htsworkflow/automation/spoolwatcher.py

   1 #!/usr/bin/env python
   2 import logging
   3 import os
   4 import re
   5 import shlex
   6 import sys
   7 import time
   8
   9 from htsworkflow.util import mount
  10
  11 # this uses pyinotify
  12 import pyinotify
  13 from pyinotify import EventsCodes
  14
  15 from benderjab import rpc
  16
  17 def get_top_dir(root, path):
  18     """
  19     Return the directory in path that is a subdirectory of root.
  20     e.g.
  21
  22     >>> print get_top_dir('/a/b/c', '/a/b/c/d/e/f')
  23     d
  24     >>> print get_top_dir('/a/b/c/', '/a/b/c/d/e/f')
  25     d
  26     >>> print get_top_dir('/a/b/c', '/g/e/f')
  27     None
  28     >>> print get_top_dir('/a/b/c', '/a/b/c')
  29     <BLANKLINE>
  30     """
  31     if path.startswith(root):
  32         subpath = path[len(root):]
  33         if subpath.startswith('/'):
  34             subpath = subpath[1:]
  35         return subpath.split(os.path.sep)[0]
  36     else:
  37         return None
  38
  39 class WatcherEvents(object):
  40     # two events need to be tracked
  41     # one to send startCopy
  42     # one to send OMG its broken
  43     # OMG its broken needs to stop when we've seen enough
  44     #  cycles
  45     # this should be per runfolder.
  46     # read the xml files
  47     def __init__(self):
  48         pass
  49
  50
  51 class Handler(pyinotify.ProcessEvent):
  52     def __init__(self, watchmanager, bot, ipar=False):
  53         """
  54         ipar flag indicates we should wait for ipar to finish, instead of
  55              just the run finishing
  56         """
  57         self.last_event = {}
  58         self.watchmanager = watchmanager
  59         self.bot = bot
  60         self.ipar_mode = ipar
  61         if self.ipar_mode:
  62             self.last_file = 'IPAR_Netcopy_Complete.txt'.lower()
  63         else:
  64             self.last_file = "run.completed".lower()
  65
  66     def process_IN_CREATE(self, event):
  67         for wdd in self.bot.wdds:
  68             for watch_path in self.bot.watchdirs:
  69                 if event.path.startswith(watch_path):
  70                     target = get_top_dir(watch_path, event.path)
  71                     self.last_event.setdefault(watch_path, {})[target] = time.time()
  72
  73                     msg = "Create: %s %s" % (event.path, event.name)
  74
  75                     if event.name.lower() == self.last_file:
  76                         try:
  77                             self.bot.sequencingFinished(event.path)
  78                         except IOError, e:
  79                             pass
  80                             logging.error("Couldn't send sequencingFinished")
  81                     logging.debug(msg)
  82
  83     def process_IN_DELETE(self, event):
  84         logging.debug("Remove: %s" %  os.path.join(event.path, event.name))
  85         pass
  86
  87     def process_IN_UNMOUNT(self, event):
  88         pathname = os.path.join(event.path, event.name)
  89         logging.debug("IN_UNMOUNT: %s" % (pathname,))
  90         self.bot.unmount_watch(event.path)
  91
  92 class SpoolWatcher(rpc.XmlRpcBot):
  93     """
  94     Watch a directory and send a message when another process is done writing.
  95
  96     This monitors a directory tree using inotify (linux specific) and
  97     after some files having been written will send a message after <timeout>
  98     seconds of no file writing.
