toil.utils.toilStats¶

Reports statistical data about a given Toil workflow.

Attributes¶

`SYS_MAX_SIZE`
`logger`
`CATEGORIES`
`CATEGORY_UNITS`
`TITLES`
`TIME_CATEGORIES`
`SPACE_CATEGORIES`
`COMPUTED_CATEGORIES`
`LONG_FORMS`
`sort_category_choices`
`sort_field_choices`

Exceptions¶

NoSuchJobStoreException

Indicates that the specified job store does not exist.

Classes¶

`Config`	Class to represent configuration operations for a toil workflow run.
`Toil`	A context manager that represents a Toil workflow.
`Job`	Class represents a unit of work in toil.
`AbstractJobStore`	Represents the physical storage for the jobs and files in a Toil workflow.
`Expando`	Pass initial attributes to the constructor:
`ColumnWidths`	Convenience object that stores the width of columns for printing. Helps make things pretty.

Functions¶

`parser_with_common_options`([provisioner_options, ...])
`set_logging_from_options`(options)
`pad_str`(s[, field])	Pad the beginning of a string with spaces, if necessary.
`pretty_space`(k[, field, alone])	Given input k as kibibytes, return a nicely formatted string.
`pretty_time`(t[, field, unit, alone])	Given input t as seconds, return a nicely formatted string.
`report_unit`(unit)	Format a unit name for display.
`report_time`(t, options[, field, unit, alone])	Given t seconds, report back the correct format as string.
`report_space`(k, options[, field, unit, alone])	Given k kibibytes, report back the correct format as string.
`report_number`(n[, field, nan_value])	Given a number, report back the correct format as string.
`report`(v, category, options[, field, alone])	Report a value of the given category formatted as a string.
`sprint_tag`(key, tag, options[, columnWidths])	Generate a pretty-print ready string from a JTTag().
`decorate_title`(category, title, options)	Add extra parts to the category titles.
`decorate_subheader`(category, columnWidths, options)	Add a marker to the correct field if the TITLE is sorted on.
`get`(tree, name)	Return a float value attribute NAME from TREE.
`sort_jobs`(jobTypes, options)	Return a jobTypes all sorted.
`report_pretty_data`(root, worker, job, job_types, options)	Print the important bits out.
`compute_column_widths`(job_types, worker, job, options)	Return a ColumnWidths() object with the correct max widths.
`update_column_widths`(tag, cw, options)	Update the column width attributes for this tag's fields.
`build_element`(element, items, item_name, defaults)	Create an element for output.
`create_summary`(element, containingItems, ...)	Figure out how many jobs (or contained items) ran on each worker (or containing item).
`get_stats`(jobStore)	Sum together all the stats information in the job store.
`process_data`(config, stats)	Collate the stats and report
`report_data`(tree, options)
`add_stats_options`(parser)
`main`()	Reports stats on the workflow, use with --stats option to toil.

Module Contents¶

class toil.utils.toilStats.Config[source]¶

Class to represent configuration operations for a toil workflow run.

logFile: str | None¶

logRotating: bool¶

cleanWorkDir: str¶

max_jobs: int¶

max_local_jobs: int¶

manualMemArgs: bool¶

run_local_jobs_on_workers: bool¶

coalesceStatusCalls: bool¶

mesos_endpoint: str | None¶

mesos_framework_id: str | None¶

mesos_role: str | None¶

mesos_name: str¶

kubernetes_host_path: str | None¶

kubernetes_owner: str | None¶

kubernetes_service_account: str | None¶

kubernetes_pod_timeout: float¶

kubernetes_privileged: bool¶

tes_endpoint: str¶

tes_user: str¶

tes_password: str¶

tes_bearer_token: str¶

aws_batch_region: str | None¶

aws_batch_queue: str | None¶

aws_batch_job_role_arn: str | None¶

scale: float¶

batchSystem: str¶

batch_logs_dir: str | None¶: The backing scheduler will be instructed, if possible, to save logs to this directory, where the leader can read them.

statePollingWait: int¶

state_polling_timeout: int¶

disableAutoDeployment: bool¶

workflowID: str | None¶: This attribute uniquely identifies the job store and therefore the workflow. It is necessary in order to distinguish between two consecutive workflows for which self.jobStore is the same, e.g. when a job store name is reused after a previous run has finished successfully and its job store has been clean up.

workflowAttemptNumber: int¶

jobStore: str¶

logLevel: str¶

colored_logs: bool¶

workDir: str | None¶

coordination_dir: str | None¶

noStdOutErr: bool¶

stats: bool¶

clean: str | None¶

clusterStats: str¶

restart: bool¶

caching: bool | None¶

symlinkImports: bool¶

moveOutputs: bool¶

provisioner: str | None¶

nodeTypes: List[Tuple[Set[str], float | None]]¶

minNodes: List[int]¶

maxNodes: List[int]¶

targetTime: float¶

betaInertia: float¶

scaleInterval: int¶

preemptibleCompensation: float¶

nodeStorage: int¶

nodeStorageOverrides: List[str]¶

metrics: bool¶

assume_zero_overhead: bool¶

maxPreemptibleServiceJobs: int¶

maxServiceJobs: int¶

deadlockWait: float | int¶

deadlockCheckInterval: float | int¶

defaultMemory: int¶

defaultCores: float | int¶

defaultDisk: int¶

defaultPreemptible: bool¶

defaultAccelerators: List[toil.job.AcceleratorRequirement]¶

maxCores: int¶

maxMemory: int¶

maxDisk: int¶

retryCount: int¶

enableUnlimitedPreemptibleRetries: bool¶

doubleMem: bool¶

maxJobDuration: int¶

rescueJobsFrequency: int¶

job_store_timeout: float¶

maxLogFileSize: int¶

writeLogs: str¶

writeLogsGzip: str¶

writeLogsFromAllJobs: bool¶

write_messages: str | None¶

realTimeLogging: bool¶

environment: Dict[str, str]¶

disableChaining: bool¶

disableJobStoreChecksumVerification: bool¶

sseKey: str | None¶

servicePollingInterval: int¶

useAsync: bool¶

forceDockerAppliance: bool¶

statusWait: int¶

disableProgress: bool¶

readGlobalFileMutableByDefault: bool¶

debugWorker: bool¶

disableWorkerOutputCapture: bool¶

badWorker: float¶

badWorkerFailInterval: float¶

kill_polling_interval: int¶

cwl: bool¶

set_from_default_config()[source]¶

Return type:: None

prepare_start()[source]¶

After options are set, prepare for initial start of workflow.

Return type:: None

prepare_restart()[source]¶

Before restart options are set, prepare for a restart of a workflow. Set up any execution-specific parameters and clear out any stale ones.

Return type:: None

setOptions(options)[source]¶

Creates a config object from the options object.

Parameters:: options (argparse.Namespace)
Return type:: None

check_configuration_consistency()[source]¶

Old checks that cannot be fit into an action class for argparse

Return type:: None

__eq__(other)[source]¶

Return self==value.

