Use a logger initialized to the module name much more consistently.

[htsworkflow.git] / htsworkflow / automation / runner.py

diff --git a/htsworkflow/automation/runner.py b/htsworkflow/automation/runner.py
index 45d4ffcdee8d52a7786dc65816fcc6b8d8d78044..7b0c4c9d7ca6b47e59254b27e2171876525e6715 100644 (file)
--- a/htsworkflow/automation/runner.py
+++ b/htsworkflow/automation/runner.py
@@ -11,6 +11,8 @@ from benderjab import rpc
 
 from htsworkflow.pipelines.configure_run import *
 
+LOGGER = logging.getLogger(__name__)
+
 #s_fc = re.compile('FC[0-9]+')
 s_fc = re.compile('_[0-9a-zA-Z]*$')
 
@@ -23,22 +25,22 @@ def _get_flowcell_from_rundir(run_dir):
     junk, dirname = os.path.split(run_dir)
     mo = s_fc.search(dirname)
     if not mo:
-        logging.error('RunDir 2 FlowCell error: %s' % (run_dir))
+        LOGGER.error('RunDir 2 FlowCell error: %s' % (run_dir))
         return None
 
     return dirname[mo.start()+1:]
-    
+
 
 
 class Runner(rpc.XmlRpcBot):
     """
     Manage running pipeline jobs.
-    """    
+    """
     def __init__(self, section=None, configfile=None):
         #if configfile is None:
         #    self.configfile = "~/.htsworkflow"
         super(Runner, self).__init__(section, configfile)
-        
+
         self.cfg['notify_users'] = None
         self.cfg['genome_dir'] = None
         self.cfg['base_analysis_dir'] = None
@@ -47,11 +49,11 @@ class Runner(rpc.XmlRpcBot):
         self.cfg['notify_postanalysis'] = None
 
         self.conf_info_dict = {}
-        
+
         self.register_function(self.sequencingFinished)
         #self.eventTasks.append(self.update)
 
-    
+
     def read_config(self, section=None, configfile=None):
         super(Runner, self).read_config(section, configfile)
 
@@ -60,8 +62,8 @@ class Runner(rpc.XmlRpcBot):
 
         self.notify_users = self._parse_user_list(self.cfg['notify_users'])
         #FIXME: process notify_postpipeline cfg
-        
-    
+
+
     def _parser(self, msg, who):
         """
         Parse xmpp chat messages
@@ -88,13 +90,13 @@ class Runner(rpc.XmlRpcBot):
         else:
             reply = u"I didn't understand '%s'" %(msg)
 
-        logging.debug("reply: " + str(reply))
+        LOGGER.debug("reply: " + str(reply))
         return reply
 
 
     def getStatusReport(self, fc_num):
         """
-        Returns text status report for flow cell number 
+        Returns text status report for flow cell number
         """
         if fc_num not in self.conf_info_dict:
             return "No record of a %s run." % (fc_num)
@@ -108,18 +110,18 @@ class Runner(rpc.XmlRpcBot):
         output = status.statusReport()
 
         return '\n'.join(output)
-    
-            
+
+
     def sequencingFinished(self, run_dir):
         """
         Sequenceing (and copying) is finished, time to start pipeline
         """
-        logging.debug("received sequencing finished message")
+        LOGGER.debug("received sequencing finished message")
 
         # Setup config info object
         ci = ConfigInfo()
         ci.base_analysis_dir = self.base_analysis_dir
-        ci.analysis_dir = os.path.join(self.base_analysis_dir, run_dir)        
+        ci.analysis_dir = os.path.join(self.base_analysis_dir, run_dir)
 
         # get flowcell from run_dir name
         flowcell = _get_flowcell_from_rundir(run_dir)
@@ -131,22 +133,22 @@ class Runner(rpc.XmlRpcBot):
         # Launch the job in it's own thread and turn.
         self.launchJob(run_dir, flowcell, ci)
         return "started"
-        
-        
+
+
     def pipelineFinished(self, run_dir):
         # need to strip off self.watch_dir from rundir I suspect.
-        logging.info("pipeline finished in" + str(run_dir))
+        LOGGER.info("pipeline finished in" + str(run_dir))
         #pattern = self.watch_dir
         #if pattern[-1] != os.path.sep:
         #    pattern += os.path.sep
         #stripped_run_dir = re.sub(pattern, "", run_dir)
-        #logging.debug("stripped to " + stripped_run_dir)
+        #LOGGER.debug("stripped to " + stripped_run_dir)
 
         # Notify each user that the run has finished.
         if self.notify_users is not None:
             for u in self.notify_users:
                 self.send(u, 'Pipeline run %s finished' % (run_dir))
-                
+
         #if self.notify_runner is not None:
         #    for r in self.notify_runner:
         #        self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
@@ -168,39 +170,39 @@ class Runner(rpc.XmlRpcBot):
                                           cfg_filepath,
                                           self.genome_dir)
         if status_retrieve_cfg:
-            logging.info("Runner: Retrieve config: success")
+            LOGGER.info("Runner: Retrieve config: success")
             self.reportMsg("Retrieve config (%s): success" % (run_dir))
         else:
-            logging.error("Runner: Retrieve config: failed")
+            LOGGER.error("Runner: Retrieve config: failed")
             self.reportMsg("Retrieve config (%s): FAILED" % (run_dir))
 
-        
+
         # configure step
         if status_retrieve_cfg:
             status = configure(conf_info)
             if status:
-                logging.info("Runner: Configure: success")
+                LOGGER.info("Runner: Configure: success")
                 self.reportMsg("Configure (%s): success" % (run_dir))
                 self.reportMsg(
                     os.linesep.join(glob(os.path.join(run_dir,'Data','C*')))
                 )
             else:
-                logging.error("Runner: Configure: failed")
+                LOGGER.error("Runner: Configure: failed")
                 self.reportMsg("Configure (%s): FAILED" % (run_dir))
 
             #if successful, continue
             if status:
                 # Setup status cmdline status monitor
                 #startCmdLineStatusMonitor(ci)
-                
+
                 # running step
                 print 'Running pipeline now!'
                 run_status = run_pipeline(conf_info)
                 if run_status is True:
-                    logging.info('Runner: Pipeline: success')
+                    LOGGER.info('Runner: Pipeline: success')
                     self.reportMsg("Pipeline run (%s): Finished" % (run_dir,))
                 else:
-                    logging.info('Runner: Pipeline: failed')
+                    LOGGER.info('Runner: Pipeline: failed')
                     self.reportMsg("Pipeline run (%s): FAILED" % (run_dir))
 
 
@@ -212,13 +214,13 @@ class Runner(rpc.XmlRpcBot):
                         args=[run_dir, flowcell, conf_info])
         t.setDaemon(True)
         t.start()
-        
 
-        
+
+
 def main(args=None):
     bot = Runner()
     return bot.main(args)
-    
+
 if __name__ == "__main__":
     sys.exit(main(sys.argv[1:]))
-    
+