def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
worklist.comment("Generated %s" % (datetime.now().ctime()))
worklist.userprompt(
"The following reagent tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt(
"The following eppendorf tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',
subject='Run started (Generate: %s)' %
(datetime.now().ctime()))
worklist.email(dest='*****@*****.**',
subject='Tecan error',
onerror=1)
self.cleanTips = 0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis = False
self.ptcrunning = False
self.overrideSanitize = False
self.pgmStartTime = None
self.pgmEndTime = None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt(
"Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms = []
self.timerStartTime = [None] * 8
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
self.checksum=md5sum(sys.argv[0])
self.checksum=self.checksum[-4:]
pyTecan=os.path.dirname(os.path.realpath(__file__))
self.gitlabel=strip(subprocess.check_output(["git", "describe","--always"],cwd=pyTecan))
worklist.comment("Generated %s (%s-%s pyTecan-%s)"%(datetime.now().ctime(),sys.argv[0],self.checksum,self.gitlabel))
worklist.userprompt("The following reagent tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt("The following eppendorf tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',subject='Run started (Generate: %s) expected runtime %.0f minutes'%(datetime.now().ctime(),clock.totalTime/60.0 if clock.totalTime is not None else 0.0 ) )
worklist.email(dest='*****@*****.**',subject='Tecan error',onerror=1)
self.cleanTips=0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis=False
self.ptcrunning=False
self.overrideSanitize=False
self.pgmStartTime=None
self.pgmEndTime=None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt("Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms=[]
self.timerStartTime=[None]*8
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
worklist.comment("Generated %s"%(datetime.now().ctime()))
worklist.userprompt("The following reagent tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt("The following eppendorf tubes should be present: %s"%Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(dest='*****@*****.**',subject='Run started (Generate: %s)'%(datetime.now().ctime()))
worklist.email(dest='*****@*****.**',subject='Tecan error',onerror=1)
self.cleanTips=0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis=False
self.ptcrunning=False
self.overrideSanitize=False
self.pgmStartTime=None
self.pgmEndTime=None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt("Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms=[]
self.timerStartTime=[None]*8
def __init__(self):
'Create a new experiment with given sample locations for water and WASTE; totalTime is expected run time in seconds, if known'
self.checksum = md5sum(sys.argv[0])
self.checksum = self.checksum[-4:]
pyTecan = os.path.dirname(os.path.realpath(__file__))
self.gitlabel = strip(
subprocess.check_output(["git", "describe", "--always"],
cwd=pyTecan))
worklist.comment("Generated %s (%s-%s pyTecan-%s)" %
(datetime.now().ctime(), sys.argv[0], self.checksum,
self.gitlabel))
worklist.userprompt(
"The following reagent tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.REAGENTPLATE))
worklist.userprompt(
"The following eppendorf tubes should be present: %s" %
Sample.getAllLocOnPlate(decklayout.EPPENDORFS))
worklist.email(
dest='*****@*****.**',
subject='Run started (Generate: %s) expected runtime %.0f minutes'
% (datetime.now().ctime(),
clock.totalTime / 60.0 if clock.totalTime is not None else 0.0))
worklist.email(dest='*****@*****.**',
subject='Tecan error',
onerror=1)
self.cleanTips = 0
# self.sanitize() # Not needed, TRP does it, also first use of tips will do this
self.useDiTis = False
self.ptcrunning = False
self.overrideSanitize = False
self.pgmStartTime = None
self.pgmEndTime = None
# Access PTC and RIC early to be sure they are working
worklist.pyrun("PTC\\ptctest.py")
# worklist.periodicWash(15,4)
worklist.userprompt(
"Verify that PTC thermocycler lid pressure is set to '2'.")
self.idlePgms = []
self.timerStartTime = [None] * 8
def volcheck(self,tipMask,well,volToRemove):
'''Check if the well contains the expected volume'''
if self.lastvolcheck is not None:
# Decide if a volume check is needed
if volToRemove==0:
# No need to check if not removing anything and it has been checked previously (i.e. lastvolcheck is not None)
return
if self.volume-volToRemove > max(30,self.lastvolcheck-200) or self.volume-volToRemove>200:
# Not needed
return
self.lastvolcheck=self.volume
height=self.plate.getliquidheight(self.volume)
gemvol=self.plate.getgemliquidvolume(height) # Volume that would be reported by Gemini for this height
if gemvol is None:
logging.warning( "No volume equation for %s, skipping initial volume check"%self.name)
return
volwarn=self.volume*0.80
heightwarn=min(self.plate.getliquidheight(volwarn),height-1.0) # threshold is lower of 1mm or 80%
gemvolwarn=self.plate.getgemliquidvolume(heightwarn) # Volume that would be reported by Gemini for this height
volcrit=self.plate.unusableVolume*0.8+volToRemove
heightcrit=self.plate.getliquidheight(volcrit)
gemvolcrit=self.plate.getgemliquidvolume(heightcrit) # Volume that would be reported by Gemini for this height
worklist.flushQueue()
worklist.comment( "Check that %s contains %.1f ul (warn< %.1f, crit<%.1f), (gemvol=%.1f (warn<%.1f,crit<%.1f); height=%.1f (>%.1f) )"%(self.name,self.volume,volwarn,volcrit,gemvol,gemvolwarn,gemvolcrit,height,heightwarn))
tipnum=0
tm=tipMask
while tm>0:
tm=tm>>1
tipnum+=1
volvar='detected_volume_%d'%tipnum
worklist.variable(volvar,-2)
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
doneLabel=worklist.getlabel()
worklist.condition(volvar,">",gemvolwarn,doneLabel)
ptmp=clock.pipetting;
warnLabel=worklist.getlabel()
worklist.condition(volvar,">",gemvolcrit,warnLabel)
worklist.moveliha(worklist.WASHLOC) # Get LiHa out of the way
msg="Failed volume check of %s - should have %.0f ul (gemvol=~%s~, crit=%.0f)"%(self.name,self.volume,volvar,gemvolcrit)
worklist.email(dest='*****@*****.**',subject=msg)
worklist.stringvariable("response","retry",msg+" Enter 'ignore' to ignore and continue, otherwise will retry.")
