figth globals: nTips implementing #8

EvoScriPy/EvoMode.py

@@ -169,7 +169,7 @@ class iRobot(Mode):
  and current volume in wells in labware, etc. One basic use of this, is to garante that the robot will be actualize
  once and only once even when multiple modes are used.
  """
- def __init__(self, index, nTips=4 , arms=None):
+ def __init__(self, index, nTips , arms=None):
  Mode.__init__(self )
  # import Robot as Rbt
  self.robot = Rbt.Robot(index=index, arms=arms, nTips=nTips)
@@ -183,5 +183,5 @@ def set_as_current(self):
  self.robot.set_as_current()
 
 
-current = None
+current = None # Oppsss !!! Define
 

EvoScriPy/Instruction_Base.py

@@ -94,7 +94,7 @@ def actualize_robot_state(self):
  pass
 
  def exec(self, mode=None):
- if not mode: mode = EvoScriPy.EvoMode.current # todo revise
+ if mode is None: mode = EvoScriPy.EvoMode.current # todo revise
  if not self.allowed(mode):
  return
  mode.exec(self)
@@ -217,7 +217,7 @@ class Pipetting(Pipette):
  def __init__(self, name, tipMask = curTipMask,
  liquidClass = def_liquidClass,
  volume = def_vol,
- labware = Lab.def_LabW,
+ labware = Lab.def_LabW, # todo ??????
  spacing = 1,
  wellSelection= None,
  LoopOptions = def_LoopOp,
@@ -237,7 +237,7 @@ def __init__(self, name, tipMask = curTipMask,
 
  def validateArg(self):
  Pipette.validateArg(self)
- nTips = Rbt.Robot.current.curArm().nTips
+ nTips = Rbt.Robot.current.curArm().nTips # todo FIX arm is arg
  self.arg[1:1] = [string1(self.liquidClass)] + expr(nTips, self.volume).split() + [int(0)] * (
  12 - nTips) # arg 2, 3 - 14
  return True

EvoScriPy/Robot.py

@@ -18,8 +18,8 @@
  tipMask += [1 << tip]
  tipsMask += [2 ** tip - 1]
 
-def_nTips = 4
-nTips = def_nTips
+# def_nTips = 4
+# nTips = def_nTips
 
 
 class Robot:
@@ -29,7 +29,7 @@ class Robot:
  Most of the changes in state are made by the implementation of the low level instructions, while the protocols can
  "observe" the state to make all kind of optimizations and organizations previous to the actual instruction call
  """
- current=None
+ current=None # use immediately, for a short time.
 
  class Arm:
  DiTi = 0
@@ -218,7 +218,7 @@ def __init__(self, index = None,
  tipsType = Arm.DiTi,
  templateFile= None): # index=Pipette.LiHa1
  """
-
+ A Robot may have 1 or more Arms, indexes by key index in a dictionary of Arms.
  :param arms:
  :param nTips:
  :param workingTips:
@@ -228,7 +228,7 @@ def __init__(self, index = None,
  Robot.current = self
  self.arms = arms if isinstance(arms, dict ) else \
  {arms.index: arms} if isinstance(arms, Robot.Arm) else \
- { index: Robot.Arm(nTips or def_nTips, index, workingTips, tipsType)}
+ { index: Robot.Arm(nTips, index, workingTips, tipsType)}
  self.set_worktable(templateFile)
  self.def_arm = index # or Pipette.LiHa1
  self.droptips = True
@@ -270,7 +270,7 @@ def where_are_preserved_tips(self, selected_reactive, TIP_MASK, type)->list: #
  :param type:
  :return: Return a list of racks with the tips-wells already selected.
  """
- TIP_MASK = TIP_MASK if TIP_MASK != -1 else tipsMask[nTips]
+ TIP_MASK = TIP_MASK if TIP_MASK != -1 else tipsMask[self.curArm().nTips]
  type = type if type else Lab.def_DiTi
  n = Lab.count_tips(TIP_MASK)
  assert n == len(selected_reactive)
@@ -293,7 +293,7 @@ def where_preserve_tips(self, TIP_MASK)->list: # [Lab.DITIrack]
  :return:
  """ # todo this in Labware??
 
