Source code for toil.test.sort.sortTest

# Copyright (C) 2015-2021 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import logging
import os
import random
import shutil
import subprocess
import unittest
from contextlib import contextmanager
from uuid import uuid4

from toil import resolveEntryPoint
from toil.batchSystems.mesos.test import MesosTestSupport
from toil.common import Toil
from toil.exceptions import FailedJobsException
from toil.job import Job
from toil.jobStores.abstractJobStore import (JobStoreExistsException,
from toil.lib.bioio import root_logger
from toil.test import (ToilTest,
from toil.test.sort.sort import (copySubRangeOfFile,

logger = logging.getLogger(__name__)

defaultLineLen = int(os.environ.get('TOIL_TEST_SORT_LINE_LEN', 10))
defaultLines = int(os.environ.get('TOIL_TEST_SORT_LINES', 10))
defaultN = int(os.environ.get('TOIL_TEST_SORT_N', defaultLineLen * defaultLines / 5))

[docs] @contextmanager def runMain(options): """ make sure the output file is deleted every time main is run """ main(options) yield if os.path.exists(options.outputFile): os.remove(options.outputFile)
[docs] @slow class SortTest(ToilTest, MesosTestSupport): """ Tests Toil by sorting a file in parallel on various combinations of job stores and batch systems. """
[docs] def setUp(self): super().setUp() self.tempDir = self._createTempDir(purpose='tempDir') self.outputFile = os.path.join(self.tempDir, 'sortedFile.txt') self.inputFile = os.path.join(self.tempDir, "fileToSort.txt")
[docs] def tearDown(self): if os.path.exists(self.tempDir): shutil.rmtree(self.tempDir) ToilTest.tearDown(self)
def _toilSort(self, jobStoreLocator, batchSystem, lines=defaultLines, N=defaultN, testNo=1, lineLen=defaultLineLen, retryCount=2, badWorker=0.5, downCheckpoints=False, caching=True): """ Generate a file consisting of the given number of random lines, each line of the given length. Sort the file with Toil by splitting the file recursively until each part is less than the given number of bytes, sorting each part and merging them back together. Then verify the result. :param jobStoreLocator: The location of the job store. :param batchSystem: the name of the batch system :param lines: the number of random lines to generate :param N: the size in bytes of each split :param testNo: the number of repeats of this test :param lineLen: the length of each random line in the file """ for test in range(testNo): try: # Specify options options = Job.Runner.getDefaultOptions(jobStoreLocator) options.logLevel = logging.getLevelName(root_logger.getEffectiveLevel()) options.retryCount = retryCount options.batchSystem = batchSystem options.clean = "never" options.badWorker = badWorker options.badWorkerFailInterval = 0.05 options.caching = caching # This is required because mesos_endpoint now defaults to the IP of the machine # that is starting the workflow while the mesos *tests* run locally. if batchSystem == 'mesos': options.mesos_endpoint = 'localhost:5050' options.downCheckpoints = downCheckpoints options.N = N options.outputFile = self.outputFile options.fileToSort = self.inputFile options.overwriteOutput = True options.realTimeLogging = True # Make the file to sort makeFileToSort(options.fileToSort, lines=lines, lineLen=lineLen) # First make our own sorted version with open(options.fileToSort) as fileHandle: l = fileHandle.readlines() l.sort() # Check we get an exception if we try to restart a workflow that doesn't exist options.restart = True with self.assertRaises(NoSuchJobStoreException): with runMain(options): # Now check the file is properly sorted.. with open(options.outputFile) as fileHandle: l2 = fileHandle.readlines() self.assertEqual(l, l2) options.restart = False # Now actually run the workflow try: with runMain(options): pass i = 0 except FailedJobsException as e: i = e.numberOfFailedJobs # Check we get an exception if we try to run without restart on an existing store with self.assertRaises(JobStoreExistsException): with runMain(options): pass options.restart = True # This loop tests the restart behavior totalTrys = 1 while i != 0: options.useExistingOptions = random.random() > 0.5 try: with runMain(options): pass i = 0 except FailedJobsException as e: i = e.numberOfFailedJobs if totalTrys > 32: # p(fail after this many restarts) = 0.5**32'Exceeded a reasonable number of restarts') totalTrys += 1 finally: subprocess.check_call([resolveEntryPoint('toil'), 'clean', jobStoreLocator]) # final test to make sure the jobStore was actually deleted self.assertRaises(NoSuchJobStoreException, Toil.resumeJobStore, jobStoreLocator)