worklist.condition("response","==","ignore",doneLabel)
# Retry
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
worklist.condition(volvar,">",gemvolcrit,doneLabel)
worklist.stringvariable("response","retry","Still have <%.0f. Enter 'ignore' to ignore and continue, otherwise will retry."%self.volume)
worklist.condition("response","==","ignore",doneLabel)
# Retry again
worklist.detectLiquid(tipMask,well,self.inliquidLC,self.plate)
worklist.condition(volvar,">",gemvolcrit,doneLabel)
worklist.stringvariable("response","ignore","Still have <%.0f. Will continue regardless."%self.volume)
worklist.condition("response","!=","warn",doneLabel)
worklist.comment(warnLabel)
msg="Warning: volume check of %s - should have %.0f ul (gemvol=~%s~, warn=%.0f, crit=%.0f)"%(self.name,self.volume,volvar,gemvolwarn,gemvolcrit)
worklist.email(dest='*****@*****.**',subject=msg)
worklist.comment(doneLabel)
clock.pipetting=ptmp # All the retries don't usually happen, so don't count in total time
self.addhistory("LD",0,tipMask)
def volcheck(self, tipMask, well, volToRemove):
'''Check if the well contains the expected volume'''
if self.lastvolcheck is not None:
# Decide if a volume check is needed
if volToRemove == 0:
# No need to check if not removing anything and it has been checked previously (i.e. lastvolcheck is not None)
return
if self.volume - volToRemove > max(
30, self.lastvolcheck -
200) or self.volume - volToRemove > 200:
# Not needed
return
self.lastvolcheck = self.volume
height = self.plate.getliquidheight(self.volume)
gemvol = self.plate.getgemliquidvolume(
height) # Volume that would be reported by Gemini for this height
if gemvol is None:
logging.warning(
"No volume equation for %s, skipping initial volume check" %
self.name)
return
volcrit = self.plate.unusableVolume * 0.8 + volToRemove
volwarn = min(volcrit, self.volume * 0.80)
heightwarn = min(self.plate.getliquidheight(volwarn),
height - 1.0) # threshold is lower of 1mm or 80%
gemvolwarn = self.plate.getgemliquidvolume(
heightwarn
) # Volume that would be reported by Gemini for this height
heightcrit = self.plate.getliquidheight(volcrit)
gemvolcrit = self.plate.getgemliquidvolume(
heightcrit
) # Volume that would be reported by Gemini for this height
worklist.flushQueue()
worklist.comment(
"Check that %s contains %.1f ul (warn< %.1f, crit<%.1f), (gemvol=%.1f (warn<%.1f,crit<%.1f); height=%.1f (>%.1f) )"
% (self.name, self.volume, volwarn, volcrit, gemvol, gemvolwarn,
gemvolcrit, height, heightwarn))
tipnum = 0
tm = tipMask
while tm > 0:
tm = tm >> 1
tipnum += 1
volvar = 'detected_volume_%d' % tipnum
worklist.variable(volvar, -2)
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
doneLabel = worklist.getlabel()
worklist.condition(volvar, ">", gemvolwarn, doneLabel)
ptmp = clock.pipetting
warnLabel = worklist.getlabel()
worklist.condition(volvar, ">", gemvolcrit, warnLabel)
worklist.moveliha(worklist.WASHLOC) # Get LiHa out of the way
msg = "Failed volume check of %s - should have %.0f ul (gemvol=~%s~, crit=%.0f)" % (
self.name, self.volume, volvar, gemvolcrit)
worklist.email(dest='*****@*****.**', subject=msg)
worklist.stringvariable(
"response", "retry", msg +
" Enter 'ignore' to ignore and continue, otherwise will retry.")
worklist.condition("response", "==", "ignore", doneLabel)
# Retry
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
worklist.condition(volvar, ">", gemvolcrit, doneLabel)
worklist.stringvariable(
"response", "retry",
"Still have <%.0f. Enter 'ignore' to ignore and continue, otherwise will retry."
% self.volume)
worklist.condition("response", "==", "ignore", doneLabel)
# Retry again
worklist.detectLiquid(tipMask, well, self.inliquidLC, self.plate)
worklist.condition(volvar, ">", gemvolcrit, doneLabel)
worklist.stringvariable(
"response", "ignore",
"Still have <%.0f. Will continue regardless." % self.volume)
worklist.condition("response", "!=", "warn", doneLabel)
worklist.comment(warnLabel)
msg = "Warning: volume check of %s - should have %.0f ul (gemvol=~%s~, warn=%.0f, crit=%.0f)" % (
self.name, self.volume, volvar, gemvolwarn, gemvolcrit)
worklist.email(dest='*****@*****.**', subject=msg)
worklist.comment(doneLabel)
clock.pipetting = ptmp # All the retries don't usually happen, so don't count in total time
self.addhistory("LD", 0, tipMask, "detect")
