Module ImportFrom alias ImportFrom alias alias ImportFrom alias ImportFrom alias ImportFrom alias Import alias Import alias Import alias ImportFrom alias Import alias Import alias Import alias Import alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias ImportFrom alias alias alias ImportFrom alias ImportFrom alias alias alias alias alias Assign NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Num Assign NameStore NameLoad Assign NameStore Call NameLoad keyword Num keyword Num keyword Num keyword NameLoad ClassDef bases body Expr Str ClassDef bases NameLoad body Expr Str Assign NameStore NameLoad FunctionDef arguments args NameParam defaults body Expr Str Raise NameLoad decorator_list NameLoad FunctionDef arguments args NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr Expr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad Call NameLoad AttributeLoad NameLoad attr NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr CompareGtE Call AttributeLoad NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Set NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Num Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Set NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr Dict Call AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad If Call AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr CompareGt NameLoad Num orelse Expr Call AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad AttributeLoad NameLoad attr attr Num Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad Num decorator_list FunctionDef arguments args NameParam defaults body FunctionDef arguments args defaults body Import alias alias Expr Call AttributeLoad NameLoad attr IfExp CompareEq Call AttributeLoad NameLoad attr Str Str Num Num decorator_list Assign NameStore Call NameLoad Call AttributeLoad Str attr SubscriptLoad Call AttributeLoad Call NameLoad NameLoad attr Str Slice Num With Call NameLoad NameLoad NameStore body Assign NameStore BinOpAdd BinOpAdd AttributeLoad NameLoad attr Str NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad AttributeLoad NameLoad attr attr Str Str Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad NameLoad Assign TupleStore NameStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body If Call NameLoad AttributeLoad NameLoad attr NameLoad body Assign NameStore AttributeLoad AttributeLoad NameLoad attr attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num keyword Num keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num keyword Num keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num keyword Num keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num keyword Num keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword NameLoad keyword Num keyword Num Expr Call AttributeLoad NameLoad attr NameLoad NameLoad keyword Num keyword NameLoad keyword Num Expr Call NameLoad keyword Num keyword Num keyword Num decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr CompareGt Call AttributeLoad AttributeLoad NameLoad attr attr Num decorator_list FunctionDef arguments args NameParam defaults body Pass decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListLoad While UnaryOpNot CompareEq Call NameLoad NameLoad NameLoad body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Assign NameStore ListLoad While UnaryOpNot CompareEq Call NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Num Assign NameStore Call AttributeLoad Call AttributeLoad AttributeLoad NameLoad attr attr attr Return NameLoad decorator_list decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr NameLoad body Expr Str FunctionDef arguments args NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias Expr Call AttributeLoad NameLoad attr NameLoad Return Call NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad keyword Num keyword Num keyword Str decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr decorator_list decorator_list NameLoad ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return Call NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad keyword Num keyword Num decorator_list decorator_list ClassDef bases NameLoad body