toil.test.batchSystems.batch_system_plugin_test¶

Attributes¶

logger

Classes¶

`AbstractBatchSystem`	An abstract base class to represent the interface the batch system must provide to Toil.
`UpdatedBatchJobInfo`
`BatchSystemCleanupSupport`	Adds cleanup support when the last running job leaves a node, for batch
`OptionSetter`	Protocol for the setOption function we get to let us set up CLI options for
`Toil`	A context manager that represents a Toil workflow.
`JobDescription`	Stores all the information that the Toil Leader ever needs to know about a Job.
`ToilTest`	A common base class for Toil tests.
`FakeBatchSystem`	Adds cleanup support when the last running job leaves a node, for batch
`BatchSystemPluginTest`	A common base class for Toil tests.

Functions¶

`add_batch_system_factory`(key, class_factory)	Adds a batch system to the registry for workflow or plugin-supplied batch systems.
`addOptions`(parser[, jobstore_as_flag, cwl, wdl])	Add all Toil command line options to a parser.

Module Contents¶

class toil.test.batchSystems.batch_system_plugin_test.AbstractBatchSystem[source]¶

Bases: abc.ABC

An abstract base class to represent the interface the batch system must provide to Toil.

classmethod supportsAutoDeployment()[source]¶

Abstractmethod:
Return type:: bool

Whether this batch system supports auto-deployment of the user script itself.

If it does, the setUserScript() can be invoked to set the resource object representing the user script.

Note to implementors: If your implementation returns True here, it should also override

classmethod supportsWorkerCleanup()[source]¶

Abstractmethod:
Return type:: bool

Whether this batch system supports worker cleanup.

Indicates whether this batch system invokes BatchSystemSupport.workerCleanup() after the last job for a particular workflow invocation finishes. Note that the term worker refers to an entire node, not just a worker process. A worker process may run more than one job sequentially, and more than one concurrent worker process may exist on a worker node, for the same workflow. The batch system is said to shut down after the last worker process terminates.

abstract setUserScript(userScript)[source]¶

Set the user script for this workflow.

This method must be called before the first job is issued to this batch system, and only if supportsAutoDeployment() returns True, otherwise it will raise an exception.

Parameters:: userScript (toil.resource.Resource) – the resource object representing the user script or module and the modules it depends on.
Return type:: None

set_message_bus(message_bus)[source]¶

Give the batch system an opportunity to connect directly to the message bus, so that it can send informational messages about the jobs it is running to other Toil components.

Parameters:: message_bus (toil.bus.MessageBus)
Return type:: None

abstract issueBatchJob(command, job_desc, job_environment=None)[source]¶

Issues a job with the specified command to the batch system and returns a unique job ID number.

Parameters:

command (str) – the command to execute somewhere to run the Toil worker process
job_desc (toil.job.JobDescription) – the JobDescription for the job being run
job_environment (Optional[Dict[str, str]]) – a collection of job-specific environment variables to be set on the worker.

Returns:

a unique job ID number that can be used to reference the newly issued job

Return type:

int

abstract killBatchJobs(jobIDs)[source]¶

Kills the given job IDs. After returning, the killed jobs will not appear in the results of getRunningBatchJobIDs. The killed job will not be returned from getUpdatedBatchJob.

Parameters:: jobIDs (List[int]) – list of IDs of jobs to kill
Return type:: None

abstract getIssuedBatchJobIDs()[source]¶

Gets all currently issued jobs

Returns:: A list of jobs (as job ID numbers) currently issued (may be running, or may be waiting to be run). Despite the result being a list, the ordering should not be depended upon.
Return type:: List[int]

abstract getRunningBatchJobIDs()[source]¶

Gets a map of jobs as job ID numbers that are currently running (not just waiting) and how long they have been running, in seconds.

Returns:: dictionary with currently running job ID number keys and how many seconds they have been running as the value
Return type:: Dict[int, float]

abstract getUpdatedBatchJob(maxWait)[source]¶

Returns information about job that has updated its status (i.e. ceased running, either successfully or with an error). Each such job will be returned exactly once.

Does not return info for jobs killed by killBatchJobs, although they may cause None to be returned earlier than maxWait.