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

__hash__()[source]¶

Return hash(self).

Return type:: int

class toil.utils.toilStats.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.utils.toilStats.parser_with_common_options(provisioner_options=False, jobstore_option=True, prog=None, default_log_level=None)[source]¶

Parameters:

provisioner_options (bool)
jobstore_option (bool)
prog (Optional[str])
default_log_level (Optional[int])

Return type:

configargparse.ArgParser

class toil.utils.toilStats.Job(memory=None, cores=None, disk=None, accelerators=None, preemptible=None, preemptable=None, unitName='', checkpoint=False, displayName='', descriptionClass=None, local=None)[source]¶

Class represents a unit of work in toil.

Parameters:

memory (Optional[ParseableIndivisibleResource])
cores (Optional[ParseableDivisibleResource])
disk (Optional[ParseableIndivisibleResource])
accelerators (Optional[ParseableAcceleratorRequirement])
preemptible (Optional[ParseableFlag])
preemptable (Optional[ParseableFlag])
unitName (Optional[str])
checkpoint (Optional[bool])
displayName (Optional[str])
descriptionClass (Optional[type])
local (Optional[bool])

__str__()[source]¶: Produce a useful logging string to identify this Job and distinguish it from its JobDescription.

check_initialized()[source]¶

Ensure that Job.__init__() has been called by any subclass __init__().

This uses the fact that the self._description instance variable should always be set after __init__().

If __init__() has not been called, raise an error.

Return type:: None

property jobStoreID: str | TemporaryID¶

Get the ID of this Job.

Return type:: Union[str, TemporaryID]

property description: JobDescription¶

Expose the JobDescription that describes this job.

Return type:: JobDescription

property disk: int¶

The maximum number of bytes of disk the job will require to run.

Return type:: int

property memory¶
The maximum number of bytes of memory the job will require to run.

property cores: int | float¶

The number of CPU cores required.

Return type:: Union[int, float]

property accelerators: List[AcceleratorRequirement]¶

Any accelerators, such as GPUs, that are needed.

Return type:: List[AcceleratorRequirement]

property preemptible: bool¶

Whether the job can be run on a preemptible node.

Return type:: bool

preemptable()[source]¶

property checkpoint: bool¶

Determine if the job is a checkpoint job or not.

Return type:: bool

assignConfig(config)[source]¶

Assign the given config object.

It will be used by various actions implemented inside the Job class.

Parameters:: config (toil.common.Config) – Config object to query
Return type:: None

run(fileStore)[source]¶

Override this function to perform work and dynamically create successor jobs.

Parameters:: fileStore (toil.fileStores.abstractFileStore.AbstractFileStore) – Used to create local and globally sharable temporary files and to send log messages to the leader process.
Returns:: The return value of the function can be passed to other jobs by means of toil.job.Job.rv().
Return type:: Any

addChild(childJob)[source]¶

Add a childJob to be run as child of this job.

Child jobs will be run directly after this job’s toil.job.Job.run() method has completed.

Returns:: childJob: for call chaining
Parameters:: childJob (Job)
Return type:: Job

hasChild(childJob)[source]¶

Check if childJob is already a child of this job.

Returns:: True if childJob is a child of the job, else False.
Parameters:: childJob (Job)
Return type:: bool

addFollowOn(followOnJob)[source]¶

Add a follow-on job.

Follow-on jobs will be run after the child jobs and their successors have been run.

Returns:: followOnJob for call chaining
Parameters:: followOnJob (Job)
Return type:: Job

hasPredecessor(job)[source]¶

Check if a given job is already a predecessor of this job.

Parameters:: job (Job)
Return type:: bool

hasFollowOn(followOnJob)[source]¶

Check if given job is already a follow-on of this job.

Returns:: True if the followOnJob is a follow-on of this job, else False.
Parameters:: followOnJob (Job)
Return type:: bool

addService(service, parentService=None)[source]¶

Add a service.

The toil.job.Job.Service.start() method of the service will be called after the run method has completed but before any successors are run. The service’s toil.job.Job.Service.stop() method will be called once the successors of the job have been run.

Services allow things like databases and servers to be started and accessed by jobs in a workflow.

Raises:

toil.job.JobException – If service has already been made the child of a job or another service.

Parameters:

service (Job) – Service to add.
parentService (Optional[Job]) – Service that will be started before ‘service’ is started. Allows trees of services to be established. parentService must be a service of this job.

Returns:

a promise that will be replaced with the return value from toil.job.Job.Service.start() of service in any successor of the job.

Return type:

Promise

hasService(service)[source]¶

Return True if the given Service is a service of this job, and False otherwise.

Parameters:: service (Job)
Return type:: bool

addChildFn(fn, *args, **kwargs)[source]¶

Add a function as a child job.

Parameters:: fn (Callable) – Function to be run as a child job with *args and **kwargs as arguments to this function. See toil.job.FunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new child job that wraps fn.
Return type:: FunctionWrappingJob

addFollowOnFn(fn, *args, **kwargs)[source]¶

Add a function as a follow-on job.

Parameters:: fn (Callable) – Function to be run as a follow-on job with *args and **kwargs as arguments to this function. See toil.job.FunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new follow-on job that wraps fn.
Return type:: FunctionWrappingJob

addChildJobFn(fn, *args, **kwargs)[source]¶

Add a job function as a child job.

See toil.job.JobFunctionWrappingJob for a definition of a job function.

Parameters:: fn (Callable) – Job function to be run as a child job with *args and **kwargs as arguments to this function. See toil.job.JobFunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new child job that wraps fn.
Return type:: FunctionWrappingJob

addFollowOnJobFn(fn, *args, **kwargs)[source]¶

Add a follow-on job function.

See toil.job.JobFunctionWrappingJob for a definition of a job function.

Parameters:: fn (Callable) – Job function to be run as a follow-on job with *args and **kwargs as arguments to this function. See toil.job.JobFunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new follow-on job that wraps fn.
Return type:: FunctionWrappingJob

property tempDir: str¶

Shortcut to calling job.fileStore.getLocalTempDir().

Temp dir is created on first call and will be returned for first and future calls :return: Path to tempDir. See job.fileStore.getLocalTempDir

Return type:: str

log(text, level=logging.INFO)[source]¶

Log using fileStore.log_to_leader().

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

static wrapFn(fn, *args, **kwargs)[source]¶

Makes a Job out of a function.

Convenience function for constructor of toil.job.FunctionWrappingJob.

Parameters:: fn – Function to be run with *args and **kwargs as arguments. See toil.job.JobFunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new function that wraps fn.
Return type:: FunctionWrappingJob

static wrapJobFn(fn, *args, **kwargs)[source]¶

Makes a Job out of a job function.

Convenience function for constructor of toil.job.JobFunctionWrappingJob.

Parameters:: fn – Job function to be run with *args and **kwargs as arguments. See toil.job.JobFunctionWrappingJob for reserved keyword arguments used to specify resource requirements.
Returns:: The new job function that wraps fn.
Return type:: JobFunctionWrappingJob

encapsulate(name=None)[source]¶

Encapsulates the job, see toil.job.EncapsulatedJob. Convenience function for constructor of toil.job.EncapsulatedJob.

