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' ]