Parameters:: maxWait (int) – the number of seconds to block, waiting for a result
Returns:: If a result is available, returns UpdatedBatchJobInfo. Otherwise it returns None. wallTime is the number of seconds (a strictly positive float) in wall-clock time the job ran for, or None if this batch system does not support tracking wall time.
Return type:: Optional[UpdatedBatchJobInfo]

getSchedulingStatusMessage()[source]¶

Get a log message fragment for the user about anything that might be going wrong in the batch system, if available.

If no useful message is available, return None.

This can be used to report what resource is the limiting factor when scheduling jobs, for example. If the leader thinks the workflow is stuck, the message can be displayed to the user to help them diagnose why it might be stuck.

Returns:: User-directed message about scheduling state.
Return type:: Optional[str]

abstract shutdown()[source]¶

Called at the completion of a toil invocation. Should cleanly terminate all worker threads.

Return type:: None

abstract setEnv(name, value=None)[source]¶

Set an environment variable for the worker process before it is launched.

The worker process will typically inherit the environment of the machine it is running on but this method makes it possible to override specific variables in that inherited environment before the worker is launched. Note that this mechanism is different to the one used by the worker internally to set up the environment of a job. A call to this method affects all jobs issued after this method returns. Note to implementors: This means that you would typically need to copy the variables before enqueuing a job.

If no value is provided it will be looked up from the current environment.

Parameters:

name (str)
value (Optional[str])

Return type:

None

classmethod add_options(parser)[source]¶

If this batch system provides any command line options, add them to the given parser.

Parameters:: parser (Union[argparse.ArgumentParser, argparse._ArgumentGroup])
Return type:: None

classmethod setOptions(setOption)[source]¶

Process command line or configuration options relevant to this batch system.

Parameters:: setOption (toil.batchSystems.options.OptionSetter) – A function with signature setOption(option_name, parsing_function=None, check_function=None, default=None, env=None) returning nothing, used to update run configuration as a side effect.
Return type:: None

getWorkerContexts()[source]¶

Get a list of picklable context manager objects to wrap worker work in, in order.

Can be used to ask the Toil worker to do things in-process (such as configuring environment variables, hot-deploying user scripts, or cleaning up a node) that would otherwise require a wrapping “executor” process.

Return type:: List[ContextManager[Any]]

class toil.test.batchSystems.batch_system_plugin_test.UpdatedBatchJobInfo[source]¶

Bases: NamedTuple

jobID: int¶

exitStatus: int¶

The exit status (integer value) of the job. 0 implies successful.

EXIT_STATUS_UNAVAILABLE_VALUE is used when the exit status is not available (e.g. job is lost, or otherwise died but actual exit code was not reported).

exitReason: BatchJobExitReason | None¶

wallTime: float | int | None¶

class toil.test.batchSystems.batch_system_plugin_test.BatchSystemCleanupSupport(config, maxCores, maxMemory, maxDisk)[source]¶

Bases: toil.batchSystems.local_support.BatchSystemLocalSupport

Adds cleanup support when the last running job leaves a node, for batch systems that can’t provide it using the backing scheduler.

Parameters:

config (toil.common.Config)
maxCores (float)
maxMemory (int)
maxDisk (int)

classmethod supportsWorkerCleanup()[source]¶

Whether this batch system supports worker cleanup.

Indicates whether this batch system invokes BatchSystemSupport.workerCleanup() after the last job for a particular workflow invocation finishes. Note that the term worker refers to an entire node, not just a worker process. A worker process may run more than one job sequentially, and more than one concurrent worker process may exist on a worker node, for the same workflow. The batch system is said to shut down after the last worker process terminates.

Return type:: bool

getWorkerContexts()[source]¶

Get a list of picklable context manager objects to wrap worker work in, in order.

Can be used to ask the Toil worker to do things in-process (such as configuring environment variables, hot-deploying user scripts, or cleaning up a node) that would otherwise require a wrapping “executor” process.

Return type:: List[ContextManager[Any]]

class toil.test.batchSystems.batch_system_plugin_test.OptionSetter[source]¶

Bases: Protocol

Protocol for the setOption function we get to let us set up CLI options for each batch system.

Actual functionality is defined in the Config class.

