# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# 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,
NoSuchJobStoreException)
from toil.lib.bioio import root_logger
from toil.test import (ToilTest,
needs_aws_ec2,
needs_google_project,
needs_google_storage,
needs_gridengine,
needs_mesos,
needs_torque,
slow)
from toil.test.sort.sort import (copySubRangeOfFile,
getMidPoint,
main,
makeFileToSort,
merge,
sort)
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
self.fail('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 = f.read()
with open(tempFile) as f:
l2 = f.read()[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 = f.read()
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()
