def setGetFloatingSpeciesByIndex(testId):
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
n = rrPython.getNumberOfFloatingSpecies()
for i in range (n):
value = random.random()*10
rrPython.setFloatingSpeciesByIndex (i, value)
if expectApproximately(rrPython.getFloatingSpeciesByIndex (i), value, 1E-6) == False:
errorFlag = True
break;
print passMsg (errorFlag)
def checkFloatingSpeciesInitialConditionIds (testId):
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
line = readLine ()
words = line.split()
expected = rrPython.getFloatingSpeciesInitialConditionIds()
m = rrPython.getNumberOfFloatingSpecies()
for i in range(0,m):
if words[i] != expected[i]:
errorFlag = True
break
print passMsg (errorFlag)
def checkFloatingSpeciesInitialConditionIds(testId):
print string.ljust("Check " + testId, rpadding),
errorFlag = False
line = readLine()
words = line.split()
expected = rrPython.getFloatingSpeciesInitialConditionIds()
m = rrPython.getNumberOfFloatingSpecies()
for i in range(0, m):
if words[i] != expected[i]:
errorFlag = True
break
print passMsg(errorFlag)
def checkGetRatesOfChangeIds(testId):
print string.ljust("Check " + testId, rpadding),
errorFlag = False
line = readLine()
words = line.split()
expected = rrPython.getRatesOfChangeIds()
n = rrPython.getNumberOfFloatingSpecies()
for i in range(0, n):
if words[i] != expected[i]:
errorFlag = True
break
print passMsg(errorFlag)
def checkGetRatesOfChangeIds (testId):
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
line = readLine ()
words = line.split()
expected = rrPython.getRatesOfChangeIds()
n = rrPython.getNumberOfFloatingSpecies()
for i in range(0,n):
if words[i] != expected[i]:
errorFlag = True
break
print passMsg (errorFlag)
def checkLinkMatrix(testId):
# Link matrix
print string.ljust("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
st = rrPython.getLinkMatrix()
for i in range(0, m):
words = readLine().split()
for j in range(0, m):
if expectApproximately(float(words[j]), st[i, j], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
def checkLinkMatrix(testId):
# Link matrix
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
st = rrPython.getLinkMatrix()
for i in range(0,m):
words = readLine ().split()
for j in range(0,m):
if expectApproximately(float (words[j]), st[i,j], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def setGetReset(testId):
print string.ljust("Check " + testId, rpadding),
errorFlag = False
values = zeros(rrPython.getNumberOfFloatingSpecies())
for i in range(len(values)):
values[i] = random.random() * 10
initial = rrPython.getFloatingSpeciesInitialConcentrations()
rrPython.setFloatingSpeciesConcentrations(values)
# Should reset the floats by to the current initial condition
rrPython.reset()
values = rrPython.getFloatingSpeciesConcentrations()
if (values != initial).all():
errorFlag = True
print passMsg(errorFlag)
def setGetReset(testId):
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
values = zeros (rrPython.getNumberOfFloatingSpecies())
for i in range (len (values)):
values[i] = random.random()*10
initial = rrPython.getFloatingSpeciesInitialConcentrations()
rrPython.setFloatingSpeciesConcentrations (values)
# Should reset the floats by to the current initial condition
rrPython.reset()
values = rrPython.getFloatingSpeciesConcentrations()
if(values != initial).all():
errorFlag = True
print passMsg (errorFlag)
def checkScaledElasticityMatrix(testId):
# Jacobian
print string.ljust("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
ee = rrPython.getScaledElasticityMatrix()
for i in range(0, m):
line = readLine()
words = line.split()
for j in range(0, m):
expectedValue = float(words[j])
if expectApproximately(expectedValue, ee[i, j], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
def checkScaledConcentrationControlMatrix(testId):
# Unscaled Concentration Control matrix
print string.ljust("Check " + testId, rpadding),
words = []
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions()
st = rrPython.getScaledConcentrationControlCoefficientMatrix()
for i in range(0, m):
words = readLine().split()
for j in range(0, n):
if expectApproximately(float(words[j]), st[i, j], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
def checkStoichiometryMatrix(testId):
# Stoichiometry matrix
print string.ljust("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions()
st = rrPython.getStoichiometryMatrix()
for i in range(0, m):
line = readLine()
words = line.split()
for j in range(0, n):
if expectApproximately(float(words[j]), st[i, j], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