OptionType¶

__call__(option_name, parsing_function=None, check_function=None, default=None, env=None, old_names=None)[source]¶

Parameters:

option_name (str)
parsing_function (Optional[Callable[[Any], OptionType]])
check_function (Optional[Callable[[OptionType], Union[None, bool]]])
default (Optional[OptionType])
env (Optional[List[str]])
old_names (Optional[List[str]])

Return type:

bool

toil.test.batchSystems.batch_system_plugin_test.add_batch_system_factory(key, class_factory)[source]¶

Adds a batch system to the registry for workflow or plugin-supplied batch systems.

Parameters:

class_factory (Callable[[], Type[toil.batchSystems.abstractBatchSystem.AbstractBatchSystem]]) – A function that returns a batch system class (NOT an instance), which implements toil.batchSystems.abstractBatchSystem.AbstractBatchSystem.
key (str)

class toil.test.batchSystems.batch_system_plugin_test.Toil(options)[source]¶

Bases: ContextManager[Toil]

A context manager that represents a Toil workflow.

Specifically the batch system, job store, and its configuration.

Parameters:: options (argparse.Namespace)

config: Config¶

__enter__()[source]¶

Derive configuration from the command line options.

Then load the job store and, on restart, consolidate the derived configuration with the one from the previous invocation of the workflow.

Return type:: Toil

__exit__(exc_type, exc_val, exc_tb)[source]¶

Clean up after a workflow invocation.

Depending on the configuration, delete the job store.

Parameters:

exc_type (Optional[Type[BaseException]])
exc_val (Optional[BaseException])
exc_tb (Optional[types.TracebackType])

Return type:

Literal[False]

start(rootJob)[source]¶

Invoke a Toil workflow with the given job as the root for an initial run.

This method must be called in the body of a with Toil(...) as toil: statement. This method should not be called more than once for a workflow that has not finished.

Parameters:: rootJob (toil.job.Job) – The root job of the workflow
Returns:: The root job’s return value
Return type:: Any

restart()[source]¶

Restarts a workflow that has been interrupted.

Returns:: The root job’s return value
Return type:: Any

classmethod getJobStore(locator)[source]¶

Create an instance of the concrete job store implementation that matches the given locator.

Parameters:: locator (str) – The location of the job store to be represent by the instance
Returns:: an instance of a concrete subclass of AbstractJobStore
Return type:: toil.jobStores.abstractJobStore.AbstractJobStore

static parseLocator(locator)[source]¶

Parameters:: locator (str)
Return type:: Tuple[str, str]

static buildLocator(name, rest)[source]¶

Parameters:

name (str)
rest (str)

Return type:

str

classmethod resumeJobStore(locator)[source]¶

Parameters:: locator (str)
Return type:: toil.jobStores.abstractJobStore.AbstractJobStore

static createBatchSystem(config)[source]¶

Create an instance of the batch system specified in the given config.

Parameters:: config (Config) – the current configuration
Returns:: an instance of a concrete subclass of AbstractBatchSystem
Return type:: toil.batchSystems.abstractBatchSystem.AbstractBatchSystem

importFile(srcUrl: str, sharedFileName: str, symlink: bool = True) → None[source]¶
importFile(srcUrl: str, sharedFileName: None = None, symlink: bool = True) → toil.fileStores.FileID

import_file(src_uri: str, shared_file_name: str, symlink: bool = True, check_existence: bool = True) → None[source]¶

import_file(src_uri: str, shared_file_name: None = None, symlink: bool = True, check_existence: bool = True) → toil.fileStores.FileID

Import the file at the given URL into the job store.

By default, returns None if the file does not exist.

Parameters:: check_existence – If true, raise FileNotFoundError if the file does not exist. If false, return None when the file does not exist.

See toil.jobStores.abstractJobStore.AbstractJobStore.importFile() for a full description

exportFile(jobStoreFileID, dstUrl)[source]¶

Parameters:

jobStoreFileID (toil.fileStores.FileID)
dstUrl (str)

Return type:

None

export_file(file_id, dst_uri)[source]¶

Export file to destination pointed at by the destination URL.