Expr Str FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr Expr Call AttributeLoad NameLoad attr keyword AttributeLoad NameLoad attr decorator_list NameLoad FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr TryFinally body TryExcept body Assert CompareEq Call AttributeLoad NameLoad attr NameLoad NameLoad Call NameLoad NameLoad handlers ExceptHandler body Expr Call AttributeLoad NameLoad attr NameLoad Raise orelse Return NameLoad finalbody Expr Call AttributeLoad NameLoad attr NameLoad decorator_list Assign AttributeStore NameLoad attr Call NameLoad Str FunctionDef arguments args defaults body Import alias alias alias alias FunctionDef arguments args NameParam defaults body Expr Str Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Num AttributeLoad NameLoad attr TryFinally body Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr TryFinally body Assign NameStore Call AttributeLoad NameLoad attr NameLoad Num Assign TupleStore NameStore NameStore Call NameLoad NameLoad Call AttributeLoad NameLoad attr Str AugAssignAdd NameStore NameLoad If CompareGt NameLoad NameLoad body Assign NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Num Num Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad Str attr Call NameLoad NameLoad TupleLoad NameLoad NameLoad finalbody Expr Call AttributeLoad NameLoad attr NameLoad AttributeLoad NameLoad attr finalbody Expr Call AttributeLoad NameLoad attr NameLoad decorator_list If CompareLt Call NameLoad AttributeLoad NameLoad attr Num body Expr Call NameLoad Num TryFinally body Expr Call AttributeLoad NameLoad attr Num finalbody Expr Call NameLoad Num orelse Expr Call NameLoad Call NameLoad SubscriptLoad AttributeLoad NameLoad attr Index Num decorator_list Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad Call AttributeLoad Str attr SubscriptLoad Call AttributeLoad Call NameLoad NameLoad attr Str Slice Num decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Return Call AttributeLoad Str attr ListLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore NameLoad Assign NameStore Call NameLoad Num Num Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad AttributeLoad NameLoad attr For NameStore Set Call NameLoad NameLoad BinOpMult NameLoad Num Call NameLoad Num Call NameLoad NameLoad Num Call NameLoad NameLoad body For NameStore Set Call NameLoad NameLoad Call NameLoad BinOpMult NameLoad Num Call NameLoad Num Call NameLoad NameLoad Num Call NameLoad NameLoad body For NameStore TupleLoad Call NameLoad Num Num Call NameLoad Num Call NameLoad Num body Assign NameStore Call NameLoad BinOpMult BinOpDiv NameLoad NameLoad NameLoad If BoolOpAnd CompareGtE NameLoad Num CompareLtELt NameLoad NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr NameLoad Call NameLoad NameLoad Assign NameStore Call NameLoad keyword Call NameLoad keyword Call NameLoad NameLoad keyword BinOpMult NameLoad Num keyword BinOpMult NameLoad Num TryFinally body Assign NameStore Call NameLoad For NameStore Call NameLoad Num Call NameLoad NameLoad body Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr keyword Call AttributeLoad NameLoad attr keyword Call NameLoad NameLoad keyword Num keyword Num keyword NameLoad Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad NameLoad While NameLoad body Assign NameStore Call AttributeLoad NameLoad attr keyword Num Expr Call AttributeLoad NameLoad attr NameLoad Assign TupleStore NameStore NameStore NameStore NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr NameLoad finalbody Expr Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Num Expr Call AttributeLoad NameLoad attr Call AttributeLoad Str attr Call NameLoad Assign NameStore Call NameLoad BinOpDiv NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body With Call NameLoad AttributeLoad NameLoad attr Str NameStore body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str NameLoad Assign TupleStore NameStore NameStore Call NameLoad NameLoad Call AttributeLoad NameLoad attr Str Return TupleLoad NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body With Call NameLoad AttributeLoad NameLoad attr Str NameStore body Expr Call AttributeLoad NameLoad