def runpgm(self,pgm,duration,waitForCompletion=True,volume=10,hotlidmode="TRACKING",hotlidtemp=1):
if self.ptcrunning:
logging.error("Attempt to start a progam on PTC when it is already running")
if len(pgm)>8:
logging.error("PTC program name (%s) too long (max is 8 char)"%pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt="run %s"%pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE,"PTC")
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode=="TRACKING" or hotlidmode=="CONSTANT"
assert (hotlidmode=="TRACKING" and hotlidtemp>=0 and hotlidtemp<=45) or (hotlidmode=="CONSTANT" and hotlidtemp>30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d'%(pgm,hotlidmode,hotlidtemp,volume))
self.pgmStartTime=clock.pipetting
self.pgmEndTime=duration*60+clock.pipetting
self.ptcrunning=True
Sample.addallhistory("{%s}"%pgm,addToEmpty=False,onlyplate=decklayout.SAMPLEPLATE.name)
if waitForCompletion:
self.waitpgm()
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
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
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 multitransfer(self, volumes, src, dests,mix=(True,False),getDITI=True,dropDITI=True,ignoreContents=False,extraFrac=0.05):
'Multi pipette from src to multiple dest. mix is (src,dest) mixing -- only mix src if needed though'
#print "multitransfer(",volumes,",",src,",",dests,",",mix,",",getDITI,",",dropDITI,")"
if self.ptcrunning and (src.plate==decklayout.SAMPLEPLATE or len([1 for d in dests if d.plate==decklayout.SAMPLEPLATE])>0):
self.waitpgm()
if isinstance(volumes,(int,long,float)):
# Same volume for each dest
volumes=[volumes for i in range(len(dests))]
assert len(volumes)==len(dests)
# if len([d.volume for d in dests if d.conc!=None])==0:
if len([dests[i].volume for i in range(0,len(dests)) if dests[i].conc != None and volumes[i]>0.01])==0:
maxval=0
else:
maxval=max([dests[i].volume for i in range(0,len(dests)) if dests[i].conc != None and volumes[i]>0.01])
# maxval=max([d.volume for d in dests if d.conc != None])
#print "volumes=",[d.volume for d in dests],", conc=",[str(d.conc) for d in dests],", maxval=",maxval
if not mix[1] and len(volumes)>1 and ( maxval<.01 or ignoreContents):
if sum(volumes)*(1+extraFrac)>self.MAXVOLUME:
#print "sum(volumes)=%.1f, MAXVOL=%.1f"%(sum(volumes),self.MAXVOLUME)
for i in range(1,len(volumes)):
if sum(volumes[0:i+1])*(1+extraFrac)>self.MAXVOLUME:
destvol=max([d.volume for d in dests[0:i]])
reuseTip=destvol<=0
# print "Splitting multi with total volume of %.1f ul into smaller chunks < %.1f ul after %d dispenses "%(sum(volumes),self.MAXVOLUME,i),
# if reuseTip:
# print "with tip reuse"
# else:
# print "without tip reuse"
self.multitransfer(volumes[0:i],src,dests[0:i],mix,getDITI,not reuseTip,extraFrac=extraFrac)
self.multitransfer(volumes[i:],src,dests[i:],(False,mix[1]),not reuseTip,dropDITI,extraFrac=extraFrac)
return
if self.useDiTis:
tipMask=4
if getDITI:
ditivol=sum(volumes)*(1+extraFrac)+src.inliquidLC.multicond+src.inliquidLC.multiexcess
worklist.getDITI(tipMask&self.DITIMASK,min(self.MAXVOLUME,ditivol),True,True)
else:
tipMask=self.cleantip()
cmt="Multi-add %s to samples %s"%(src.name,",".join("%s[%.1f]"%(dests[i].name,volumes[i]) for i in range(len(dests))))
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask,sum(volumes)*(1+extraFrac),True) # Aspirate extra
for i in range(len(dests)):
if volumes[i]>0.01:
dests[i].dispense(tipMask,volumes[i],src)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask&self.DITIMASK,decklayout.WASTE)
else:
for i in range(len(dests)):
if volumes[i]>0.01:
self.transfer(volumes[i],src,dests[i],(mix[0] and i==0,mix[1]),getDITI,dropDITI)
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 waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime-clock.pipetting > 120:
