19     """
  20     Returns flowcell string based on run_dir.
  21     Returns None and logs error if flowcell can't be found.
  22     """
  23     junk, dirname = os.path.split(run_dir)
  24     mo = s_fc.search(dirname)
  25     if not mo:
  26         logging.error('RunDir 2 FlowCell error: %s' % (run_dir))
  27         return None
  28
  29     return dirname[mo.start()+1:]
  30
  31
  32
  33 class Runner(rpc.XmlRpcBot):
  34     """
  35     Manage running pipeline jobs.
  36     """
  37     def __init__(self, section=None, configfile=None):
  38         #if configfile is None:
  39         #    self.configfile = "~/.htsworkflow"
  40         super(Runner, self).__init__(section, configfile)
  41
  42         self.cfg['notify_users'] = None
  43         self.cfg['genome_dir'] = None
  44         self.cfg['base_analysis_dir'] = None
  45
  46         self.cfg['notify_users'] = None
  47         self.cfg['notify_postanalysis'] = None
  48
  49         self.conf_info_dict = {}
  50
  51         self.register_function(self.sequencingFinished)
  52         #self.eventTasks.append(self.update)
  53
  54
  55     def read_config(self, section=None, configfile=None):
  56         super(Runner, self).read_config(section, configfile)
  57
  58         self.genome_dir = self._check_required_option('genome_dir')
  59         self.base_analysis_dir = self._check_required_option('base_analysis_dir')
  60
  61         self.notify_users = self._parse_user_list(self.cfg['notify_users'])
  62         #FIXME: process notify_postpipeline cfg
  63
  64
  65     def _parser(self, msg, who):
  66         """
  67         Parse xmpp chat messages
  68         """
  69         help = u"I can send [start] a run, or report [status]"
  70         if re.match(u"help", msg):
  71             reply = help
  72         elif re.match("status", msg):
  73             words = msg.split()
  74             if len(words) == 2:
  75                 reply = self.getStatusReport(words[1])
  76             else:
  77                 reply = u"Status available for: %s" \
  78                         % (', '.join([k for k in self.conf_info_dict.keys()]))
  79         elif re.match(u"start", msg):
  80             words = msg.split()
  81             if len(words) == 2:
  82                 self.sequencingFinished(words[1])
  83                 reply = u"starting run for %s" % (words[1])
  84             else:
  85                 reply = u"need runfolder name"
  86         elif re.match(u"path", msg):
  87             reply = u"My path is: " + unicode(os.environ['PATH'])
  88         else:
  89             reply = u"I didn't understand '%s'" %(msg)
  90
  91         logging.debug("reply: " + str(reply))
  92         return reply
  93
  94
  95     def getStatusReport(self, fc_num):
  96         """
  97         Returns text status report for flow cell number
  98         """
  99         if fc_num not in self.conf_info_dict:
 100             return "No record of a %s run." % (fc_num)
 101
 102         status = self.conf_info_dict[fc_num].status
 103
 104         if status is None:
 105             return "No status information for %s yet." \
 106                    " Probably still in configure step. Try again later." % (fc_num)
 107
 108         output = status.statusReport()
 109
 110         return '\n'.join(output)
 111
 112
 113     def sequencingFinished(self, run_dir):
 114         """
 115         Sequenceing (and copying) is finished, time to start pipeline
 116         """
 117         logging.debug("received sequencing finished message")
 118
 119         # Setup config info object
 120         ci = ConfigInfo()
 121         ci.base_analysis_dir = self.base_analysis_dir
 122         ci.analysis_dir = os.path.join(self.base_analysis_dir, run_dir)
 123
 124         # get flowcell from run_dir name
 125         flowcell = _get_flowcell_from_rundir(run_dir)
 126
 127         # Store ci object in dictionary
 128         self.conf_info_dict[flowcell] = ci
 129
 130
 131         # Launch the job in it's own thread and turn.
 132         self.launchJob(run_dir, flowcell, ci)
 133         return "started"
 134
 135
 136     def pipelineFinished(self, run_dir):
 137         # need to strip off self.watch_dir from rundir I suspect.
 138         logging.info("pipeline finished in" + str(run_dir))
 139         #pattern = self.watch_dir
 140         #if pattern[-1] != os.path.sep:
 141         #    pattern += os.path.sep
 142         #stripped_run_dir = re.sub(pattern, "", run_dir)
 143         #logging.debug("stripped to " + stripped_run_dir)
 144
 145         # Notify each user that the run has finished.
 146         if self.notify_users is not None:
 147             for u in self.notify_users:
 148                 self.send(u, 'Pipeline run %s finished' % (run_dir))
 149
 150         #if self.notify_runner is not None:
 151         #    for r in self.notify_runner:
 152         #        self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
 153
 154     def reportMsg(self, msg):
 155
 156         if self.notify_users is not None:
 157             for u in self.notify_users:
 158                 self.send(u, msg)
 159
 160
 161     def _runner(self, run_dir, flowcell, conf_info):
 162
 163         # retrieve config step
 164         cfg_filepath = os.path.join(conf_info.analysis_dir,
 165                                     'config-auto.txt')
 166         status_retrieve_cfg = retrieve_config(conf_info,
 167                                           flowcell,
 168                                           cfg_filepath,
 169                                           self.genome_dir)
 170         if status_retrieve_cfg:
 171             logging.info("Runner: Retrieve config: success")
 172             self.reportMsg("Retrieve config (%s): success" % (run_dir))
 173         else:
 174             logging.error("Runner: Retrieve config: failed")
 175             self.reportMsg("Retrieve config (%s): FAILED" % (run_dir))
 176
 177
 178         # configure step
 179         if status_retrieve_cfg:
 180             status = configure(conf_info)
 181             if status:
 182                 logging.info("Runner: Configure: success")
 183                 self.reportMsg("Configure (%s): success" % (run_dir))
 184                 self.reportMsg(
 185                     os.linesep.join(glob(os.path.join(run_dir,'Data','C*')))
 186                 )
 187             else:
 188                 logging.error("Runner: Configure: failed")
 189                 self.reportMsg("Configure (%s): FAILED" % (run_dir))
 190
 191             #if successful, continue
 192             if status:
 193                 # Setup status cmdline status monitor
 194                 #startCmdLineStatusMonitor(ci)
 195
 196                 # running step
 197                 print 'Running pipeline now!'
 198                 run_status = run_pipeline(conf_info)
 199                 if run_status is True:
 200                     logging.info('Runner: Pipeline: success')
 201                     self.reportMsg("Pipeline run (%s): Finished" % (run_dir,))
 202                 else:
 203                     logging.info('Runner: Pipeline: failed')
 204                     self.reportMsg("Pipeline run (%s): FAILED" % (run_dir))
 205
 206
 207     def launchJob(self, run_dir, flowcell, conf_info):
 208         """
 209         Starts up a thread for running the pipeline
 210         """
 211         t = threading.Thread(target=self._runner,
 212                         args=[run_dir, flowcell, conf_info])
 213         t.setDaemon(True)
 214         t.start()
 215
 216
 217
 218 def main(args=None):
 219     bot = Runner()
 220     return bot.main(args)
 221
 222 if __name__ == "__main__":
 223     sys.exit(main(sys.argv[1:]))
 224