See toil.jobStores.abstractJobStore.AbstractJobStore.exportFile() for a full description

Parameters:

file_id (toil.fileStores.FileID)
dst_uri (str)

Return type:

None

static normalize_uri(uri, check_existence=False)[source]¶

Given a URI, if it has no scheme, prepend “file:”.

Parameters:

check_existence (bool) – If set, raise FileNotFoundError if a URI points to a local file that does not exist.
uri (str)

Return type:

str

static getToilWorkDir(configWorkDir=None)[source]¶

Return a path to a writable directory under which per-workflow directories exist.

This directory is always required to exist on a machine, even if the Toil worker has not run yet. If your workers and leader have different temp directories, you may need to set TOIL_WORKDIR.

Parameters:: configWorkDir (Optional[str]) – Value passed to the program using the –workDir flag
Returns:: Path to the Toil work directory, constant across all machines
Return type:: str

classmethod get_toil_coordination_dir(config_work_dir, config_coordination_dir)[source]¶

Return a path to a writable directory, which will be in memory if convenient. Ought to be used for file locking and coordination.

Parameters:

config_work_dir (Optional[str]) – Value passed to the program using the –workDir flag
config_coordination_dir (Optional[str]) – Value passed to the program using the –coordinationDir flag
workflow_id – Used if a tmpdir_prefix exists to create full directory paths unique per workflow

Returns:

Path to the Toil coordination directory. Ought to be on a POSIX filesystem that allows directories containing open files to be deleted.

Return type:

str

static get_workflow_path_component(workflow_id)[source]¶

Get a safe filesystem path component for a workflow.

Will be consistent for all processes on a given machine, and different for all processes on different machines.

Parameters:: workflow_id (str) – The ID of the current Toil workflow.
Return type:: str

classmethod getLocalWorkflowDir(workflowID, configWorkDir=None)[source]¶

Return the directory where worker directories and the cache will be located for this workflow on this machine.

Parameters:

configWorkDir (Optional[str]) – Value passed to the program using the –workDir flag
workflowID (str)

Returns:

Path to the local workflow directory on this machine

Return type:

str

classmethod get_local_workflow_coordination_dir(workflow_id, config_work_dir, config_coordination_dir)[source]¶

Return the directory where coordination files should be located for this workflow on this machine. These include internal Toil databases and lock files for the machine.

If an in-memory filesystem is available, it is used. Otherwise, the local workflow directory, which may be on a shared network filesystem, is used.

Parameters:

workflow_id (str) – Unique ID of the current workflow.
config_work_dir (Optional[str]) – Value used for the work directory in the current Toil Config.
config_coordination_dir (Optional[str]) – Value used for the coordination directory in the current Toil Config.

Returns:

Path to the local workflow coordination directory on this machine.

Return type:

str

toil.test.batchSystems.batch_system_plugin_test.addOptions(parser, jobstore_as_flag=False, cwl=False, wdl=False)[source]¶

Add all Toil command line options to a parser.

Support for config files if using configargparse. This will also check and set up the default config file.

Parameters:

jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.
cwl (bool) – Whether CWL options are expected. If so, CWL options won’t be suppressed.
wdl (bool) – Whether WDL options are expected. If so, WDL options won’t be suppressed.
parser (argparse.ArgumentParser)

Return type:

None

class toil.test.batchSystems.batch_system_plugin_test.JobDescription(requirements, jobName, unitName='', displayName='', local=None)[source]¶

Bases: Requirer

Stores all the information that the Toil Leader ever needs to know about a Job.

This includes:

Resource requirements.
Which jobs are children or follow-ons or predecessors of this job.
A reference to the Job object in the job store.

Can be obtained from an actual (i.e. executable) Job object, and can be used to obtain the Job object from the JobStore.

Never contains other Jobs or JobDescriptions: all reference is by ID.

Subclassed into variants for checkpoint jobs and service jobs that have their specific parameters.

Parameters:

requirements (Mapping[str, Union[int, str, bool]])
jobName (str)
unitName (Optional[str])
displayName (Optional[str])
local (Optional[bool])

get_names()[source]¶

Get the names and ID of this job as a named tuple.

Return type:: toil.bus.Names

get_chain()[source]¶

Get all the jobs that executed in this job’s chain, in order.

