/
prparser.py
executable file
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/
prparser.py
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#!/usr/bin/env python3.3
# prparser.py, a part of PR-PR (previously known as PaR-PaR), a biology-friendly language for liquid-handling robots
# Author: Nina Stawski, nstawski@lbl.gov, me@ninastawski.com
# Copyright 2012-2013, Lawrence Berkeley National Laboratory
# http://github.com/JBEI/prpr/blob/master/license.txt
__author__ = 'Nina Stawski'
__version__ = '1.1'
import sys
import os
import argparse
import sqlite3
from prpr import *
from shutil import copyfile
from prpr_commands import *
from itertools import cycle
from copy import deepcopy
# from prpr_tecan import *
# from prpr_mf import *
#todo: switch to postgres
class Experiment:
def __init__(self, maxVolume, tips, db, platform, userMethods='', language = 'en'):
"""
New experiment with parameters:
robotTips - maximum amount of tips the robot has
maxVolume - maximum capacity of a tip
"""
self.name = ''
self.platform = platform
self.language = language
self.components = {}
self.plates = {}
self.volumes = {}
self.recipes = {}
self.tableAdded = False
self.dosStringAdded = False
self.docString = []
self.transactionList = []
self.logger = []
self.wells = []
self.testindex = 0
self.ID = str(db.selectMax('Experiments'))
self.robotTips = tips
self.maxVolume = maxVolume
db.insert('Experiments', [self.ID, self.robotTips, self.maxVolume, '"' + self.platform + '"', '"' + self.language + '"'])
self.log('Experiment ID: ' + str(self.ID))
self.errorLogger = []
self.protocols = {}
self.addMethods(userMethods, db.getMethods())
self.groups = {} #note: group{name:[component1, component2]}
self.mfWellLocations = {}
self.mfWellConnections = {}
# self.tableSize = 31
def addName(self, name):
self.name = name
self.log('Experiment name: ' + str(self.name))
def addDocString(self, line):
self.docString.append(line)
def add(self, target, itemName, itemInfo):
"""
usage: add(target, name, info)
target: component|plate|volume|recipe|protocol|group
"""
self.log('Added a ' + target + ' "' + itemName + '"')
if target == 'component':
platform = __import__('prpr_'+ self.platform)
location = platform.PRPR.parseLocation(self, itemInfo.location) #self.parseLocation
method = self.checkMethod(itemInfo.method)
if method:
itemInfo.method = method
if location:
itemInfo.location = location
self.components[itemName] = itemInfo
elif target == 'plate':
self.plates[itemName] = itemInfo
elif target == 'volume':
self.volumes[itemName] = itemInfo
elif target == 'recipe':
self.recipes[itemName] = itemInfo
elif target == 'protocol':
self.protocols[itemName] = itemInfo
elif target == 'group':
self.groups[itemName] = itemInfo
def addMFWellLocations(self, wellLocationString):
locations = wellLocationString.split(';')[:-1]
for location in locations:
wellInfo = location.split(':')
well = wellInfo[0]
coords = wellInfo[1]#.split(',')
self.mfWellLocations[well] = coords
def addMFWellConnections(self, wellConnectionString):
for welInfo in wellConnectionString:
wellConnections = welInfo.strip().split(':')
well = wellConnections[0]
connections = wellConnections[1].split(',')
for connection in connections:
if well in self.mfWellConnections:
self.mfWellConnections[well].append(connection)
else:
self.mfWellConnections[well] = [connection]
if connection in self.mfWellConnections:
self.mfWellConnections[connection].append(well)
else:
self.mfWellConnections[connection] = [well]
def addMethods(self, userMethods, methods):
if userMethods:
if userMethods[0]:
self.methods = userMethods + methods
else:
self.methods = methods + userMethods[1:]
else:
self.methods = methods
def checkMethod(self, method):
if self.platform == 'tecan' or self.platform == 'human':
if method in self.methods:
return method
else:
if method != '' and method != 'Error' and method != 'None' and method != 'empty':
self.errorLog('Error. No such method on file: "' + str(method) + '"')
return 'Error'
else:
return self.methods[0]
elif self.platform == 'microfluidics':
if isNumber(method):
return method
else:
return '100'
#self.errorLog('Error in method "' + str(method) + '". Microfluidic methods should be numbers.')