attr Str decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr Num Expr Call AttributeLoad NameLoad attr CompareLtE AttributeLoad NameLoad attr AttributeLoad NameLoad attr Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr NameLoad Call AttributeLoad NameLoad attr NameLoad With Call NameLoad AttributeLoad NameLoad attr Str NameStore body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Str NameLoad Expr Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr TupleLoad Num Num decorator_list Call NameLoad CompareLt AttributeLoad NameLoad attr Num Str decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad NameLoad attr NameLoad keyword NameLoad decorator_list ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr Assign AttributeStore NameLoad attr NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad NameLoad attr BinOpAdd AttributeLoad NameLoad attr Str keyword NameLoad decorator_list FunctionDef arguments args NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Call AttributeLoad NameLoad attr BinOpAdd AttributeLoad NameLoad attr Str keyword NameLoad decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr NameLoad body Expr Str FunctionDef arguments args NameParam defaults body Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad Call NameLoad NameLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad Num Expr Call AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad Return Call NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad keyword NameLoad keyword Num decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr Expr Call AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str keyword BinOpLShift Num Num keyword Num keyword Num keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str keyword BinOpLShift Num Num keyword Num keyword Num keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Num Expr Call AttributeLoad NameLoad attr SubscriptLoad SubscriptLoad NameLoad Index Num Index Str SubscriptLoad SubscriptLoad NameLoad Index Num Index Str Expr Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad NameLoad Assign NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Str keyword BinOpLShift Num Num keyword Num keyword Num keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Num decorator_list FunctionDef arguments args NameParam NameParam defaults body Import alias Assign NameStore Call NameLoad Assign NameStore Call AttributeLoad NameLoad attr Str Assign NameStore Call AttributeLoad NameLoad attr Assign SubscriptStore NameLoad Index Str Call NameLoad SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad SubscriptLoad NameLoad Index Num Assign NameStore Call AttributeLoad NameLoad attr SubscriptLoad NameLoad Index Num Assign NameStore Call NameLoad Call AttributeLoad NameLoad attr Num Assign NameStore Call AttributeLoad NameLoad attr Num Assign NameStore Dict Str Str Str Str Str Num Num Num Num Num Assign SubscriptStore NameLoad Index Str BinOpMult NameLoad SubscriptLoad NameLoad Index NameLoad Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr ListLoad Str Str Expr Call AttributeLoad NameLoad attr NameLoad Num Return ListComp Call AttributeLoad NameLoad attr NameLoad comprehension NameStore SubscriptLoad NameLoad Slice Num NameLoad decorator_list decorator_list NameLoad ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad Call NameLoad NameLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias Return Call NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad keyword Num keyword Num decorator_list decorator_list NameLoad ClassDef bases AttributeLoad NameLoad attr body Expr Str FunctionDef arguments args NameParam defaults body Assign NameStore Call AttributeLoad Call NameLoad NameLoad NameLoad attr Assign AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Str Return NameLoad decorator_list FunctionDef arguments args NameParam defaults body ImportFrom alias Return Call NameLoad keyword AttributeLoad NameLoad attr keyword NameLoad keyword Num keyword Num decorator_list FunctionDef arguments args NameParam defaults body Expr Call AttributeLoad Call NameLoad NameLoad NameLoad attr ImportFrom alias For NameStore Call NameLoad Str body Expr Call AttributeLoad NameLoad attr NameLoad decorator_list decorator_list NameLoad FunctionDef arguments args NameParam defaults body Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr keyword Str TryFinally body TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad handlers ExceptHandler body Expr Call AttributeLoad NameLoad attr NameLoad Raise orelse Expr Call AttributeLoad NameLoad attr NameLoad Expr Yield NameLoad finalbody Expr Call AttributeLoad NameLoad attr NameLoad decorator_list NameLoad