  99
 100     (Basically when the solexa machine finishes dumping a round of data
 101     this'll hopefully send out a message saying hey look theres data available
 102
 103     """
 104     # these params need to be in the config file
 105     # I wonder where I should put the documentation
 106     #:Parameters:
 107     #    `watchdirs` - list of directories to monitor for modifications
 108     #    `profile` - specify which .htsworkflow profile to use
 109     #    `write_timeout` - how many seconds to wait for writes to finish to
 110     #                      the spool
 111     #    `notify_timeout` - how often to timeout from notify
 112
 113     def __init__(self, section=None, configfile=None):
 114         #if configfile is None:
 115         #    self.configfile = "~/.htsworkflow"
 116         super(SpoolWatcher, self).__init__(section, configfile)
 117
 118         self.cfg['watchdirs'] = None
 119         self.cfg['write_timeout'] = 10
 120         self.cfg['notify_users'] = None
 121         self.cfg['notify_runner'] = None
 122         self.cfg['wait_for_ipar'] = 0
 123
 124         self.watchdirs = []
 125         self.watchdir_url_map = {}
 126         self.notify_timeout = 0.001
 127
 128         self.wm = None
 129         self.notify_users = None
 130         self.notify_runner = None
 131         self.wdds = []
 132
 133         # keep track if the specified mount point is currently mounted
 134         self.mounted_points = {}
 135         # keep track of which mount points tie to which watch directories
 136         # so maybe we can remount them.
 137         self.mounts_to_watches = {}
 138
 139         self.eventTasks.append(self.process_notify)
 140
 141     def read_config(self, section=None, configfile=None):
 142         super(SpoolWatcher, self).read_config(section, configfile)
 143
 144         self.watchdirs = shlex.split(self._check_required_option('watchdirs'))
 145         # see if there's an alternate url that should be used for the watchdir
 146         for watchdir in self.watchdirs:
 147             self.watchdir_url_map[watchdir] = self.cfg.get(watchdir, watchdir)
 148
 149         self.write_timeout = int(self.cfg['write_timeout'])
 150         self.wait_for_ipar = int(self.cfg['wait_for_ipar'])
 151
 152         self.notify_users = self._parse_user_list(self.cfg['notify_users'])
 153         try:
 154           self.notify_runner = \
 155              self._parse_user_list(self.cfg['notify_runner'],
 156                                    require_resource=True)
 157         except bot.JIDMissingResource:
 158             msg = 'need a full jabber ID + resource for xml-rpc destinations'
 159             raise bot.JIDMissingResource(msg)
 160
 161         self.handler = None
 162         self.notifier = None
 163
 164     def add_watch(self, watchdirs=None):
 165         """
 166         start watching watchdir or self.watchdir
 167         we're currently limited to watching one directory tree.
 168         """
 169         # create the watch managers if we need them
 170         if self.wm is None:
 171             self.wm = pyinotify.WatchManager()
 172             self.handler = Handler(self.wm, self, self.wait_for_ipar)
 173             self.notifier = pyinotify.Notifier(self.wm, self.handler)
 174
 175         # the one tree limit is mostly because self.wdd is a single item
 176         # but managing it as a list might be a bit more annoying
 177         if watchdirs is None:
 178             watchdirs = self.watchdirs
 179
 180         mask = EventsCodes.IN_CREATE | EventsCodes.IN_UNMOUNT
 181         # rec traverses the tree and adds all the directories that are there
 182         # at the start.
 183         # auto_add will add in new directories as they are created
 184         for w in watchdirs:
 185             mount_location = mount.find_mount_point_for(w)
 186             self.mounted_points[mount_location] = True
 187             mounts = self.mounts_to_watches.get(mount_location, [])
 188             if w not in mounts:
 189                 mounts.append(w)
 190                 self.mounts_to_watches[mount_location] = mounts
 191
 192             logging.info(u"Watching:"+unicode(w))
 193             self.wdds.append(self.wm.add_watch(w, mask, rec=True, auto_add=True))
 194
 195     def unmount_watch(self, event_path):
 196         # remove backwards so we don't get weirdness from
 197         # the list getting shorter
 198         for i in range(len(self.wdds),0, -1):
 199             wdd = self.wdds[i]
 200             logging.info(u'unmounting: '+unicode(wdd.items()))
 201             self.wm.rm_watch(wdd.values())
 202             del self.wdds[i]
 203         self.mounted = False
 204
 205     def process_notify(self, *args):
 206         if self.notifier is None:
 207             # nothing to do yet
 208             return
 209         # process the queue of events as explained above
 210         self.notifier.process_events()
 211         #check events waits timeout
 212         if self.notifier.check_events(self.notify_timeout):
 213             # read notified events and enqeue them
 214             self.notifier.read_events()
 215             # should we do something?
