9 from benderjab import rpc
11 from gaworkflow.pipeline.configure_run import *
12 from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor
14 #s_fc = re.compile('FC[0-9]+')
15 s_fc = re.compile('_[0-9a-zA-Z]*$')
18 def _get_flowcell_from_rundir(run_dir):
20 Returns flowcell string based on run_dir.
21 Returns None and logs error if flowcell can't be found.
23 junk, dirname = os.path.split(run_dir)
24 mo = s_fc.search(dirname)
26 logging.error('RunDir 2 FlowCell error: %s' % (run_dir))
29 return dirname[mo.start()+1:]
33 class Runner(rpc.XmlRpcBot):
35 Manage running pipeline jobs.
37 def __init__(self, section=None, configfile=None):
38 #if configfile is None:
39 # self.configfile = "~/.gaworkflow"
40 super(Runner, self).__init__(section, configfile)
42 self.cfg['notify_users'] = None
43 self.cfg['genome_dir'] = None
44 self.cfg['base_analysis_dir'] = None
46 self.cfg['notify_users'] = None
47 self.cfg['notify_postanalysis'] = None
49 self.conf_info_dict = {}
51 self.register_function(self.sequencingFinished)
52 #self.eventTasks.append(self.update)
55 def read_config(self, section=None, configfile=None):
56 super(Runner, self).read_config(section, configfile)
58 self.genome_dir = self._check_required_option('genome_dir')
59 self.base_analysis_dir = self._check_required_option('base_analysis_dir')
61 self.notify_users = self._parse_user_list(self.cfg['notify_users'])
62 #FIXME: process notify_postpipeline cfg
65 def _parser(self, msg, who):
67 Parse xmpp chat messages
69 help = u"I can send [start] a run, or report [status]"
70 if re.match(u"help", msg):
72 elif re.match("status", msg):
73 reply = u"not implemented"
74 elif re.match(u"start", msg):
77 self.sequencingFinished(words[1])
78 reply = u"starting run for %s" % (words[1])
80 reply = u"need runfolder name"
82 reply = u"I didn't understand '%s'" %(msg)
84 logging.debug("reply: " + str(reply))
88 def start(self, daemonize):
92 super(Runner, self).start(daemonize)
99 super(Runner, self).stop()
102 def sequencingFinished(self, run_dir):
104 Sequenceing (and copying) is finished, time to start pipeline
106 logging.debug("received sequencing finished message")
108 # Setup config info object
110 ci.base_analysis_dir = self.base_analysis_dir
111 ci.analysis_dir = os.path.join(self.base_analysis_dir, run_dir)
113 # get flowcell from run_dir name
114 flowcell = _get_flowcell_from_rundir(run_dir)
116 # Store ci object in dictionary
117 self.conf_info_dict[flowcell] = ci
120 # Launch the job in it's own thread and turn.
121 self.launchJob(run_dir, flowcell, ci)
124 def pipelineFinished(self, run_dir):
125 # need to strip off self.watch_dir from rundir I suspect.
126 logging.info("pipeline finished in" + str(run_dir))
127 #pattern = self.watch_dir
128 #if pattern[-1] != os.path.sep:
129 # pattern += os.path.sep
130 #stripped_run_dir = re.sub(pattern, "", run_dir)
131 #logging.debug("stripped to " + stripped_run_dir)
133 # Notify each user that the run has finished.
134 if self.notify_users is not None:
135 for u in self.notify_users:
136 self.send(u, 'Pipeline run %s finished' % (run_dir))
138 #if self.notify_runner is not None:
139 # for r in self.notify_runner:
140 # self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
142 def reportMsg(self, msg):
144 if self.notify_users is not None:
145 for u in self.notify_users:
149 def _runner(self, run_dir, flowcell, conf_info):
151 # retrieve config step
152 cfg_filepath = os.path.join(conf_info.analysis_dir,
154 status_retrieve_cfg = retrieve_config(conf_info,
158 if status_retrieve_cfg:
159 logging.info("Runner: Retrieve config: success")
160 self.reportMsg("Retrieve config (%s): success" % (run_dir))
162 logging.error("Runner: Retrieve config: failed")
163 self.reportMsg("Retrieve config (%s): FAILED" % (run_dir))
167 if status_retrieve_cfg:
168 status = configure(conf_info)
170 logging.info("Runner: Configure: success")
171 self.reportMsg("Configure (%s): success" % (run_dir))
173 logging.error("Runner: Configure: failed")
174 self.reportMsg("Configure (%s): FAILED" % (run_dir))
176 #if successful, continue
178 # Setup status cmdline status monitor
179 #startCmdLineStatusMonitor(ci)
182 print 'Running pipeline now!'
183 run_status = run_pipeline(conf_info)
184 if run_status is True:
185 logging.info('Runner: Pipeline: success')
186 self.piplineFinished(run_dir)
188 logging.info('Runner: Pipeline: failed')
189 self.reportMsg("Pipeline run (%s): FAILED" % (run_dir))
192 def launchJob(self, run_dir, flowcell, conf_info):
194 Starts up a thread for running the pipeline
196 t = threading.Thread(target=self._runner,
197 args=[run_dir, flowcell, conf_info])
204 bot = Runner('demobot')
205 bot.cfg['loglevel'] = 'DEBUG'
206 return bot.main(args)
208 if __name__ == "__main__":
209 sys.exit(main(sys.argv[1:]))