Parameters:: name (Optional[str]) – Human-readable name for the encapsulated job.
Returns:: an encapsulated version of this job.
Return type:: EncapsulatedJob

rv(*path)[source]¶

Create a promise (toil.job.Promise).

The “promise” representing a return value of the job’s run method, or, in case of a function-wrapping job, the wrapped function’s return value.

Parameters:: path ((Any)) – Optional path for selecting a component of the promised return value. If absent or empty, the entire return value will be used. Otherwise, the first element of the path is used to select an individual item of the return value. For that to work, the return value must be a list, dictionary or of any other type implementing the __getitem__() magic method. If the selected item is yet another composite value, the second element of the path can be used to select an item from it, and so on. For example, if the return value is [6,{‘a’:42}], .rv(0) would select 6 , rv(1) would select {‘a’:3} while rv(1,’a’) would select 3. To select a slice from a return value that is slicable, e.g. tuple or list, the path element should be a slice object. For example, assuming that the return value is [6, 7, 8, 9] then .rv(slice(1, 3)) would select [7, 8]. Note that slicing really only makes sense at the end of path.
Returns:: A promise representing the return value of this jobs toil.job.Job.run() method.
Return type:: Promise

registerPromise(path)[source]¶

prepareForPromiseRegistration(jobStore)[source]¶

Set up to allow this job’s promises to register themselves.

Prepare this job (the promisor) so that its promises can register themselves with it, when the jobs they are promised to (promisees) are serialized.

The promissee holds the reference to the promise (usually as part of the job arguments) and when it is being pickled, so will the promises it refers to. Pickling a promise triggers it to be registered with the promissor.

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

checkJobGraphForDeadlocks()[source]¶

Ensures that a graph of Jobs (that hasn’t yet been saved to the JobStore) doesn’t contain any pathological relationships between jobs that would result in deadlocks if we tried to run the jobs.

See toil.job.Job.checkJobGraphConnected(), toil.job.Job.checkJobGraphAcyclic() and toil.job.Job.checkNewCheckpointsAreLeafVertices() for more info.

Raises:: toil.job.JobGraphDeadlockException – if the job graph is cyclic, contains multiple roots or contains checkpoint jobs that are not leaf vertices when defined (see toil.job.Job.checkNewCheckpointsAreLeaves()).

getRootJobs()[source]¶

Return the set of root job objects that contain this job.

A root job is a job with no predecessors (i.e. which are not children, follow-ons, or services).

Only deals with jobs created here, rather than loaded from the job store.

Return type:: Set[Job]

checkJobGraphConnected()[source]¶

Raises:: toil.job.JobGraphDeadlockException – if toil.job.Job.getRootJobs() does not contain exactly one root job.

As execution always starts from one root job, having multiple root jobs will cause a deadlock to occur.

Only deals with jobs created here, rather than loaded from the job store.

checkJobGraphAcylic()[source]¶

Raises:: toil.job.JobGraphDeadlockException – if the connected component of jobs containing this job contains any cycles of child/followOn dependencies in the augmented job graph (see below). Such cycles are not allowed in valid job graphs.

A follow-on edge (A, B) between two jobs A and B is equivalent to adding a child edge to B from (1) A, (2) from each child of A, and (3) from the successors of each child of A. We call each such edge an edge an “implied” edge. The augmented job graph is a job graph including all the implied edges.

For a job graph G = (V, E) the algorithm is O(|V|^2). It is O(|V| + |E|) for a graph with no follow-ons. The former follow-on case could be improved!

Only deals with jobs created here, rather than loaded from the job store.

checkNewCheckpointsAreLeafVertices()[source]¶

A checkpoint job is a job that is restarted if either it fails, or if any of its successors completely fails, exhausting their retries.

A job is a leaf it is has no successors.

A checkpoint job must be a leaf when initially added to the job graph. When its run method is invoked it can then create direct successors. This restriction is made to simplify implementation.

Only works on connected components of jobs not yet added to the JobStore.

Raises:: toil.job.JobGraphDeadlockException – if there exists a job being added to the graph for which checkpoint=True and which is not a leaf.
Return type:: None

defer(function, *args, **kwargs)[source]¶

Register a deferred function, i.e. a callable that will be invoked after the current attempt at running this job concludes. A job attempt is said to conclude when the job function (or the toil.job.Job.run() method for class-based jobs) returns, raises an exception or after the process running it terminates abnormally. A deferred function will be called on the node that attempted to run the job, even if a subsequent attempt is made on another node. A deferred function should be idempotent because it may be called multiple times on the same node or even in the same process. More than one deferred function may be registered per job attempt by calling this method repeatedly with different arguments. If the same function is registered twice with the same or different arguments, it will be called twice per job attempt.

Examples for deferred functions are ones that handle cleanup of resources external to Toil, like Docker containers, files outside the work directory, etc.

Parameters:

function (callable) – The function to be called after this job concludes.
args (list) – The arguments to the function
kwargs (dict) – The keyword arguments to the function

Return type:

None

class Runner[source]¶

Used to setup and run Toil workflow.

static getDefaultArgumentParser(jobstore_as_flag=False)[source]¶

Get argument parser with added toil workflow options.

Parameters:: jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.
Returns:: The argument parser used by a toil workflow with added Toil options.
Return type:: argparse.ArgumentParser

static getDefaultOptions(jobStore=None, jobstore_as_flag=False)[source]¶

Get default options for a toil workflow.

Parameters:

jobStore (Optional[str]) – A string describing the jobStore for the workflow.
jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.

Returns:

The options used by a toil workflow.

Return type:

argparse.Namespace

static addToilOptions(parser, jobstore_as_flag=False)[source]¶

Adds the default toil options to an optparse or argparse parser object.

Parameters:

parser (Union[optparse.OptionParser, argparse.ArgumentParser]) – Options object to add toil options to.
jobstore_as_flag (bool) – make the job store option a –jobStore flag instead of a required jobStore positional argument.

Return type:

None

static startToil(job, options)[source]¶

Run the toil workflow using the given options.

Deprecated by toil.common.Toil.start.

(see Job.Runner.getDefaultOptions and Job.Runner.addToilOptions) starting with this job. :param job: root job of the workflow :raises: toil.exceptions.FailedJobsException if at the end of function there remain failed jobs. :return: The return value of the root job’s run function.

Parameters:: job (Job)
Return type:: Any

class Service(memory=None, cores=None, disk=None, accelerators=None, preemptible=None, unitName=None)[source]¶

Bases: Requirer

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.

abstract start(job)[source]¶

Start the service.

Parameters:: 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:: Any

abstract stop(job)[source]¶

Stops the service. Function can block until complete.

