def register_monitor(self, facilities):
# we have to import 'logging' not at the top of the module
import logging
self.setup_listener_gettext()
t = current_thread()
t.monitor_facilities = ltrace_str_to_int(facilities)
t.monitor_uuid = uuid.uuid4()
logging.notice(_(u'New trace session started with UUID {0}, '
u'facilities {1}.').format(stylize(ST_UGID, t.monitor_uuid),
stylize(ST_COMMENT, facilities)))
# The monitor_lock avoids collisions on listener.verbose
# modifications while a flood of messages are beiing sent
# on the wire. Having a per-thread lock avoids locking
# the master `options.monitor_lock` from the client side
# when only one monitor changes its verbose level. This
# is more fine grained.
t.monitor_lock = RLock()
with options.monitor_lock:
options.monitor_listeners.append(t)
# return the UUID of the thread, so that the remote side
# can detach easily when it terminates.
return t.monitor_uuid
def find_server_Linux(favorite, group):
""" Return the hostname (or IP, in some conditions) of our Licorn® server.
These are tried in turn:
- ``LICORN_SERVER`` environment variable (always takes precedence, with
a message; this variable should be used for debug / development purposes only;
- `zeroconf` lookup; this the "standard" way of discovery our server.
- LAN dhcp server on distros where it is supported (currently Ubuntu and Debian).
:param favorite: UUID of our optional favorite server, as a string
formated like `LMC.configuration.system_uuid` (no dashes).
:param group: an LXC cpuset. This is an undocumented feature. please do
not use outside of debugging / testing environments.
"""
env_server = os.getenv('LICORN_SERVER', None)
if env_server:
logging.notice(_(u'Using environment variable value {0} for our '
u'server; unset {1} if you prefer automatic detection.').format(
stylize(ST_IMPORTANT, env_server),
stylize(ST_NAME, 'LICORN_SERVER')))
if ':' in env_server:
return env_server.split(':')
return env_server, None
return find_zeroconf_server_Linux(favorite, group)
"""
def write_file(self, local_path, remote_path):
filename = os.path.basename(local_path)
try:
logging.debug("Changing remote directory to %s",
remote_path)
self.client.cwd(remote_path)
except ftplib.error_perm:
if not self.dry_run:
logging.notice("Creating remote directory %s" % remote_path)
self.client.mkd(remote_path)
else:
logging.warn("Remote path %s does not exist and will be created on write" % remote_path)
# Just test that we can perform the necessary operations
# without writing anything
logging.info(
"%s writing %s to %s" % (
"Not" if self.dry_run else "",
local_path,
remote_path))
if self.dry_run: return
with open(local_path, "rb") as f:
self.client.storbinary("STOR %s" % filename,f)
def _run(self, ns):
config = Configuration(ns.configdir)
config.use_badlog = ns.known_bad
if not is_sorted(ns.actions):
logging.warning("Actions will be performed in the order of the respective command-line arguments")
logging.notice("Action order as requested: " + ', '.join(a.name for a in ns.actions))
logging.notice("Suggested natural order of actions: " + ', '.join(a.name for a in sorted(set(ns.actions))))
for (action, constants) in itertools.groupby(sorted(ns.actions)):
count = sum(1 for c in constants)
if count != 1:
logging.warning("Redundant action {:s} will be performed {:d} times".format(action.name, count))
with Manager(ns.bindir, ns.datadir, timeout=ns.timeout, config=config) as mngr:
with _make_badlog(ns, logfile=mngr.badlog) as badlog:
if ns.clean == 0:
if not ns.actions:
logging.warning("Nothing will be done")
for action in ns.actions:
_perform_action(mngr, action, badlog)
elif ns.clean == 1:
if not ns.actions:
logging.warning("Nothing will be cleaned")
for action in ns.actions:
_perform_cleaning(mngr, action)
elif ns.clean == 2:
if ns.actions:
raise FatalError("No action must be specified in combination with {!r}".format('-cc'))
if ns.datadir == '.':
raise FatalError("Cowardly refusing to recursively delete the current working directory")
mngr.clean_all()
else:
raise AssertionError(ns.clean)
def _gen_generic(mngr : Manager, gen : Generators, bl : _BucketList):
assert not gen.imported
while bl:
size = bl.pick()
with mngr.make_tempdir() as tempdir:
try:
logging.info("Generating {:s} graph with {:s} ...".format(size.name, gen.name))
meta = _call_generic_tool(mngr, gen, size, tempdir=tempdir)
except RecoverableError as e:
logging.error("Cannot generate graph: {!s}".format(e))
continue
actualsize = GraphSizes.classify(meta['nodes'])
if actualsize != size:
if bl.offer(actualsize):
logging.notice(
"Asked {:s} for a {:s} graph but got a {:s} one which is still useful though".format(
gen.name, size.name, actualsize.name))
else:
logging.warning(
"Asked {:s} for a {:s} graph but got a {:s} one which I'll have to discard".format(
gen.name, size.name, actualsize.name))
continue
if _insert_graph(mngr, gen, meta):
bl.decrement(actualsize)
if meta.get('layout'):
_insert_layout(mngr, meta, native=True)
def parse_args2(default_log_filename=None, parser = None):
import argparse
if not parser:
parser= argparse.ArgumentParser()
parser.add_argument('-v', '--verbose', action='count', help="verbose", default=0)
parser.add_argument('-o', '--logfile', default=default_log_filename)
try:
import argcomplete
argcomplete.autocomplete(parser)
except:
pass
args = parser.parse_args()
loggers = [logging.root]
if args.verbose == 0:
for logger in loggers:
init_logging(logger, logging.NOTICE, True, args.logfile)
elif args.verbose == 1:
for logger in loggers:
init_logging(logger, logging.INFO, True, args.logfile)
elif args.verbose > 1:
for logger in loggers:
init_logging(logger, logging.DEBUG, True, args.logfile)
logging.notice("start running: " + ' '.join(sys.argv))
logging.info(args)
return args
def run(board, path, name):
path = os.path.expandvars(path)
path = os.path.expanduser(path)
if not os.path.exists(path):
raise RuntimeError('File ' + path + ' not found')
vs = {}
execfile(path, vs)
if name not in vs:
raise RuntimeError('Menu ' + name + ' not found in ' + path)
menu = vs[name]
logging.notice('Updating event sizes')
evszs = board.computeEventSizes(menu)
for i, s in evszs.iteritems():
logging.info('mode %d: %d', i, s)
menu.mode(i).eventSize = s
for l in str(menu).split('\n'):
logging.debug('%s', l)
rc = board.getReadout().getNode('readout_control')
rc.configureMenu(menu)
def testTTS(self):
self.resetEverything()
self.configMP7DAQ()
self.configAMC13()
# AMC13 must go in Run Mode
self._amc13.startRun()
self.linkStatus('TTS check - initial')
time.sleep(1)
ttsStates = [
('Warning', 0x1),
('OOS', 0x2),
('Busy', 0x4),
('Ready', 0x8),
('Error', 0xc),
('Disconnected', 0xf),
]
for state, code in ttsStates:
logging.notice('TTS check: Force %s', state)
mp7daq.hw().getNode('readout.tts_csr.ctrl.tts_force').write(1)
mp7daq.hw().getNode('readout.tts_csr.ctrl.tts').write(code)
mp7daq.hw().dispatch()
time.sleep(2)
self.linkStatus('TTS check')
def evapcheck(self, op, thresh=0.20):
'Update amount of evaporation and check for issues'
if self.plate.name == "Samples":
dt = clock.pipetting - self.lastevapupdate # Assume no evaporation while in PTC
if dt < -0.1:
# This may happen during thermocycler operation since pipetting while thermocycling is moved to pipthermotime after waitpgm() is called
logging.notice(
"%s: clock went backwards: pipetting=%f, lastevapupdate=%f, dt=%f -- probably OK due to counting pipetting time during PTC operation"
% (self.name, clock.pipetting, self.lastevapupdate, dt))
else:
dt = clock.elapsed() - self.lastevapupdate
if dt < -0.1:
logging.error(
"%s: clock went backwards: elapsed=%f, lastevapupdate=%f, dt=%f"
% (self.name, clock.elapsed(), self.lastevapupdate, dt))
if dt <= 0.1:
return
for i in range(
10): # Break it into smaller steps since volume affects rate
evaprate = self.plate.getevaprate(max(0, self.volume - self.evap))
self.evap += evaprate * dt / 3600 / 10
if op == 'aspirate' and self.evap > thresh * self.volume and self.evap > 2.0 and self.volume > 0:
pctevap = self.evap / self.volume * 100
logging.warning(
" %s (%s.%s, vol=%.1f ul) may have %.1f ul of evaporation (%.0f%%)"
% (self.name, str(self.plate), self.plate.wellname(
self.well), self.volume, self.evap, pctevap))
if "evap" in __historyOptions:
self.history = self.history + (' [Evap: %0.1f ul]' %
(self.evap))
self.lastevapupdate += dt
def _insert_layout(mngr: Manager, meta : dict, native : bool = False):
with mngr.sql_ctx as curs:
layout = Layouts.NATIVE if native else None
graphid = Id(meta['graph'])
fingerprint = prepare_fingerprint(meta.get('layout'))
if not native and mngr.sql_select_curs(curs, 'Layouts', graph=graphid, layout=layout, fingerprint=fingerprint):
logging.notice(
"Discarding unknown layout of graph {gid!s} with fingerprint {fp!s} (already exists)"
.format(gid=graphid, fp=Id(fingerprint))
)
return False
layoutid = mngr.make_unique_layout_id(curs)
filename = mngr.make_layout_filename(graphid, layoutid, layout=layout)
mngr.sql_insert_curs(
curs, 'Layouts', id=layoutid, graph=graphid, layout=layout, file=filename, fingerprint=fingerprint
)
os.makedirs(os.path.dirname(filename), exist_ok=True)
if native:
graphfilename = get_one(r['file'] for r in mngr.sql_select_curs(curs, 'Graphs', id=graphid))
directory = os.path.dirname(filename)
symlinktarget = os.path.relpath(graphfilename, start=directory)
logging.info("Creating symbolic link: {!r} -> {!r}".format(filename, symlinktarget))
os.symlink(symlinktarget, filename)
else:
logging.debug("Renaming layout file {!r} to {!r}".format(meta['filename-layout'], filename))
os.rename(meta['filename-layout'], filename)
return True
def pip_install_packages(packages_list, warn_only=False):
""" Install one or more packages, via PIP. The function just spawns :program:`pip`
with argument ``install``.