N/A __future__ absolute_import abc ABCMeta abstractmethod contextlib contextmanager fractions Fraction inspect getsource N/A logging N/A os N/A tempfile textwrap dedent N/A time N/A multiprocessing N/A sys N/A subprocess unittest skipIf toil.common Config toil.batchSystems.mesos.test MesosTestSupport toil.batchSystems.parasolTestSupport ParasolTestSupport toil.batchSystems.parasol ParasolBatchSystem toil.batchSystems.singleMachine SingleMachineBatchSystem toil.batchSystems.abstractBatchSystem InsufficientSystemResources AbstractBatchSystem BatchSystemSupport toil.job Job toil.test ToilTest needs_mesos needs_parasol needs_gridengine needs_slurm N/A log N/A N/A logging getLogger __name__ N/A numCores 2 N/A preemptable True N/A defaultRequirements N/A dict memory 100000000.0 cores 1 disk 1000 preemptable preemptable hidden N/A N/A N/A 
    Hide abstract base class from unittest's test case loader

    http://stackoverflow.com/questions/1323455/python-unit-test-with-base-and-sub-class#answer-25695512
     AbstractBatchSystemTest N/A ToilTest N/A N/A 
        A base test case with generic tests that every batch system should pass
         N/A __metaclass__ ABCMeta createBatchSystem N/A N/A self N/A N/A N/A 
            :rtype: AbstractBatchSystem
             N/A NotImplementedError N/A abstractmethod supportsWallTime N/A N/A self N/A N/A N/A False N/A _createDummyConfig N/A N/A self N/A N/A N/A N/A Config N/A setUpClass N/A N/A cls N/A N/A N/A N/A N/A N/A super N/A hidden AbstractBatchSystemTest cls setUpClass N/A N/A N/A logging basicConfig level N/A logging DEBUG N/A classmethod setUp N/A N/A self N/A N/A N/A N/A N/A N/A super N/A hidden AbstractBatchSystemTest self setUp N/A N/A self config N/A N/A self _createDummyConfig N/A N/A self batchSystem N/A N/A self createBatchSystem N/A N/A self tempDir N/A N/A self _createTempDir testFiles N/A tearDown N/A N/A self N/A N/A N/A N/A N/A N/A self batchSystem shutdown N/A N/A N/A N/A super N/A hidden AbstractBatchSystemTest self tearDown N/A testAvailableCores N/A N/A self N/A N/A N/A N/A N/A self assertTrue N/A N/A N/A multiprocessing cpu_count numCores N/A testRunJobs N/A N/A self N/A N/A N/A testPath N/A N/A N/A os path join N/A self tempDir test.txt N/A job1 N/A N/A N/A self batchSystem issueBatchJob sleep 1000 defaultRequirements N/A job2 N/A N/A N/A self batchSystem issueBatchJob sleep 1000 defaultRequirements N/A issuedIDs N/A N/A self _waitForJobsToIssue 2 N/A N/A N/A self assertEqual N/A set issuedIDs N/A job1 job2 N/A runningJobIDs N/A N/A self _waitForJobsToStart 2 N/A N/A N/A self assertEqual N/A set runningJobIDs N/A job1 job2 N/A N/A N/A N/A self batchSystem killBatchJobs N/A job1 job2 N/A N/A N/A self assertEqual N/A N/A N/A N/A self batchSystem getRunningBatchJobIDs N/A N/A N/A self assertFalse N/A N/A N/A os path exists testPath N/A job3 N/A N/A N/A self batchSystem issueBatchJob N/A touch %s testPath defaultRequirements N/A N/A updatedID exitStatus wallTime N/A N/A N/A self batchSystem getUpdatedBatchJob maxWait 1000 N/A N/A N/A self assertEqual exitStatus 0 N/A N/A N/A self assertEqual updatedID job3 N/A N/A N/A self supportsWallTime N/A N/A N/A N/A self assertTrue N/A wallTime 0 N/A N/A N/A N/A self assertIsNone wallTime N/A N/A N/A self assertTrue N/A N/A N/A os path exists testPath N/A N/A N/A self assertFalse N/A N/A N/A self batchSystem getUpdatedBatchJob 0 N/A N/A N/A N/A self batchSystem killBatchJobs N/A 10 N/A testSetEnv N/A N/A self N/A N/A assertEnv N/A N/A N/A N/A N/A os sys N/A N/A N/A sys exit N/A N/A N/A N/A os getenv FOO bar 0 42 N/A N/A script_body N/A dedent N/A N/A join N/A