toil.test.src.jobServiceTest

Attributes

logger

Classes

TestJobService

Tests testing the Job.Service class

TestPerfectServicet

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, ...)

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

Module Contents

toil.test.src.jobServiceTest.logger
class toil.test.src.jobServiceTest.TestJobService

Tests testing the Job.Service class

testServiceSerialization(tmp_path)

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

Parameters:

tmp_path (pathlib.Path)

Return type:

None

testService(tmp_path, checkpoint=False)

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

Parameters:
Return type:

None

testServiceDeadlock(tmp_path)

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

Parameters:

tmp_path (pathlib.Path)

Return type:

None

testServiceWithCheckpoints(tmp_path)

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

Parameters:

tmp_path (pathlib.Path)

Return type:

None

testServiceRecursive(tmp_path, checkpoint=True)

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

Parameters:
Return type:

None

testServiceParallelRecursive(tmp_path, checkpoint=True)

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

Parameters:
Return type:

None

runToil(tmp_path, rootJob, retryCount=1, badWorker=0.5, badWorkedFailInterval=0.1, maxServiceJobs=sys.maxsize, deadlockWait=60, max_attempts=50)
Parameters:
Return type:

None

class toil.test.src.jobServiceTest.TestPerfectServicet

Bases: TestJobService

Tests testing the Job.Service class

runToil(*args, **kwargs)

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

Parameters:

  • args (Any)

  • kwargs (Any)

Return type:

None

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.

Parameters:
Return type:

None

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

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

Parameters:
Return type:

None

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

Creates multiple chains of services and accessing jobs.

Parameters:
Return type:

None

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.

Parameters:

  • messageInt (int)

  • args (Any)

  • kwargs (Any)

messageInt
start(job)

Start the service.

Parameters:

job (toil.job.ServiceHostJob) – 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()).

Return type:

tuple[str, str]

stop(job)

Stops the service. Function can block until complete.

Parameters:

job (toil.job.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.

Return type:

None

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!

Return type:

Literal[True]

static serviceWorker(jobStore, terminate, error, inJobStoreID, outJobStoreID, messageInt)
Parameters:
Return type:

None

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

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.

Parameters:
Return type:

None

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.

Parameters:

  • messageInt (str)

  • args (Any)

  • kwargs (Any)

messageInt
start(job)

Start the service.

Parameters:

job (toil.job.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()).

Return type:

str

stop(job)

Stops the service. Function can block until complete.

Parameters:

job (toil.job.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.

Return type:

None

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!

Return type:

Literal[True]

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

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

Parameters:
Return type:

None