# Run any idle programs
oldElapsed=clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime-clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime-clock.pipetting-120)
if oldElapsed==clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime+=(clock.pipetting-self.pgmStartTime)
clock.thermotime+=(self.pgmEndTime-clock.pipetting)
clock.pipetting=self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
self.lihahome()
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector("Hotel 1 Lid",decklayout.HOTELPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle2",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200Wiggle2Pos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE,True)
worklist.vector("PTC200Wiggle",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.OPEN,True)
worklist.vector("PTC200WigglePos",decklayout.PTCPOS,worklist.ENDTOSAFE,False,worklist.DONOTMOVE,worklist.DONOTMOVE)
self.ptcrunning=False
self.moveplate(decklayout.SAMPLEPLATE,"Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.SAFETOEND,False,worklist.DONOTMOVE,worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,decklayout.SAMPLEPLATE,worklist.ENDTOSAFE,False,worklist.OPEN,worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15,1,5,True)
def mix(self, src, nmix=4):
if self.ptcrunning and src.plate == decklayout.SAMPLEPLATE:
self.waitpgm()
cmt = "Mix %s" % (src.name)
tipMask = self.cleantip()
worklist.comment(cmt)
src.lastMixed = None # Force a mix
src.mix(tipMask, False, nmix=nmix)
def mix(self, src, nmix=4):
if self.ptcrunning and src.plate==decklayout.SAMPLEPLATE:
self.waitpgm()
cmt="Mix %s"%(src.name)
tipMask=self.cleantip()
worklist.comment(cmt)
src.lastMixed=None # Force a mix
src.mix(tipMask,False,nmix=nmix)
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
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul " % (
volume, self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
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 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():
if src.plate == decklayout.SAMPLEPLATE or src.plate == decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
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 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 moveplate(self,plate,dest="Home",returnHome=True):
if self.ptcrunning and plate==decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate!=decklayout.SAMPLEPLATE and plate!=decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s"%(decklayout.SAMPLEPLATE.name,decklayout.DILPLATE.name,plate.name)
assert False
if plate.curloc==dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt="moveplate %s %s"%(plate.name,dest)
worklist.comment(cmt)
if plate.curloc=="Home":
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Magnet":
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="Shaker":
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
elif plate.curloc=="PTC":
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s"%(plate.name,plate.curloc)
assert False
if dest=="Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName,plate,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Magnet":
plate.movetoloc(dest,decklayout.MAGPLATELOC)
worklist.vector("Magplate",decklayout.MAGPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="Shaker":
plate.movetoloc(dest,decklayout.SHAKERPLATELOC)
worklist.vector("Shaker",decklayout.SHAKERPLATELOC,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
elif dest=="PTC":
plate.movetoloc(dest,decklayout.PTCPOS)
worklist.vector("PTC200",decklayout.PTCPOS,worklist.SAFETOEND,True,worklist.DONOTMOVE,worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s"%(plate.name,dest)
assert False
Sample.addallhistory("{->%s}"%dest,onlyplate=plate.name)
if returnHome:
worklist.romahome()
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