:param packages_list: a list of strings representing PIP packages names. For
real-life examples, see the `upgrades` modules (notably `daemon`).
:param warn_only: see :func:`install_packages`.
.. versionadded:: 1.3
Before the WMI2, the package management foundations didn't exist.
"""
tname = stylize(ST_NAME, current_thread().name)
pnames = u', '.join(stylize(ST_NAME, x) for x in packages_list)
logging.notice(_(u'{0}: Installing needed packages {1} from source before '
u'continuing. Please wait…').format(tname, pnames))
out, err = process.execute([ 'pip', 'install' ] + packages_list)
if err:
logging.warn_or_raise(_(u'An error occured while installing package(s) '
u'{0}! PIP install Log follows:').format(pnames) + u'\n' + err, warn_only=warn_only)
else:
logging.notice(_(u'{0}: Successfully installed package(s) {1} via {2}.').format(
tname, pnames, stylize(ST_NAME, 'PIP')))
def unregister_monitor(self, muuid):
# we have to import 'logging' not at the top of the module
import logging
self.setup_listener_gettext()
found = None
with options.monitor_lock:
for t in options.monitor_listeners[:]:
if t.monitor_uuid == muuid:
found = t
options.monitor_listeners.remove(t)
break
if found:
del t.monitor_facilities
del t.monitor_uuid
del t.monitor_lock
else:
logging.warning(_(u'Monitor listener with UUID %s not found!') % muuid)
logging.notice(_(u'Trace session UUID {0} ended.').format(
stylize(ST_UGID, muuid)))
def logwrite(logcontents,loglevel = "error"):
"""
Get the error message and store in the log file
"""
logpath='/var/log/k8s-manager/'
global hostname
hostname = os.uname()[1]
if not os.path.isdir(logpath):
os.makedirs(logpath)
logdata=datetime.datetime.now()
logtime=logdata.strftime('%Y-%m-%d %H:%M:%S')
daylogfile=logpath+'/'+'k8s-manager' + '.log'
logging.basicConfig(filename = daylogfile,level = logging.DEBUG)
if str(loglevel) == "info":
logging.info(" " + str(logtime) + " " + hostname + " " + os.path.basename(sys.argv[0]).split(".")[0] \
+ ": " + str(logcontents))
elif str(loglevel) == "warning":
logging.warning(" " + str(logtime) + " " + hostname + " " + os.path.basename(sys.argv[0]).split(".")[0] \
+ ": " + str(logcontents))
elif str(loglevel) == "notice":
logging.notice(" " + str(logtime) + " " + hostname + " " + os.path.basename(sys.argv[0]).split(".")[0] \
+ ": " + str(logcontents))
else:
logging.error(" " + str(logtime) + " " + hostname + " " + os.path.basename(sys.argv[0]).split(".")[0] \
+ ": " + str(logcontents))
def parse_args2(default_log_filename=None, parser=None):
import argparse
if not parser:
parser = argparse.ArgumentParser()
parser.add_argument('-v',
'--verbose',
action='count',
help="verbose",
default=0)
parser.add_argument('-o', '--logfile', default=default_log_filename)
try:
import argcomplete
argcomplete.autocomplete(parser)
except:
pass
args = parser.parse_args()
loggers = [logging.root]
if args.verbose == 0:
for logger in loggers:
init_logging(logger, logging.NOTICE, True, args.logfile)
elif args.verbose == 1:
for logger in loggers:
init_logging(logger, logging.INFO, True, args.logfile)
elif args.verbose > 1:
for logger in loggers:
init_logging(logger, logging.DEBUG, True, args.logfile)
logging.notice("start running: " + ' '.join(sys.argv))
logging.info(args)
return args
def _compute_prop_outer(mngr: Manager,
prop: Properties,
kern: Kernels,
badlog: BadLog,
graphid: Id = None,
layoutid: Id = None,
layoutfile: str = None,
progress: float = None):
what = {
Kernels.BOXED: "discrete",
Kernels.GAUSSIAN: "continuous"
}.get(kern, "other")
if badlog.get_bad(Actions.PROPERTIES, layoutid, prop):
logging.notice(
"Skipping computation of {:s} property {:s} for layout {!s}".
format(what, prop.name, layoutid))
return
prefix = "[{:6.2f} %] ".format(
100.0 * min(1.0, progress)) if progress is not None else ""
logging.info(prefix +
"Computing {:s} property {:s} for layout {!s} ...".format(
what, prop.name, layoutid))
directory = _get_directory(mngr, layoutid, prop, kern, make=True)
try:
_compute_prop_inner(mngr,
prop,
kern,
layoutid,
layoutfile,
directory=directory)
except RecoverableError as e:
badlog.set_bad(Actions.PROPERTIES, layoutid, prop, msg=str(e))
logging.error(
"Cannot compute {:s} property {:s} for layout {!s} of graph {!s}: {!s}"
.format(what, prop.name, layoutid, graphid, e))
def fill_empty_var(var):
''' sets variable to e (estimate in phyml) if empty '''
if var is None:
logging.notice('unable to parse %s; PhyML will estimate this in subsequent runs' % var)
return 'e'
else:
return var
def run(board, enablechans=None, tdr_fmt=None, dmx_hdrfmt=None, dmx_valfmt=None, s1_bc0fmt=None):
'''
Configures the MP7 formatter. Arguments:
* board - The MP7Controller FunctorInterface for that board
* tdr_fmt - TDR header formatter options. Valid values: None , or map with keys 'strip' and 'insert', each value True or False
* dmx_hdrfmt - Demux header formatter options. Valid values: same as tdr_fmt
* dmx_valfmt - Demux datavalid-override formatter options. Valid values: None, 'disable', or map with keys 'start' and 'stop', each value a 2-tuple of ints (i.e. (bx, clock_cycle))
* s1_bc0fmt - Stage-1 formatter options. Valid values: None, 'disable', or int (the bx number)
'''
logging.notice("Configuring formatters")
cm = hlp.channelMgr(board,enablechans)
fmt = board.getFormatter()
ctrl = board.getCtrl()
datapath = board.getDatapath()
if ( not any([tdr_fmt, dmx_hdrfmt, dmx_valfmt, s1_bc0fmt]) ):
logging.warn('Nothing to do')
return
if tdr_fmt is not None:
cm.configureHdrFormatters(mp7.FormatterKind.kTDRFormatter, tdr_fmt['strip'], tdr_fmt['insert'])
if dmx_hdrfmt is not None :
cm.configureHdrFormatters(mp7.FormatterKind.kDemuxFormatter, dmx_hdrfmt['strip'], dmx_hdrfmt['insert'])
if dmx_valfmt is not None:
# print mp7.orbit.Point(*dmx_valfmt['start']),mp7.orbit.Point(*dmx_valfmt['stop'])
if dmx_valfmt == 'disable':
cm.disableDVFormatters()
else:
cm.configureDVFormatters(mp7.orbit.Point(*dmx_valfmt['start']),mp7.orbit.Point(*dmx_valfmt['stop']))
def clean_model(self):
assert os.path.realpath(os.getcwd()) == os.path.realpath(
self.abs_datadir)
logging.notice("Deleting existing model ...")