def splitAmount(self, volume):
maxVolume = int(self.maxVolume)
if volume.isdigit():
splitAmount = volume.split('.')
if len(splitAmount) > 1: # works for small volumes only
amount = float(volume)
else:
amount = int(volume)
if amount < maxVolume:
return amount, 1
else:
times = amount / maxVolume
left = amount - maxVolume * int(times)
if left > 0:
tipsNeeded = int(times)
newAmount = (maxVolume, tipsNeeded, left)
else:
tipsNeeded = int(times)
newAmount = (maxVolume, tipsNeeded)
return newAmount
else:
self.errorLog('Error, volume "' + volume + '" is not defined. Please correct the error and try again.')
def get(self, target, itemName):
if target == 'component':
item = self.components
elif target == 'plate':
item = self.plates
elif target == 'volume':
item = self.volumes
elif target == 'recipe':
item = self.recipes
else:
item = False
assert item, 'Wrong target name, "' + target + '"'
if itemName in item.keys():
return item[itemName]
else:
self.log('Error. No ' + target + ' "' + itemName + '" defined.')
self.errorLog('Error. No ' + target + ' "' + itemName + '" defined. Please correct the error and try again.')
def prepareLocation(self, component):
location = []
for comp in component:
if len(comp) == 2:
times = int(comp[1][1])
if comp[1][0] == '|':
for well in comp[0].location:
for i in range(0, times):
location.append(well)
if comp[1][0] == '*':
for i in range(0, times):
for well in comp[0].location:
location.append(well)
else:
for well in comp[0].location:
location.append(well)
return location
def createTransfer(self, source, destination, volume, transferMethod, line, wellsOnly = False):
method = ''
methodError = False
if transferMethod == 'DEFAULT':
if self.platform == 'tecan' or self.platform == 'human':
method = self.methods[0]
elif self.platform == 'microfluidics':
method = 100
else:
m = self.checkMethod(transferMethod)
if m:
method = m
else:
if self.platform == 'microscope':
method = transferMethod
else:
methodError = True
self.log('Wrong method "' + transferMethod + '"')
self.errorLog('Error. Wrong method "' + transferMethod + '" in line "' + line + '"')
if method:
if volume in self.volumes:
amount = self.volumes[volume].amount
else:
amount = volume
if self.platform == 'tecan':
volumeInfo = [self.splitAmount(x) for x in amount.split(',')]
else:
volumeInfo = amount
if wellsOnly:
src = source
dst = destination
else:
src = self.prepareLocation(source)
dst = self.prepareLocation(destination)
transferDict = {'src': src, 'dst': dst, 'volume': volumeInfo, 'method': method, 'type': 'transfer'}
return transferDict
else:
if not methodError:
self.errorLog('Error. No method defined in line "' + line + '"')
#else:
