toil.test.src.jobServiceTest

Module Contents

Classes

JobServiceTest	Tests testing the Job.Service class
PerfectServiceTest	Tests testing the Job.Service class
ToyService	Abstract class used to define the interface to a service.
ToySerializableService	Abstract class used to define the interface to a service.

Functions

serviceTest(job, outFile, messageInt)	Creates one service and one accessing job, which communicate with two files to establish
serviceTestRecursive(job, outFile, messages)	Creates a chain of services and accessing jobs, each paired together.
serviceTestParallelRecursive(job, outFiles, messageBundles)	Creates multiple chains of services and accessing jobs.
serviceAccessor(job, communicationFiles, outFile, randInt)	Writes a random integer iinto the inJobStoreFileID file, then tries 10 times reading
fnTest(strings, outputFile)	Function concatenates the strings together and writes them to the output file

Attributes

logger

toil.test.src.jobServiceTest.logger

class toil.test.src.jobServiceTest.JobServiceTest(methodName='runTest')

Bases: toil.test.ToilTest

Tests testing the Job.Service class

testServiceSerialization()

Tests that a service can receive a promise without producing a serialization error.

testService(checkpoint=False)

Tests the creation of a Job.Service with random failures of the worker.

testServiceDeadlock()

Creates a job with more services than maxServices, checks that deadlock is detected.

testServiceWithCheckpoints()

Tests the creation of a Job.Service with random failures of the worker, making the root job use checkpointing to restart the subtree.

testServiceRecursive(checkpoint=True)

Tests the creation of a Job.Service, creating a chain of services and accessing jobs. Randomly fails the worker.

testServiceParallelRecursive(checkpoint=True)

Tests the creation of a Job.Service, creating parallel chains of services and accessing jobs. Randomly fails the worker.

runToil(rootJob, retryCount=1, badWorker=0.5, badWorkedFailInterval=0.1, maxServiceJobs=sys.maxsize, deadlockWait=60)

class toil.test.src.jobServiceTest.PerfectServiceTest(methodName='runTest')

Bases: JobServiceTest

Tests testing the Job.Service class

runToil(rootJob, retryCount=1, badWorker=0, badWorkedFailInterval=1000, maxServiceJobs=sys.maxsize, deadlockWait=60)

Let us run all the tests in the other service test class, but without worker failures.

toil.test.src.jobServiceTest.serviceTest(job, outFile, messageInt)

Creates one service and one accessing job, which communicate with two files to establish that both run concurrently.

toil.test.src.jobServiceTest.serviceTestRecursive(job, outFile, messages)

Creates a chain of services and accessing jobs, each paired together.

toil.test.src.jobServiceTest.serviceTestParallelRecursive(job, outFiles, messageBundles)

Creates multiple chains of services and accessing jobs.

class toil.test.src.jobServiceTest.ToyService(messageInt, *args, **kwargs)

Bases: toil.job.Job.Service

Abstract class used to define the interface to a service.

Should be subclassed by the user to define services.

Is not executed as a job; runs within a ServiceHostJob.

start(job)

Start the service.

Parameters

job – The underlying host job that the service is being run in. Can be used to register deferred functions, or to access the fileStore for creating temporary files.

Returns

An object describing how to access the service. The object must be pickleable and will be used by jobs to access the service (see toil.job.Job.addService()).

stop(job)

Stops the service. Function can block until complete.

Parameters

job – The underlying host job that the service is being run in. Can be used to register deferred functions, or to access the fileStore for creating temporary files.

check()

Checks the service is still running.

Raises

exceptions.RuntimeError – If the service failed, this will cause the service job to be labeled failed.

Returns

True if the service is still running, else False. If False then the service job will be terminated, and considered a success. Important point: if the service job exits due to a failure, it should raise a RuntimeError, not return False!

static serviceWorker(jobStore, terminate, error, inJobStoreID, outJobStoreID, messageInt)

toil.test.src.jobServiceTest.serviceAccessor(job, communicationFiles, outFile, randInt)

Writes a random integer iinto the inJobStoreFileID file, then tries 10 times reading from outJobStoreFileID to get a pair of integers, the first equal to i the second written into the outputFile.

class toil.test.src.jobServiceTest.ToySerializableService(messageInt, *args, **kwargs)

Bases: toil.job.Job.Service

Abstract class used to define the interface to a service.

Should be subclassed by the user to define services.

Is not executed as a job; runs within a ServiceHostJob.

start(job)

Start the service.

Parameters

job – The underlying host job that the service is being run in. Can be used to register deferred functions, or to access the fileStore for creating temporary files.

Returns

An object describing how to access the service. The object must be pickleable and will be used by jobs to access the service (see toil.job.Job.addService()).

stop(job)

Stops the service. Function can block until complete.

Parameters

job – The underlying host job that the service is being run in. Can be used to register deferred functions, or to access the fileStore for creating temporary files.

check()

Checks the service is still running.

Raises

exceptions.RuntimeError – If the service failed, this will cause the service job to be labeled failed.

Returns

True if the service is still running, else False. If False then the service job will be terminated, and considered a success. Important point: if the service job exits due to a failure, it should raise a RuntimeError, not return False!

toil.test.src.jobServiceTest.fnTest(strings, outputFile)

Function concatenates the strings together and writes them to the output file