def testToilStats_SortSimple(self):
"""
Tests the toilStats utility using the scriptTree_sort example.
"""
for test in xrange(self.testNo):
tempDir = getTempDirectory(os.getcwd())
tempFile = getTempFile(rootDir=tempDir)
outputFile = getTempFile(rootDir=tempDir)
toilDir = os.path.join(tempDir, "testToil")
lines = 10000
maxLineLength = 10
N = 1000
makeFileToSort(tempFile, lines, maxLineLength)
# Sort the file
rootPath = os.path.join(toilPackageDirPath(), "test", "sort")
system("{rootPath}/sort.py "
"--toil {toilDir} "
"--logLevel=DEBUG "
"--fileToSort={tempFile} "
"--N {N} --stats "
"--jobTime 0.5 "
"--retryCount 99".format(**locals()))
# Now get the stats
toilStats = self.getScriptPath('toilStats')
system("{toilStats} "
"--toil {toilDir} "
"--outputFile {outputFile}".format(**locals()))
# Cleanup
system("rm -rf %s" % tempDir)
def setUp(self):
super(UtilsTest, self).setUp()
self.tempDir = self._createTempDir()
self.tempFile = getTempFile(rootDir=self.tempDir)
self.outputFile = getTempFile(rootDir=self.tempDir)
self.toilDir = os.path.join(self.tempDir, "jobstore")
self.assertFalse(os.path.exists(self.toilDir))
self.lines = 1000
self.lineLen = 10
self.N = 1000
makeFileToSort(self.tempFile, self.lines, self.lineLen)
# First make our own sorted version
with open(self.tempFile, 'r') as fileHandle:
self.correctSort = fileHandle.readlines()
self.correctSort.sort()
def setUp(self):
super(UtilsTest, self).setUp()
self.tempDir = self._createTempDir()
self.tempFile = getTempFile(rootDir=self.tempDir)
self.outputFile = getTempFile(rootDir=self.tempDir)
self.toilDir = os.path.join(self.tempDir, "jobstore")
self.assertFalse(os.path.exists(self.toilDir))
self.lines = 1000
self.lineLen = 10
self.N = 1000
makeFileToSort(self.tempFile, self.lines, self.lineLen)
# First make our own sorted version
with open(self.tempFile, "r") as fileHandle:
self.correctSort = fileHandle.readlines()
self.correctSort.sort()
def setUp(self):
super(UtilsTest, self).setUp()
self.tempDir = self._createTempDir()
self.tempFile = getTempFile(rootDir=self.tempDir)
self.outputFile = 'someSortedStuff.txt'
self.toilDir = os.path.join(self.tempDir, "jobstore")
self.assertFalse(os.path.exists(self.toilDir))
self.lines = 1000
self.lineLen = 10
self.N = 1000
makeFileToSort(self.tempFile, self.lines, self.lineLen)
# First make our own sorted version
with open(self.tempFile, 'r') as fileHandle:
self.correctSort = fileHandle.readlines()
self.correctSort.sort()
self.sort_workflow_cmd = [
'python', '-m', 'toil.test.sort.sort', 'file:' + self.toilDir,
'--clean=never', '--numLines=1', '--lineLength=1'
]