# self.log('Error. Wrong component "' + component + '".')
# self.errorLog('Error. Component "' + component + '" is not defined. Please correct the error and try again.')
# return False
### todo: separate by '/', ',' and '*' before calling platform location parse, common for all platforms, then parse location for both source and destination
def parseGivenLocation(self, location, method=''):
def CheckMultiplier(componentInfo):
"""
Checks for additional actions on components
"""
if self.platform == 'microscope':
return [componentInfo]
else:
pipe = componentInfo.split('|')
times = componentInfo.split('*')
if len(pipe) == 2:
pipe[1] = ('|', pipe[1])
return pipe
elif len(times) == 2:
times[1] = ('*', times[1])
return times
else:
return [componentInfo]
def CheckIfPlatePreDefined(locationInfo):
plateAndWells = locationInfo.split(':')
if len(plateAndWells) >1:
if plateAndWells[0] in self.plates:
print('plateAndWell is in selfplates:::::::::::::::::', self.plates)
splitLocations = []
locationPerPlate = location.split('/')
tempLocations = []
for plateLocation in locationPerPlate:
singleLocations = plateLocation.split(',')
for l in singleLocations:
location = CheckMultiplier(l)
if location[0] in self.components:
prevLocations = ','.join(tempLocations)
location[0] = self.components[location[0]]
splitLocations.append(location)
if prevLocations != '':
lc = CheckMultiplier(prevLocations)
if self.platform == 'tecan':
method = self.methods[0]
CheckIfPlatePreDefined(lc[0])
tempComponent = Component({'name': lc[0], 'location': lc[0], 'method': method})
self.add('component', tempComponent.name, tempComponent)
lc[0] = self.components[location[0]]
self.locations.append(lc)
tempLocations = []
else:
print('location is NOT in self.components', l)
tempLocations.append(l)
prevLocations = ','.join(tempLocations)
if prevLocations != '':
location = CheckMultiplier(prevLocations)
if self.platform == 'tecan':
method = self.methods[0]
CheckIfPlatePreDefined(location[0])
tempComponent = Component({'name': location[0], 'location': location[0], 'method': method})
self.add('component', tempComponent.name, tempComponent)
location[0] = self.components[location[0]]
splitLocations.append(location)
return splitLocations
def make(self, splitLine):
originalLine = ' '.join(splitLine)
line = splitLine[1:]
if len(line) >= 3:
if self.platform != 'human':
self.addComment('------ BEGIN MAKE ' + line[0] + ' in ' + line[1] + ' ------')
self.testindex += 1
recipeInfo = line[0].split(':')
if recipeInfo[0] in self.recipes:
subrecipeError = False
recipeName = self.recipes[recipeInfo[0]]
recipe = []
destination = self.parseGivenLocation(line[1])
dstLocation = self.prepareLocation(destination)
if len(recipeInfo) == 2:
subrecipes = recipeInfo[1].split(',')
for sub in subrecipes:
if sub in recipeName.subrecipes:
recipe.append(recipeName.subrecipes[sub]['recipe'])
else:
subrecipeError = True
self.errorLog('Error. No such line "' + str(sub) + '" in recipe "' + recipeInfo[0] + '"')
else:
recipeLines = sorted(recipeName.subrecipes.values(), key=lambda k: k['line'])
for rLine in recipeLines:
recipe.append(rLine['recipe'])
if not subrecipeError:
if len(recipe) == len(dstLocation):
a = zip(*recipe)
for element in a:
transferString = []
for i, z in enumerate(element):
if len(dstLocation) == 1:
dst = dstLocation[0]
else:
dst = dstLocation[i]
source = self.parseGivenLocation(z[0])
src = self.prepareLocation(source)[0]
volume = z[1]
transferMethod = line[2]
transaction = self.createTransfer(src, dst, volume, transferMethod, originalLine, wellsOnly=True)
if transaction:
if self.platform != "microfluidics" and self.platform != "human":
transaction['volume'] = transaction['volume'][0]
transferString.append(transaction)
if transferString:
self.transactionList.append(transferString)
else:
self.log('Error. Please specify the correct amount of wells in line: "' + originalLine + '".')
self.errorLog('Error. Please specify the correct amount of wells in line: "' + originalLine + '".')
if len(line) > 3:
options = line[3].split(',')
for option in options:
a = option.lower()
if a.startswith('mix'):
mixoptions = a.split(':')
if len(mixoptions) == 2:
transaction = {'type': 'command', 'action': 'mix', 'options': mixoptions[1], 'location': self.prepareLocation(destination), 'recipe': line[0]}
self.transactionList.append([transaction])
else:
self.log('Error. Wrong mixing options in line "' + originalLine + '"')
self.errorLog('Error. Wrong mixing options in line "' + originalLine + '". Please correct the error and try again.')
else:
pass
else:
self.errorLog('Error. No such recipe as "' + recipeInfo[0] + '".')
