[project @ add skeleton for runner]

this is the basic outline of the runner bot. Important functions like
sequencingFinished and pipelineFinish still need to be filled in.

diff --git a/gaworkflow/runner.py b/gaworkflow/runner.py
new file mode 100644 (file)
index 0000000..40eae64
--- /dev/null
+++ b/gaworkflow/runner.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+import logging
+import os
+import re
+import sys
+import time
+
+from benderjab import rpc
+
+class Runner(rpc.XmlRpcBot):
+    """
+    Manage running pipeline jobs.
+    """    
+    def __init__(self, section=None, configfile=None):
+        #if configfile is None:
+        #    self.configfile = "~/.gaworkflow"
+        super(Runner, self).__init__(section, configfile)
+        
+        self.cfg['notify_users'] = None
+        
+        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)
+    
+    def _parser(self, msg, who):
+        """
+        Parse xmpp chat messages
+        """
+        help = u"I can send [start] a run, or report [status]"
+        if re.match(u"help", msg):
+            reply = help
+        elif re.match("status", msg):            
+            reply = u"not implemented"
+        elif re.match(u"start", msg):
+            words = msg.split()
+            if len(words) == 2:
+                self.sequencingFinished(words[1])
+                reply = u"starting run for %s" % (words[1])
+            else:
+                reply = u"need runfolder name"
+        else:
+            reply = u"I didn't understand '%s'" %(msg)            
+        return reply
+        
+    def start(self, daemonize):
+        """
+        Start application
+        """
+        super(Runner, self).start(daemonize)
+        
+    def stop(self):
+        """
+        shutdown application
+        """
+        super(Runner, self).stop()
+            
+    def sequencingFinished(self, run_dir):
+        """
+        Sequenceing (and copying) is finished, time to start pipeline
+        """
+        logging.debug("received sequencing finished message")
+        
+    def pipelineFinished(self, run_dir):
+        # need to strip off self.watch_dir from rundir I suspect.
+        logging.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)
+        #if self.notify_users is not None:
+        #    for u in self.notify_users:
+        #        self.send(u, 'Sequencing run %s finished' % #(stripped_run_dir))
+        #if self.notify_runner is not None:
+        #    for r in self.notify_runner:
+        #        self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
+        
+def main(args=None):
+    bot = Runner()
+    return bot.main(args)
+    
+if __name__ == "__main__":
+    sys.exit(main(sys.argv[1:]))
+    
\ No newline at end of file