toil.jobStores.abstractJobStore

Attributes

memoize

Memoize a function result based on its parameters using this decorator.

logger

Exceptions

JobException

General job exception.

ProxyConnectionError

Dummy class.

LocatorException

Base exception class for all locator exceptions.

InvalidImportExportUrlException

Common base class for all non-exit exceptions.

UnimplementedURLException

Unspecified run-time error.

NoSuchJobException

Indicates that the specified job does not exist.

ConcurrentFileModificationException

Indicates that the file was attempted to be modified by multiple processes at once.

NoSuchFileException

Indicates that the specified file does not exist.

NoSuchJobStoreException

Indicates that the specified job store does not exist.

JobStoreExistsException

Indicates that the specified job store already exists.

Classes

Config

Class to represent configuration operations for a toil workflow run.

FileID

A small wrapper around Python's builtin string class.

CheckpointJobDescription

A description of a job that is a checkpoint.

JobDescription

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

ServiceJobDescription

A description of a job that hosts a service.

WriteWatchingStream

A stream wrapping class that calls any functions passed to onWrite() with the number of bytes written for every write.

ErrorCondition

A wrapper describing an error condition.

AbstractJobStore

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

JobStoreSupport

A mostly fake JobStore to access URLs not really associated with real job

Functions

getNodeID()

Return unique ID of the current node (host). The resulting string will be convertible to a uuid.UUID.

safeUnpickleFromStream(stream)

deprecated(new_function_name)

retry([intervals, infinite_retries, errors, ...])

Retry a function if it fails with any Exception defined in "errors".

Module Contents

class toil.jobStores.abstractJobStore.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

toil.jobStores.abstractJobStore.getNodeID()[source]

Return unique ID of the current node (host). The resulting string will be convertible to a uuid.UUID.

Tries several methods until success. The returned ID should be identical across calls from different processes on the same node at least until the next OS reboot.

The last resort method is uuid.getnode() that in some rare OS configurations may return a random ID each time it is called. However, this method should never be reached on a Linux system, because reading from /proc/sys/kernel/random/boot_id will be tried prior to that. If uuid.getnode() is reached, it will be called twice, and exception raised if the values are not identical.

Return type:

str

toil.jobStores.abstractJobStore.safeUnpickleFromStream(stream)[source]
Parameters:

stream (IO[Any])

Return type:

Any

class toil.jobStores.abstractJobStore.FileID(fileStoreID, size, executable=False)[source]

Bases: str

A small wrapper around Python’s builtin string class.

It is used to represent a file’s ID in the file store, and has a size attribute that is the file’s size in bytes. This object is returned by importFile and writeGlobalFile.

Calls into the file store can use bare strings; size will be queried from the job store if unavailable in the ID.

Parameters:
pack()[source]

Pack the FileID into a string so it can be passed through external code.

Return type:

str

classmethod forPath(fileStoreID, filePath)[source]
Parameters:

  • fileStoreID (str)

  • filePath (str)

Return type:

FileID

classmethod unpack(packedFileStoreID)[source]

Unpack the result of pack() into a FileID object.

Parameters:

packedFileStoreID (str)

Return type:

FileID

class toil.jobStores.abstractJobStore.CheckpointJobDescription(*args, **kwargs)[source]

Bases: JobDescription

A description of a job that is a checkpoint.

set_checkpoint()[source]

Save a body checkpoint into self.checkpoint

Return type:

str

restore_checkpoint()[source]

Restore the body checkpoint from self.checkpoint

Return type:

None

restartCheckpoint(jobStore)[source]

Restart a checkpoint after the total failure of jobs in its subtree.

Writes the changes to the jobStore immediately. All the checkpoint’s successors will be deleted, but its try count will not be decreased.

Returns a list with the IDs of any successors deleted.

Parameters:

jobStore (toil.jobStores.abstractJobStore.AbstractJobStore)

Return type:

List[str]

class toil.jobStores.abstractJobStore.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:
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:
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

exception toil.jobStores.abstractJobStore.JobException(message)[source]

Bases: Exception

General job exception.

Parameters:

message (str)

class toil.jobStores.abstractJobStore.ServiceJobDescription(*args, **kwargs)[source]

Bases: JobDescription

A description of a job that hosts a service.

onRegistration(jobStore)[source]

Setup flag files.

When a ServiceJobDescription first meets the JobStore, it needs to set up its flag files.

toil.jobStores.abstractJobStore.deprecated(new_function_name)[source]
Parameters:

new_function_name (str)

Return type:

Callable[Ellipsis, Any]

class toil.jobStores.abstractJobStore.WriteWatchingStream(backingStream)[source]

A stream wrapping class that calls any functions passed to onWrite() with the number of bytes written for every write.

Not seekable.