if self.platform != 'human':
self.addComment('------ END MAKE ' + line[0] + ' in ' + line[1] + ' ------')
else:
self.errorLog('Error. Not enough parameters in line "' + originalLine + '". Please correct your script.')
def transfer(self, splitLine, type):
originalLine = ' '.join(splitLine)
transferInfo = splitLine[1:]
method = ''
source = self.parseGivenLocation(transferInfo[0], method)
destination = self.parseGivenLocation(transferInfo[1], method)
if len(transferInfo) >= 4:
if self.platform != 'human':
self.addComment('------ BEGIN ' + type.upper() + ' ' + transferInfo[0] + ' to ' + transferInfo[1] + ' ------')
self.testindex += 1
volume = transferInfo[2]
method = transferInfo[3]
if self.platform == 'microfluidics':
#method = transferInfo[3]
if not isNumber(method):
if method == 'DEFAULT':
method = 100
elif method in self.volumes:
method = self.volumes[method].amount
else:
self.errorLog('Error in method "' + str(method) + '". Not found in defined methods.')
transferLine = self.createTransfer(source, destination, volume, method, originalLine)
if transferLine:
newTr = False
if type == 'transfer':
if len(transferLine['src']) == len(transferLine['dst']):
newTr = enumerate(zip(transferLine['src'], transferLine['dst']))
elif type == 'spread':
newTr = enumerate(zip(cycle(transferLine['src']), transferLine['dst']))
transfer = []
if newTr:
vol = transferLine['volume']
for i, tr in newTr:
trLine = deepcopy(transferLine)
trLine['src'] = tr[0]
trLine['dst'] = tr[1]
if self.platform == "tecan":
if len(vol) == 1:
trLine['volume'] = vol[0]
else:
try:
trLine['volume'] = vol[i] #volume is the problem!!!
except IndexError:
self.errorLog('Error in line "' + originalLine + '". The number of volumes in "' + volume + '" is less than number of source wells.')
transfer.append(trLine)
if transfer:
self.transactionList.append(transfer)
if len(transferInfo) > 4:
options = transferInfo[4].split(',')
for option in options:
a = option.lower()
if a.startswith('mix'):
mixoptions = a.split(':')
if len(mixoptions) == 2:
transaction = {'type': 'command', 'action': 'mix', 'options': mixoptions[1], 'location': self.prepareLocation(destination)}
self.transactionList.append([transaction])
else:
self.log('Error. Wrong mixing options in line "' + originalLine + '"')
if self.platform != 'human':
self.addComment('------ END ' + type.upper() + ' ' + transferInfo[0] + ' to ' + transferInfo[1] + ' ------')
else:
self.errorLog('Error in line "' + originalLine + '"')
else:
self.errorLog('Error. Not enough parameters in line "' + originalLine + '". Please correct your script.')
def move(self, line, commandName): #todo: add support for TRANSFER and COMPONENT commands
if self.platform == 'microscope':
self.testindex += 1
self.addComment('------ BEGIN MOVE' + ' at location ' + line[0] + ' ' + line[2] + ' times with increments ' + line[1] + ' ------')
transaction = []
coords = line[0].split(',')
increment = line[1].split(',')
times = line[2]
action = line[3]
from ast import literal_eval
coord_x = int(coords[0])
coord_y = int(coords[1])
coord_z = int(coords[2])
transaction.append({'type': 'command', 'action': 'move', 'options': action, 'location': (coord_x, coord_y, coord_z)})
for m in range(int(times)):
coord_x = literal_eval(str(coord_x) + increment[0])
coord_y = literal_eval(str(coord_y) + increment[1])
coord_z = literal_eval(str(coord_z) + increment[2])
transaction.append({'type': 'command', 'action': 'move', 'options': action, 'location': (coord_x, coord_y, coord_z)})
self.transactionList.append(transaction)
self.addComment('------ END MOVE' + ' at location ' + line[0] + ' ' + line[2] + ' times with increments ' + line[1] + ' ------')
def message(self, line):
message = {'type': 'command', 'action': 'message', 'options': line}
self.transactionList.append([message])