Parameters:: 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()[source]¶

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:: bool

getUserScript()[source]¶

Return type:: toil.resource.ModuleDescriptor

getTopologicalOrderingOfJobs()[source]¶

Returns:: a list of jobs such that for all pairs of indices i, j for which i < j, the job at index i can be run before the job at index j.
Return type:: List[Job]

Only considers jobs in this job’s subgraph that are newly added, not loaded from the job store.

Ignores service jobs.

saveBody(jobStore)[source]¶

Save the execution data for just this job to the JobStore, and fill in the JobDescription with the information needed to retrieve it.

The Job’s JobDescription must have already had a real jobStoreID assigned to it.

Does not save the JobDescription.

Parameters:: jobStore (toil.jobStores.abstractJobStore.AbstractJobStore) – The job store to save the job body into.
Return type:: None

saveAsRootJob(jobStore)[source]¶

Save this job to the given jobStore as the root job of the workflow.

Returns:: the JobDescription describing this job.
Parameters:: jobStore (toil.jobStores.abstractJobStore.AbstractJobStore)
Return type:: JobDescription

classmethod loadJob(job_store, job_description)[source]¶

Retrieves a toil.job.Job instance from a JobStore

Parameters:

job_store (toil.jobStores.abstractJobStore.AbstractJobStore) – The job store.
job_description (JobDescription) – the JobDescription of the job to retrieve.

Returns:

The job referenced by the JobDescription.

Return type:

Job

set_debug_flag(flag)[source]¶

Enable the given debug option on the job.

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

has_debug_flag(flag)[source]¶

Return true if the given debug flag is set.

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

files_downloaded_hook(host_and_job_paths=None)[source]¶

Function that subclasses can call when they have downloaded their input files.

Will abort the job if the “download_only” debug flag is set.

Can be hinted a list of file path pairs outside and inside the job container, in which case the container environment can be reconstructed.

Parameters:: host_and_job_paths (Optional[List[Tuple[str, str]]])
Return type:: None

class toil.utils.toilStats.AbstractJobStore(locator)[source]¶

Bases: abc.ABC

Represents the physical storage for the jobs and files in a Toil workflow.

JobStores are responsible for storing toil.job.JobDescription (which relate jobs to each other) and files.

Actual toil.job.Job objects are stored in files, referenced by JobDescriptions. All the non-file CRUD methods the JobStore provides deal in JobDescriptions and not full, executable Jobs.

To actually get ahold of a toil.job.Job, use toil.job.Job.loadJob() with a JobStore and the relevant JobDescription.

Parameters:: locator (str)

initialize(config)[source]¶

Initialize this job store.

Create the physical storage for this job store, allocate a workflow ID and persist the given Toil configuration to the store.

Parameters:: config (toil.common.Config) – the Toil configuration to initialize this job store with. The given configuration will be updated with the newly allocated workflow ID.
Raises:: JobStoreExistsException – if the physical storage for this job store already exists
Return type:: None

writeConfig()[source]¶

Return type:: None

write_config()[source]¶

Persists the value of the AbstractJobStore.config attribute to the job store, so that it can be retrieved later by other instances of this class.

Return type:: None

resume()[source]¶

Connect this instance to the physical storage it represents and load the Toil configuration into the AbstractJobStore.config attribute.

Raises:: NoSuchJobStoreException – if the physical storage for this job store doesn’t exist
Return type:: None

property config: toil.common.Config¶

Return the Toil configuration associated with this job store.

Return type:: toil.common.Config

property locator: str¶

Get the locator that defines the job store, which can be used to connect to it.

Return type:: str

rootJobStoreIDFileName = 'rootJobStoreID'¶

setRootJob(rootJobStoreID)[source]¶

Set the root job of the workflow backed by this job store.

Parameters:: rootJobStoreID (toil.fileStores.FileID)
Return type:: None

set_root_job(job_id)[source]¶

Set the root job of the workflow backed by this job store.

Parameters:: job_id (toil.fileStores.FileID) – The ID of the job to set as root
Return type:: None

loadRootJob()[source]¶

Return type:: toil.job.JobDescription

load_root_job()[source]¶

Loads the JobDescription for the root job in the current job store.

Raises:: toil.job.JobException – If no root job is set or if the root job doesn’t exist in this job store
Returns:: The root job.
Return type:: toil.job.JobDescription

createRootJob(desc)[source]¶

Parameters:: desc (toil.job.JobDescription)
Return type:: toil.job.JobDescription

create_root_job(job_description)[source]¶

Create the given JobDescription and set it as the root job in this job store.

Parameters:: job_description (toil.job.JobDescription) – JobDescription to save and make the root job.
Return type:: toil.job.JobDescription

getRootJobReturnValue()[source]¶

Return type:: Any

get_root_job_return_value()[source]¶

Parse the return value from the root job.

Raises an exception if the root job hasn’t fulfilled its promise yet.

Return type:: Any

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

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

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

Imports the file at the given URL into job store. The ID of the newly imported file is returned. If the name of a shared file name is provided, the file will be imported as such and None is returned. If an executable file on the local filesystem is uploaded, its executability will be preserved when it is downloaded.

Currently supported schemes are:

‘s3’ for objects in Amazon S3
e.g. s3://bucket/key

‘file’ for local files
e.g. file:///local/file/path

‘http’
e.g. http://someurl.com/path

‘gs’
e.g. gs://bucket/file

Raises FileNotFoundError if the file does not exist.

Parameters:

src_uri (str) – URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an AWS s3 bucket. It must be a file, not a directory or prefix.
shared_file_name (str) – Optional name to assign to the imported file within the job store

Returns:

The jobStoreFileID of the imported file or None if shared_file_name was given

Return type:

toil.fileStores.FileID or None

exportFile(jobStoreFileID, dstUrl)[source]¶

Parameters:

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

Return type:

None

export_file(file_id, dst_uri)[source]¶

Exports file to destination pointed at by the destination URL. The exported file will be executable if and only if it was originally uploaded from an executable file on the local filesystem.

Refer to AbstractJobStore.import_file() documentation for currently supported URL schemes.

Note that the helper method _exportFile is used to read from the source and write to destination. To implement any optimizations that circumvent this, the _exportFile method should be overridden by subclasses of AbstractJobStore.

Parameters:

file_id (str) – The id of the file in the job store that should be exported.
dst_uri (str) – URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an AWS s3 bucket.

Return type:

None

classmethod url_exists(src_uri)[source]¶

Return True if the file at the given URI exists, and False otherwise.

Parameters:: src_uri (str) – URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an AWS s3 bucket.
Return type:: bool

classmethod get_size(src_uri)[source]¶

Get the size in bytes of the file at the given URL, or None if it cannot be obtained.

Parameters:: src_uri (str) – URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an AWS s3 bucket.
Return type:: Optional[int]

classmethod get_is_directory(src_uri)[source]¶

Return True if the thing at the given URL is a directory, and False if it is a file. The URL may or may not end in ‘/’.

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

classmethod list_url(src_uri)[source]¶

List the directory at the given URL. Returned path components can be joined with ‘/’ onto the passed URL to form new URLs. Those that end in ‘/’ correspond to directories. The provided URL may or may not end with ‘/’.