N/A N/A N/A getsource assertEnv split N/A 1 N/A N/A tempFileContaining script_body script_path N/A N/A command N/A N/A N/A sys executable script_path N/A job4 N/A N/A N/A self batchSystem issueBatchJob command defaultRequirements N/A N/A updatedID exitStatus wallTime N/A N/A N/A self batchSystem getUpdatedBatchJob maxWait 1000 N/A N/A N/A self assertEqual exitStatus 42 N/A N/A N/A self assertEqual updatedID job4 N/A N/A N/A N/A self batchSystem setEnv FOO bar N/A job5 N/A N/A N/A self batchSystem issueBatchJob command defaultRequirements N/A N/A updatedID exitStatus wallTime N/A N/A N/A self batchSystem getUpdatedBatchJob maxWait 1000 N/A N/A N/A self assertEqual exitStatus 0 N/A N/A N/A self assertEqual updatedID job5 N/A testCheckResourceRequest N/A N/A self N/A N/A N/A N/A isinstance N/A self batchSystem BatchSystemSupport N/A N/A checkResourceRequest N/A N/A self batchSystem checkResourceRequest N/A N/A N/A self assertRaises InsufficientSystemResources checkResourceRequest memory 1000 cores 200 disk 1000000000.0 N/A N/A N/A self assertRaises InsufficientSystemResources checkResourceRequest memory 5 cores 200 disk 1000000000.0 N/A N/A N/A self assertRaises InsufficientSystemResources checkResourceRequest memory 1.001e+12 cores 1 disk 1000000000.0 N/A N/A N/A self assertRaises InsufficientSystemResources checkResourceRequest memory 5 cores 1 disk 2000000000.0 N/A N/A N/A self assertRaises AssertionError checkResourceRequest memory None cores 1 disk 1000 N/A N/A N/A self assertRaises AssertionError checkResourceRequest memory 10 cores None disk 1000 N/A N/A checkResourceRequest memory 10 cores 1 disk 100 N/A testGetRescueJobFrequency N/A N/A self N/A N/A N/A N/A N/A self assertTrue N/A N/A N/A N/A self batchSystem getRescueBatchJobFrequency 0 N/A testScalableBatchSystem N/A N/A self N/A N/A N/A N/A _waitForJobsToIssue N/A N/A self numJobs N/A N/A N/A issuedIDs N/A N/A N/A N/A N/A len issuedIDs numJobs N/A N/A issuedIDs N/A N/A N/A self batchSystem getIssuedBatchJobIDs N/A issuedIDs N/A _waitForJobsToStart N/A N/A self numJobs N/A N/A N/A runningIDs N/A N/A N/A N/A N/A len runningIDs numJobs N/A N/A N/A N/A time sleep 0.1 N/A runningIDs N/A N/A N/A N/A N/A self batchSystem getRunningBatchJobIDs keys N/A runningIDs N/A N/A N/A MesosBatchSystemTest N/A N/A hidden AbstractBatchSystemTest MesosTestSupport N/A N/A 
    Tests against the Mesos batch system
     supportsWallTime N/A N/A self N/A N/A N/A True N/A createBatchSystem N/A N/A self N/A N/A toil.batchSystems.mesos.batchSystem MesosBatchSystem N/A N/A N/A self _startMesos numCores N/A N/A MesosBatchSystem config N/A self config maxCores numCores maxMemory 1000000000.0 maxDisk 1001 masterAddress 127.0.0.1:5050 N/A tearDown N/A N/A self N/A N/A N/A N/A N/A self _stopMesos N/A N/A N/A N/A super MesosBatchSystemTest self tearDown N/A N/A needs_mesos SingleMachineBatchSystemTest N/A N/A hidden AbstractBatchSystemTest N/A N/A 
    Tests against the single-machine batch system
     supportsWallTime N/A N/A self N/A N/A N/A True N/A createBatchSystem N/A N/A self N/A N/A N/A N/A SingleMachineBatchSystem config N/A self config maxCores numCores maxMemory 1000000000.0 maxDisk 1001 N/A N/A MaxCoresSingleMachineBatchSystemTest N/A ToilTest N/A N/A 
    This test ensures that single machine batch system doesn't exceed the configured number of
    cores
     setUpClass N/A N/A cls N/A N/A N/A N/A N/A N/A super MaxCoresSingleMachineBatchSystemTest cls setUpClass N/A N/A N/A logging basicConfig level N/A logging DEBUG N/A classmethod setUp N/A N/A self N/A N/A N/A N/A N/A N/A super MaxCoresSingleMachineBatchSystemTest self setUp writeTempFile N/A N/A s N/A N/A N/A N/A fd path N/A N/A tempfile mkstemp N/A N/A N/A N/A N/A N/A N/A N/A os write fd s N/A len s N/A N/A N/A N/A N/A N/A os unlink path N/A N/A N/A path N/A N/A N/A N/A os close fd N/A N/A N/A self counterPath N/A writeTempFile 0,0 script N/A N/A N/A N/A N/A os sys fcntl time count N/A N/A delta N/A N/A N/A 
                Adjust the first integer value in a file by the given amount. If the result
                exceeds the second integer value, set the second one to the first.