def addComment(self, line):
comment = {'type': 'command', 'action': 'comment', 'options': line}
self.transactionList.append([comment])
def wait(self, line):
comment = {'type': 'command', 'action': 'wait', 'options': line}
self.addComment('------ WAIT ' + line + ' ms ------')
self.transactionList.append([comment])
def log(self, item):
from datetime import datetime
time = str(datetime.now())
print(item)
self.logger.append(time + ': ' + item)
def errorLog(self, item):
self.errorLogger.append(item)
class Protocol:
def __init__(self, protocolInfo):
self.name = protocolInfo['name']
self.variables = protocolInfo['variables']
self.info = []
def addInfo(self, info):
self.info.append(info)
def addValues(self, values, experiment):
if len(self.variables) == len(values):
readyProtocol = self.info
newProtocol = []
for i in range(0, len(readyProtocol)):
mystring = readyProtocol[i]
newProtocol.append(mystring)
for v in range(0, len(values)):
newProtocol[i] = newProtocol[i].replace(self.variables[v], values[v])
from tempfile import TemporaryFile
protocolFile = TemporaryFile(mode='r+')
protocolFile.writelines(newProtocol)
protocolFile.seek(0)
line = protocolFile.readline()
if experiment.platform != 'human':
experiment.addComment('------ BEGIN PROTOCOL ' + self.name + ', variables: ' + ' '.join(self.variables) + '; values: ' + ' '.join(values) + ' ------')
else:
experiment.addComment('$')
while line != '':
splitline = line.split()
LineToList(splitline, protocolFile, experiment)
line = protocolFile.readline()
if experiment.platform != 'human':
experiment.addComment('------ END PROTOCOL ' + self.name + ' ------')
else:
experiment.addComment('$')
class DBHandler:
def __init__(self):
self.conn = sqlite3.connect('prpr.db')
self.crsr = self.conn.cursor()
def createExperiment(self, experiment):
self.experiment = experiment
expID = experiment.ID
maxTips = experiment.robotTips
maxVolume = experiment.maxVolume
platform = experiment.platform
language = 'en'
self.insert('Experiments', [expID, maxTips, maxVolume, '"' + platform + '"', '"' + language + '"'])
def insert(self, destination, items):
list = []
for item in items:
list.append(str(item))
values = ', '.join(list)
message = 'INSERT INTO ' + destination + ' Values(' + values + ');'
try:
self.crsr.execute(message)
except sqlite3.IntegrityError:
pass
self.conn.commit()
def update(self, destination, items, filter=''):
message = 'UPDATE ' + destination + ' SET ' + items + ' WHERE ExpID = ' + self.experiment.ID
if filter != '':
message += ' AND ' + filter
self.crsr.execute(message)
self.conn.commit()
def selectMax(self, destination, expID=''):
destinations = {
'Experiments': 'ExpID',
'Components': 'ComponentID',
'Wells': 'WellID',
'Transfers': 'TransferID'
}
if destination in destinations:
message = 'SELECT Max(' + destinations[destination] + ') FROM ' + destination
if destination != 'Experiments':
message += ' WHERE ExpID=' + expID
self.crsr.execute(message)
id = self.crsr.fetchone()
if id is None:
return 1
else:
return id[0] + 1
def updateExperiment(self, experiment):
"""
Dumps experiment information into database
"""
self.experiment = experiment
list = [experiment.name,
experiment.docString,
experiment.wells,
experiment.components,
experiment.plates,
experiment.volumes,
experiment.recipes,
experiment.transactionList,
experiment.mfWellLocations,
experiment.mfWellConnections]
expID = str(experiment.ID)
for element in list:
if element:
if element == experiment.name:
self.insert('ExperimentInfo', [experiment.ID, '"' + element + '"', '"' + '\n'.join(experiment.docString) + '"'])
elif element == experiment.components:
for component in experiment.components:
c = experiment.components[component]
componentID = str(id(c))
method = '"' + c.method + '"'
name = '"' + c.name + '"'
for well in c.location:
wellID = str(id(well))
plate = '"' + str(well.plate) + '"'
location = '"' + str(well.location) + '"'
self.insert('Components', [expID, componentID, wellID])
self.insert('ComponentMethods', [expID, componentID, method])
self.insert('ComponentNames', [expID, componentID, name])
elif element == experiment.wells:
for well in experiment.wells:
wellID = str(id(well))
plate = '"' + str(well.plate) + '"'
location = '"' + str(well.location) + '"'
self.insert('Wells', [expID, wellID, plate, location])
elif element == experiment.plates:
for plate in experiment.plates:
p = experiment.plates[plate]
grid = p.location[0]
site = p.location[1]
factoryName = '"' + p.factoryName + '"'
name = '"' + p.name + '"'
plateLocationDescription = '"' + p.plateLocationDescription + '"'
if plate != p.name:
nickname = '"' + plate + '"'
self.insert('PlateNicknames', [expID, name, nickname])
else:
self.insert('PlateLocations', [expID, name, factoryName, grid, site, plateLocationDescription])
elif element == experiment.volumes:
for volume in experiment.volumes:
v = experiment.volumes[volume]
volumeName = '"' + v.name + '"'
volumeValue = '"' + v.amount + '"'
self.insert('Volumes', [expID, volumeName, volumeValue])
elif element == experiment.recipes:
for recipe in experiment.recipes:
r = experiment.recipes[recipe]
recipe = '"' + r.name + '"'
for subrecipe in r.subrecipes:
s = r.subrecipes[subrecipe]
row = str(s['line'])
name = '"' + s['name'] + '"'
self.insert('Subrecipes', [expID, recipe, row, name])
for element in s['recipe']:
column = str(s['recipe'].index(element))
rName = '"' + element[0] + '"'
rVolume = '"' + element[1] + '"'
self.insert('Recipes', [expID, recipe, row, column, rName, rVolume])
elif element == experiment.transactionList:
for i in range(0, len(experiment.transactionList)):
actionID = str(i)
transaction = experiment.transactionList[i]
trType = '"' + transaction[0]['type'] + '"'
self.insert('Actions', [expID, actionID, trType])
for t in range(0, len(transaction)):
tr = transaction[t]
trOrder = str(t)
if tr['type'] == 'transfer':
srcWellID = str(id(tr['src']))
dstWellID = str(id(tr['dst']))
volume = '"' + str(tr['volume']) + '"'
method = '"' + str(tr['method']) + '"'
self.insert('Transfers', [expID, actionID, trOrder, srcWellID, dstWellID, volume, method])
if tr['type'] == 'command':
command = '"' + tr['action'] + '"'
options = '"' + tr['options'] + '"'
self.insert('Commands', [expID, actionID, trOrder, command, options])
if tr['action'] == 'mix':
locationList = tr['location']
m = t
for l in locationList:
self.insert('CommandLocations', [expID, actionID, str(m), str(id(l))])
m += 1
elif tr['action'] == 'move':
location = '"' + str(tr['location']) + '"'
self.insert('CommandLocations', [expID, actionID, str(t), location])
elif element == experiment.mfWellLocations:
for key in element:
name = '"' + key + '"'
coords = '"' + element[key] + '"'
self.insert('mfWellLocations', [expID, name, coords])
elif element == experiment.mfWellConnections:
for key in element:
well = '"' + key + '"'
for item in element[key]:
connection = '"' + item + '"'
self.insert('mfWellConnections', [expID, well, connection])
def close(self):
self.conn.commit()
self.crsr.close()
self.conn.close()
def getMethods(self):
methods = []
message = 'SELECT Method FROM DefaultMethod'
default = DBHandler.db(message)[0][0]
methods.append(default)
message = 'SELECT Method FROM Methods'
list_ = DBHandler.db(message)
for row in list_:
methods.append(row[0])
self.conn.commit()
return methods
def getPlates(self):
plates = []
message = 'SELECT * FROM Plates'
plate_list = DBHandler.db(message)
for row in plate_list:
plates.append(row)
self.conn.commit()
return plates
@staticmethod
def checkIfMethodExists(method):
"""
Checks if the method entered by the user exists in the database.