print "Splitting large transfer of %.1f ul into smaller chunks < %.1f ul "%(volume,self.MAXVOLUME),
if reuseTip:
print "with tip reuse"
else:
print "without tip reuse"
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 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():
if src.plate==decklayout.SAMPLEPLATE or src.plate==decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
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 runpgm(self,
pgm,
duration,
waitForCompletion=True,
volume=10,
hotlidmode="TRACKING",
hotlidtemp=1):
if self.ptcrunning:
logging.error(
"Attempt to start a progam on PTC when it is already running")
if len(pgm) > 8:
logging.error("PTC program name (%s) too long (max is 8 char)" %
pgm)
# move to thermocycler
worklist.flushQueue()
self.lihahome()
cmt = "run %s" % pgm
worklist.comment(cmt)
#print "*",cmt
worklist.pyrun("PTC\\ptclid.py OPEN")
self.moveplate(decklayout.SAMPLEPLATE, "PTC")
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.romahome()
worklist.pyrun("PTC\\ptclid.py CLOSE")
# pgm="PAUSE30" # For debugging
assert hotlidmode == "TRACKING" or hotlidmode == "CONSTANT"
assert (hotlidmode == "TRACKING" and hotlidtemp >= 0
and hotlidtemp <= 45) or (hotlidmode == "CONSTANT"
and hotlidtemp > 30)
worklist.pyrun('PTC\\ptcrun.py %s CALC %s,%d %d' %
(pgm, hotlidmode, hotlidtemp, volume))
self.pgmStartTime = clock.pipetting
self.pgmEndTime = duration * 60 + clock.pipetting
self.ptcrunning = True
Sample.addallhistory("{%s}" % pgm,
addToEmpty=False,
onlyplate=decklayout.SAMPLEPLATE.name,
type="ptc")
if waitForCompletion:
self.waitpgm()
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 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 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 sanitize(self,nmix=1,deepvol=20,force=False):
'Deep wash including RNase-Away treatment'
fixedTips=(~self.DITIMASK)&15
worklist.flushQueue()
if not force and fixedTips==self.cleanTips:
# print no sanitize needed
worklist.comment("Sanitize not needed cleanTips=%d"%self.cleanTips)
return
worklist.comment("Sanitize (cleanTips=%d)"%self.cleanTips)
worklist.wash(15,1,2)
fixedWells=[]
if not self.overrideSanitize:
for i in range(4):
if (fixedTips & (1<<i)) != 0:
fixedWells.append(i)
decklayout.BLEACH.addhistory("SANITIZE",0,1<<i)
worklist.mix(fixedTips,fixedWells,decklayout.BLEACH.mixLC,200,decklayout.BLEACH.plate,nmix,False)
worklist.wash(fixedTips,1,deepvol,True)
self.cleanTips|=fixedTips
# print "* Sanitize"
worklist.comment(clock.statusString())
def sanitize(self, nmix=1, deepvol=20, force=False):
'Deep wash including RNase-Away treatment'
fixedTips = (~self.DITIMASK) & 15
worklist.flushQueue()
if not force and fixedTips == self.cleanTips:
# print no sanitize needed
worklist.comment("Sanitize not needed cleanTips=%d" %
self.cleanTips)
return
worklist.comment("Sanitize (cleanTips=%d)" % self.cleanTips)
worklist.wash(15, 1, 2)
fixedWells = []
if not self.overrideSanitize:
for i in range(4):
if (fixedTips & (1 << i)) != 0:
fixedWells.append(i)
decklayout.BLEACH.addhistory("SANITIZE", 0, 1 << i)
worklist.mix(fixedTips, fixedWells, decklayout.BLEACH.mixLC, 200,
decklayout.BLEACH.plate, nmix, False)
worklist.wash(fixedTips, 1, deepvol, True)
self.cleanTips |= fixedTips
# print "* Sanitize"
worklist.comment(clock.statusString())
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:
print "No samples\n"
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:
print "Error: Ingredients add up to more than desired volume by %.1f ul" % (
-min(watervols))
for s in samples:
if s.volume > 0:
print "Note: %s already contains %.1f ul\n" % (s.name,
s.volume)
assert False
if sum(watervols) > 0.01:
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 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 savegem(self, filename):