with self.sql_ctx as curs:
curs.execute("DROP TABLE `TestScores`")
if os.path.isdir(self.nndir):
shutil.rmtree(self.nndir)
def clean_layouts(self):
assert os.path.realpath(os.getcwd()) == os.path.realpath(
self.abs_datadir)
logging.notice("Deleting all existing layouts ...")
with self.sql_ctx as curs:
curs.execute("DROP TABLE `Layouts`")
if os.path.isdir(self.layoutdir):
shutil.rmtree(self.layoutdir)
def print_errors(self):
items = self.get_errors()
if not items:
logging.notice("No errors")
else:
logging.error(f"{len(items)} Errors:")
for w in items:
logging.error(f"\t{w.msg}")
def ps(self):
logging.notice("ps %s" % self)
for mongod in self.mongod_arr:
Mongod(mongod).ps()
try:
self._get_primary()
except:
pass
def print_warnings(self):
items = self.get_warnings()
if not items:
logging.notice("No warnings")
else:
logging.warning(f"{len(items)} Warnings:")
for w in items:
logging.warning(f"\t{w.msg}")
def ps(self):
logging.notice("ps %s" % self)
for mongod in self.mongod_arr:
Mongod(mongod).ps()
try:
self._get_primary()
except:
pass
def shake(self,plate,dur=60,speed=None,accel=5,returnPlate=True,samps=None,force=False):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# Move the plate to the shaker, run for the given time, and bring plate back
allsamps=Sample.getAllOnPlate(plate)
if samps is None:
samps=allsamps
if all([x.isMixed() for x in samps]) and not force:
logging.notice( "No need to shake "+plate.name+", but doing so anyway.")
minspeed=0
maxspeed=2000
for x in samps:
(a,b)=x.getmixspeeds()
minspeed=max([a,minspeed])
maxspeed=min([b,maxspeed])
if speed is None:
if minspeed<maxspeed:
speed=max((maxspeed+minspeed)/2,maxspeed-50) # Mix as fast as safely possible (but always above minspeed)
else:
speed=maxspeed
if speed<minspeed-2 or speed>maxspeed+2:
others=""
for x in allsamps:
(a,b)=x.getmixspeeds()
if b<minspeed or a>maxspeed:
if a is not None and a>0:
others+=" {%s: %.1ful,G=%.2f%%,min=%.0f,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,a,b)
else:
others+=" {%s: %.1ful,G=%.2f%%,max=%.0f}"%(x.name,x.volume,x.glycerolfrac()*100,b)
logging.mixwarning("Mixing %s at %.0f RPM; minspeed(%.0f) > maxspeed(%.0f), limits=[%s]"%(plate.name,speed,minspeed,maxspeed,others))
else:
logging.notice("Mixing %s at %.0f RPM ( min RPM=%.0f, max RPM=%.f)"%(plate.name, speed, minspeed, maxspeed))
oldloc=plate.curloc
self.moveplate(plate,"Shaker",returnHome=False)
global __shakerActive
__shakerActive=True
worklist.pyrun("BioShake\\bioexec.py setElmLockPos")
worklist.pyrun("BioShake\\bioexec.py setShakeTargetSpeed%d"%speed)
worklist.pyrun("BioShake\\bioexec.py setShakeAcceleration%d"%accel)
worklist.pyrun("BioShake\\bioexec.py shakeOn")
self.starttimer()
Sample.shaken(plate.name,speed)
Sample.addallhistory("(S%d@%.0f)"%(dur,speed),onlyplate=plate.name)
self.waittimer(dur)
worklist.pyrun("BioShake\\bioexec.py shakeOff")
self.starttimer()
self.waittimer(accel+4)
worklist.pyrun("BioShake\\bioexec.py setElmUnlockPos")
__shakerActive=False
if returnPlate:
self.moveplate(plate,oldloc)
def run(board):
# if not command.startswith('board'):
# throw ArgumentError('Alakazham!')
try:
import IPython
except ImportError:
logging.notice('Failed to load IPython')
return
logging.notice('Starting IPython - %s connected to variable \'board\'', board.id())
IPython.embed()
def stage(self,stagename,reagents,sources,samples,volume,finalx=1.0,destMix=True,dilutant=None):
# Add water to sample wells as needed (multi)
# Pipette reagents into sample wells (multi)
# Pipette sources into sample wells
# Concs are in x (>=1)
# Sample.printallsamples("Before "+stagename)
# print "\nStage: ", stagename, "reagents=",[str(r) for r in reagents], ",sources=",[str(s) for s in sources],",samples=",[str(s) for s in samples],str(volume)
if len(samples)==0:
logging.notice("No samples")
return
if dilutant is None:
dilutant=decklayout.WATER
worklist.comment("Stage: "+stagename)
if not isinstance(volume,list):
volume=[volume for i in range(len(samples))]
for i in range(len(volume)):
assert volume[i]>0
volume[i]=float(volume[i])
reagentvols=[1.0/x.conc.dilutionneeded()*finalx for x in reagents]
if len(sources)>0:
sourcevols=[volume[i]*1.0/sources[i].conc.dilutionneeded()*finalx for i in range(len(sources))]
while len(sourcevols)<len(samples):
sourcevols.append(0)
watervols=[volume[i]*(1-sum(reagentvols))-samples[i].volume-sourcevols[i] for i in range(len(samples))]
else:
watervols=[volume[i]*(1-sum(reagentvols))-samples[i].volume for i in range(len(samples))]
if min(watervols)<-0.01:
msg="Error: Ingredients add up to more than desired volume by %.1f ul"%(-min(watervols))
for s in samples:
if s.volume>0:
msg=msg+" Note: %s already contains %.1f ul\n"%(s.name,s.volume)
logging.error(msg)
watervols2=[w if w<=2 else 0 for w in watervols] # Move later since volume is low
watervols=[w if w>2 else 0 for w in watervols] # Only move>=2 at beginning
if any([w>0.01 for w in watervols]):
self.multitransfer(watervols,dilutant,samples,(False,destMix and (len(reagents)+len(sources)==0)))
for i in range(len(reagents)):
self.multitransfer([reagentvols[i]*v for v in volume],reagents[i],samples,(True,destMix and (len(sources)==0 and i==len(reagents)-1)))
if any([w>0.01 for w in watervols2]):
self.multitransfer(watervols2,dilutant,samples,(False,destMix and (len(reagents)+len(sources)==0)))
if len(sources)>0:
assert len(sources)<=len(samples)
for i in range(len(sources)):
self.transfer(sourcevols[i],sources[i],samples[i],(True,destMix))
def run(board,
enablechans=None,
alignTo=None,
alignMargin=3,
alignFreeze=False,
dmx_delays=False):
cm = hlp.channelMgr(board, enablechans)
logging.notice('Aligning links')
delays = None
if dmx_delays:
#delays = {}
#nMaxMps = 12
#clockRatio = 6
#nMpOutputs = 6
#for mp in xrange(nMaxMps):
# for c in xrange(nMpOutputs):
# delays[c*nMaxMps+mp] = mp*clockRatio
delays = {}
nMaxMps = 6
nMaxMps_2 = 12
clockRatio = 6
nMpOutputs = 6