Currently supported schemes are:

‘s3’ for objects in Amazon S3
e.g. s3://bucket/prefix/

‘file’ for local files
e.g. file:///local/dir/path/

Parameters:: src_uri (str) – URL that points to a directory or prefix in the storage mechanism of a supported URL scheme e.g. a prefix in an AWS s3 bucket.
Returns:: A list of URL components in the given directory, already URL-encoded.
Return type:: List[str]

classmethod read_from_url(src_uri, writable)[source]¶

Read the given URL and write its content into the given writable stream.

Raises FileNotFoundError if the URL doesn’t exist.

Returns:

The size of the file in bytes and whether the executable permission bit is set

Parameters:

src_uri (str)
writable (IO[bytes])

Return type:

Tuple[int, bool]

classmethod open_url(src_uri)[source]¶

Read from the given URI.

Raises FileNotFoundError if the URL doesn’t exist.

Has a readable stream interface, unlike read_from_url() which takes a writable stream.

Parameters:: src_uri (str)
Return type:: IO[bytes]

abstract destroy()[source]¶

The inverse of initialize(), this method deletes the physical storage represented by this instance. While not being atomic, this method is at least idempotent, as a means to counteract potential issues with eventual consistency exhibited by the underlying storage mechanisms. This means that if the method fails (raises an exception), it may (and should be) invoked again. If the underlying storage mechanism is eventually consistent, even a successful invocation is not an ironclad guarantee that the physical storage vanished completely and immediately. A successful invocation only guarantees that the deletion will eventually happen. It is therefore recommended to not immediately reuse the same job store location for a new Toil workflow.

Return type:: None

getEnv()[source]¶

Return type:: Dict[str, str]

get_env()[source]¶

Returns a dictionary of environment variables that this job store requires to be set in order to function properly on a worker.

Return type:: dict[str,str]

clean(jobCache=None)[source]¶

Function to cleanup the state of a job store after a restart.

Fixes jobs that might have been partially updated. Resets the try counts and removes jobs that are not successors of the current root job.

Parameters:: jobCache (Optional[Dict[Union[str, toil.job.TemporaryID], toil.job.JobDescription]]) – if a value it must be a dict from job ID keys to JobDescription object values. Jobs will be loaded from the cache (which can be downloaded from the job store in a batch) instead of piecemeal when recursed into.
Return type:: toil.job.JobDescription

assignID(jobDescription)[source]¶

Parameters:: jobDescription (toil.job.JobDescription)
Return type:: None

abstract assign_job_id(job_description)[source]¶

Get a new jobStoreID to be used by the described job, and assigns it to the JobDescription.

Files associated with the assigned ID will be accepted even if the JobDescription has never been created or updated.

Parameters:: job_description (toil.job.JobDescription) – The JobDescription to give an ID to
Return type:: None

batch()[source]¶

If supported by the batch system, calls to create() with this context manager active will be performed in a batch after the context manager is released.

Return type:: Iterator[None]

create(jobDescription)[source]¶

Parameters:: jobDescription (toil.job.JobDescription)
Return type:: toil.job.JobDescription

abstract create_job(job_description)[source]¶

Writes the given JobDescription to the job store. The job must have an ID assigned already.

Must call jobDescription.pre_update_hook()

Returns:: The JobDescription passed.
Return type:: toil.job.JobDescription
Parameters:: job_description (toil.job.JobDescription)

exists(jobStoreID)[source]¶

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

abstract job_exists(job_id)[source]¶

Indicates whether a description of the job with the specified jobStoreID exists in the job store

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

publicUrlExpiration¶

getPublicUrl(fileName)[source]¶

Parameters:: fileName (str)
Return type:: str

abstract get_public_url(file_name)[source]¶

Returns a publicly accessible URL to the given file in the job store. The returned URL may expire as early as 1h after its been returned. Throw an exception if the file does not exist.

Parameters:: file_name (str) – the jobStoreFileID of the file to generate a URL for
Raises:: NoSuchFileException – if the specified file does not exist in this job store
Return type:: str

getSharedPublicUrl(sharedFileName)[source]¶

Parameters:: sharedFileName (str)
Return type:: str

abstract get_shared_public_url(shared_file_name)[source]¶

Differs from getPublicUrl() in that this method is for generating URLs for shared files written by writeSharedFileStream().

Returns a publicly accessible URL to the given file in the job store. The returned URL starts with ‘http:’, ‘https:’ or ‘file:’. The returned URL may expire as early as 1h after its been returned. Throw an exception if the file does not exist.

Parameters:: shared_file_name (str) – The name of the shared file to generate a publically accessible url for.
Raises:: NoSuchFileException – raised if the specified file does not exist in the store
Return type:: str

load(jobStoreID)[source]¶

Parameters:: jobStoreID (str)
Return type:: toil.job.JobDescription

abstract load_job(job_id)[source]¶

Loads the description of the job referenced by the given ID, assigns it the job store’s config, and returns it.

May declare the job to have failed (see toil.job.JobDescription.setupJobAfterFailure()) if there is evidence of a failed update attempt.

Parameters:: job_id (str) – the ID of the job to load
Raises:: NoSuchJobException – if there is no job with the given ID
Return type:: toil.job.JobDescription

update(jobDescription)[source]¶

Parameters:: jobDescription (toil.job.JobDescription)
Return type:: None

abstract update_job(job_description)[source]¶

Persists changes to the state of the given JobDescription in this store atomically.

Must call jobDescription.pre_update_hook()

Parameters:

job (toil.job.JobDescription) – the job to write to this job store
job_description (toil.job.JobDescription)

Return type:

None

delete(jobStoreID)[source]¶

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

abstract delete_job(job_id)[source]¶

Removes the JobDescription from the store atomically. You may not then subsequently call load(), write(), update(), etc. with the same jobStoreID or any JobDescription bearing it.

This operation is idempotent, i.e. deleting a job twice or deleting a non-existent job will succeed silently.

Parameters:: job_id (str) – the ID of the job to delete from this job store
Return type:: None

abstract jobs()[source]¶

Best effort attempt to return iterator on JobDescriptions for all jobs in the store. The iterator may not return all jobs and may also contain orphaned jobs that have already finished successfully and should not be rerun. To guarantee you get any and all jobs that can be run instead construct a more expensive ToilState object

Returns:: Returns iterator on jobs in the store. The iterator may or may not contain all jobs and may contain invalid jobs
Return type:: Iterator[toil.job.jobDescription]

writeFile(localFilePath, jobStoreID=None, cleanup=False)[source]¶

Parameters:

localFilePath (str)
jobStoreID (Optional[str])
cleanup (bool)

Return type:

str

abstract write_file(local_path, job_id=None, cleanup=False)[source]¶

Takes a file (as a path) and places it in this job store. Returns an ID that can be used to retrieve the file at a later time. The file is written in a atomic manner. It will not appear in the jobStore until the write has successfully completed.