worklist.comment("Completed (%s-%s)" % (sys.argv[0], self.checksum))
worklist.flushQueue()
worklist.savegem(decklayout.headerfile, filename)
def multitransfer(self,
volumes,
src,
dests,
mix=(True, False),
getDITI=True,
dropDITI=True,
ignoreContents=False,
extraFrac=0.05):
'Multi pipette from src to multiple dest. mix is (src,dest) mixing -- only mix src if needed though'
#print "multitransfer(",volumes,",",src,",",dests,",",mix,",",getDITI,",",dropDITI,")"
if self.ptcrunning and (src.plate == decklayout.SAMPLEPLATE or len(
[1 for d in dests if d.plate == decklayout.SAMPLEPLATE]) > 0):
self.waitpgm()
if isinstance(volumes, (int, long, float)):
# Same volume for each dest
volumes = [volumes for i in range(len(dests))]
assert len(volumes) == len(dests)
# if len([d.volume for d in dests if d.conc!=None])==0:
if len([
dests[i].volume for i in range(0, len(dests))
if dests[i].conc != None and volumes[i] > 0.01
]) == 0:
maxval = 0
else:
maxval = max([
dests[i].volume for i in range(0, len(dests))
if dests[i].conc != None and volumes[i] > 0.01
])
# maxval=max([d.volume for d in dests if d.conc != None])
#print "volumes=",[d.volume for d in dests],", conc=",[str(d.conc) for d in dests],", maxval=",maxval
if not mix[1] and len(volumes) > 1 and (maxval < .01
or ignoreContents):
if sum(volumes) * (1 + extraFrac) > self.MAXVOLUME:
#print "sum(volumes)=%.1f, MAXVOL=%.1f"%(sum(volumes),self.MAXVOLUME)
for i in range(1, len(volumes)):
if sum(volumes[0:i + 1]) * (1 +
extraFrac) > self.MAXVOLUME:
destvol = max([d.volume for d in dests[0:i]])
reuseTip = destvol <= 0
# print "Splitting multi with total volume of %.1f ul into smaller chunks < %.1f ul after %d dispenses "%(sum(volumes),self.MAXVOLUME,i),
# if reuseTip:
# print "with tip reuse"
# else:
# print "without tip reuse"
self.multitransfer(volumes[0:i],
src,
dests[0:i],
mix,
getDITI,
not reuseTip,
extraFrac=extraFrac)
self.multitransfer(volumes[i:],
src,
dests[i:], (False, mix[1]),
not reuseTip,
dropDITI,
extraFrac=extraFrac)
return
if self.useDiTis:
tipMask = 4
if getDITI:
ditivol = sum(volumes) * (
1 + extraFrac
) + src.inliquidLC.multicond + src.inliquidLC.multiexcess
worklist.getDITI(tipMask & self.DITIMASK,
min(self.MAXVOLUME, ditivol), True, True)
else:
tipMask = self.cleantip()
cmt = "Multi-add %s to samples %s" % (src.name, ",".join(
"%s[%.1f]" % (dests[i].name, volumes[i])
for i in range(len(dests))))
#print "*",cmt
worklist.comment(cmt)
if mix[0] and not src.isMixed():
if src.plate == decklayout.SAMPLEPLATE or src.plate == decklayout.DILPLATE:
self.shakeSamples([src])
else:
src.mix(tipMask)
src.aspirate(tipMask,
sum(volumes) * (1 + extraFrac),
True) # Aspirate extra
for i in range(len(dests)):
if volumes[i] > 0.01:
dests[i].dispense(tipMask, volumes[i], src)
if self.useDiTis and dropDITI:
worklist.dropDITI(tipMask & self.DITIMASK, decklayout.WASTE)
else:
for i in range(len(dests)):
if volumes[i] > 0.01:
self.transfer(volumes[i], src, dests[i],
(mix[0] and i == 0, mix[1]), getDITI,
dropDITI)
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 savegem(self,filename):
worklist.comment("Completed (%s-%s)"%(sys.argv[0],self.checksum))
worklist.flushQueue()
worklist.savegem(decklayout.headerfile,filename)
def moveplate(self, plate, dest="Home", returnHome=True):
if self.ptcrunning and plate == decklayout.SAMPLEPLATE:
self.waitpgm()
# move to given destination (one of "Home","Magnet","Shaker","PTC" )
if plate != decklayout.SAMPLEPLATE and plate != decklayout.DILPLATE:
print "Only able to move %s or %s plates, not %s" % (
decklayout.SAMPLEPLATE.name, decklayout.DILPLATE.name,
plate.name)
assert False
if plate.curloc == dest:
#print "Plate %s is already at %s"%(plate.name,dest)
return
#print "Move plate %s from %s to %s"%(plate.name,plate.curloc,dest)
worklist.flushQueue()
self.lihahome()
