Refactor batch daemon to not be a full UNIX daemon implementation

Do not try to implement a full UNIX daemon suitable for init.d with the
batch daemon, but rather keep it simple and depend on something like
supervisord to implement process control.

We now also correctly handle SIGINT (Ctrl+C) and SIGTERM signals.

bin/mutalyzer-batchd

@@ -2,24 +2,16 @@
 """
 Daemon for processing scheduled batch jobs.
 
-We use python-daemon [1] for daemonizing the job processing. This file
-should be run with the mutalyzer directory as working directory.
+The process can be shutdown gracefully by sending a SIGINT (Ctrl+C) or SIGTERM
+signal.
 
-@todo: Check if PID dir is writable.
 @todo: Get rid of ugly exception logging.
 @todo: Reload configuration without restarting (for example, on SIGHUP).
-@todo: Use [2] to set process name (and use that in init script).
-
-[1] http://pypi.python.org/pypi/python-daemon/
-[2] http://code.google.com/p/py-setproctitle/
 """
 
 
-import os
-import sys
-from daemon import pidfile, DaemonContext
-from lockfile import LockTimeout
 import signal
+import sys
 import time
 import traceback
 
@@ -28,76 +20,44 @@ from mutalyzer.Db import Batch, Counter
 from mutalyzer.Scheduler import Scheduler
 
 
-def cleanup(signum, stack_frame):
-    """
-    Generate a normal exit signal.
-    """
-    sys.exit(1)
-
-
 def daemonize():
     """
-    Write PID file when it is not locked and daemonize a loop processing
-    scheduled batch jobs.
+    Run forever in a loop processing scheduled batch jobs.
     """
-    pidfile_path = os.path.realpath(config.get('PIDfile'))
-
-    lockfile = pidfile.TimeoutPIDLockFile(pidfile_path, acquire_timeout=1,
-                                          threaded=False)
-
-    context = DaemonContext(working_directory=os.getcwd(),
-                            pidfile=lockfile)
-
-    # To preserve stderr and stdout, add these arguments.
-    #stdin=sys.stdin,
-    #stdout=sys.stdout,
-    #files_preserve=[sys.stdin, sys.stdout]
-
-    # Writing the PID file as root before changing user/group does not seem
-    # to work.
-    #uid=pwd.getpwnam('www-data').pw_uid
-    #gid=grp.getgrnam('www-data').gr_gid
-
-    context.signal_map = {
-        signal.SIGTERM: cleanup,
-        signal.SIGHUP:  'terminate'
-    }
-
-    with context:
-        # Note that any opened files are now closed. This is not a problem for
-        # the config module, since it does not read its file again after
-        # initialisation.
-        database = Batch()
-        counter = Counter()
-
-        scheduler = Scheduler(database)
-
-        def stop_scheduler(signum, stack_frame):
-            scheduler.stop()
-        signal.signal(signal.SIGTERM, stop_scheduler)
-
-        while not scheduler.stopped():
-            # Process batch jobs. This process() method runs while there
-            # exist jobs to run.
-            try:
-                scheduler.process(counter)
-            except Exception as e:
-                f = open('/tmp/batcherror.log', 'a+')
-                f.write('Error (%s): %s\n' % (type(e), str(e)))
-                f.write('%s\n\n' % repr(traceback.format_exc()))
-                f.flush()
-                f.close()
-            if scheduler.stopped():
-                break
-            # Wait a bit and process any possible new jobs.
-            time.sleep(5)
+    database = Batch()
+    counter = Counter()
+    scheduler = Scheduler(database)
+
+    def handle_exit(signum, stack_frame):
+        if scheduler.stopped():
+            sys.stderr.write('mutalyzer-batchd: Terminated\n')
+            sys.exit(1)
+        if signum == signal.SIGINT:
+            sys.stderr.write('mutalyzer-batchd: Hitting Ctrl+C again will terminate any running job!\n')
+        scheduler.stop()
+
+    signal.signal(signal.SIGTERM, handle_exit)
+    signal.signal(signal.SIGINT, handle_exit)
+
+    while not scheduler.stopped():
+        # Process batch jobs. This process() method runs while there
+        # exist jobs to run.
+        try:
+            scheduler.process(counter)
+        except Exception as e:
+            f = open('/tmp/batcherror.log', 'a+')
+            f.write('Error (%s): %s\n' % (type(e), str(e)))
+            f.write('%s\n\n' % repr(traceback.format_exc()))
+            f.flush()
+            f.close()
+        if scheduler.stopped():
+            break
+        # Wait a bit and process any possible new jobs.
+        time.sleep(1)
+
+    sys.stderr.write('mutalyzer-batchd: Graceful shutdown\n')
+    sys.exit(0)
 
 
 if __name__ == '__main__':
-    try:
-        daemonize()
-    except LockTimeout:
-        # If we want to see something on stdout, we have to add it to the
-        # {files_preserve} argument of the DaemonContext.
-        #print 'Mutalyzer batch daemon is already running.'
-        sys.exit(1)
+    daemonize()

requirements.txt

 MySQL-python==1.2.4
-argparse==1.2.1
 biopython==1.63b
 configobj==4.7.2
-lockfile==0.9.1
 lxml==3.2.4
 nose==1.3.0
 pyparsing==2.0.1
-python-daemon==1.6
 pytz==2013.8
 requests==2.0.1
 simplejson==3.3.1