Example #1
0
 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()
Example #2
0
 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()
Example #3
0
    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)
Example #4
0
    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()
Example #5
0
import worklist
import plate

#aspirate(1,"LC",[1,3,4],1,2,3,"wells")
plate1=plate.Plate("Samples",4,3,12,8)
worklist.aspirate(7,['B3','D3','E3'],"Water",[10,20,30],plate1)
worklist.aspirate(7,['B4','D4','F4'],"Water",[10,20,30],plate1)
worklist.aspirate(1,['B1'],"Water",[10],plate1)
worklist.dispense(2,['B1'],"Water",[10],plate1)
worklist.mix(2,['B1'],"Water",[10],plate1,7)
worklist.vector("ROMAVector",plate1,worklist.SAFETOEND,True,worklist.OPEN,worklist.CLOSE)
worklist.execute("python test",True,"result")
worklist.userprompt("Script done")
worklist.dump()
Example #6
0
    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)
Example #7
0
    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:
            logging.error("Only able to move %s or %s plates, not %s"%(decklayout.SAMPLEPLATE.name,decklayout.DILPLATE.name,plate.name))

        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:
            logging.error("Plate %s is in unknown location: %s"%(plate.name,plate.curloc))

        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:
            logging.error("Attempt to move plate %s to unknown location: %s"%(plate.name,dest))

        #Sample.addallhistory("{->%s}"%dest,onlyplate=plate.name)
        if returnHome:
            worklist.romahome()
Example #8
0
import worklist
import plate

#aspirate(1,"LC",[1,3,4],1,2,3,"wells")
plate1 = plate.Plate("Samples", 4, 3, 12, 8)
worklist.aspirate(7, ['B3', 'D3', 'E3'], "Water", [10, 20, 30], plate1)
worklist.aspirate(7, ['B4', 'D4', 'F4'], "Water", [10, 20, 30], plate1)
worklist.aspirate(1, ['B1'], "Water", [10], plate1)
worklist.dispense(2, ['B1'], "Water", [10], plate1)
worklist.mix(2, ['B1'], "Water", [10], plate1, 7)
worklist.vector("ROMAVector", plate1, worklist.SAFETOEND, True, worklist.OPEN,
                worklist.CLOSE)
worklist.execute("python test", True, "result")
worklist.userprompt("Script done")
worklist.dump()