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 is_runfolder(name):
  18     """
  19     Is it a runfolder?
  20
  21     >>> print is_runfolder('090630_HWUSI-EAS999_0006_30LNFAAXX')
  22     True
  23     >>> print is_runfolder('hello')
  24     False
  25     """
  26     if re.match("[0-9]{6}_.*", name):
  27         return True
  28     else:
  29         return False
  30
  31 def get_top_dir(root, path):
  32     """
  33     Return the directory in path that is a subdirectory of root.
  34     e.g.
  35
  36     >>> print get_top_dir('/a/b/c', '/a/b/c/d/e/f')
  37     d
  38     >>> print get_top_dir('/a/b/c/', '/a/b/c/d/e/f')
  39     d
  40     >>> print get_top_dir('/a/b/c', '/g/e/f')
  41     None
  42     >>> print get_top_dir('/a/b/c', '/a/b/c')
  43     <BLANKLINE>
  44     """
  45     if path.startswith(root):
  46         subpath = path[len(root):]
  47         if subpath.startswith('/'):
  48             subpath = subpath[1:]
  49         return subpath.split(os.path.sep)[0]
  50     else:
  51         return None
  52
  53 class WatcherEvent(object):
  54     """
  55     Track information about a file event
  56
  57     Currently its time, and if it was an indication we've completed the run.
  58     """
  59     def __init__(self, event_root=None):
  60         self.time = time.time()
  61         self.event_root = event_root
  62         self.complete = False
  63
  64     def __unicode__(self):
  65         if self.complete:
  66            complete = "(completed)"
  67         else:
  68            complete = ""
  69         return u"<WatchEvent: %s %s %s>" % (time.ctime(self.time), self.event_root, complete)
  70
  71 class Handler(pyinotify.ProcessEvent):
  72     def __init__(self, watchmanager, bot, completion_file=None):
  73         """
  74         Completion file contains current "completion" filename
  75         """
  76         self.last_event = {}
  77         self.watchmanager = watchmanager
  78         self.bot = bot
  79         if completion_file is not None:
  80             completion_file = completion_file.lower()
  81         self.completion_file = completion_file
  82
  83     def process_IN_CREATE(self, event):
  84         for wdd in self.bot.wdds:
  85             for watch_path in self.bot.watchdirs:
  86                 run_already_complete = False
  87                 # I only care about things created inside the watch directory, so
  88                 # the event path needs to be longer than the watch path in addition to
  89                 # starting with the watch_path
  90                 if len(event.path) > len(watch_path) and event.path.startswith(watch_path):
  91                     # compute name of the top level directory that had an event
  92                     # in the current watch path
  93                     target = get_top_dir(watch_path, event.path)
  94
  95                     if not is_runfolder(target):
  96                         logging.debug("Skipping %s, not a runfolder" % (target,))
  97                         continue
  98
  99                     # grab the previous events for this watch path
 100                     watch_path_events = self.last_event.setdefault(watch_path, {})
 101
 102                     # if we've already seen an event in this directory (AKA runfolder)
 103                     # keep track if its already hit the "completed" flag
 104                     if watch_path_events.has_key(target):
 105                        run_already_complete = watch_path_events[target].complete
 106
 107                     watch_path_events[target] = WatcherEvent(target)
 108                     #self.last_event.setdefault(watch_path, {})[target] = WatcherEvent(target)
 109
 110                     msg = "Create: %s %s %s %s" % (watch_path, target, event.path, event.name)
 111
 112                     if self.completion_file == event.name.lower() or run_already_complete:
 113                         self.last_event[watch_path][target].complete = True
 114                         msg += "(completed)"
 115
 116                     logging.debug(msg)
 117
 118     def process_IN_DELETE(self, event):
 119         logging.debug("Remove: %s" %  os.path.join(event.path, event.name))
 120         pass
 121
 122     def process_IN_UNMOUNT(self, event):
 123         pathname = os.path.join(event.path, event.name)
 124         logging.debug("IN_UNMOUNT: %s" % (pathname,))
 125         self.bot.unmount_watch(event.path)
 126
 127 class SpoolWatcher(rpc.XmlRpcBot):
 128     """
 129     Watch a directory and send a message when another process is done writing.
 130
 131     This monitors a directory tree using inotify (linux specific) and
 132     after some files having been written will send a message after <timeout>
 133     seconds of no file writing.