def checkStoichiometryMatrix(testId):
# Stoichiometry matrix
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions();
st = rrPython.getStoichiometryMatrix()
for i in range(0,m):
line = readLine ()
words = line.split()
for j in range(0,n):
if expectApproximately(float (words[j]), st[i,j], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkScaledElasticityMatrix(testId):
# Jacobian
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
ee = rrPython.getScaledElasticityMatrix()
for i in range(0,m):
line = readLine ()
words = line.split()
for j in range(0,m):
expectedValue = float(words[j])
if expectApproximately (expectedValue, ee[i,j], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkScaledConcentrationControlMatrix(testId):
# Unscaled Concentration Control matrix
print string.ljust ("Check " + testId, rpadding),
words = []
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions();
st = rrPython.getScaledConcentrationControlCoefficientMatrix();
for i in range(0,m):
words = readLine ().split()
for j in range(0,n):
if expectApproximately(float (words[j]), st[i,j], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkIndividualEigenvalues(testId):
# Eigenvalues
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
try:
for i in range(0,m):
line = readLine ()
words = line.split()
eigenvalueName = words[0]
realPart = rrPython.getValue ('eigen(' + eigenvalueName + ')')
realPart = float (realPart)
if expectApproximately (realPart, float(words[1]), 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
except:
print 'Unexpected error in checkIndividualEigenvalues:', sys.exc_info()[0]
def checkSpeciesConcentrations(testId):
words = []
species = []
m = rrPython.getNumberOfFloatingSpecies()
for i in range (0,m):
line = readLine ()
words = line.split()
words.append (rrPython.getValue(words[0]))
species.append (words)
# Steady State Concentrations
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
for i in range (0,m):
expectedValue = float (species[i][1])
if expectApproximately (expectedValue, species[i][2], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkSpeciesConcentrations(testId):
words = []
species = []
m = rrPython.getNumberOfFloatingSpecies()
for i in range(0, m):
line = readLine()
words = line.split()
words.append(rrPython.getValue(words[0]))
species.append(words)
# Steady State Concentrations
print string.ljust("Check " + testId, rpadding),
errorFlag = False
for i in range(0, m):
expectedValue = float(species[i][1])
if expectApproximately(expectedValue, species[i][2], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
def checkEigenvalueMatrix(testId):
# Eigenvalues
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
eigenvalues = rrPython.getEigenvalues()
for i in range(0,m):
line = readLine ()
words = line.split()
realPart = float (words[0])
# Check if there is an imaginary part
if len (words) == 1:
imagPart = 0
else:
imagPart= float (words[1])
if (expectApproximately (realPart, eigenvalues[i,0], 1E-6) == False) or (expectApproximately (imagPart, eigenvalues[i,1], 1E-6)) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkFluxes(testId):
words = []
fluxes = []
# Steady State Fluxes
print string.ljust ("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions();
for i in range (0,n):
line = readLine ()
words = line.split()
words.append (rrPython.getValue(words[0]))
fluxes.append (words)
for i in range (0,n):
expectedValue = float (fluxes[i][1])
if expectApproximately (expectedValue, fluxes[i][2], 1E-6) == False:
errorFlag = True
break
print passMsg (errorFlag)
def checkFluxes(testId):
words = []
fluxes = []
# Steady State Fluxes
print string.ljust("Check " + testId, rpadding),
errorFlag = False
m = rrPython.getNumberOfFloatingSpecies()
n = rrPython.getNumberOfReactions()
for i in range(0, n):
line = readLine()
words = line.split()
words.append(rrPython.getValue(words[0]))
fluxes.append(words)
for i in range(0, n):
expectedValue = float(fluxes[i][1])
if expectApproximately(expectedValue, fluxes[i][2], 1E-6) == False:
errorFlag = True
break
print passMsg(errorFlag)
import rrPython
import os
import csv
os.chdir('C:\\RoadRunner\\bin')
function = 'getNumberOfFloatingSpecies'
try:
num = rrPython.getNumberOfFloatingSpecies()
if str(num) 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 os
import csv
os.chdir('C:\\RoadRunner\\bin')
function = 'getNumberOfFloatingSpecies'
try:
num = rrPython.getNumberOfFloatingSpecies()
if str(num) 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()