- TIP_MASK = TIP_MASK if TIP_MASK != -1 else tipsMask[nTips]
+ TIP_MASK = TIP_MASK if TIP_MASK != -1 else tipsMask[self.curArm().nTips]
  types = []
  t_masks = []
  racks = []

EvoScriPy/protocol_steps.py

@@ -18,7 +18,7 @@ def not_implemented(NumOfSamples):
  print('This protocols have yet to be implemented.')
 
 
-output_filename = '../current/AWL'
+# output_filename = '../current/AWL'
 
 
 class Protocol:
@@ -36,11 +36,11 @@ class Parameter:
 
  def __init__(self, GUI = None,
  worktable_template_filename = None,
- output_filename = output_filename,
+ output_filename = None,
  firstTip = None):
 
  self.worktable_template_filename = worktable_template_filename or ""
- self.output_filename = output_filename
+ self.output_filename = output_filename or '../current/AWL'
  self.GUI = GUI
  self.firstTip = firstTip or 'A01'
 
@@ -56,7 +56,7 @@ def __init__(self, # worktable_template_fn ,
  self.parameters = parameters or Protocol.Parameter()
  self.initialized = False
  self.Reactives = []
- self. nTips = nTips
+ self.nTips = nTips
  self.EvoMode = None
 
  self.set_EvoMode()
@@ -77,7 +77,9 @@ def init_EvoMode(self):
  self.comments_
  ])
  EvoMode.current = self.EvoMode
- self.worktable = self.iRobot.robot.worktable
+ self.worktable = self.iRobot.robot.worktable # shortcut !!
+ self.robot = self.iRobot.robot
+ assert (self.iRobot.robot.curArm().nTips == self.nTips )
 
  def set_EvoMode(self):
  if not self.EvoMode:
@@ -181,9 +183,9 @@ def moveTips(zMove, zTarget, offset, speed, TIP_MASK=-1):
  pass # Itr.moveLiha
 
 def getTips(TIP_MASK=-1, type=None, selected_samples=None):
- robot = Rbt.Robot.current
- mask = TIP_MASK = TIP_MASK if TIP_MASK != -1 else Rbt.tipsMask[Rbt.nTips]
+ robot = Rbt.Robot.current # todo revice !!!
  assert isinstance(robot, Rbt.Robot)
+ mask = TIP_MASK = TIP_MASK if TIP_MASK != -1 else Rbt.tipsMask[robot.curArm().nTips]
  #if not Rbt.Robot.reusetips: # and Rbt.Robot.droptips
 
  if robot.usePreservedtips:

protocols/KingFisher_RNAextNucleoMag_EtOH80p/KingFisher_RNAextNucleoMag_EtOH80p.py

@@ -71,7 +71,7 @@ def Run(self):
  SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
 
  all_samples = range(NumOfSamples)
- maxTips = min (Rbt.nTips, NumOfSamples)
+ maxTips = min (self.nTips, NumOfSamples)
  maxMask = Rbt.tipsMask[maxTips]
 
 

protocols/PreKingFisher_RNAextNucleoMag/PreKingFisher_RNAextNucleoMag.py

@@ -76,7 +76,7 @@ def Run(self):
 
 
  all_samples = range(NumOfSamples)
- maxTips = min (Rbt.nTips, NumOfSamples)
+ maxTips = min (self.nTips, NumOfSamples)
  maxMask = Rbt.tipsMask[maxTips]
 
 

protocols/PreKingFisher_RNAextNucleoMag_EtOH80p/PreKingFisher_RNAextNucleoMag_EtOH80p.py