nMpOutputs_2 = 12
for mp in xrange(nMaxMps - 1):
for c in xrange(nMpOutputs):
delays[c * nMaxMps + mp] = mp * clockRatio
for mp in xrange(nMaxMps, nMaxMps_2):
for c in xrange(nMpOutputs, nMpOutputs_2):
delays[c * nMaxMps + mp - 6] = mp * clockRatio - 6
if alignTo:
p = mp7.orbit.Point(alignTo[0], alignTo[1])
args = (p, ) if delays == None else (p, delays)
cm.align(*args)
else:
args = (alignMargin, ) if delays == None else (delays, alignMargin)
cm.minimizeAndAlign(*args)
if alignFreeze:
cm.freezeAlignment()
def console_start(self, is_tty=True):
# we have to import 'logging' not at the top of the module
import logging, events
from _settings import settings
# other foundations
from workers import workers
# import things that we need in the remote console
from licorn.core import version, LMC
from threads import RLock, Event
# This is a little too much
#self._console_namespace = sys._getframe(1).f_globals
self._console_isatty = is_tty
self._console_namespace = {
'version' : version,
'settings' : settings,
'options' : options,
'exceptions' : exceptions,
'workers' : workers,
'events' : events,
'LicornEvent' : events.LicornEvent,
'daemon' : self.licornd,
'threads' : self.licornd.threads,
'uptime' : self.licornd.uptime,
'LMC' : LMC,
'dump' : ltrace_dump,
'fulldump' : ltrace_fulldump,
'dumpstacks' : ltrace_dumpstacks,
'RLock' : RLock,
'Event' : Event,
}
self._console_interpreter = self.__class__.BufferedInterpreter(
self._console_namespace)
self._console_completer = rlcompleter.Completer(self._console_namespace)
t = current_thread()
logging.notice(_(u'{0}: Interactive console requested by {1} '
u'from {2}.').format(self.licornd,
stylize(ST_NAME, t._licorn_remote_user),
stylize(ST_ADDRESS, '%s:%s' % (t._licorn_remote_address,
t._licorn_remote_port))),
to_listener=False)
if is_tty:
remote_output(_(u'Welcome into licornd\'s arcanes…') + '\n',
clear_terminal=True, char_delay=0.025)
else:
remote_output(_(u'>>> Entered batched remote console.') + '\n',
_message_channel_=2)
def _get_same_graph_id_curs(mngr, curs, lhslid, rhslid, exception=FatalError):
lhsgid = _get_graph_id_curs(mngr, curs, lhslid, exception=exception)
rhsgid = _get_graph_id_curs(mngr, curs, rhslid, exception=exception)
if lhsgid != rhsgid:
logging.notice("Layout {!s} corresponds to graph {!s}".format(
lhslid, lhsgid))
logging.notice("Layout {!s} corresponds to graph {!s}".format(
rhslid, rhsgid))
raise exception(
"The layouts {!s} and {!s} correspond to different graphs".format(
lhslid, rhslid))
return lhsgid
def transfer(self, volume, src, dest, mix=(True,False), getDITI=True, dropDITI=True):
if self.ptcrunning and (src.plate==decklayout.SAMPLEPLATE or dest.plate==decklayout.SAMPLEPLATE)>0:
self.waitpgm()
if volume>self.MAXVOLUME:
destvol=dest.volume
reuseTip=destvol<=0
msg="Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME)
if reuseTip:
msg+= "with tip reuse"
else:
msg+= "without tip reuse"
logging.notice(msg)
self.transfer(self.MAXVOLUME,src,dest,mix,getDITI,False)
self.transfer(volume-self.MAXVOLUME,src,dest,(mix[0] and not reuseTip,mix[1]),False,dropDITI)
return
cmt="Add %.1f ul of %s to %s"%(volume, src.name, dest.name)
ditivolume=volume+src.inliquidLC.singletag
if mix[0] and not src.isMixed():
cmt=cmt+" with src mix"
ditivolume=max(ditivolume,src.volume)
if mix[1] and dest.volume>0 and not src.isMixed():
cmt=cmt+" with dest mix"
ditivolume=max(ditivolume,volume+dest.volume)
# print "Mix volume=%.1f ul"%(ditivolume)
if mix[0] and not src.isMixed() and (src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE):
worklist.comment("shaking for src mix of "+src.name)
self.shakeSamples([src]) # Need to do this before allocating a tip since washing during this will modify the tip clean states
if self.useDiTis:
tipMask=4
if getDITI:
worklist.getDITI(tipMask&self.DITIMASK,ditivolume)
else:
tipMask=self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix[0] and (not src.isMixed() or not src.wellMixed):
if (src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE):
logging.notice("Forcing pipette mix of "+src.name)
worklist.comment("pipette mix for src mix of "+src.name)
src.mix(tipMask) # Manual mix (after allocating a tip for this)
src.aspirate(tipMask,volume)
dest.dispense(tipMask,volume,src)
if mix[1]:
dest.mix(tipMask,True)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
def clean_properties(self):
assert os.path.realpath(os.getcwd()) == os.path.realpath(
self.abs_datadir)
logging.notice("Deleting all existing properties ...")
tables = [
'PropertiesDisc', 'PropertiesCont', 'Histograms',
'SlidingAverages', 'MajorAxes', 'MinorAxes'
]
with self.sql_ctx as curs:
for table in tables:
curs.execute("DROP TABLE `{table:s}`".format(table=table))
if os.path.isdir(self.propsdir):
shutil.rmtree(self.propsdir)
def handle_error(self, *args, **kwargs):
try:
raise
except BrokenPipeError:
logging.notice(
"Could not send complete reply; client closed connection prematurely"
)
except Exception as e:
logging.critical(
"Uncaught exception of type {:s} in main loop of HTTP server".
format(type(e).__name__))
dump_current_exception_trace()
raise SystemExit(True)
def _get_log_level_environment():
envval = os.environ.get(LOG_LEVEL_ENVVAR)
if envval is None:
return LOG_LEVEL_DEFAULT
try:
return LogLevels.parse(envval)
except ValueError as e:
logging.warning(
"Ignoring bogous value of environment variable {:s}: {!r}".format(
LOG_LEVEL_ENVVAR, envval))
logging.notice("Valid logging levels are: " +
', '.join(l.name for l in LogLevels))
return LOG_LEVEL_DEFAULT
def overrideDataValidPattern(bData, replaceChs, masterCh):
'''
Returns copy of board data with data valid pattern of several channels updated
to match the data valid pattern of a master channel. Arguments:
- bData : Input board data object
- replaceChs : List of IDs of channels whose data valid bits will be updated
- masterCh : ID of channel whose data valid pattern will be used.