Parameters:

local_path (str) – the path to the local file that will be uploaded to the job store. The last path component (basename of the file) will remain associated with the file in the file store, if supported, so that the file can be searched for by name or name glob.
job_id (str) – the id of a job, or None. If specified, the may be associated with that job in a job-store-specific way. This may influence the returned ID.
cleanup (bool) – Whether to attempt to delete the file when the job whose jobStoreID was given as jobStoreID is deleted with jobStore.delete(job). If jobStoreID was not given, does nothing.

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method
NoSuchJobException – if the job specified via jobStoreID does not exist

Return type:

str

FIXME: some implementations may not raise this

Returns:

an ID referencing the newly created file and can be used to read the file in the future.

Return type:

str

Parameters:

local_path (str)
job_id (Optional[str])
cleanup (bool)

writeFileStream(jobStoreID=None, cleanup=False, basename=None, encoding=None, errors=None)[source]¶

Parameters:

jobStoreID (Optional[str])
cleanup (bool)
basename (Optional[str])
encoding (Optional[str])
errors (Optional[str])

Return type:

ContextManager[Tuple[IO[bytes], str]]

abstract write_file_stream(job_id=None, cleanup=False, basename=None, encoding=None, errors=None)[source]¶

Similar to writeFile, but returns a context manager yielding a tuple of 1) a file handle which can be written to and 2) the ID of the resulting file in the job store. The yielded file handle does not need to and should not be closed explicitly. The file is written in a atomic manner. It will not appear in the jobStore until the write has successfully completed.

Parameters:

job_id (str) – the id of a job, or None. If specified, the may be associated with that job in a job-store-specific way. This may influence the returned ID.
cleanup (bool) – Whether to attempt to delete the file when the job whose jobStoreID was given as jobStoreID is deleted with jobStore.delete(job). If jobStoreID was not given, does nothing.
basename (str) – If supported by the implementation, use the given file basename so that when searching the job store with a query matching that basename, the file will be detected.
encoding (str) – the name of the encoding used to encode the file. Encodings are the same as for encode(). Defaults to None which represents binary mode.
errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method
NoSuchJobException – if the job specified via jobStoreID does not exist

Return type:

Iterator[Tuple[IO[bytes], str]]

FIXME: some implementations may not raise this

Returns:

a context manager yielding a file handle which can be written to and an ID that references the newly created file and can be used to read the file in the future.

Return type:

Iterator[Tuple[IO[bytes], str]]

Parameters:

job_id (Optional[str])
cleanup (bool)
basename (Optional[str])
encoding (Optional[str])
errors (Optional[str])

getEmptyFileStoreID(jobStoreID=None, cleanup=False, basename=None)[source]¶

Parameters:

jobStoreID (Optional[str])
cleanup (bool)
basename (Optional[str])

Return type:

str

abstract get_empty_file_store_id(job_id=None, cleanup=False, basename=None)[source]¶

Creates an empty file in the job store and returns its ID. Call to fileExists(getEmptyFileStoreID(jobStoreID)) will return True.

Parameters:

job_id (str) – the id of a job, or None. If specified, the may be associated with that job in a job-store-specific way. This may influence the returned ID.
cleanup (bool) – Whether to attempt to delete the file when the job whose jobStoreID was given as jobStoreID is deleted with jobStore.delete(job). If jobStoreID was not given, does nothing.
basename (str) – If supported by the implementation, use the given file basename so that when searching the job store with a query matching that basename, the file will be detected.

Returns:

a jobStoreFileID that references the newly created file and can be used to reference the file in the future.

Return type:

str

readFile(jobStoreFileID, localFilePath, symlink=False)[source]¶

Parameters:

jobStoreFileID (str)
localFilePath (str)
symlink (bool)

Return type:

None

abstract read_file(file_id, local_path, symlink=False)[source]¶

Copies or hard links the file referenced by jobStoreFileID to the given local file path. The version will be consistent with the last copy of the file written/updated. If the file in the job store is later modified via updateFile or updateFileStream, it is implementation-defined whether those writes will be visible at localFilePath. The file is copied in an atomic manner. It will not appear in the local file system until the copy has completed.

The file at the given local path may not be modified after this method returns!

Note! Implementations of readFile need to respect/provide the executable attribute on FileIDs.

Parameters:

file_id (str) – ID of the file to be copied
local_path (str) – the local path indicating where to place the contents of the given file in the job store
symlink (bool) – whether the reader can tolerate a symlink. If set to true, the job store may create a symlink instead of a full copy of the file or a hard link.

Return type:

None

readFileStream(jobStoreFileID, encoding=None, errors=None)[source]¶

Parameters:

jobStoreFileID (str)
encoding (Optional[str])
errors (Optional[str])

Return type:

Union[ContextManager[IO[bytes]], ContextManager[IO[str]]]

read_file_stream(file_id: toil.fileStores.FileID | str, encoding: Literal[None] = None, errors: str | None = None) → ContextManager[IO[bytes]][source]¶

read_file_stream(file_id: toil.fileStores.FileID | str, encoding: str, errors: str | None = None) → ContextManager[IO[str]]

Similar to readFile, but returns a context manager yielding a file handle which can be read from. The yielded file handle does not need to and should not be closed explicitly.

Parameters:

file_id (str) – ID of the file to get a readable file handle for
encoding (str) – the name of the encoding used to decode the file. Encodings are the same as for decode(). Defaults to None which represents binary mode.
errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Returns:

a context manager yielding a file handle which can be read from

Return type:

Iterator[Union[IO[bytes], IO[str]]]

deleteFile(jobStoreFileID)[source]¶

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

abstract delete_file(file_id)[source]¶

Deletes the file with the given ID from this job store. This operation is idempotent, i.e. deleting a file twice or deleting a non-existent file will succeed silently.

Parameters:: file_id (str) – ID of the file to delete
Return type:: None

fileExists(jobStoreFileID)[source]¶

Determine whether a file exists in this job store.

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

abstract file_exists(file_id)[source]¶

Determine whether a file exists in this job store.

Parameters:: file_id (str) – an ID referencing the file to be checked
Return type:: bool

getFileSize(jobStoreFileID)[source]¶

Get the size of the given file in bytes.

Parameters:: jobStoreFileID (str)
Return type:: int

abstract get_file_size(file_id)[source]¶

Get the size of the given file in bytes, or 0 if it does not exist when queried.

Note that job stores which encrypt files might return overestimates of file sizes, since the encrypted file may have been padded to the nearest block, augmented with an initialization vector, etc.

Parameters:: file_id (str) – an ID referencing the file to be checked
Return type:: int

updateFile(jobStoreFileID, localFilePath)[source]¶

Replaces the existing version of a file in the job store.

Parameters:

jobStoreFileID (str)
localFilePath (str)

Return type:

None

abstract update_file(file_id, local_path)[source]¶

Replaces the existing version of a file in the job store.

Throws an exception if the file does not exist.