 134
 135     (Basically when the solexa machine finishes dumping a round of data
 136     this'll hopefully send out a message saying hey look theres data available
 137
 138     """
 139     # these params need to be in the config file
 140     # I wonder where I should put the documentation
 141     #:Parameters:
 142     #    `watchdirs` - list of directories to monitor for modifications
 143     #    `profile` - specify which .htsworkflow profile to use
 144     #    `write_timeout` - how many seconds to wait for writes to finish to
 145     #                      the spool
 146     #    `notify_timeout` - how often to timeout from notify
 147     #    `completion_file` - what file indicates we've finished sequencing
 148     #                        defaults to: netcopy_complete.txt
 149
 150     def __init__(self, section=None, configfile=None):
 151         #if configfile is None:
 152         #    self.configfile = "~/.htsworkflow"
 153         super(SpoolWatcher, self).__init__(section, configfile)
 154
 155         self.cfg['watchdirs'] = None
 156         self.cfg['write_timeout'] = 10
 157         self.cfg['notify_users'] = None
 158         self.cfg['notify_runner'] = None
 159         self.cfg['completion_file'] = 'netcopy_complete.txt'
 160
 161         self.watchdirs = []
 162         self.watchdir_url_map = {}
 163         self.notify_timeout = 0.001
 164
 165         self.wm = None
 166         self.notify_users = None
 167         self.notify_runner = None
 168         self.wdds = []
 169
 170         # keep track if the specified mount point is currently mounted
 171         self.mounted_points = {}
 172         # keep track of which mount points tie to which watch directories
 173         # so maybe we can remount them.
 174         self.mounts_to_watches = {}
 175
 176         self.eventTasks.append(self.process_notify)
 177
 178     def read_config(self, section=None, configfile=None):
 179         # Don't give in to the temptation to use logging functions here,
 180         # need to wait until after we detach in start
 181         super(SpoolWatcher, self).read_config(section, configfile)
 182
 183         self.watchdirs = shlex.split(self._check_required_option('watchdirs'))
 184         # see if there's an alternate url that should be used for the watchdir
 185         for watchdir in self.watchdirs:
 186             self.watchdir_url_map[watchdir] = self.cfg.get(watchdir, watchdir)
 187
 188         self.write_timeout = int(self.cfg['write_timeout'])
 189         self.completion_file = self.cfg['completion_file']
 190
 191         self.notify_users = self._parse_user_list(self.cfg['notify_users'])
 192         try:
 193           self.notify_runner = \
 194              self._parse_user_list(self.cfg['notify_runner'],
 195                                    require_resource=True)
 196         except bot.JIDMissingResource:
 197             msg = 'need a full jabber ID + resource for xml-rpc destinations'
 198             raise bot.JIDMissingResource(msg)
 199
 200         self.handler = None
 201         self.notifier = None
 202
 203     def add_watch(self, watchdirs=None):
 204         """
 205         start watching watchdir or self.watchdir
 206         we're currently limited to watching one directory tree.
 207         """
 208         # create the watch managers if we need them
 209         if self.wm is None:
 210             self.wm = pyinotify.WatchManager()
 211             self.handler = Handler(self.wm, self, self.completion_file)
 212             self.notifier = pyinotify.Notifier(self.wm, self.handler)
 213
 214         # the one tree limit is mostly because self.wdd is a single item
 215         # but managing it as a list might be a bit more annoying
 216         if watchdirs is None:
 217             watchdirs = self.watchdirs
 218
 219         mask = EventsCodes.IN_CREATE | EventsCodes.IN_UNMOUNT
 220         # rec traverses the tree and adds all the directories that are there
 221         # at the start.
 222         # auto_add will add in new directories as they are created
 223         for w in watchdirs:
 224             mount_location = mount.find_mount_point_for(w)
 225             self.mounted_points[mount_location] = True
 226             mounts = self.mounts_to_watches.get(mount_location, [])
 227             if w not in mounts:
 228                 mounts.append(w)
 229                 self.mounts_to_watches[mount_location] = mounts
 230
 231             logging.info(u"Watching:"+unicode(w))
 232             self.wdds.append(self.wm.add_watch(w, mask, rec=True, auto_add=True))
 233
 234     def unmount_watch(self, event_path):
 235         # remove backwards so we don't get weirdness from
 236         # the list getting shorter
 237         for i in range(len(self.wdds),0, -1):
 238             wdd = self.wdds[i]
 239             logging.info(u'unmounting: '+unicode(wdd.items()))
 240             self.wm.rm_watch(wdd.values())
 241             del self.wdds[i]
 242         self.mounted = False
 243
 244     def make_copy_url(self, watchdir, list_event_dir):
 245         root_copy_url = self.watchdir_url_map[watchdir]
 246         if root_copy_url[-1] != '/':
 247             root_copy_url += '/'
 248         copy_url = root_copy_url + list_event_dir
 249         logging.debug('Copy url: %s' % (copy_url,))
 250         return copy_url
 251
 252     def process_notify(self, *args):
 253         if self.notifier is None:
 254             # nothing to do yet
 255             return
 256         # process the queue of events as explained above
 257         self.notifier.process_events()
 258         #check events waits timeout
 259         if self.notifier.check_events(self.notify_timeout):
 260             # read notified events and enqeue them
 261             self.notifier.read_events()
 262             # should we do something?