'''
assert( isinstance(bData, mp7.BoardData) )
assert( isinstance(replaceChs, list) )
assert( isinstance(masterCh, int) )
indata = bData
logging.notice('Master is %d', masterCh)
master = indata[masterCh]
valids = [ (f.data>>32) for f in master ]
fakedata = mp7.LinkData()
for m in master:
f = mp7.Frame()
f.valid = m.valid
fakedata.append(f)
# if args.offset == 0:
# pass
# elif args.offset < 0:
# fakedata = fakedata[-args.offset:] + [0]*-args.offset
# elif args.offset > 0:
# fakedata = [0]*args.offset + fakedata[:-args.offset]
# print 'len',len(valids),len(fakedata)
# for v,f in zip(valids,fakedata):
# print v,hex(f)
# for i,v in enumerate(valids):
# print i,v
outdata = mp7.BoardData(indata.name())
for l in indata:
if not l.first in replaceChs:
outdata.add(l.first, l.second)
continue
outdata.add(l.first,fakedata)
return outdata
def _log_data(data, description="Bogus data"):
logging.notice(description + " was {:d} bytes long".format(len(data)))
try:
text = data if isinstance(data, str) else data.decode()
for (i, line) in enumerate(map(str.rstrip, text.splitlines())):
logging.notice("{:6d}: {:s}".format(i + 1, line))
except UnicodeError as e:
(dumpfd, dumpfilename) = tempfile.mkstemp(prefix='dump-',
suffix='.dat')
logging.error(
description + " could not be decoded as Unicode data;" +
" dumping binary data to file {!r} ...".format(dumpfilename))
with os.fdopen(dumpfd, 'wb') as ostr:
ostr.write(data)
def _gen_import(mngr : Manager, gen : Generators, src : ImportSource, bl : _BucketList):
assert gen.imported
total = bl.total()
with src as archive, mngr.make_tempdir() as tempdir:
cmd = [
os.path.join(mngr.abs_bindir, 'src', 'generators', 'import'),
'--format={:s}'.format(src.format),
'--output={:s}'.format(os.path.join(tempdir, enum_to_json(gen) + GRAPH_FILE_SUFFIX)),
'--meta={:s}'.format('STDIO'),
]
if src.layout is not None:
cmd.append('--layout={:d}'.format(int(src.layout)))
else:
cmd.append('--output-layout={:s}'.format(os.path.join(tempdir, 'layout' + GRAPH_FILE_SUFFIX)))
if src.simplify:
cmd.append('--simplify')
native = src.layout is True
poisoned = src.layout is None
cmd.append('STDIO' if src.compression is None else 'STDIO:' + src.compression) # Let me open that file for you
archlen = len(archive) # This is a potentially expensive operation so do it only once
count = 0
logging.info("{:s} archive {!r} contains {:d} graphs in total".format(gen.name, archive.name, archlen))
for (i, cand) in enumerate(archive):
if not bl: break
progress = i / archlen if total is None else count / total
pretty = archive.prettyname(cand)
logging.info("[{:6.2f} %] Considering {:s} graph {:d} of {:d} from {!r} of {!r} ...".format(
100.0 * progress, gen.name, i + 1, archlen, pretty, archive.name))
try:
with archive.get(cand) as istr:
meta = mngr.call_graphstudy_tool(cmd, meta='stdout', stdin=istr)
except Exception as e:
if not isinstance(e, RecoverableError) and not archive.is_likely_read_error(e): raise
logging.error("Cannot import {:s} graph {!r}: {!s}".format(gen.name, pretty, e))
continue
actualsize = GraphSizes.classify(meta['nodes'])
if not bl.offer(actualsize):
logging.notice("Discarding {:s} {:s} graph (not wanted)".format(actualsize.name, gen.name))
continue
if _insert_graph(mngr, gen, meta, native=native, poisoned=poisoned):
bl.decrement(actualsize)
count += 1
if meta.get('layout'):
_insert_layout(mngr, meta, native=native)
logging.info("[{:6.2f} %] Imported {:d} {:s} graphs from {!r}".format(100.0, count, gen.name, archive.name))
for (size, diff) in bl.items():
logging.warning("{:s} archive exhausted but {:d} {:s} graphs are still missing".format(
gen.name, diff, size.name))
def chooseLC(self, aspirateVolume=0):
if self.volume - aspirateVolume >= MINLIQUIDDETECTVOLUME:
if aspirateVolume == 0:
return self.inliquidLC # Not aspirating, should be fine
# Try using liquid detection
initheight = self.plate.getliquidheight(
self.volume) # True height at start
finalheight = self.plate.getliquidheight(
self.volume - aspirateVolume) # True height at end of aspirate
initgemvolume = self.plate.getgemliquidvolume(
initheight) # How much will Gemini think we have at start
if initgemvolume < aspirateVolume + 15:
# Not enough
msg = "Aspirate %.1f ul from %.1f ul, gem will think initial volume is %.1ful which is too low to reliably work - not using LD" % (
aspirateVolume, self.volume, initgemvolume)
logging.notice(msg)
else:
finalgemvolume = initgemvolume - aspirateVolume
finalgemheight = self.plate.getgemliquidheight(finalgemvolume)
finaltipdepth = self.inliquidLC.submerge - (finalgemheight -
finalheight)
msg = "Aspirate %.1f ul from %.1f ul in %s: height goes from %.1f to %.1f mm, gem will think initial volume is %.1ful and final height %.1f mm" % (
aspirateVolume, self.volume, self.name, initheight,
finalheight, initgemvolume, finalgemheight)
if finalgemheight - 0.1 < self.inliquidLC.submerge:
# Gemini won't be able to submerge as much as requested
logging.notice(
msg +
": Gemini would think there's not enough liquid to submerge %.1f mm - not using LD"
% self.inliquidLC.submerge)
elif finaltipdepth < 0.1:
# Tracking is off so much that tip will break surface of water during operation
logging.warning(
msg +
": tip will not be submerged enough (depth=%.1f mm) - not using LD"
% finaltipdepth)
else:
# Should be good
#logging.notice(msg)
return self.inliquidLC
# No liquid detect:
if self.volume == 0 and aspirateVolume == 0:
return self.emptyLC
elif self.hasBeads and self.plate.curloc == "Magnet":
return self.beadsLC
else:
return self.bottomLC
def get_localdata(dbpool, locale):
# localdata 에서 최신 data를 가져옴
with dbpool.scoped_get_group("common", readonly=True) as db:
rs = db.query("select version, country, localdata from localdata where country=%s and mdate=(select MAX(mdate) from localedata where country=%s)", (locale, locale,))
if not rs:
raise DBAccessError("get_localedata not found error")
for ld in rs:
localedata_version, country, localedata = ld
if country == locale:
localedata_pb = localedata_pb2.LocaleData()
localedata_pb.ParseFromString(localedata)
LDManager.set_localedata_with_key(localedata_pb, (localedata_version, country))
logging.notice("localedata load complete version: %s country: %s", localedata_version, country)
return (localedata_version, country)
def __dump_model(self):
try:
time_ = datetime.datetime.fromtimestamp(time.time())
year = time_.year
day = time_.day
month = time_.month
path = os.path.join(self.dump_path, str(year), str(month), str(day))
if not os.path.exists(path):
os.makedirs(path)
self.logger('create {0} dir : '.format(path))
filename_model = path+str(time.time())+' model '+self.method+'.sav'
with open(filename_model, 'wb') as file:
pickle.dump(self.result, file)
logging.notice('Create dump {0} '.format(filename_model))
except Exception as e:
logging.notice('Dump processing errors : {0}'.format(repr(e)))
def get_PhyML_stats(value=None):
''' parses PhyML stats '''
if os.path.isfile('init_phyml_stats.txt') and os.path.getsize('init_phyml_stats.txt') > 0:
for phymlstats in open('init_phyml_stats.txt', 'r'):
if phymlstats.startswith('. Log-likelihood:'):
loglike = phymlstats.strip().split()[-1]
logging.info('calculated %s log-likelihood from PhyML statistics' % loglike)
elif phymlstats.startswith(' - Gamma shape parameter:'):
alpha = phymlstats.strip().split()[-1]
logging.info('calculated %s gamma shape from PhyML statistics' % alpha)
elif phymlstats.startswith(' - f(A)='):
fA = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' - f(C)='):
