toil.toilState

Attributes

logger

Exceptions

NoSuchJobException

Indicates that the specified job does not exist.

Classes

JobUpdatedMessage

Produced when a job is "updated" and ready to have something happen to it.

MessageBus

Holds messages that should cause jobs to change their scheduling states.

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.

AbstractJobStore

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

ToilState

Holds the leader's scheduling information.

Module Contents

class toil.toilState.JobUpdatedMessage[source]

Bases: NamedTuple

Produced when a job is “updated” and ready to have something happen to it.

job_id: str
result_status: int
class toil.toilState.MessageBus[source]

Holds messages that should cause jobs to change their scheduling states. Messages are put in and buffered, and can be taken out and handled as batches when convenient.

All messages are NamedTuple objects of various subtypes.

Message order is guaranteed to be preserved within a type.

publish(message)[source]

Put a message onto the bus. Can be called from any thread.

Parameters:

message (Any)

Return type:

None

check()[source]

If we are in the owning thread, deliver any messages that are in the queue for us. Must be called every once in a while in the main thread, possibly through inbox objects.

Return type:

None

MessageType
subscribe(message_type, handler)[source]

Register the given callable to be called when messages of the given type are sent. It will be called with messages sent after the subscription is created. Returns a subscription object; when the subscription object is GC’d the subscription will end.

Parameters:

  • message_type (Type[MessageType])

  • handler (Callable[[MessageType], Any])

Return type:

pubsub.core.listener.Listener

connect(wanted_types)[source]

Get a connection object that serves as an inbox for messages of the given types. Messages of those types will accumulate in the inbox until it is destroyed. You can check for them at any time.

Parameters:

wanted_types (List[type])

Return type:

MessageBusConnection

outbox()[source]

Get a connection object that only allows sending messages.

Return type:

MessageOutbox

connect_output_file(file_path)[source]

Send copies of all messages to the given output file.

Returns connection data which must be kept alive for the connection to persist. That data is opaque: the user is not supposed to look at it or touch it or do anything with it other than store it somewhere or delete it.

Parameters:

file_path (str)

Return type:

Any

classmethod scan_bus_messages(stream, message_types)[source]

Get an iterator over all messages in the given log stream of the given types, in order. Discard any trailing partial messages.

Parameters:

  • stream (IO[bytes])

  • message_types (List[Type[NamedTuple]])

Return type:

Iterator[Any]

class toil.toilState.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.toilState.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

class toil.toilState.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

exception toil.toilState.NoSuchJobException(jobStoreID)[source]

Bases: Exception

Indicates that the specified job does not exist.

Parameters:

jobStoreID (toil.fileStores.FileID)

toil.toilState.logger
class toil.toilState.ToilState(jobStore)[source]

Holds the leader’s scheduling information.

But onlt that which does not need to be persisted back to the JobStore (such as information on completed and outstanding predecessors)

Holds the true single copies of all JobDescription objects that the Leader and ServiceManager will use. The leader and service manager shouldn’t do their own load() and update() calls on the JobStore; they should go through this class.

Everything in the leader should reference JobDescriptions by ID.

Only holds JobDescription objects, not Job objects, and those JobDescription objects only exist in single copies.

Parameters:

jobStore (toil.jobStores.abstractJobStore.AbstractJobStore)

load_workflow(rootJob, jobCache=None)[source]

Load the workflow rooted at the given job.

If jobs are loaded that have updated and need to be dealt with by the leader, JobUpdatedMessage messages will be sent to the message bus.

The jobCache is a map from jobStoreID to JobDescription or None. Is used to speed up the building of the state when loading initially from the JobStore, and is not preserved.

Parameters:
Return type:

None

job_exists(job_id)[source]

Test if the givin job exists now.

Returns True if the given job exists right now, and false if it hasn’t been created or it has been deleted elsewhere.

Doesn’t guarantee that the job will or will not be gettable, if racing another process, or if it is still cached.

Parameters:

job_id (str)

Return type:

bool

get_job(job_id)[source]

Get the one true copy of the JobDescription with the given ID.

Parameters:

job_id (str)

Return type:

toil.job.JobDescription

commit_job(job_id)[source]

Save back any modifications made to a JobDescription.

(one retrieved from get_job())

Parameters:

job_id (str)

Return type:

None

delete_job(job_id)[source]

Destroy a JobDescription.

May raise an exception if the job could not be cleaned up (i.e. files belonging to it failed to delete).

Parameters:

job_id (str)

Return type:

None

reset_job(job_id)[source]

Discard any local modifications to a JobDescription.

Will make modifications from other hosts visible.

Parameters:

job_id (str)

Return type:

None

reset_job_expecting_change(job_id, timeout)[source]

Discard any local modifications to a JobDescription.

Will make modifications from other hosts visible.

Will wait for up to timeout seconds for a modification (or deletion) from another host to actually be visible.

Always replaces the JobDescription with what is stored in the job store, even if no modification ends up being visible.

Returns True if an update was detected in time, and False otherwise.

Parameters:
Return type:

bool

successors_pending(predecessor_id, count)[source]

Remember that the given job has the given number more pending successors.

(that have not yet succeeded or failed.)

Parameters:

  • predecessor_id (str)

  • count (int)

Return type:

None

successor_returned(predecessor_id)[source]

Remember that the given job has one fewer pending successors.

(because one has succeeded or failed.)

Parameters:

predecessor_id (str)

Return type:

None

count_pending_successors(predecessor_id)[source]

Count number of pending successors of the given job.

Pending successors are those which have not yet succeeded or failed.

Parameters:

predecessor_id (str)

Return type:

int