def runTester(pathToModels, testModel):
global fHandle
global sbmlStr
global JarnacStr
print "Starting Tester on ", testModel
sys.path.append(pathToModels)
#print 'Version: ', rrPython.getVersion()
#print 'Build Date: ', rrPython.getBuildDate()
#print 'Copyright Message: ', rrPython.getCopyright()
fHandle = open(pathToModels + testModel, 'r')
sbmlStr = loadSBMLModelFromTestFile()
JarnacStr = loadJarnacModelFromTestFile()
print "\n", "Info:" + "\n"
rrPython.enableLogging()
info = rrPython.getInfo()
for item in info:
print item
print
# Load any initialization actions
testId = jumpToNextTest()
if testId == '[INITIALIZATION]':
testId = jumpToNextTest()
while testId != '[END_INITIALIZATION]':
if functions.has_key(testId):
func = functions[testId]
func(testId)
else:
print 'No initialization function found for ' + testId
testId = jumpToNextTest()
# Load the model into RoadRunner
if rrPython.loadSBML(sbmlStr) == False:
print 'Failed to load model'
print rrPython.getLastError()
sys.exit(-1)
print rrPython.getuCC('J1', 'k1')
print rrPython.getuCC('J1', 'k_1')
print rrPython.getuCC('J1', 'k2')
print rrPython.getuCC('J1', 'k_2')
print rrPython.getuCC('J1', 'k3')
print rrPython.getuCC('J1', 'k_3')
print rrPython.getuCC('J1', 'k4')
print rrPython.getuCC('J1', 'k_4')
# Now start the tests proper
testId = jumpToNextTest()
if testId == '[START_TESTS]':
testId = jumpToNextTest()
while testId != '[END_TESTS]':
if functions.has_key(testId):
func = functions[testId]
func(testId)
else:
print string.ljust(testId, rpadding), 'NO TEST'
testId = jumpToNextTest()
else:
print 'No Tests found'
scriptTests()
import rrPython
import numpy
import matplotlib.pyplot as plot
model = open('C:\\roadRunner\\models\\feedback.xml', 'r').read()
rrPython.loadSBML(model)
timeStart = 0.0
timeEnd = 10.0
numPoints = 50
results = rrPython.simulateEx(timeStart, timeEnd, numPoints)
print results
S1 = results[:,2]
S2 = results[:,3]
S3 = results[:,4]
x = numpy.arange(timeStart, timeEnd, (timeEnd - timeStart)/numPoints)
plot.plot(x, S1, label="S1")
plot.plot(x, S2, label="S2")
plot.plot(x, S3, label="S3")
plot.legend(bbox_to_anchor=(1.05, 1), loc=5, borderaxespad=0.)
plot.ylabel('Concentration (moles/L)')
plot.xlabel('time (s)')
plot.show()
import rrPython
import os
import csv
os.chdir('C:\\RoadRunner\\bin')
function = 'writeSBML'
rrPython.loadSBML('abc123')
try:
sbml = rrPython.writeSBML()
if str(sbml) is not False:
result = 'True'
else:
result = 'False'
except:
result = 'False'
PythonTestResults = open('C:\\RoadRunner\\PythonTestResults.csv', 'a')
writer = csv.writer(PythonTestResults)
writevar = function + '=' + result
writer.writerow([writevar])
PythonTestResults.close()
def runTester (pathToModels, testModel):
global fHandle
global sbmlStr
global JarnacStr
print "Starting Tester on ", testModel
sys.path.append (pathToModels)
#print 'Version: ', rrPython.getVersion()
#print 'Build Date: ', rrPython.getBuildDate()
#print 'Copyright Message: ', rrPython.getCopyright()
fHandle = open (pathToModels + testModel, 'r')
sbmlStr = loadSBMLModelFromTestFile ()
JarnacStr = loadJarnacModelFromTestFile ()
print "\n", "Info:"+ "\n"
rrPython.enableLogging()
info = rrPython.getInfo()
for item in info:
print item
print
# Load any initialization actions
testId = jumpToNextTest()
if testId == '[INITIALIZATION]':
testId = jumpToNextTest ()
while testId != '[END_INITIALIZATION]':
if functions.has_key(testId):
func = functions[testId]
func(testId)
else:
print 'No initialization function found for ' + testId
testId = jumpToNextTest()
# Load the model into RoadRunner
if rrPython.loadSBML(sbmlStr) == False:
print 'Failed to load model'
print rrPython.getLastError()
sys.exit(-1)
print rrPython.getuCC ('J1', 'k1')
print rrPython.getuCC ('J1', 'k_1')
print rrPython.getuCC ('J1', 'k2')
