class CopierBot(rpc.XmlRpcBot):
def __init__(self, section=None, configfile=None):
#if configfile is None:
- # configfile = '~/.gaworkflow'
+ # configfile = '~/.htsworkflow'
super(CopierBot, self).__init__(section, configfile)
#!/usr/bin/env python
+from glob import glob
import logging
import os
import re
from benderjab import rpc
-from gaworkflow.pipeline.configure_run import *
-from gaworkflow.pipeline.monitors import _percentCompleted
+from htsworkflow.pipelines.configure_run import *
#s_fc = re.compile('FC[0-9]+')
s_fc = re.compile('_[0-9a-zA-Z]*$')
"""
def __init__(self, section=None, configfile=None):
#if configfile is None:
- # self.configfile = "~/.gaworkflow"
+ # self.configfile = "~/.htsworkflow"
super(Runner, self).__init__(section, configfile)
self.cfg['notify_users'] = None
reply = u"starting run for %s" % (words[1])
else:
reply = u"need runfolder name"
+ elif re.match(u"path", msg):
+ reply = u"My path is: " + unicode(os.environ['PATH'])
else:
reply = u"I didn't understand '%s'" %(msg)
return "No status information for %s yet." \
" Probably still in configure step. Try again later." % (fc_num)
- fc,ft = status.statusFirecrest()
- bc,bt = status.statusBustard()
- gc,gt = status.statusGerald()
-
- tc,tt = status.statusTotal()
-
- fp = _percentCompleted(fc, ft)
- bp = _percentCompleted(bc, bt)
- gp = _percentCompleted(gc, gt)
- tp = _percentCompleted(tc, tt)
-
- output = []
-
- output.append(u'Firecrest: %s%% (%s/%s)' % (fp, fc, ft))
- output.append(u' Bustard: %s%% (%s/%s)' % (bp, bc, bt))
- output.append(u' Gerald: %s%% (%s/%s)' % (gp, gc, gt))
- output.append(u'-----------------------')
- output.append(u' Total: %s%% (%s/%s)' % (tp, tc, tt))
+ output = status.statusReport()
return '\n'.join(output)
# retrieve config step
cfg_filepath = os.path.join(conf_info.analysis_dir,
- 'config32auto.txt')
+ 'config-auto.txt')
status_retrieve_cfg = retrieve_config(conf_info,
flowcell,
cfg_filepath,
if status:
logging.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")
self.reportMsg("Configure (%s): FAILED" % (run_dir))
run_status = run_pipeline(conf_info)
if run_status is True:
logging.info('Runner: Pipeline: success')
- self.piplineFinished(run_dir)
+ self.reportMsg("Pipeline run (%s): Finished" % (run_dir,))
else:
logging.info('Runner: Pipeline: failed')
self.reportMsg("Pipeline run (%s): FAILED" % (run_dir))
import time
#import glob
-#from gaworkflow.pipeline.recipe_parser import get_cycles
+from htsworkflow.util import mount
# this uses pyinotify
import pyinotify
logging.debug("Remove: %s" % os.path.join(event.path, event.name))
def process_IN_UNMOUNT(self, event):
+ pathname = os.path.join(event.path, event.name)
+ logging.debug("IN_UNMOUNT: %s" % (pathname,))
self.bot.unmount_watch()
class SpoolWatcher(rpc.XmlRpcBot):
# I wonder where I should put the documentation
#:Parameters:
# `watchdir` - which directory tree to monitor for modifications
- # `profile` - specify which .gaworkflow profile to use
+ # `profile` - specify which .htsworkflow profile to use
# `write_timeout` - how many seconds to wait for writes to finish to
# the spool
# `notify_timeout` - how often to timeout from notify
def __init__(self, section=None, configfile=None):
#if configfile is None:
- # self.configfile = "~/.gaworkflow"
+ # self.configfile = "~/.htsworkflow"
super(SpoolWatcher, self).__init__(section, configfile)
self.cfg['watchdir'] = None
self.handler = Handler(self.wm, self)
self.notifier = pyinotify.Notifier(self.wm, self.handler)
self.wdd = None
+ self.mount_point = None
+ self.mounted = True
self.notify_users = None
self.notify_runner = None
msg = 'need a full jabber ID + resource for xml-rpc destinations'
logging.FATAL(msg)
raise bot.JIDMissingResource(msg)
-
+
def add_watch(self, watchdir=None):
"""
start watching watchdir or self.watch_dir
if watchdir is None:
watchdir = self.watch_dir
logging.info("Watching:"+str(watchdir))
+
+ self.mount_point = mount.find_mount_point_for(watchdir)
+
mask = EventsCodes.IN_CREATE | EventsCodes.IN_UNMOUNT
# rec traverses the tree and adds all the directories that are there
# at the start.
def unmount_watch(self):
if self.wdd is not None:
- logging.debug("disabling watch")
- logging.debug(str(self.wdd))
self.wm.rm_watch(self.wdd.values())
self.wdd = None
+ self.mounted = False
def process_notify(self, *args):
# process the queue of events as explained above
# read notified events and enqeue them
self.notifier.read_events()
# should we do something?
+ # has something happened?
last_event_time = self.handler.last_event_time
if last_event_time is not None:
time_delta = time.time() - last_event_time
if time_delta > self.write_timeout:
self.startCopy()
self.handler.last_event_time = None
-
+ # handle unmounted filesystems
+ if not self.mounted:
+ if mount.is_mounted(self.mount_point):
+ # we've been remounted. Huzzah!
+ # restart the watch
+ self.add_watch()
+ self.mounted = True
+ logging.info(
+ "%s was remounted, restarting watch" % \
+ (self.mount_point)
+ )
+
def _parser(self, msg, who):
"""
Parse xmpp chat messages
--- /dev/null
+import unittest
+
+
+import os
+from htsworkflow.automation.copier import runfolder_validate
+
+def extract_runfolder_path(watchdir, event):
+ runfolder_path = watchdir
+ path = event.path
+ if not path.startswith(watchdir):
+ return None
+
+ fragments = path[len(watchdir):].split(os.path.sep)
+ for f in fragments:
+ runfolder_path = os.path.join(runfolder_path, f)
+ if runfolder_validate(f):
+ return runfolder_path
+ return None
+
+class Event(object):
+ def __init__(self, path=None, name=None):
+ self.path = path
+ self.name = name
+
+class testRunner(unittest.TestCase):
+
+ def test_extract_runfolder(self):
+ watchdir = os.path.join('root', 'server', 'mount')
+ runfolder = os.path.join(watchdir, '080909_HWI-EAS229_0052_1234ABCD')
+ ipar = os.path.join(runfolder, 'Data', 'IPAR_1.01')
+ other = os.path.join(watchdir, 'other')
+
+ event = Event( path=runfolder )
+ self.failUnlessEqual(extract_runfolder_path(watchdir, event), runfolder)
+
+ event = Event( path=ipar )
+ self.failUnlessEqual(extract_runfolder_path(watchdir, event), runfolder)
+
+ event = Event( path=other)
+ self.failUnlessEqual(extract_runfolder_path(watchdir, event), None )
+
+def suite():
+ return unittest.makeSuite(testRunner,'test')
+
+if __name__ == "__main__":
+ unittest.main(defaultTest="suite")
projects / htsworkflow.git / commitdiff