Parameters:

file_id (str) – the ID of the file in the job store to be updated
local_path (str) – the local path to a file that will overwrite the current version in the job store

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method
NoSuchFileException – if the specified file does not exist

Return type:

None

updateFileStream(jobStoreFileID, encoding=None, errors=None)[source]¶

Parameters:

jobStoreFileID (str)
encoding (Optional[str])
errors (Optional[str])

Return type:

ContextManager[IO[Any]]

abstract update_file_stream(file_id, encoding=None, errors=None)[source]¶

Replaces the existing version of a file in the job store. Similar to writeFile, but returns a context manager yielding a file handle which can be written to. The yielded file handle does not need to and should not be closed explicitly.

Parameters:

file_id (str) – the ID of the file in the job store to be updated
encoding (str) – the name of the encoding used to encode the file. Encodings are the same as for encode(). Defaults to None which represents binary mode.
errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method
NoSuchFileException – if the specified file does not exist

Return type:

Iterator[IO[Any]]

sharedFileNameRegex¶

writeSharedFileStream(sharedFileName, isProtected=None, encoding=None, errors=None)[source]¶

Parameters:

sharedFileName (str)
isProtected (Optional[bool])
encoding (Optional[str])
errors (Optional[str])

Return type:

ContextManager[IO[bytes]]

abstract write_shared_file_stream(shared_file_name, encrypted=None, encoding=None, errors=None)[source]¶

Returns a context manager yielding a writable file handle to the global file referenced by the given name. File will be created in an atomic manner.

Parameters:

shared_file_name (str) – A file name matching AbstractJobStore.fileNameRegex, unique within this job store
encrypted (bool) – True if the file must be encrypted, None if it may be encrypted or False if it must be stored in the clear.
encoding (str) – the name of the encoding used to encode the file. Encodings are the same as for encode(). Defaults to None which represents binary mode.
errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method

Returns:

a context manager yielding a writable file handle

Return type:

Iterator[IO[bytes]]

readSharedFileStream(sharedFileName, encoding=None, errors=None)[source]¶

Parameters:

sharedFileName (str)
encoding (Optional[str])
errors (Optional[str])

Return type:

ContextManager[IO[bytes]]

abstract read_shared_file_stream(shared_file_name, encoding=None, errors=None)[source]¶

Returns a context manager yielding a readable file handle to the global file referenced by the given name.

Parameters:

shared_file_name (str) – A file name matching AbstractJobStore.fileNameRegex, unique within this job store
encoding (str) – the name of the encoding used to decode the file. Encodings are the same as for decode(). Defaults to None which represents binary mode.
errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Returns:

a context manager yielding a readable file handle

Return type:

Iterator[IO[bytes]]

writeStatsAndLogging(statsAndLoggingString)[source]¶

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

abstract write_logs(msg)[source]¶

Stores a message as a log in the jobstore.

Parameters:: msg (str) – the string to be written
Raises:: ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method
Return type:: None

readStatsAndLogging(callback, readAll=False)[source]¶

Parameters:

callback (Callable[Ellipsis, Any])
readAll (bool)

Return type:

int

abstract read_logs(callback, read_all=False)[source]¶

Reads logs accumulated by the write_logs() method. For each log this method calls the given callback function with the message as an argument (rather than returning logs directly, this method must be supplied with a callback which will process log messages).

Only unread logs will be read unless the read_all parameter is set.

Parameters:

callback (Callable) – a function to be applied to each of the stats file handles found
read_all (bool) – a boolean indicating whether to read the already processed stats files in addition to the unread stats files

Raises:

ConcurrentFileModificationException – if the file was modified concurrently during an invocation of this method

Returns:

the number of stats files processed

Return type:

int

write_leader_pid()[source]¶

Write the pid of this process to a file in the job store.

Overwriting the current contents of pid.log is a feature, not a bug of this method. Other methods will rely on always having the most current pid available. So far there is no reason to store any old pids.

Return type:: None

read_leader_pid()[source]¶

Read the pid of the leader process to a file in the job store.

Raises:: NoSuchFileException – If the PID file doesn’t exist.
Return type:: int

write_leader_node_id()[source]¶

Write the leader node id to the job store. This should only be called by the leader.

Return type:: None

read_leader_node_id()[source]¶

Read the leader node id stored in the job store.

Raises:: NoSuchFileException – If the node ID file doesn’t exist.
Return type:: str

write_kill_flag(kill=False)[source]¶

Write a file inside the job store that serves as a kill flag.

The initialized file contains the characters “NO”. This should only be changed when the user runs the “toil kill” command.

Changing this file to a “YES” triggers a kill of the leader process. The workers are expected to be cleaned up by the leader.

Parameters:: kill (bool)
Return type:: None

read_kill_flag()[source]¶

Read the kill flag from the job store, and return True if the leader has been killed. False otherwise.

Return type:: bool

default_caching()[source]¶

Jobstore’s preference as to whether it likes caching or doesn’t care about it. Some jobstores benefit from caching, however on some local configurations it can be flaky.

see https://github.com/DataBiosphere/toil/issues/4218

Return type:: bool

exception toil.utils.toilStats.NoSuchJobStoreException(locator, prefix)[source]¶

Bases: LocatorException

Indicates that the specified job store does not exist.

Parameters:

locator (str)
prefix (str)

class toil.utils.toilStats.Expando(*args, **kwargs)[source]¶

Bases: dict

Pass initial attributes to the constructor:

>>> o = Expando(foo=42)
>>> o.foo
42

Dynamically create new attributes:

>>> o.bar = 'hi'
>>> o.bar
'hi'

Expando is a dictionary:

>>> isinstance(o,dict)
True
>>> o['foo']
42

Works great with JSON:

>>> import json
>>> s='{"foo":42}'
>>> o = json.loads(s,object_hook=Expando)
>>> o.foo
42
>>> o.bar = 'hi'
>>> o.bar
'hi'

And since Expando is a dict, it serializes back to JSON just fine:

>>> json.dumps(o, sort_keys=True)
'{"bar": "hi", "foo": 42}'

Attributes can be deleted, too:

>>> o = Expando(foo=42)
>>> o.foo
42
>>> del o.foo
>>> o.foo
Traceback (most recent call last):
...
AttributeError: 'Expando' object has no attribute 'foo'
>>> o['foo']
Traceback (most recent call last):
...
KeyError: 'foo'

>>> del o.foo
Traceback (most recent call last):
...
AttributeError: foo

And copied:

>>> o = Expando(foo=42)
>>> p = o.copy()
>>> isinstance(p,Expando)
True
>>> o == p
True
>>> o is p
False

Same with MagicExpando …

>>> o = MagicExpando()
>>> o.foo.bar = 42
>>> p = o.copy()
>>> isinstance(p,MagicExpando)
True
>>> o == p
True
>>> o is p
False

… but the copy is shallow:

>>> o.foo is p.foo
True

copy()[source]¶: D.copy() -> a shallow copy of D

toil.utils.toilStats.SYS_MAX_SIZE = 9223372036854775807¶

toil.utils.toilStats.set_logging_from_options(options)[source]¶

Parameters:: options (Union[toil.common.Config, argparse.Namespace])
Return type:: None

toil.utils.toilStats.logger¶

toil.utils.toilStats.CATEGORIES = ['time', 'clock', 'wait', 'memory', 'disk']¶

toil.utils.toilStats.CATEGORY_UNITS¶

toil.utils.toilStats.TITLES¶

toil.utils.toilStats.TIME_CATEGORIES¶

toil.utils.toilStats.SPACE_CATEGORIES¶

toil.utils.toilStats.COMPUTED_CATEGORIES¶

toil.utils.toilStats.LONG_FORMS¶

class toil.utils.toilStats.ColumnWidths[source]¶

Convenience object that stores the width of columns for printing. Helps make things pretty.

title(category)[source]¶

Return the total printed length of this category item.