Parameters:

backingStream (IO[Any])

onWrite(listener)[source]

Call the given listener with the number of bytes written on every write.

Parameters:

listener (Callable[[int], None])

Return type:

None

write(data)[source]

Write the given data to the file.

writelines(datas)[source]

Write each string from the given iterable, without newlines.

flush()[source]

Flush the backing stream.

close()[source]

Close the backing stream.

toil.jobStores.abstractJobStore.memoize

Memoize a function result based on its parameters using this decorator.

For example, this can be used in place of lazy initialization. If the decorating function is invoked by multiple threads, the decorated function may be called more than once with the same arguments.

class toil.jobStores.abstractJobStore.ErrorCondition(error=None, error_codes=None, boto_error_codes=None, error_message_must_include=None, retry_on_this_condition=True)[source]

A wrapper describing an error condition.

ErrorCondition events may be used to define errors in more detail to determine whether to retry.

Parameters:

  • error (Optional[Any])

  • error_codes (List[int])

  • boto_error_codes (List[str])

  • error_message_must_include (str)

  • retry_on_this_condition (bool)

toil.jobStores.abstractJobStore.retry(intervals=None, infinite_retries=False, errors=None, log_message=None, prepare=None)[source]

Retry a function if it fails with any Exception defined in “errors”.

Does so every x seconds, where x is defined by a list of numbers (ints or floats) in “intervals”. Also accepts ErrorCondition events for more detailed retry attempts.

Parameters:

  • intervals (Optional[List]) – A list of times in seconds we keep retrying until returning failure. Defaults to retrying with the following exponential back-off before failing: 1s, 1s, 2s, 4s, 8s, 16s

  • infinite_retries (bool) – If this is True, reset the intervals when they run out. Defaults to: False.

  • errors (Optional[Sequence[Union[ErrorCondition, Type[Exception]]]]) –

    A list of exceptions OR ErrorCondition objects to catch and retry on. ErrorCondition objects describe more detailed error event conditions than a plain error. An ErrorCondition specifies: - Exception (required) - Error codes that must match to be retried (optional; defaults to not checking) - A string that must be in the error message to be retried (optional; defaults to not checking) - A bool that can be set to False to always error on this condition.

    If not specified, this will default to a generic Exception.

  • log_message (Optional[Tuple[Callable, str]]) – Optional tuple of (“log/print function()”, “message string”) that will precede each attempt.

  • prepare (Optional[List[Callable]]) – Optional list of functions to call, with the function’s arguments, between retries, to reset state.

Returns:

The result of the wrapped function or raise.

Return type:

Callable[[Callable[Ellipsis, RT]], Callable[Ellipsis, RT]]

toil.jobStores.abstractJobStore.logger
exception toil.jobStores.abstractJobStore.ProxyConnectionError[source]

Bases: BaseException

Dummy class.

exception toil.jobStores.abstractJobStore.LocatorException(error_msg, locator, prefix=None)[source]

Bases: Exception

Base exception class for all locator exceptions. For example, job store/aws bucket exceptions where they already exist

Parameters:

  • error_msg (str)

  • locator (str)

  • prefix (Optional[str])

exception toil.jobStores.abstractJobStore.InvalidImportExportUrlException(url)[source]

Bases: Exception

Common base class for all non-exit exceptions.

Parameters:

url (urllib.parse.ParseResult)

exception toil.jobStores.abstractJobStore.UnimplementedURLException(url, operation)[source]

Bases: RuntimeError

Unspecified run-time error.

Parameters:
exception toil.jobStores.abstractJobStore.NoSuchJobException(jobStoreID)[source]

Bases: Exception

Indicates that the specified job does not exist.

Parameters:

jobStoreID (toil.fileStores.FileID)

exception toil.jobStores.abstractJobStore.ConcurrentFileModificationException(jobStoreFileID)[source]

Bases: Exception

Indicates that the file was attempted to be modified by multiple processes at once.

Parameters:

jobStoreFileID (toil.fileStores.FileID)

exception toil.jobStores.abstractJobStore.NoSuchFileException(jobStoreFileID, customName=None, *extra)[source]

Bases: Exception

Indicates that the specified file does not exist.

Parameters:
exception toil.jobStores.abstractJobStore.NoSuchJobStoreException(locator, prefix)[source]

Bases: LocatorException

Indicates that the specified job store does not exist.

Parameters:
exception toil.jobStores.abstractJobStore.JobStoreExistsException(locator, prefix)[source]

Bases: LocatorException

Indicates that the specified job store already exists.

Parameters:
class toil.jobStores.abstractJobStore.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:

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:
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:

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:
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:
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:
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:
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:
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:
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

class toil.jobStores.abstractJobStore.JobStoreSupport(locator)[source]

Bases: AbstractJobStore

A mostly fake JobStore to access URLs not really associated with real job stores.

Parameters:

locator (str)