/
prpr_microscope.py
executable file
·156 lines (136 loc) · 5.45 KB
/
prpr_microscope.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
#!/usr/bin/env python3
# prpr_human.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 os
from prpr import *
class PRPR:
def __init__(self, ID):
print('_yay, microscope!_')
self.expID = ID
db = DatabaseHandler(ID)
self.transfers = db.transfers
self.logger = []
self.robotConfig = []
self.transactions = []
self.createTransfer()
self.saveLog()
self.saveConfig()
def createTransfer(self):
self.config('import microscope')
self.config('import os')
self.config('')
self.config('d = microscope.director')
self.config('proj_dir = os.path.join(d.root_directory, "Local Storage", "Dropbox/experiment_' + str(self.expID) + '")')
self.config('if not os.path.exists(proj_dir):')
self.config('\tos.makedirs(proj_dir)')
self.config('d.set_working_directory(proj_dir)')
self.config('')
self.config('d.turn_light(1, True)')
self.config('')
allTransfers = self.transfers
print('allTransfers', allTransfers)
for transfer in allTransfers:
trType = transfer['type']
els = transfer['info']
if trType == 'command':
self.parseCommand(els)
else:
self.parseTransfer(els)
def config(self, line):
self.robotConfig.append(line)
def saveConfig(self):
def writeLines(file):
for line in self.robotConfig:
file.write(line.rstrip() + '\n')
fileName = 'esc' + os.sep + 'config' + self.expID + '.py'
with open(fileName, 'a') as myfile:
writeLines(myfile)
def log(self, item):
from datetime import datetime
time = str(datetime.now())
self.logger.append(time + ': ' + item)
def saveLog(self):
logname = 'logs/experiment' + self.expID + '.log'
self.log('Translation log location: ' + logname)
writefile = open(logname, "a")
writefile.writelines( "%s\n" % item for item in self.logger )
print('Translation log location: ' + logname)
def message(self, message):
command = '# ' + message
self.config(command)
def comment(self, comment):
command = '# ' + comment
self.config(command)
def parseCommand(self, transferList):
tr = transferList
for option in tr:
if option['command'] == 'move':
loc = option['location']
self.config('d.reset_position' + loc)
self.config('d.take_snapshot()')
if option['command'] == 'comment':
self.config('# ' + option['message'])
def parseTransfer(self, transferList):
tr = transferList
for option in tr:
print('option!!!+++', option)
snapAmount = option['volume']
method = option['method']
src = option['source']['well']
# if method == 'lighton':
# self.config('d.turn_light(1, True)')
# self.config('')
dstLine = option['destination']['well'].split('*')
if len(dstLine) == 2:
times = dstLine[1]
import re
dstMod = re.split('[(|)]', dstLine[0])[:-1]
if len(dstMod) > 1:
self.config('d.reset_position(' + dstMod[0] + ')')
dest = dstMod[1].replace('+', '')
else:
self.config('d.reset_position(' + src + ')')
dest = dstLine[0].replace('+', '')
print(dest, '!!!')
dst = src
self.config('for i in range(' + times + '):')
self.config('\td.adjust_position' + '(' + dest + ')')
self.config('\tfor s in range(' + snapAmount + '):')
self.config('\t\td.take_snapshot()')
else:
self.config('d.reset_position(' + dstLine[0] + ')')
self.config('for s in range(' + snapAmount + '):')
self.config('\td.take_snapshot()')
def parseLocation(self, location):
print('location is: ', location)
loc = []
print('location__', location)
#splitting the component from everything
compl = location.split('(')
if location not in self.components:
if compl[0] in self.components:
resLoc = self.components[compl[0]].shortLocation + '(' + ''.join(compl[1:])
print('resLoc....', resLoc)
w = Well({'Plate' : self.platform, 'Location' : resLoc})
self.wells.append(w)
loc.append(w)
else:
w = Well({'Plate' : self.platform, 'Location' : location})
self.wells.append(w)
loc.append(w)
else:
w = Well({'Plate' : self.platform, 'Location' : location})
self.wells.append(w)
loc.append(w)
return loc
class defaults:
fileExtensions = {'py' : 'py'}
if __name__ == '__main__':
prpr = PRPR(310)
print('Config:')
for element in prpr.robotConfig:
print(element)