Parameters:: category (str)
Return type:: int

get_width(category, field)[source]¶

Parameters:

category (str)
field (str)

Return type:

int

set_width(category, field, width)[source]¶

Parameters:

category (str)
field (str)
width (int)

Return type:

None

report()[source]¶

Return type:: None

toil.utils.toilStats.pad_str(s, field=None)[source]¶

Pad the beginning of a string with spaces, if necessary.

Parameters:

s (str)
field (Optional[int])

Return type:

str

toil.utils.toilStats.pretty_space(k, field=None, alone=False)[source]¶

Given input k as kibibytes, return a nicely formatted string.

Parameters:

k (float)
field (Optional[int])
alone (bool)

Return type:

str

toil.utils.toilStats.pretty_time(t, field=None, unit='s', alone=False)[source]¶

Given input t as seconds, return a nicely formatted string.

Parameters:

t (float)
field (Optional[int])
unit (str)
alone (bool)

Return type:

str

toil.utils.toilStats.report_unit(unit)[source]¶

Format a unit name for display.

Parameters:: unit (str)
Return type:: str

toil.utils.toilStats.report_time(t, options, field=None, unit='s', alone=False)[source]¶

Given t seconds, report back the correct format as string.

Parameters:

t (float)
options (argparse.Namespace)
field (Optional[int])
unit (str)
alone (bool)

Return type:

str

toil.utils.toilStats.report_space(k, options, field=None, unit='KiB', alone=False)[source]¶

Given k kibibytes, report back the correct format as string.

If unit is set to B, convert to KiB first.

Parameters:

k (float)
options (argparse.Namespace)
field (Optional[int])
unit (str)
alone (bool)

Return type:

str

toil.utils.toilStats.report_number(n, field=None, nan_value='NaN')[source]¶

Given a number, report back the correct format as string.

If it is a NaN or None, use nan_value to represent it instead.

Parameters:

n (Union[int, float, None])
field (Optional[int])
nan_value (str)

Return type:

str

toil.utils.toilStats.report(v, category, options, field=None, alone=False)[source]¶

Report a value of the given category formatted as a string.

Uses the given field width if set.

If alone is set, the field is being formatted outside a table and might need a unit.

Parameters:

v (float)
category (str)
options (argparse.Namespace)
field (Optional[int])

Return type:

str

toil.utils.toilStats.sprint_tag(key, tag, options, columnWidths=None)[source]¶

Generate a pretty-print ready string from a JTTag().

Parameters:

key (str)
tag (toil.lib.expando.Expando)
options (argparse.Namespace)
columnWidths (Optional[ColumnWidths])

Return type:

str

toil.utils.toilStats.decorate_title(category, title, options)[source]¶

Add extra parts to the category titles.

Add units to title if they won’t appear in the formatted values. Add a marker to TITLE if the TITLE is sorted on.

Parameters:

category (str)
title (str)
options (argparse.Namespace)

Return type:

str

toil.utils.toilStats.decorate_subheader(category, columnWidths, options)[source]¶

Add a marker to the correct field if the TITLE is sorted on.

Parameters:

category (str)
columnWidths (ColumnWidths)
options (argparse.Namespace)

Return type:

str

toil.utils.toilStats.get(tree, name)[source]¶

Return a float value attribute NAME from TREE.

Parameters:

tree (toil.lib.expando.Expando)
name (str)

Return type:

float

toil.utils.toilStats.sort_jobs(jobTypes, options)[source]¶

Return a jobTypes all sorted.

Parameters:

jobTypes (List[Any])
options (argparse.Namespace)

Return type:

List[Any]

toil.utils.toilStats.report_pretty_data(root, worker, job, job_types, options)[source]¶

Print the important bits out.

Parameters:

root (toil.lib.expando.Expando)
worker (toil.lib.expando.Expando)
job (toil.lib.expando.Expando)
job_types (List[Any])
options (argparse.Namespace)

Return type:

str

toil.utils.toilStats.compute_column_widths(job_types, worker, job, options)[source]¶

Return a ColumnWidths() object with the correct max widths.

Parameters:

job_types (List[Any])
worker (toil.lib.expando.Expando)
job (toil.lib.expando.Expando)
options (argparse.Namespace)

Return type:

ColumnWidths

toil.utils.toilStats.update_column_widths(tag, cw, options)[source]¶

Update the column width attributes for this tag’s fields.

Parameters:

Return type:

None

toil.utils.toilStats.build_element(element, items, item_name, defaults)[source]¶

Create an element for output.

Parameters:

element (toil.lib.expando.Expando)
items (List[toil.job.Job])
item_name (str)
defaults (Dict[str, float])

Return type:

toil.lib.expando.Expando

toil.utils.toilStats.create_summary(element, containingItems, containingItemName, count_contained)[source]¶

Figure out how many jobs (or contained items) ran on each worker (or containing item).

Stick a bunch of xxx_number_per_xxx stats into element to describe this.

Parameters:

count_contained (Callable[[toil.lib.expando.Expando], int]) – function that maps from containing item to number of contained items.
element (toil.lib.expando.Expando)
containingItems (List[toil.lib.expando.Expando])
containingItemName (str)

Return type:

None

toil.utils.toilStats.get_stats(jobStore)[source]¶

Sum together all the stats information in the job store.

Produces one object containing lists of the values from all the summed objects.

Parameters:: jobStore (toil.jobStores.abstractJobStore.AbstractJobStore)
Return type:: toil.lib.expando.Expando

toil.utils.toilStats.process_data(config, stats)[source]¶

Collate the stats and report

Parameters:

config (toil.common.Config)
stats (toil.lib.expando.Expando)

Return type:

toil.lib.expando.Expando

toil.utils.toilStats.report_data(tree, options)[source]¶

Parameters:

tree (toil.lib.expando.Expando)
options (argparse.Namespace)

Return type:

None

toil.utils.toilStats.sort_category_choices¶

toil.utils.toilStats.sort_field_choices = ['min', 'med', 'ave', 'max', 'total']¶

toil.utils.toilStats.add_stats_options(parser)[source]¶

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

toil.utils.toilStats.main()[source]¶

Reports stats on the workflow, use with –stats option to toil.

Return type:: None

toil.utils.toilStats¶

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