For each job, produces a named tuple with its various names and its original job store ID. The jobs in the chain are in execution order.

If the job hasn’t run yet or it didn’t chain, produces a one-item list.

Return type:: List[toil.bus.Names]

serviceHostIDsInBatches()[source]¶

Find all batches of service host job IDs that can be started at the same time.

(in the order they need to start in)

Return type:: Iterator[List[str]]

successorsAndServiceHosts()[source]¶

Get an iterator over all child, follow-on, and service job IDs.

Return type:: Iterator[str]

allSuccessors()[source]¶

Get an iterator over all child, follow-on, and chained, inherited successor job IDs.

Follow-ons will come before children.

Return type:: Iterator[str]

successors_by_phase()[source]¶

Get an iterator over all child/follow-on/chained inherited successor job IDs, along with their phase numbere on the stack.

Phases ececute higher numbers to lower numbers.

Return type:: Iterator[Tuple[int, str]]

property services¶
Get a collection of the IDs of service host jobs for this job, in arbitrary order.: Will be empty if the job has no unfinished services.

has_body()[source]¶

Returns True if we have a job body associated, and False otherwise.

Return type:: bool

attach_body(file_store_id, user_script)[source]¶

Attach a job body to this JobDescription.

Takes the file store ID that the body is stored at, and the required user script module.

The file store ID can also be “firstJob” for the root job, stored as a shared file instead.

Parameters:

file_store_id (str)
user_script (toil.resource.ModuleDescriptor)

Return type:

None

detach_body()[source]¶

Drop the body reference from a JobDescription.

Return type:: None

get_body()[source]¶

Get the information needed to load the job body.

Returns:: a file store ID (or magic shared file name “firstJob”) and a user script module.
Return type:: Tuple[str, toil.resource.ModuleDescriptor]

Fails if no body is attached; check has_body() first.

nextSuccessors()[source]¶

Return the collection of job IDs for the successors of this job that are ready to run.

If those jobs have multiple predecessor relationships, they may still be blocked on other jobs.

Returns None when at the final phase (all successors done), and an empty collection if there are more phases but they can’t be entered yet (e.g. because we are waiting for the job itself to run).

Return type:: Optional[Set[str]]

filterSuccessors(predicate)[source]¶

Keep only successor jobs for which the given predicate function approves.

The predicate function is called with the job’s ID.

Treats all other successors as complete and forgets them.

Parameters:: predicate (Callable[[str], bool])
Return type:: None

filterServiceHosts(predicate)[source]¶

Keep only services for which the given predicate approves.

The predicate function is called with the service host job’s ID.

Treats all other services as complete and forgets them.

Parameters:: predicate (Callable[[str], bool])
Return type:: None

clear_nonexistent_dependents(job_store)[source]¶

Remove all references to child, follow-on, and associated service jobs that do not exist.

That is to say, all those that have been completed and removed.

Parameters:: job_store (toil.jobStores.abstractJobStore.AbstractJobStore)
Return type:: None

clear_dependents()[source]¶

Remove all references to successor and service jobs.

Return type:: None

is_subtree_done()[source]¶

Check if the subtree is done.

Returns:: True if the job appears to be done, and all related child, follow-on, and service jobs appear to be finished and removed.
Return type:: bool

replace(other)[source]¶

Take on the ID of another JobDescription, retaining our own state and type.

When updated in the JobStore, we will save over the other JobDescription.

Useful for chaining jobs: the chained-to job can replace the parent job.

Merges cleanup state and successors other than this job from the job being replaced into this one.

Parameters:: other (JobDescription) – Job description to replace.
Return type:: None

assert_is_not_newer_than(other)[source]¶

Make sure this JobDescription is not newer than a prospective new version of the JobDescription.

Parameters:: other (JobDescription)
Return type:: None

is_updated_by(other)[source]¶

Return True if the passed JobDescription is a distinct, newer version of this one.

Parameters:: other (JobDescription)
Return type:: bool

addChild(childID)[source]¶

Make the job with the given ID a child of the described job.

Parameters:: childID (str)
Return type:: None

addFollowOn(followOnID)[source]¶

Make the job with the given ID a follow-on of the described job.