@@ -71,7 +71,7 @@ def Run(self):
  SampleLiqClass = "Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
 
  all_samples = range(NumOfSamples)
- maxTips = min (Rbt.nTips, NumOfSamples)
+ maxTips = min (self.nTips, NumOfSamples)
  maxMask = Rbt.tipsMask[maxTips]
 
 

protocols/Prefill_plates_VEW1_ElutionBuffer_VEW2/Prefill_plates_VEW1_ElutionBuffer_VEW2.py

@@ -17,7 +17,7 @@ class Prefill_plates_VEW1_ElutionBuffer_VEW2(Evo100_FLI):
  """
  Prefill plates with VEW1, Elution buffer and VEW2 for the
  Implementation of the protocol for RNA extraction using the NucleoMag® VET kit from MACHEREY-NAGEL
- with watching in the Fischer Robot.
+ with washes in the Fischer Robot.
  """
 
  name = "Prefill plates with VEW1, Elution buffer and VEW2 for KingFisher"
@@ -73,7 +73,7 @@ def Run(self):
 
 
  all_samples = range(NumOfSamples)
- maxTips = min (Rbt.nTips, NumOfSamples)
+ maxTips = min (self.nTips, NumOfSamples)
  maxMask = Rbt.tipsMask[maxTips]
 
 

protocols/RNAextractionMN_Mag/RNAextractionMN_Mag_Vet.py

@@ -91,9 +91,9 @@ def Run(self):
  SampleLiqClass ="Serum Asp" # = TissueHomLiqClass # SerumLiqClass="Serum Asp preMix3"
 
  all_samples = range(NumOfSamples)
- maxTips = min(Rbt.nTips, NumOfSamples)
+ maxTips = min(self.nTips, NumOfSamples)
  maxMask = Rbt.tipsMask[maxTips]
- par = TeMag.parallelOrder(Rbt.nTips, all_samples)
+ par = TeMag.parallelOrder(self.nTips, all_samples)
 
  LysisBuffer = Rtv.Reactive("VL - Lysis Buffer " ,
  LysBuf, volpersample=LysisBufferVolume ,defLiqClass=B_liquidClass)
@@ -178,7 +178,7 @@ def Run(self):
  with group("Wash in TeMag with " + EtOH80p.name), tips():
  spread( reactive=EtOH80p,to_labware_region= TeMag.selectOnly(all_samples))
 
- with parallel_execution_of(mix_mag_sub, repeat=NumOfSamples//Rbt.nTips +1):
+ with parallel_execution_of(mix_mag_sub, repeat=NumOfSamples//self.nTips +1):
  mix( TeMag.selectOnly(all_samples), EtOH80p.defLiqClass)
  with incubation(minutes=0.5):
  Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Aspirate, z_pos=24).exec()
@@ -195,7 +195,7 @@ def Run(self):
  Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Incubation).exec()
 
  Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
- with parallel_execution_of(mix_mag_eluat, repeat=NumOfSamples//Rbt.nTips+1):
+ with parallel_execution_of(mix_mag_eluat, repeat=NumOfSamples//self.nTips+1):
  mix(TeMag.selectOnly(all_samples), ElutionBuffer.defLiqClass)
 
  with tips(usePreserved=preserveingTips(), preserve=False, drop=True):
@@ -228,7 +228,7 @@ def wash_in_TeMag( self, reactive, wells=None, using_liquid_class=None, vol=None
  Te_MagS_MoveToPosition(Te_MagS_MoveToPosition.Dispense).exec()
  spread(reactive=reactive, to_labware_region=self.TeMag.selectOnly(wells))
 
- with parallel_execution_of(mix_mag_sub, repeat=self.NumOfSamples//Rbt.nTips +1):
+ with parallel_execution_of(mix_mag_sub, repeat=self.NumOfSamples//self.nTips +1):
  mix(self.TeMag.selectOnly(wells), using_liquid_class, vol)
 
  with incubation(minutes=0.5, timer=2):