print rrPython.getuCC ('J1', 'k_2')
print rrPython.getuCC ('J1', 'k3')
print rrPython.getuCC ('J1', 'k_3')
print rrPython.getuCC ('J1', 'k4')
print rrPython.getuCC ('J1', 'k_4')
# Now start the tests proper
testId = jumpToNextTest()
if testId == '[START_TESTS]':
testId = jumpToNextTest()
while testId != '[END_TESTS]':
if functions.has_key(testId):
func = functions[testId]
func(testId)
else:
print string.ljust (testId, rpadding), 'NO TEST'
testId = jumpToNextTest()
else:
print 'No Tests found'
scriptTests()
import rrPython
import os
import csv
os.chdir('C:\\RoadRunner\\bin')
function = 'loadSBML'
file = open('C:\\RoadRunner\\Models\\feedback.xml','r').read()
#rrPython.loadSBML(file)
try:
sbml = rrPython.loadSBML(file)
if str(sbml) is not False:
result = 'True'
else:
result = 'False'
except:
result = 'False'
PythonTestResults = open('C:\\RoadRunner\\PythonTestResults.csv','a')
writer = csv.writer(PythonTestResults)
writevar = function + '=' + result
writer.writerow([writevar])
PythonTestResults.close()
import rrPython
import numpy
import matplotlib.pyplot as plot
model = open('C:\\roadRunner\\models\\feedback.xml', 'r').read()
rrPython.loadSBML(model)
timeStart = 0.0
timeEnd = 10.0
numPoints = 50
results = rrPython.simulateEx(timeStart, timeEnd, numPoints)
print results
S1 = results[:, 2]
S2 = results[:, 3]
S3 = results[:, 4]
x = numpy.arange(timeStart, timeEnd, (timeEnd - timeStart) / numPoints)
plot.plot(x, S1, label="S1")
plot.plot(x, S2, label="S2")
plot.plot(x, S3, label="S3")
plot.legend(bbox_to_anchor=(1.05, 1), loc=5, borderaxespad=0.)
plot.ylabel('Concentration (moles/L)')
plot.xlabel('time (s)')
plot.show()
import rrPython
import os
import csv
os.chdir('C:\\RoadRunner\\bin')
function = 'writeSBML'
rrPython.loadSBML('abc123')
try:
sbml = rrPython.writeSBML()
if str(sbml) is not False:
result = 'True'
else:
result = 'False'
except:
result = 'False'
PythonTestResults = open('C:\\RoadRunner\\PythonTestResults.csv','a')
writer = csv.writer(PythonTestResults)
writevar = function + '=' + result
writer.writerow([writevar])
PythonTestResults.close()
import csv
import re
import rrPython
path = 'C:/SBML_test_cases/'
os.chdir(path)
it = []#for name of xml file
ip = []#for name of settings file
ic = []#for name of results file
for path, dirs, files in os.walk(os.getcwd()):
for xml in [os.path.abspath(os.path.join(path, filename)) for filename in files if fnmatch.fnmatch(filename, '*l2v4.xml')]:
it.append(xml)
ip.append(xml)
ic.append(xml)
f = open(xml,'r').read()
rrPython.loadSBML(f)
b = ""
j=0
while j<len(it[-1])-13:
b+=it[-1][j]
j+=1
ip[-1]=b+"settings.txt"
ic[-1]=b+"results.csv"
concheck = 0 #used later to check if values should be concentrations or amounts
f=open(ip[-1]) #loading model parameters
for line in f: # reads all parameters from settings.txt
text = line.split()
if len(text) > 0: #checks for something in line
if text[0] == 'start:':
startTime = float(text[1])
if text[0] == 'duration:':
path = 'C:/SBML_test_cases/'
os.chdir(path)
it = [] #for name of xml file
ip = [] #for name of settings file
ic = [] #for name of results file
for path, dirs, files in os.walk(os.getcwd()):
for xml in [
os.path.abspath(os.path.join(path, filename)) for filename in files
if fnmatch.fnmatch(filename, '*l2v4.xml')
]:
it.append(xml)
ip.append(xml)
ic.append(xml)
f = open(xml, 'r').read()
rrPython.loadSBML(f)
b = ""
j = 0
while j < len(it[-1]) - 13:
b += it[-1][j]
j += 1
ip[-1] = b + "settings.txt"
ic[-1] = b + "results.csv"
concheck = 0 #used later to check if values should be concentrations or amounts
f = open(ip[-1]) #loading model parameters
for line in f: # reads all parameters from settings.txt
text = line.split()
if len(text) > 0: #checks for something in line
if text[0] == 'start:':
startTime = float(text[1])
if text[0] == 'duration:':