                 N/A fd N/A N/A os open N/A N/A sys argv N/A 1 N/A os O_RDWR N/A N/A N/A N/A N/A fcntl flock fd N/A fcntl LOCK_EX N/A N/A N/A s N/A N/A os read fd 10 N/A N/A value maxValue N/A map int N/A N/A s split , N/A value delta N/A N/A value maxValue N/A N/A maxValue value N/A N/A N/A os lseek fd 0 0 N/A N/A N/A os ftruncate fd 0 N/A N/A N/A os write fd N/A N/A , join N/A map str N/A value maxValue N/A N/A N/A N/A fcntl flock fd N/A fcntl LOCK_UN N/A N/A N/A N/A os close fd N/A N/A N/A N/A len N/A sys argv 3 N/A N/A N/A count 1 N/A N/A N/A N/A N/A time sleep 1 N/A N/A N/A count -1 N/A N/A N/A count N/A int N/A N/A sys argv N/A 2 N/A N/A N/A self scriptPath N/A writeTempFile N/A dedent N/A N/A join N/A N/A N/A N/A getsource script split N/A 1 N/A tearDown N/A N/A self N/A N/A N/A N/A N/A os unlink N/A self scriptPath N/A N/A N/A os unlink N/A self counterPath N/A scriptCommand N/A N/A self N/A N/A N/A N/A N/A join N/A N/A sys executable N/A self scriptPath N/A self counterPath N/A test N/A N/A self N/A N/A N/A F Fraction N/A minCores N/A F 1 10 N/A N/A N/A self assertEquals N/A float minCores N/A SingleMachineBatchSystem minCores N/A maxCores N/A N/A F minCores N/A minCores 10 N/A F 1 N/A F numCores 2 N/A F numCores N/A N/A coresPerJob N/A N/A F minCores N/A F N/A minCores 10 N/A F 1 N/A F maxCores 2 N/A F maxCores N/A N/A load N/A N/A F 1 10 N/A F 1 N/A F 10 N/A N/A jobs N/A int N/A N/A maxCores coresPerJob load N/A N/A N/A jobs 1 N/A minCores coresPerJob maxCores N/A N/A N/A N/A self assertEquals maxCores N/A float maxCores N/A bs N/A SingleMachineBatchSystem config N/A Config maxCores N/A float maxCores maxMemory N/A jobs 10 maxDisk N/A jobs 10 N/A N/A N/A jobIds N/A set N/A i N/A range 0 N/A int jobs N/A N/A N/A N/A jobIds add N/A N/A bs issueBatchJob command N/A N/A self scriptCommand cores N/A float coresPerJob memory 1 disk 1 preemptable preemptable N/A N/A N/A self assertEquals N/A len jobIds jobs N/A jobIds N/A N/A job N/A N/A bs getUpdatedBatchJob maxWait 10 N/A N/A N/A self assertIsNotNone job N/A N/A jobId status wallTime job N/A N/A N/A self assertEquals status 0 N/A N/A N/A jobIds remove jobId N/A N/A N/A N/A bs shutdown N/A N/A concurrentTasks maxConcurrentTasks N/A N/A self getCounters N/A N/A N/A self assertEquals concurrentTasks 0 N/A N/A N/A log info N/A N/A maxCores: {maxCores}, coresPerJob: {coresPerJob}, load: {load} format N/A locals N/A expectedMaxConcurrentTasks N/A min N/A maxCores coresPerJob jobs N/A N/A N/A self assertEquals maxConcurrentTasks expectedMaxConcurrentTasks N/A N/A N/A self resetCounters N/A getCounters N/A N/A self N/A N/A N/A N/A open N/A self counterPath r+ f N/A N/A s N/A N/A f read N/A N/A N/A log info Counter is %s s N/A N/A concurrentTasks maxConcurrentTasks N/A map int N/A N/A s split , N/A