cmt = "moveplate %s %s" % (plate.name, dest)
worklist.comment(cmt)
if plate.curloc == "Home":
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.CLOSE)
elif plate.curloc == "Magnet":
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "Shaker":
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.CLOSE)
elif plate.curloc == "PTC":
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
else:
print "Plate %s is in unknown location: %s" % (plate.name,
plate.curloc)
assert False
if dest == "Home":
plate.movetoloc(dest)
worklist.vector(plate.vectorName, plate, worklist.SAFETOEND, True,
worklist.DONOTMOVE, worklist.OPEN)
elif dest == "Magnet":
plate.movetoloc(dest, decklayout.MAGPLATELOC)
worklist.vector("Magplate", decklayout.MAGPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "Shaker":
plate.movetoloc(dest, decklayout.SHAKERPLATELOC)
worklist.vector("Shaker", decklayout.SHAKERPLATELOC,
worklist.SAFETOEND, True, worklist.DONOTMOVE,
worklist.OPEN)
elif dest == "PTC":
plate.movetoloc(dest, decklayout.PTCPOS)
worklist.vector("PTC200", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
else:
print "Attempt to move plate %s to unknown location: %s" % (
plate.name, dest)
assert False
Sample.addallhistory("{->%s}" % dest, onlyplate=plate.name)
if returnHome:
worklist.romahome()
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")
def waitpgm(self, sanitize=True):
if not self.ptcrunning:
return
#print "* Wait for PTC to finish"
if sanitize:
self.sanitize() # Sanitize tips before waiting for this to be done
worklist.comment("Wait for PTC")
while self.pgmEndTime - clock.pipetting > 120:
# Run any idle programs
oldElapsed = clock.pipetting
for ip in self.idlePgms:
if self.pgmEndTime - clock.pipetting > 120:
#print "Executing idle program with %.0f seconds"%(self.pgmEndTime-clock.pipetting)
ip(self.pgmEndTime - clock.pipetting - 120)
if oldElapsed == clock.pipetting:
# Nothing was done
break
worklist.flushQueue() # Just in case
clock.pipandthermotime += (clock.pipetting - self.pgmStartTime)
clock.thermotime += (self.pgmEndTime - clock.pipetting)
clock.pipetting = self.pgmStartTime
#print "Waiting for PTC with %.0f seconds expected to remain"%(self.pgmEndTime-clock.pipetting)
worklist.pyrun('PTC\\ptcwait.py')
worklist.pyrun("PTC\\ptclid.py OPEN")
# worklist.pyrun('PTC\\ptcrun.py %s CALC ON'%"COOLDOWN")
# worklist.pyrun('PTC\\ptcwait.py')
worklist.vector("PTC200lid", decklayout.PTCPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector("Hotel 1 Lid", decklayout.HOTELPOS, worklist.SAFETOEND,
True, worklist.DONOTMOVE, worklist.OPEN)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle2", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200Wiggle2Pos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.SAFETOEND, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.SAFETOEND,
False, worklist.DONOTMOVE, worklist.CLOSE, True)
worklist.vector("PTC200Wiggle", decklayout.PTCPOS, worklist.ENDTOSAFE,
False, worklist.DONOTMOVE, worklist.OPEN, True)
worklist.vector("PTC200WigglePos", decklayout.PTCPOS,
worklist.ENDTOSAFE, False, worklist.DONOTMOVE,
worklist.DONOTMOVE)
self.ptcrunning = False
self.moveplate(decklayout.SAMPLEPLATE, "Home")
# Mark all samples on plate as unmixed (due to condensation)
Sample.notMixed(decklayout.SAMPLEPLATE.name)
# Verify plate is in place
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.SAFETOEND, False,
worklist.DONOTMOVE, worklist.CLOSE)
worklist.vector(decklayout.SAMPLEPLATE.vectorName,
decklayout.SAMPLEPLATE, worklist.ENDTOSAFE, False,
worklist.OPEN, worklist.DONOTMOVE)
worklist.romahome()
#worklist.userprompt("Plate should be back on deck. Press return to continue")
# Wash tips again to remove any drips that may have formed while waiting for PTC
worklist.wash(15, 1, 5, True)
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)