fC = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' - f(G)='):
fG = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' - f(T)='):
fT = phymlstats.strip().split()[-1]
freqs = '%s,%s,%s,%s' % (fA, fC, fG, fT) # Order (A,C,G,T) matters for PhyML
logging.info('calculated %s frequencies of A,C,G,T from PhyML statistics' % freqs)
elif phymlstats.startswith(' A <-> C'):
A2C = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' A <-> G'):
A2G = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' A <-> T'):
A2T = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' C <-> G'):
C2G = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' C <-> T'):
C2T = phymlstats.strip().split()[-1]
elif phymlstats.startswith(' G <-> T'):
G2T = phymlstats.strip().split()[-1]
Transitions = (Decimal(A2G) + Decimal(C2T)) # A<->G && C<->T
logging.info('calculated %s transitions from PhyML statistics' % Transitions)
Transversions = (Decimal(A2C) + Decimal(A2T) + Decimal(C2G) + Decimal(G2T)) # All (4) others
logging.info('calculated %s transversions from PhyML statistics' % Transversions)
TsTv = (Transitions / Transversions).quantize(Decimal('.000001'), rounding=ROUND_UP)
logging.info('calculated %s Ts:Tv from PhyML statistics' % TsTv)
for var in [alpha, freqs, TsTv]:
var = fill_empty_var(var)
else:
logging.notice('unable to open phyml stats file to optimize parameters')
logging.notice('gamma shape, Ts:Tv, and f(A),f(T),f(C),f(G) values will be estimated in subsequent runs')
alpha = 'e'
TsTv = 'e'
freqs = 'm'
return alpha, TsTv, freqs
def _quick_archive_import_eh(__cache=[ ]):
global _QUICK_ARCHIVE_IMPORT
if _QUICK_ARCHIVE_IMPORT is None:
_QUICK_ARCHIVE_IMPORT = False
envvar = 'MSC_QUICK_ARCHIVE_IMPORT'
envval = os.getenv(envvar)
if envval is not None:
try:
quick = int(envval)
except ValueError:
logging.warning("Ignoing bogous value of environment variable {!s}={!r}".format(envvar, envval))
else:
_QUICK_ARCHIVE_IMPORT = (quick > 0)
if _QUICK_ARCHIVE_IMPORT:
logging.notice("Archives won't be scanned if requested graph count is unbounded ({!s}={!r})"
.format(envvar, quick))
return _QUICK_ARCHIVE_IMPORT
def __dump_result(self):
try:
time_ = datetime.datetime.fromtimestamp(time.time())
year = time_.year
day = time_.day
month = time_.month
path = os.path.join(self.dump_path, str(year), str(month), str(day))
if not os.path.exists(path):
os.makedirs(path)
self.logger('create {0} dir : '.format(path))
filename_data = path+str(time.time())+' centers '+self.method
with open(filename_data, 'wb') as file:
file.write('cluster_centers\n')
file.write(self.get_centers())
logging.notice('Create dump data {0} '.format(filename_data))
except Exception as e:
logging.notice('Dump processing errors : {0} '.format(repr(e)))
def _insert_graph(mngr : Manager, gen : Generators, meta : dict, native : bool = False, poisoned : bool = False):
assert not (native and poisoned)
graphid = Id(meta['graph'])
filename = mngr.make_graph_filename(graphid, generator=gen)
with mngr.sql_ctx as curs:
if mngr.sql_select_curs(curs, 'Graphs', id=graphid):
logging.notice("Discarding {:s} graph {!s} (already exists)".format(gen.name, graphid))
return False
mngr.sql_insert_curs(
curs, 'Graphs',
id=graphid, generator=gen, file=filename, nodes=meta['nodes'], edges=meta['edges'],
native=native, poisoned=poisoned, seed=encoded(meta.get('seed')),
)
os.makedirs(os.path.dirname(filename), exist_ok=True)
logging.debug("Renaming graph file {!r} to {!r}".format(meta['filename'], filename))
os.rename(meta['filename'], filename)
return True
def _compute_all_metrics(mngr : Manager, metr : Metrics, sizes : set, badlog):
for row in mngr.sql_select('Layouts'):
graphid = row['graph']
if _get_graph_size(mngr, graphid) not in sizes:
continue
layoutid = row['id']
layoutfile = row['file']
if mngr.sql_select('Metrics', layout=layoutid, metric=metr):
continue
if badlog.get_bad(Actions.METRICS, layoutid, metr):
logging.notice("Skipping computation of metric {:s} for layout {!s}".format(metr.name, layoutid))
continue
logging.info("Computing metric {m:s} for layout {l!s} ...".format(m=metr.name, l=layoutid))
try:
_compute_metric(mngr, metr, layoutid, layoutfile)
except RecoverableError as e:
badlog.set_bad(Actions.METRICS, layoutid, metr, msg=str(e))
logging.error("Cannot compute metric {metr:s} for layout {lid!s} of graph {gid!s}: {!s}".format(
e, metr=metr.name, lid=layoutid, gid=graphid))
def job(self, job ):
if self.queue.full():
logging.notice( "didn't queue job, queue is full" )
return False
jid = self.nextjid
info = dict( zip( ("url","pollid","choice","count"), job ) )
info['jid'] = jid
info['qtime'] = time()
info['stime'] = None
info['etime'] = None
info['status'] = "queued"
self.jobs[jid] = info
self.queue.put( jid, False )
logging.info( "job #%d queued", jid )
self.nextjid += 1
return jid
def _merger(self, src, dst, dryRun):
try:
if dryRun:
# Be less verbose for dry runs. More detailed information is
# likely to be misleading because of dry run limitations.
logger.notice(lit("INFO_MIGRATE_MOVE_DRYRUN__S") % src)
return
root, ext = os.path.splitext(src)
if ext == ".conf":
if os.path.lexists(dst):
# Combine src and dst confs; don't override anything in dst.
combinedConf = comm.readConfFile(src)
dstConf = comm.readConfFile(dst)
for k in dstConf.keys():
if combinedConf.has_key(k):
combinedConf[k].update(dstConf[k])
else:
combinedConf[k] = dstConf[k]
# In case we don't have permission to truncate the
# file, just remove it preemptively.
safe_remove(dst)
logger.notice(lit("INFO_MIGRATE_MERGE_CONF__S_S") % (src, dst))
comm.writeConfFile(dst, combinedConf)
else:
comm.copyItem(src, dst)
else:
if os.path.lexists(dst):
logger.notice(lit("INFO_MIGRATE_IGNORE_DUP__S_S") % (src, dst))
else:
comm.copyItem(src, dst)
except Exception, e:
logger.warn(lit("WARN_MIGRATE_NO_CREATE__S") % dst)
logger.exception(e)
def migrate(self, dryRun=False):
self._verify()
if not self.is_legacy():
return
name = self.name()
src = self.location()
cleanup = True
if (name == self._DEFAULT) or (name == "README"):
logger.notice(lit("INFO_MIGRATE_OMIT__S") % name)
elif name == self._LOCAL:
if not dryRun:
self._rearrange_conf_files(self._LOCAL)
comm.mergeDirs(src, get_system_bundle_path(), dryRun, self._merger)
else:
if not dryRun:
self._rearrange_conf_files(self._DEFAULT)
collision = get_bundle(name)
if collision is None:
comm.moveItem(src, make_bundle_install_path(name), dryRun)
cleanup = False
else:
logger.notice(lit("INFO_MIGRATE_COLLISION__S_S") %
(collision.name(), collision.location()))
logger.notice(lit("INFO_MIGRATE_OMIT__S") % name)
if cleanup and not dryRun:
logger.info(lit("INFO_MIGRATE_CLEANUP__S") % src)
self.delete()
def chooseLC(self,aspirateVolume=0):
if self.volume-aspirateVolume>=MINLIQUIDDETECTVOLUME:
if aspirateVolume==0:
return self.inliquidLC # Not aspirating, should be fine
# Try using liquid detection
initheight=self.plate.getliquidheight(self.volume) # True height at start
finalheight=self.plate.getliquidheight(self.volume-aspirateVolume) # True height at end of aspirate
initgemvolume=self.plate.getgemliquidvolume(initheight) # How much will Gemini think we have at start
if initgemvolume<aspirateVolume+15:
# Not enough
msg="Aspirate %.1f ul from %.1f ul, gem will think initial volume is %.1ful which is too low to reliably work - not using LD"%(aspirateVolume,self.volume,initgemvolume)
logging.notice(msg)
else:
finalgemvolume=initgemvolume-aspirateVolume
finalgemheight=self.plate.getgemliquidheight(finalgemvolume)