 216         # has something happened?
 217         for watchdir, last_events in self.handler.last_event.items():
 218             #logging.debug('last_events: %s %s' % (watchdir, last_events))
 219             for last_event_dir, last_event_time in last_events.items():
 220                 time_delta = time.time() - last_event_time
 221                 if time_delta > self.write_timeout:
 222                     self.startCopy(watchdir, last_event_dir)
 223                     self.handler.last_event[watchdir] = {}
 224         # handle unmounted filesystems
 225         for mount_point, was_mounted in self.mounted_points.items():
 226             if not was_mounted and mount.is_mounted(mount_point):
 227                 # we've been remounted. Huzzah!
 228                 # restart the watch
 229                 for watch in self.mounts_to_watches[mount_point]:
 230                     self.add_watch(watch)
 231                     logging.info(
 232                         "%s was remounted, restarting watch" % \
 233                             (mount_point)
 234                     )
 235                 self.mounted_points[mount_point] = True
 236
 237     def _parser(self, msg, who):
 238         """
 239         Parse xmpp chat messages
 240         """
 241         help = u"I can send [copy] message, or squencer [finished]"
 242         if re.match(u"help", msg):
 243             reply = help
 244         elif re.match("copy", msg):
 245             self.startCopy()
 246             reply = u"sent copy message"
 247         elif re.match(u"finished", msg):
 248             words = msg.split()
 249             if len(words) == 2:
 250                 self.sequencingFinished(words[1])
 251                 reply = u"sending sequencing finished for %s" % (words[1])
 252             else:
 253                 reply = u"need runfolder name"
 254         else:
 255             reply = u"I didn't understand '%s'" %(msg)
 256         return reply
 257
 258     def run(self):
 259         """
 260         Start application
 261         """
 262         # we have to configure pyinotify after BenderJab.start is called
 263         # as weird things happen to pyinotify if the stdio is closed
 264         # after it's initialized.
 265         self.add_watch()
 266         super(SpoolWatcher, self).run()
 267
 268     def stop(self):
 269         """
 270         shutdown application
 271         """
 272         # destroy the inotify's instance on this interrupt (stop monitoring)
 273         if self.notifier is not None:
 274             self.notifier.stop()
 275         super(SpoolWatcher, self).stop()
 276
 277     def startCopy(self, watchdir=None, event_path=None):
 278         logging.debug("writes seem to have stopped")
 279         if self.notify_runner is not None:
 280             for r in self.notify_runner:
 281                 self.rpc_send(r, tuple(), 'startCopy')
 282         if self.notify_users is not None:
 283             for u in self.notify_users:
 284                 self.send(u, 'startCopy %s %s' % (watchdir, event_path))
 285
 286     def sequencingFinished(self, run_dir):
 287         # need to strip off self.watchdirs from rundir I suspect.
 288         logging.info("run.completed in " + str(run_dir))
 289         pattern = self.watch_dir
 290         if pattern[-1] != os.path.sep:
 291             pattern += os.path.sep
 292         stripped_run_dir = re.sub(pattern, "", run_dir)
 293         logging.debug("stripped to " + stripped_run_dir)
 294         if self.notify_users is not None:
 295             for u in self.notify_users:
 296                 self.send(u, 'Sequencing run %s finished' % (stripped_run_dir))
 297         if self.notify_runner is not None:
 298             for r in self.notify_runner:
 299                 self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
 300
 301 def main(args=None):
 302     bot = SpoolWatcher()
 303     return bot.main(args)
 304
 305 if __name__ == "__main__":
 306     ret = main(sys.argv[1:])
 307     #sys.exit(ret)
 308
 309 # TODO:
 310 # send messages to copier specifying which mount to copy