Parameters:: followOnID (str)
Return type:: None

addServiceHostJob(serviceID, parentServiceID=None)[source]¶

Make the ServiceHostJob with the given ID a service of the described job.

If a parent ServiceHostJob ID is given, that parent service will be started first, and must have already been added.

hasChild(childID)[source]¶

Return True if the job with the given ID is a child of the described job.

Parameters:: childID (str)
Return type:: bool

hasFollowOn(followOnID)[source]¶

Test if the job with the given ID is a follow-on of the described job.

Parameters:: followOnID (str)
Return type:: bool

hasServiceHostJob(serviceID)[source]¶

Test if the ServiceHostJob is a service of the described job.

Return type:: bool

renameReferences(renames)[source]¶

Apply the given dict of ID renames to all references to jobs.

Does not modify our own ID or those of finished predecessors. IDs not present in the renames dict are left as-is.

Parameters:: renames (Dict[TemporaryID, str]) – Rename operations to apply.
Return type:: None

addPredecessor()[source]¶

Notify the JobDescription that a predecessor has been added to its Job.

Return type:: None

onRegistration(jobStore)[source]¶

Perform setup work that requires the JobStore.

Called by the Job saving logic when this JobDescription meets the JobStore and has its ID assigned.

Overridden to perform setup work (like hooking up flag files for service jobs) that requires the JobStore.

Parameters:: jobStore (toil.jobStores.abstractJobStore.AbstractJobStore) – The job store we are being placed into
Return type:: None

setupJobAfterFailure(exit_status=None, exit_reason=None)[source]¶

Configure job after a failure.

Reduce the remainingTryCount if greater than zero and set the memory to be at least as big as the default memory (in case of exhaustion of memory, which is common).

Requires a configuration to have been assigned (see toil.job.Requirer.assignConfig()).

Parameters:

exit_status (Optional[int]) – The exit code from the job.
exit_reason (Optional[toil.batchSystems.abstractBatchSystem.BatchJobExitReason]) – The reason the job stopped, if available from the batch system.

Return type:

None

getLogFileHandle(jobStore)[source]¶

Create a context manager that yields a file handle to the log file.

Assumes logJobStoreFileID is set.

property remainingTryCount¶
Get the number of tries remaining.: The try count set on the JobDescription, or the default based on the retry count from the config if none is set.

clearRemainingTryCount()[source]¶

Clear remainingTryCount and set it back to its default value.

Returns:: True if a modification to the JobDescription was made, and False otherwise.
Return type:: bool

__str__()[source]¶

Produce a useful logging string identifying this job.

Return type:: str

__repr__()[source]¶: Return repr(self).

reserve_versions(count)[source]¶

Reserve a job version number for later, for journaling asynchronously.

Parameters:: count (int)
Return type:: None

pre_update_hook()[source]¶

Run before pickling and saving a created or updated version of this job.

Called by the job store.

Return type:: None

class toil.test.batchSystems.batch_system_plugin_test.ToilTest(methodName='runTest')[source]¶

Bases: unittest.TestCase

A common base class for Toil tests.

Please have every test case directly or indirectly inherit this one.

When running tests you may optionally set the TOIL_TEST_TEMP environment variable to the path of a directory where you want temporary test files be placed. The directory will be created if it doesn’t exist. The path may be relative in which case it will be assumed to be relative to the project root. If TOIL_TEST_TEMP is not defined, temporary files and directories will be created in the system’s default location for such files and any temporary files or directories left over from tests will be removed automatically removed during tear down. Otherwise, left-over files will not be removed.

setup_method(method)[source]¶

Parameters:: method (Any)
Return type:: None

classmethod setUpClass()[source]¶

Hook method for setting up class fixture before running tests in the class.

Return type:: None

classmethod tearDownClass()[source]¶

Hook method for deconstructing the class fixture after running all tests in the class.

Return type:: None

setUp()[source]¶

Hook method for setting up the test fixture before exercising it.

Return type:: None

tearDown()[source]¶

Hook method for deconstructing the test fixture after testing it.

Return type:: None

classmethod awsRegion()[source]¶

Pick an appropriate AWS region.