finaltipdepth=self.inliquidLC.submerge-(finalgemheight-finalheight)
msg="Aspirate %.1f ul from %.1f ul: height goes from %.1f to %.1f mm, gem will think initial volume is %.1ful and final height %.1f mm"%(aspirateVolume,self.volume,initheight,finalheight,initgemvolume,finalgemheight)
if finalgemheight-0.1<self.inliquidLC.submerge:
# Gemini won't be able to submerge as much as requested
logging.notice(msg+": Gemini would think there's not enough liquid to submerge %.1f mm - not using LD"%self.inliquidLC.submerge)
elif finaltipdepth<0.1:
# Tracking is off so much that tip will break surface of water during operation
logging.notice(msg+": tip will not be submerged enough (depth=%.1f mm) - not using LD"%finaltipdepth)
else:
# Should be good
#logging.notice(msg)
return self.inliquidLC
# No liquid detect:
if self.volume==0 and aspirateVolume==0:
return self.emptyLC
elif self.hasBeads and self.plate.curloc=="Magnet":
return self.beadsLC
else:
return self.bottomLC
def getmixspeeds(self):
'Get minimum, maximum speed for mixing this sample'
if self.isMixed():
minspeed=0
else:
minspeed=interpolate(self.plate.minspeeds,self.volume)
if minspeed is None:
assumeSpeed=1900
logging.notice("No shaker min speed data for volume of %.0f ul, assuming %.0f rpm"%(self.volume,assumeSpeed))
minspeed=assumeSpeed
maxspeed=interpolate(self.plate.maxspeeds,self.volume)
glycerol=self.glycerolfrac()
if glycerol>0:
gmaxspeed=interpolate(self.plate.glycerolmaxspeeds,self.volume)
if glycerol>self.plate.glycerol:
logging.notice("Sample %s contains %.1f%% Glycerol (more than tested of %.1f%%)"%(self.name,glycerol*100,self.plate.glycerol*100))
maxspeed=gmaxspeed
else:
maxspeed=maxspeed+(gmaxspeed-maxspeed)*(glycerol/self.plate.glycerol)
if maxspeed<minspeed:
logging.notice("%s with %.1ful and %.1f%% glycerol has minspeed of %.0f greater than maxspeed of %.0f"%(self.name,self.volume,glycerol*100,minspeed,maxspeed))
minspeed=maxspeed # Glycerol presence should also reduce minspeed
return (minspeed,maxspeed)
def sharding_start(sharding):
auth = sharding['auth']
configdb = ['%s:%d' % (i[0], i[1]) for i in sharding['configserver']]
configdb = ','.join(configdb)
logging.notice('............. start shard ')
for shard in sharding['shard']:
if shard['type'] == 'replset':
replset_start(shard, auth)
elif shard['type'] == 'mongod':
mongod_start(shard['server'], auth=auth)
logging.notice('............. start configserver ')
for configserver in sharding['configserver']:
configserver_start(configserver, auth)
logging.notice('............. start mongos ')
for mongos in sharding['mongos']:
mongos_start(mongos, configdb, auth)
@common.retry(Exception, tries=2)
def add_shard(shard):
if shard['type'] == 'replset':
members = ['%s:%d'%(host,port) for (id, (host, port, path)) in enumerate(shard['mongod'])]
members = ','.join(members)
js ='''
//use admin;
sh.addShard( "%s/%s" );
''' % (shard['replset_name'], members)
elif shard['type'] == 'mongod':
host,port,path = shard['server']
members = '%s:%d'%(host,port)
js ='''
//use admin;
sh.addShard( "%s" );
''' % (members)
[ip, port, path] = sharding['mongos'][0]
try:
_run_js(ip, port, js, auth)
except Exception as e:
if str(e).find('E11000 duplicate key error index: config.shards.$_id_') >= 0:
logging.warning('shard already added !!!')
return
if str(e).find('host already used') >= 0:
logging.warning('shard already added !!!')
return
logging.warning('add shard return error with: \n' + str(e))
for shard in sharding['shard']:
add_shard(shard)
_sharding_status(sharding, auth)
print "please run:"
print "sh.enableSharding('report')"
print "sh.shardCollection('report.jomo_report_2013053116', {uuid:1})"
def console_stop(self):
# we have to import 'logging' not at the top of the module
import logging
t = current_thread()
logging.notice(_(u'{0}: Interactive console terminated by {1} '
u'from {2}.').format(self.licornd,
stylize(ST_NAME, t._licorn_remote_user),
stylize(ST_ADDRESS, '%s:%s' % (
t._licorn_remote_address,
t._licorn_remote_port))),
to_listener=False)
if self._console_isatty:
# NOTE: there are console non-breakable spaces at choosen
# places in the sentences for enhanced graphical effect.
remote_output(_(u'Welcome back to Real World™. Have a nice day!')
+ u'\n', word_delay=0.25)
else:
remote_output(_(u'>>> batched remote console terminated.') + '\n',
_message_channel_=2)
def start(self):
logging.notice("+++ start replset")
for x in self.shard_arr:
Replset(x).start()
logging.notice("+++ start configserve")
for x in self.configserver_arr:
Configserver(x).start()
logging.notice("+++ start mongos")
for x in self.mongos_arr:
Mongos(x).start()
self._adduser()
logging.notice("+++ add shard")
for shard in self.args["shard"]:
self._do_addshard(shard)
logging.notice("done!!")
print common.shorten(self._runjs("sh.status()"), 1024)
print "hint:"
print "sh.enableSharding('db')"
print "sh.shardCollection('db.collection', {uuid:1})"
def save(self, filename=None, batch=False, auto_answer=None):
""" If the configuration file changed, backup the current file on disk,
and save the current data into a new version (same name).
If the current instance is a "memory-only" one, and no filename
is given, raise an exception.
"""
if filename is None:
filename = self.filename
if self.__changed:
if filename:
if batch or logging.ask_for_repair(_(u'{0}: system file {1} '
u'must be modified for the configuration to be '
u'complete. Do it?').format(
stylize(ST_NAME, self._caller),
stylize(ST_PATH, self.filename)),
auto_answer=auto_answer):
fsapi.backup_file(filename)
self.__save(filename)
# Alter the property via the underlying private attribute,
# else modifications are not allowed.
self.__changed = False
logging.notice(_(u'{0}: altered configuration file {1}.').format(
stylize(ST_NAME, self._caller),
stylize(ST_PATH, self.filename)))
else:
raise exceptions.LicornModuleError(_(u'{0}: configuration '
u'file {1} must be altered to continue.').format(
self._caller, self.filename))
else:
raise exceptions.LicornRuntimeError(_(u'%s: cannot save a '
u'file without any filename!') % self.name)
def execute(command, input_data='', dry_run=None):
""" Execute a command (passed as a list or tuple) and roughly pipe some
data into the executed program.
Return the (eventual) stdout and stderr in a tuple. """
assert ltrace(TRACE_PROCESS, 'execute(%s)%s, dry_run=%s.' % (command,
' with input_data="%s"' % input_data if input_data != '' else '', dry_run))
from subprocess import Popen, PIPE
if dry_run:
logging.notice(_(u'{0:s}: dry_run({1}){2}.').format(
stylize(ST_NAME, u'execute'),
stylize(ST_COMMENT, u' '.join(command)),
_(u' → sleep({0})').format(dry_run)))
if type(dry_run) in (IntType, LongType, FloatType):
time.sleep(float(dry_run))
return ('', '')
try:
if input_data != '':
p = Popen(command, shell=False, stdin=PIPE, stdout=PIPE, stderr=PIPE,
close_fds=True)
return p.communicate(input_data)
else:
p = Popen(command, shell=False, stdout=PIPE, stderr=PIPE,
close_fds=True)
return p.communicate()
except (OSError, IOError), e:
logging.warning2(_(u'{0}: exception "{1}" while trying to '
u'process.execute({2}).').format(
stylize(ST_NAME, current_thread().name),
stylize(ST_ATTR, e),
stylize(ST_COMMENT, ' '.join(command))))
raise
def send(cls, user_key, title, message, severity_level, url=None):
'''
:param to: str
pushover user key
:param title: str
:param message: str
:param severity_level: int
:param url: str - Default: None
:returns: boolean
'''
if not Config.data['pushover']['enabled']:
logging.notice('pushover is not enabled in the config.')
