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:':