"""
methods = []
list = DBHandler.db('select * from Methods')
for row in list:
methods.append(row[0])
if method in methods: return method
@staticmethod
def db(request):
conn = sqlite3.connect('prpr.db')
c = conn.cursor()
c.execute(request)
q = c.fetchall()
conn.commit()
c.close()
conn.close()
return q
def ParseLocation(locationLine):
"""
ParseLocation gets a string and splits it a few times.
As a result, it returns a list of dictionaries that contain plate/well locations for a certain reagent.
"""
locationStore = []
for item in locationLine.split('/'):
locationDict = {}
location = item.split(':')
locationDict['Plate'] = location[0]
locationDict['Wells'] = location[1]
locationStore.append(locationDict)
return locationStore
def PlateFileParse(plateFile, experiment, plateNicknames, plateIndexes):
"""
Gets plate names and locations from the table file
"""
plateLine = plateFile.readline()
global stringCounter
stringCounter = 0
while plateLine != '':
parts = plateLine.strip().split(';')
PlateNameParse(parts, plateFile, experiment, plateNicknames, plateIndexes)
plateLine = plateFile.readline()
def PlateNameParse(parts, plateFile, experiment, plateNicknames, plateIndexes):
global stringCounter
if stringCounter < 69:
if parts[0] == '998':
if len(parts) >= 2:
n_plates = parts[1]
if n_plates.isdigit():
if n_plates != '0':
plates = parts[2:int(n_plates) + 2]
counter = len(plates)
tempPlates = []
for plate in plates:
tempPlates.append(plate)
plateLine = plateFile.readline()
plateNames = plateLine.strip().split(';')[1:-1]
for i in range(counter):
if (plateNames[i] != '') and (tempPlates[i] != ''):
plateNicknames[plateNames[i]] = tempPlates[i]
plateIndexes[plateNames[i]] = (stringCounter, i)
if experiment:
experiment.plates[plateNames[i]] = Plate(plateNames[i], tempPlates[i],(stringCounter, i), experiment.platform)
experiment.log('Added a plate "' + tempPlates[i] + '" codename "' + plateNames[i] + '" at location ' + str((stringCounter, i + 1)))
stringCounter += 1
return plateNicknames
def SaveToFile(information, filename):
"""
Writes something to a file. Saves a log.
"""
writefile = open(filename, "w")
writefile.writelines("%s\n" % item for item in information)
print('Experiment log saved as ' + filename)
def ParseRecipe(configFileName, recipeName, experiment):
"""
Goes through the recipe line-by-line and adds it to the list until the end of the recipe found.
"""
unsplitline = configFileName.readline()
line = unsplitline.split()
if line:
if not CheckCommand(line[0]):
if unsplitline[0] != '#':
lineName = line[0][0:-1]
uncutLine = line[1:]
experiment.recipes[recipeName].lineCounter += 1
lineNo = experiment.recipes[recipeName].lineCounter
recipeLine = []
for reagent, volume in zip(uncutLine[::2], uncutLine[1::2]):
recipeLine.append((reagent, volume))
experiment.recipes[recipeName].addSubrecipe(lineName, {'name': lineName, 'line': lineNo, 'recipe': recipeLine})
ParseRecipe(configFileName, recipeName, experiment)
else:
LineToList(line, configFileName, experiment)
def ParseProtocol(configFileName, protocolName, experiment):
line = configFileName.readline()
command = ''
protocol = experiment.protocols[protocolName]
if line.strip():
test = CheckCommand(line.split()[0])
if test:
command = test['name']
if command != 'endprotocol':
protocol.addInfo(line)
ParseProtocol(configFileName, protocolName, experiment)
else:
LineToList(line.split(), configFileName, experiment)
def ParseDocstring(fileName, experiment):
line = fileName.readline().split()
if line:
c = CheckCommand(line[0])
if c:
if c['name'] == '"""':
return
else:
