def reatInput_dne_test(self):
'''
main.readInput should raise exceptions if listed files don't exist
'''
try:
main.readInput('dne.json')
except AssertionError:
assert True
return
assert False, "readInput failed to raise an exception when a listed data file was not found."
def readInput_list_test(self):
'''
main.readInput should assert it gets a list back
'''
try:
main.readInput('notalist.json')
except AssertionError:
assert True
return
assert False, "readInput failed to raise an exception when given json that wasn't a list"
def reatInput_dne_test(self):
'''
main.readInput should raise exceptions if listed files don't exist
'''
try:
main.readInput('dne.json')
except AssertionError:
assert True
return
assert False, "readInput failed to raise an exception when a listed data file was not found."
def readInput_list_test(self):
'''
main.readInput should assert it gets a list back
'''
try:
main.readInput('notalist.json')
except AssertionError:
assert True
return
assert False, "readInput failed to raise an exception when given json that wasn't a list"
def setUp(self):
filenames = main.readInput('datafiles.json')
profiles = main.extractProfiles(filenames)
# identify and import tests
testNames = main.importQC('qctests')
testNames.sort()
for testName in testNames:
exec('from qctests import ' + testName)
# Set up any keyword arguments needed by tests.
kwargs = {'profiles': profiles}
testResults = []
testVerbose = []
trueResults = []
trueVerbose = []
firstProfile = True
delete = []
currentFile = ''
self.profiles = []
for iprofile, pinfo in enumerate(profiles):
# Load the profile data.
if pinfo.file_name != currentFile:
if currentFile != '': f.close()
currentFile = pinfo.file_name
f = open(currentFile)
if f.tell() != pinfo.file_position: f.seek(pinfo.file_position)
self.profiles.append(wod.WodProfile(f))
def setUp(self):
filenames = main.readInput('datafiles.json')
profiles = main.extractProfiles(filenames)
# identify and import tests
testNames = main.importQC('qctests')
testNames.sort()
for testName in testNames:
exec('from qctests import ' + testName)
# Set up any keyword arguments needed by tests.
kwargs = {'profiles' : profiles}
testResults = []
testVerbose = []
trueResults = []
trueVerbose = []
firstProfile = True
delete = []
currentFile = ''
self.profiles = []
for iprofile, pinfo in enumerate(profiles):
# Load the profile data.
if pinfo.file_name != currentFile:
if currentFile != '': f.close()
currentFile = pinfo.file_name
f = open(currentFile)
if f.tell() != pinfo.file_position: f.seek(pinfo.file_position)
self.profiles.append(wod.WodProfile(f))
# main
########################################
if len(sys.argv) > 2:
# Identify and import tests
testNames = main.importQC('qctests')
testNames.sort()
print('{} quality control checks have been found'.format(len(testNames)))
testNames = main.checkQCTestRequirements(testNames)
print('{} quality control checks are able to be run:'.format(
len(testNames)))
for testName in testNames:
print(' {}'.format(testName))
# Identify data files and create a profile list.
filenames = main.readInput('datafiles.json')
profiles = main.extractProfiles(filenames)
data.ds.profiles = profiles
print('\n{} file(s) will be read containing {} profiles'.format(
len(filenames), len(profiles)))
# Parallel processing.
print('\nPlease wait while QC is performed\n')
processFile.parallel = main.parallel_function(processFile, sys.argv[2])
parallel_result = processFile.parallel(filenames)
# Recombine results
truth, results, profileIDs = main.combineArrays(parallel_result)
# Print summary statistics and write output file.
main.printSummary(truth, results, testNames)
########################################
# main
########################################
if len(sys.argv)>2:
# Identify and import tests
testNames = main.importQC('qctests')
testNames.sort()
print('{} quality control checks have been found'.format(len(testNames)))
testNames = main.checkQCTestRequirements(testNames)
print('{} quality control checks are able to be run:'.format(len(testNames)))
for testName in testNames:
print(' {}'.format(testName))
# Identify data files and create a profile list.
filenames = main.readInput('datafiles.json')
profiles = main.extractProfiles(filenames)
data.ds.profiles = profiles
print('\n{} file(s) will be read containing {} profiles'.format(len(filenames), len(profiles)))
# Parallel processing.
print('\nPlease wait while QC is performed\n')
processFile.parallel = main.parallel_function(processFile, sys.argv[2])
parallel_result = processFile.parallel(filenames)
# Recombine results
truth, results, profileIDs = main.combineArrays(parallel_result)
# Print summary statistics and write output file.
main.printSummary(truth, results, testNames)
main.generateCSV(truth, results, testNames, profileIDs, sys.argv[1])