N/A concurrentTasks maxConcurrentTasks N/A resetCounters N/A N/A self N/A N/A N/A N/A open N/A self counterPath w f N/A N/A N/A N/A f write 0,0 N/A testServices N/A N/A self N/A N/A N/A options N/A N/A N/A Job Runner getDefaultOptions N/A N/A self _getTestJobStorePath N/A N/A options logDebug True N/A N/A options maxCores 3 N/A N/A N/A self assertTrue N/A N/A options maxCores N/A SingleMachineBatchSystem numCores N/A N/A N/A N/A Job Runner startToil N/A N/A Job wrapJobFn parentJob N/A N/A self scriptCommand options N/A N/A open N/A self counterPath r+ f N/A N/A s N/A N/A f read N/A N/A N/A log info Counter is %s s N/A N/A N/A self assertEqual N/A N/A self getCounters N/A 0 3 N/A N/A skipIf N/A N/A SingleMachineBatchSystem numCores 3 Need at least three cores to run this test N/A parentJob N/A N/A job cmd N/A N/A N/A N/A N/A job addChildJobFn childJob cmd N/A childJob N/A N/A job cmd N/A N/A N/A N/A N/A job addService N/A Service cmd N/A N/A N/A job addChildJobFn grandChildJob cmd N/A N/A N/A subprocess check_call cmd shell True N/A grandChildJob N/A N/A job cmd N/A N/A N/A N/A N/A job addService N/A Service cmd N/A N/A N/A job addChildFn greatGrandChild cmd N/A N/A N/A subprocess check_call cmd shell True N/A greatGrandChild N/A N/A cmd N/A N/A N/A N/A N/A subprocess check_call cmd shell True N/A Service N/A N/A Job Service N/A __init__ N/A N/A self cmd N/A N/A N/A N/A N/A N/A super Service self __init__ N/A N/A self cmd cmd N/A start N/A N/A self fileStore N/A N/A N/A N/A N/A subprocess check_call N/A N/A self cmd  1 shell True N/A check N/A N/A self N/A N/A N/A True N/A stop N/A N/A self fileStore N/A N/A N/A N/A N/A subprocess check_call N/A N/A self cmd  -1 shell True N/A N/A ParasolBatchSystemTest N/A N/A hidden AbstractBatchSystemTest ParasolTestSupport N/A N/A 
    Tests the Parasol batch system
     supportsWallTime N/A N/A self N/A N/A N/A True N/A _createDummyConfig N/A N/A self N/A N/A N/A config N/A N/A N/A super ParasolBatchSystemTest self _createDummyConfig N/A N/A config jobStore N/A N/A self _createTempDir jobStore N/A config N/A createBatchSystem N/A N/A self N/A N/A N/A memory N/A int 3000000000.0 N/A N/A N/A self _startParasol numCores numCores memory memory N/A N/A ParasolBatchSystem config N/A self config maxCores numCores maxMemory memory maxDisk 1001 N/A tearDown N/A N/A self N/A N/A N/A N/A N/A N/A super ParasolBatchSystemTest self tearDown N/A N/A N/A self _stopParasol N/A testBatchResourceLimits N/A N/A self N/A N/A N/A job1 N/A N/A N/A self batchSystem issueBatchJob sleep 1000 memory N/A 1 30 cores 1 disk 1000 preemptable preemptable N/A N/A N/A self assertIsNotNone job1 N/A job2 N/A N/A N/A self batchSystem issueBatchJob sleep 1000 memory N/A 2 30 cores 1 disk 1000 preemptable preemptable N/A N/A N/A self assertIsNotNone