return False
if severity_level < 3:
priority = 2
elif severity_level < 5:
priority = 1
else:
priority = 0
params = {
'user': user_key,
'token': Config.data['pushover']['token'],
'title': '{}: {}'.format(Config.data['notification_prefix'], title),
'message': message,
'priority': priority,
}
if url:
params['url'] = url
if priority == 2:
params['retry'] = 60
params['expire'] = 14400 # 4 hours
requests.post(
'https://api.pushover.net/1/messages.json',
params=params,
)
return True
def dispose(self, volume, src, mix=False, getDITI=True, dropDITI=True):
'Dispose of a given volume by aspirating and not dispensing (will go to waste during next wash)'
if self.ptcrunning and src.plate==decklayout.SAMPLEPLATE:
self.waitpgm()
if volume>self.MAXVOLUME:
reuseTip=False # Since we need to wash to get rid of it
msg="Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME),
if reuseTip:
msg+= "with tip reuse"
else:
msg+= "without tip reuse"
logging.notice(msg)
self.dispose(self.MAXVOLUME,src,mix,getDITI,dropDITI)
self.dispose(volume-self.MAXVOLUME,src,False,getDITI,dropDITI)
return
cmt="Remove and dispose of %.1f ul from %s"%(volume, src.name)
ditivolume=volume+src.inliquidLC.singletag
if mix and not src.isMixed():
cmt=cmt+" with src mix"
ditivolume=max(ditivolume,src.volume)
if self.useDiTis:
tipMask=4
if getDITI:
worklist.getDITI(tipMask&self.DITIMASK,ditivolume)
else:
tipMask=self.cleantip()
#print "*",cmt
worklist.comment(cmt)
if mix and not src.isMixed():
src.mix(tipMask)
src.aspirate(tipMask,volume)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
def _do_at_all(self, cmd):
logging.notice("+++ %s replset" % cmd)
for x in self.shard_arr:
eval("Replset(x).%s()" % cmd)
logging.notice("+++ %s configserver" % cmd)
for x in self.configserver_arr:
eval("Configserver(x).%s()" % cmd)
logging.notice("+++ %s mongos" % cmd)
for x in self.mongos_arr:
eval("Mongos(x).%s()" % cmd)
def test_logging():
logging.debug("this is debug")
logging.info("this is info")
logging.notice("this is notice")
logging.warn("this is warn")
logging.error("this is error")
def check_file_against_dict(conf_file, defaults, configuration,
batch=False, auto_answer=None):
''' Check if a file has some configuration directives,
and check against values if given.
If the value is None, only the directive existence is tested. '''
# FIXME: move out configuration and use LMC.configuration
# FIXME 2: move this method out of here (if it needs LMC,
# it must not be in foundations)!!
from licorn.foundations import readers
conf_file_alter = False
conf_file_data = open(conf_file, 'r').read()
conf_file_dict = readers.simple_conf_load_dict(data=conf_file_data)
for (directive, value) in defaults:
if not conf_file_dict.has_key(directive):
logging.warning(_(u'Inserted missing directive {1} in {0}.').format(
stylize(ST_PATH, conf_file),
stylize(ST_COMMENT, directive)))
conf_file_alter = True
conf_file_dict[directive] = value
conf_file_data = '%s %s\n%s' % (
directive, value, conf_file_data)
if value != None and conf_file_dict[directive] != value:
logging.warning(_(u'modified {0} directive {1} to be equal to {2} '
u'(was originaly {3}).').format(
stylize(ST_PATH, conf_file),
stylize(ST_REGEX, directive),
stylize(ST_OK, value),
stylize(ST_BAD, conf_file_dict[directive])))
conf_file_alter = True
conf_file_dict[directive] = value
conf_file_data = re.sub(r'%s.*' % directive,
r'%s %s' % (directive, value), conf_file_data)
# else:
# everything is OK, just pass.
if conf_file_alter:
if batch or logging.ask_for_repair(_(u'Modify {0} on disk to '
u'reflect current in-memory changes?').format(
stylize(ST_PATH, conf_file)), auto_answer):
try:
open(conf_file, 'w').write(conf_file_data)
logging.notice(_(u'Altered {0} to match {1} '
u'pre-requisites.').format(
stylize(ST_PATH, conf_file),
stylize(ST_NAME, configuration.app_name)))
except (IOError, OSError), e:
if e.errno == 13:
raise exceptions.LicornRuntimeError(_(u'Insufficient '
u'permissions. Are you root?\n\t{0}').format(e))
else:
raise e
else:
raise exceptions.LicornRuntimeError(_(u'Modifications in {0} are '
u'mandatory for {1} to work properly. Cannot continue without '
u'this, sorry!').format(stylize(ST_PATH, conf_file),
stylize(ST_NAME, configuration.app_name)))
def __init__(self,name,plate,well=None,conc=None,volume=0,hasBeads=False,extraVol=50,mixLC=liquidclass.LCMixBottom,firstWell=None,extrainfo=[],ingredients=None,atEnd=False):
# If firstWell is not None, then it is a hint of the first well position that should be used
if well!=None and well!=-1:
if not isinstance(well,int):
well=plate.wellnumber(well)
if well not in plate.wells:
logging.warning("Attempt to assign sample %s to well %d (%s) which is not legal on plate %s"%(name,well,plate.wellname(well),plate.name))
for s in __allsamples:
if s.well==well and s.plate==plate:
logging.warning("Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name))
well=None
break
if well is None:
# Find first unused well
found=False
if firstWell is not None:
# First check only wells>=firstWell
for well in plate.wells:
if well<firstWell:
continue
found=True
for s in __allsamples:
if s.plate==plate and s.well==well:
well=well+1
found=False
break
if found:
break
if not found:
well=max(plate.wells) if atEnd else min(plate.wells)
while (well>=0) if atEnd else (well<=max(plate.wells)):
found=True
for s in __allsamples:
if s.plate==plate and s.well==well:
well=well+(-1 if atEnd else 1)
found=False
break
if found:
break
elif well==-1:
well=None
for s in __allsamples:
if s.plate==plate and s.well==well:
logging.error("Attempt to assign sample %s to plate %s, well %s that already contains %s"%(name,str(plate),plate.wellname(well),s.name))
if name in [s.name for s in __allsamples]:
while name in [s.name for s in __allsamples]:
name=name+"#"
logging.notice("renaming sample to %s"%name)
self.name=name
self.plate=plate
if well>=plate.nx*plate.ny:
logging.error("Overflow of plate %s while adding %s"%(str(plate),name))
self.well=well
if isinstance(conc,Concentration) or conc is None:
self.conc=conc
else:
self.conc=Concentration(conc)
self.volume=volume
self.initVol=volume
if volume>0:
if ingredients is None:
self.ingredients={name:volume}
else:
self.ingredients=ingredients
total=sum([v for v in ingredients.values()])
for k in self.ingredients:
self.ingredients[k]=self.ingredients[k]*volume/total
self.lastvolcheck=None
else:
self.ingredients={}
self.lastvolcheck=0 # Assume that it has already been checked for 0 (since it can't be any less...)
if plate.pierce:
self.bottomLC=liquidclass.LCWaterPierce
self.bottomSideLC=self.bottomLC # Can't use side with piercing
self.inliquidLC=self.bottomLC # Can't use liquid detection when piercing
else:
self.bottomLC=liquidclass.LCWaterBottom
self.bottomSideLC=liquidclass.LCWaterBottomSide
self.inliquidLC=liquidclass.LCWaterInLiquid
self.beadsLC=liquidclass.LCWaterBottomBeads
self.mixLC=mixLC
self.airLC=liquidclass.LCAir
# Same as bottom for now
self.emptyLC=self.bottomLC
self.history=""
__allsamples.append(self)
if hasBeads:
self.lastMixed=None
else:
self.lastMixed=clock.elapsed()-20*60 # Assume it was last mixed an 20 min before start of run
self.wellMixed=True
self.initHasBeads=hasBeads
self.hasBeads=hasBeads # Setting this to true overrides the manual conditioning
self.extraVol=extraVol # Extra volume to provide
self.evap=0 # Amount that has evaporated
if self.plate.name=="Samples":
self.lastevapupdate=clock.pipetting
else:
self.lastevapupdate=clock.elapsed()
self.extrainfo=extrainfo
self.emptied=False