Use us-west-2 unless running on EC2, in which case use the region in which the instance is located

Return type:: str

toil.test.batchSystems.batch_system_plugin_test.logger¶

class toil.test.batchSystems.batch_system_plugin_test.FakeBatchSystem(config, maxCores, maxMemory, maxDisk)[source]¶

Bases: toil.batchSystems.cleanup_support.BatchSystemCleanupSupport

Adds cleanup support when the last running job leaves a node, for batch systems that can’t provide it using the backing scheduler.

Parameters:

config (toil.common.Config)
maxCores (float)
maxMemory (int)
maxDisk (int)

classmethod supportsAutoDeployment()[source]¶

Whether this batch system supports auto-deployment of the user script itself.

If it does, the setUserScript() can be invoked to set the resource object representing the user script.

Note to implementors: If your implementation returns True here, it should also override

Return type:: bool

issueBatchJob(command, job_desc, job_environment=None)[source]¶

Issues a job with the specified command to the batch system and returns a unique job ID number.

Parameters:

command (str) – the command to execute somewhere to run the Toil worker process
job_desc (toil.job.JobDescription) – the JobDescription for the job being run
job_environment (Optional[Dict[str, str]]) – a collection of job-specific environment variables to be set on the worker.

Returns:

a unique job ID number that can be used to reference the newly issued job

Return type:

int

killBatchJobs(jobIDs)[source]¶

Kills the given job IDs. After returning, the killed jobs will not appear in the results of getRunningBatchJobIDs. The killed job will not be returned from getUpdatedBatchJob.

Parameters:: jobIDs (List[int]) – list of IDs of jobs to kill
Return type:: None

getIssuedBatchJobIDs()[source]¶

Gets all currently issued jobs

Returns:: A list of jobs (as job ID numbers) currently issued (may be running, or may be waiting to be run). Despite the result being a list, the ordering should not be depended upon.
Return type:: List[int]

getRunningBatchJobIDs()[source]¶

Gets a map of jobs as job ID numbers that are currently running (not just waiting) and how long they have been running, in seconds.

Returns:: dictionary with currently running job ID number keys and how many seconds they have been running as the value
Return type:: Dict[int, float]

getUpdatedBatchJob(maxWait)[source]¶

Returns information about job that has updated its status (i.e. ceased running, either successfully or with an error). Each such job will be returned exactly once.

Does not return info for jobs killed by killBatchJobs, although they may cause None to be returned earlier than maxWait.

Parameters:: maxWait (int) – the number of seconds to block, waiting for a result
Returns:: If a result is available, returns UpdatedBatchJobInfo. Otherwise it returns None. wallTime is the number of seconds (a strictly positive float) in wall-clock time the job ran for, or None if this batch system does not support tracking wall time.
Return type:: Optional[toil.batchSystems.abstractBatchSystem.UpdatedBatchJobInfo]

shutdown()[source]¶

Called at the completion of a toil invocation. Should cleanly terminate all worker threads.

Return type:: None

classmethod add_options(parser)[source]¶

If this batch system provides any command line options, add them to the given parser.

Parameters:: parser (configargparse.ArgumentParser)
Return type:: None

classmethod setOptions(setOption)[source]¶

Process command line or configuration options relevant to this batch system.

Parameters:: setOption (toil.batchSystems.options.OptionSetter) – A function with signature setOption(option_name, parsing_function=None, check_function=None, default=None, env=None) returning nothing, used to update run configuration as a side effect.
Return type:: None

class toil.test.batchSystems.batch_system_plugin_test.BatchSystemPluginTest(methodName='runTest')[source]¶

Bases: toil.test.ToilTest

A common base class for Toil tests.

Please have every test case directly or indirectly inherit this one.

When running tests you may optionally set the TOIL_TEST_TEMP environment variable to the path of a directory where you want temporary test files be placed. The directory will be created if it doesn’t exist. The path may be relative in which case it will be assumed to be relative to the project root. If TOIL_TEST_TEMP is not defined, temporary files and directories will be created in the system’s default location for such files and any temporary files or directories left over from tests will be removed automatically removed during tear down. Otherwise, left-over files will not be removed.

test_batchsystem_plugin_installable()[source]¶: Test that installing a batch system plugin works. :return:

toil.test.batchSystems.batch_system_plugin_test¶

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