 263         # has something happened?
 264         for watchdir, last_events in self.handler.last_event.items():
 265             for last_event_dir, last_event_detail in last_events.items():
 266                 time_delta = time.time() - last_event_detail.time
 267                 if time_delta > self.write_timeout:
 268                     print "timeout", unicode(last_event_detail)
 269                     copy_url = self.make_copy_url(watchdir, last_event_dir)
 270                     self.startCopy(copy_url)
 271                     if last_event_detail.complete:
 272                         self.sequencingFinished(last_event_detail.event_root)
 273
 274                     self.handler.last_event[watchdir] = {}
 275         # handle unmounted filesystems
 276         for mount_point, was_mounted in self.mounted_points.items():
 277             if not was_mounted and mount.is_mounted(mount_point):
 278                 # we've been remounted. Huzzah!
 279                 # restart the watch
 280                 for watch in self.mounts_to_watches[mount_point]:
 281                     self.add_watch(watch)
 282                     logging.info(
 283                         "%s was remounted, restarting watch" % \
 284                             (mount_point)
 285                     )
 286                 self.mounted_points[mount_point] = True
 287
 288     def _parser(self, msg, who):
 289         """
 290         Parse xmpp chat messages
 291         """
 292         help = u"I can send [copy] message, or squencer [finished]"
 293         if re.match(u"help", msg):
 294             reply = help
 295         elif re.match("copy", msg):
 296             self.startCopy(msg)
 297             reply = u"sent copy message"
 298         elif re.match(u"finished", msg):
 299             words = msg.split()
 300             if len(words) == 2:
 301                 self.sequencingFinished(words[1])
 302                 reply = u"sending sequencing finished for %s" % (words[1])
 303             else:
 304                 reply = u"need runfolder name"
 305         else:
 306             reply = u"I didn't understand '%s'" %(msg)
 307         return reply
 308
 309     def run(self):
 310         """
 311         Start application
 312         """
 313         # we have to configure pyinotify after BenderJab.start is called
 314         # as weird things happen to pyinotify if the stdio is closed
 315         # after it's initialized.
 316         self.add_watch()
 317         super(SpoolWatcher, self).run()
 318
 319     def stop(self):
 320         """
 321         shutdown application
 322         """
 323         # destroy the inotify's instance on this interrupt (stop monitoring)
 324         if self.notifier is not None:
 325             self.notifier.stop()
 326         super(SpoolWatcher, self).stop()
 327
 328     def startCopy(self, copy_url=None):
 329         logging.debug("writes seem to have stopped")
 330         if self.notify_runner is not None:
 331             for r in self.notify_runner:
 332                 self.rpc_send(r, tuple([copy_url]), 'startCopy')
 333         if self.notify_users is not None:
 334             for u in self.notify_users:
 335                 self.send(u, 'startCopy %s.' % (copy_url,))
 336
 337     def sequencingFinished(self, run_dir):
 338         # need to strip off self.watchdirs from rundir I suspect.
 339         logging.info("run.completed in " + str(run_dir))
 340         for watch in self.watchdirs:
 341             if not run_dir.startswith(watch):
 342                 print "%s didn't start with %s" % (run_dir, watch)
 343                 continue
 344             if watch[-1] != os.path.sep:
 345                 watch += os.path.sep
 346             stripped_run_dir = re.sub(watch, "", run_dir)
 347         else:
 348             stripped_run_dir = run_dir
 349
 350         logging.debug("stripped to " + stripped_run_dir)
 351         if self.notify_users is not None:
 352             for u in self.notify_users:
 353                 self.send(u, 'Sequencing run %s finished' % \
 354                           (stripped_run_dir))
 355         if self.notify_runner is not None:
 356             for r in self.notify_runner:
 357                 self.rpc_send(r, (stripped_run_dir,), 'sequencingFinished')
 358
 359 def main(args=None):
 360     bot = SpoolWatcher()
 361     return bot.main(args)
 362
 363 if __name__ == "__main__":
 364     ret = main(sys.argv[1:])
 365     #sys.exit(ret)
 366
 367 # TODO:
 368 # send messages to copier specifying which mount to copy