[docs] @needs_aws_ec2 def testAwsSingle(self): self._toilSort(jobStoreLocator=self._awsJobStore(), batchSystem='single_machine')
[docs] @needs_aws_ec2 @needs_mesos def testAwsMesos(self): self._startMesos() try: self._toilSort(jobStoreLocator=self._awsJobStore(), batchSystem="mesos") finally: self._stopMesos()
[docs] @needs_mesos def testFileMesos(self): self._startMesos() try: self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem="mesos") finally: self._stopMesos()
[docs] @needs_google_project @needs_google_storage def testGoogleSingle(self): self._toilSort(jobStoreLocator=self._googleJobStore(), batchSystem="single_machine")
[docs] @needs_google_project @needs_google_storage @needs_mesos def testGoogleMesos(self): self._startMesos() try: self._toilSort(jobStoreLocator=self._googleJobStore(), batchSystem="mesos") finally: self._stopMesos()
[docs] def testFileSingle(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='single_machine')
[docs] def testFileSingleNonCaching(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='single_machine', caching=False)
[docs] def testFileSingleCheckpoints(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='single_machine', retryCount=2, downCheckpoints=True)
[docs] def testFileSingle10000(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='single_machine', lines=10000, N=10000)
[docs] @needs_gridengine @unittest.skip('GridEngine does not support shared caching') def testFileGridEngine(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='gridengine')
[docs] @needs_torque @unittest.skip('PBS/Torque does not support shared caching') def testFileTorqueEngine(self): self._toilSort(jobStoreLocator=self._getTestJobStorePath(), batchSystem='torque')
testNo = 5
[docs] def testSort(self): for test in range(self.testNo): tempFile1 = os.path.join(self.tempDir, "fileToSort.txt") makeFileToSort(tempFile1) lines1 = self._loadFile(tempFile1) lines1.sort() sort(tempFile1) with open(tempFile1) as f: lines2 = f.readlines() self.assertEqual(lines1, lines2)
[docs] def testMerge(self): for test in range(self.testNo): tempFile1 = os.path.join(self.tempDir, "fileToSort1.txt") tempFile2 = os.path.join(self.tempDir, "fileToSort2.txt") tempFile3 = os.path.join(self.tempDir, "mergedFile.txt") makeFileToSort(tempFile1) makeFileToSort(tempFile2) sort(tempFile1) sort(tempFile2) with open(tempFile3, 'w') as fileHandle: with open(tempFile1) as tempFileHandle1: with open(tempFile2) as tempFileHandle2: merge(tempFileHandle1, tempFileHandle2, fileHandle) lines1 = self._loadFile(tempFile1) + self._loadFile(tempFile2) lines1.sort() with open(tempFile3) as f: lines2 = f.readlines() self.assertEqual(lines1, lines2)
[docs] def testCopySubRangeOfFile(self): for test in range(self.testNo): tempFile = os.path.join(self.tempDir, "fileToSort1.txt") outputFile = os.path.join(self.tempDir, "outputFileToSort1.txt") makeFileToSort(tempFile, lines=10, lineLen=defaultLineLen) fileSize = os.path.getsize(tempFile) assert fileSize > 0 fileStart = random.choice(range(0, fileSize)) fileEnd = random.choice(range(fileStart, fileSize)) with open(outputFile, 'w') as f: f.write(copySubRangeOfFile(tempFile, fileStart, fileEnd)) with open(outputFile) as f: l = with open(tempFile) as f: l2 =[fileStart:fileEnd] self.assertEqual(l, l2)
[docs] def testGetMidPoint(self): for test in range(self.testNo): makeFileToSort(self.inputFile) with open(self.inputFile) as f: sorted_contents = fileSize = os.path.getsize(self.inputFile) midPoint = getMidPoint(self.inputFile, 0, fileSize) print(f"The mid point is {midPoint} of a file of {fileSize} bytes.") assert midPoint < fileSize assert sorted_contents[midPoint] == '\n' assert midPoint >= 0
def _awsJobStore(self): return f'aws:{self.awsRegion()}:sort-test-{uuid4()}' def _googleJobStore(self): return f'google:{os.getenv("TOIL_GOOGLE_PROJECTID")}:sort-test-{uuid4()}' def _loadFile(self, path): with open(path) as f: return f.readlines()