experiment.addDocString(' '.join(line))
ParseDocstring(fileName, experiment)
else:
experiment.addDocString(' '.join(line))
ParseDocstring(fileName, experiment)
else:
experiment.addDocString(' '.join(line))
ParseDocstring(fileName, experiment)
def LineToList(line, configFileName, experiment):
if line:
command = CheckCommand(line[0])
if command:
if command['name'] == 'name':
experiment.addName(' '.join(line[1:]))
elif command['name'] == 'component':
componentInfo = {'name': line[1], 'location': line[2]}
if len(line) > 3:
componentInfo['method'] = experiment.checkMethod(line[3])
experiment.add(command['name'], componentInfo['name'], Component(componentInfo))
elif command['name'] == 'table':
print('table is added', line[1], experiment.platform)
if not experiment.tableAdded:
experiment.tableAdded = True
if __name__ == "__main__":
fileName = 'default_tables' + os.sep + line[1]
else:
fileName = line[1]
plateFile = open(fileName, "r")
experiment.log('Table file location: "' + fileName + '"')
if experiment.platform == 'microfluidics':
import prpr_microfluidics as platform
mfPlateFileParse(plateFile, experiment)
else:
import prpr_tecan as platform
fileExtension = fileName[-3:]
# copyfile(fileName, 'esc' + os.sep + 'config' + experiment.ID + '.esc')
copyfile(fileName, 'esc' + os.sep + 'config' + experiment.ID + '.' + platform.defaults.fileExtensions[fileExtension])
# copyfile(fileName, 'esc' + os.sep + 'config' + experiment.ID + '.gem')
PlateFileParse(plateFile, experiment, plateNicknames={}, plateIndexes={})
elif command['name'] == 'volume':
if len(line) == 3:
#if line[2].isdigit():
volumeInfo = {'name': line[1], 'amount': line[2]}
experiment.add(command['name'], volumeInfo['name'], Volume(volumeInfo))
#else:
# experiment.errorLog('Error. Volume value should be a digit in line "' + ' '.join(line) + '"')
else:
experiment.errorLog('Error. Please correct the volume info in line "' + ' '.join(line) + '"')
elif command['name'] == 'recipe':
recipe = Recipe(line[1])
experiment.add(command['name'], recipe.name, recipe)
ParseRecipe(configFileName, recipe.name, experiment)
elif command['name'] == '"""':
if not experiment.dosStringAdded:
ParseDocstring(configFileName, experiment)
experiment.dosStringAdded = True
else:
experiment.log('Docstring already added for this experiment.')
elif command['name'] == 'plate':
if len(line) >= 3:
plateNickname = line[1]
plateName = line[2]
plateLocationDescription = ''
if len(line) > 3:
plateLocationDescription = ' '.join(line[3:])
plateCoords = []
if plateName.find('*') != -1:
plateCoords = plateName.split('*')
elif plateName.find('x') != -1:
plateCoords = plateName.split('x')
if len(plateCoords) == 2:
row = plateCoords[0]
col = plateCoords[1]
plateInfo = Plate(plateNickname, plateNickname, plateCoords, experiment.platform, plateLocationDescription=plateLocationDescription, dimensions=(int(row), int(col)))
experiment.add('plate', plateNickname, plateInfo)
else:
experiment.plates[plateNickname] = experiment.plates[plateName]
experiment.log('Added a nickname "' + plateNickname + '" to the plate name "' + plateName + '"')
else:
experiment.errorLog('Error. Wrong parameter count in line "' + ' '.join(line) + '"')
elif command['name'] == 'protocol':
protocolInfo = {'name': line[1], 'variables': line[2:]}
protocol = Protocol(protocolInfo)
experiment.add(command['name'], protocol.name, protocol)
ParseProtocol(configFileName, protocol.name, experiment)
elif command['name'] == 'use':
protocolName = line[1]
values = line[2:]
experiment.protocols[protocolName].addValues(values, experiment)
elif command['name'] == 'make':