job2 N/A batches N/A N/A self _getBatchList N/A N/A N/A self assertEqual N/A len batches 2 N/A N/A N/A self assertNotEqual N/A N/A batches N/A 0 N/A ram N/A N/A batches N/A 1 N/A ram N/A N/A N/A N/A self batchSystem killBatchJobs N/A job2 N/A job3 N/A N/A N/A self batchSystem issueBatchJob sleep 1000 memory N/A 1 30 cores 1 disk 1000 preemptable preemptable N/A N/A N/A self assertIsNotNone job3 N/A batches N/A N/A self _getBatchList N/A N/A N/A self assertEqual N/A len batches 1 N/A _parseBatchString N/A N/A self batchString N/A N/A N/A re N/A batchInfo N/A dict N/A memPattern N/A N/A re compile (\d+\.\d+)([kgmbt]) N/A items N/A N/A batchString split N/A N/A batchInfo N/A cores N/A int N/A items N/A 7 N/A name N/A str N/A items N/A 11 N/A memMatch N/A N/A memPattern match N/A items N/A 8 N/A ramValue N/A float N/A N/A memMatch group 1 N/A ramUnits N/A N/A memMatch group 2 N/A ramConversion N/A b k m g t 1.0 1000.0 1000000.0 1000000000.0 1e+12 N/A N/A batchInfo N/A ram N/A ramValue N/A ramConversion N/A ramUnits N/A batchInfo N/A _getBatchList N/A N/A self N/A N/A N/A N/A exitStatus batchLines N/A N/A N/A self batchSystem _runParasol N/A list batches N/A N/A N/A self assertEqual exitStatus 0 N/A N/A N/A N/A self _parseBatchString line N/A line N/A batchLines N/A 1 line N/A N/A needs_parasol GridEngineBatchSystemTest N/A N/A hidden AbstractBatchSystemTest N/A N/A 
    Tests against the GridEngine batch system
     _createDummyConfig N/A N/A self N/A N/A N/A config N/A N/A N/A super GridEngineBatchSystemTest self _createDummyConfig N/A N/A config jobStore N/A N/A self _createTempDir jobStore N/A config N/A createBatchSystem N/A N/A self N/A N/A toil.batchSystems.gridengine GridengineBatchSystem N/A N/A GridengineBatchSystem config N/A self config maxCores numCores maxMemory 1e+12 maxDisk 1000000000.0 N/A N/A needs_gridengine SlurmBatchSystemTest N/A N/A hidden AbstractBatchSystemTest N/A N/A 
    Tests against the Slurm batch system
     _createDummyConfig N/A N/A self N/A N/A N/A config N/A N/A N/A super SlurmBatchSystemTest self _createDummyConfig N/A N/A config jobStore N/A N/A self _createTempDir jobStore N/A config N/A createBatchSystem N/A N/A self N/A N/A toil.batchSystems.slurm SlurmBatchSystem N/A N/A SlurmBatchSystem config N/A self config maxCores numCores maxMemory 1e+12 maxDisk 1000000000.0 N/A tearDown N/A N/A self N/A N/A N/A N/A N/A N/A super SlurmBatchSystemTest self tearDown glob glob N/A f N/A glob slurm-*.out N/A N/A N/A N/A os unlink f N/A N/A needs_slurm tempFileContaining N/A N/A content N/A N/A N/A N/A fd path N/A N/A tempfile mkstemp suffix .py N/A N/A N/A N/A N/A N/A N/A os write fd content N/A N/A N/A N/A N/A N/A os close fd N/A N/A N/A N/A N/A os close fd N/A N/A path N/A N/A N/A N/A os unlink path N/A contextmanager