toil.jobStores.fileJobStore

Attributes

logger

Classes

FileJobStore

A job store that uses a directory on a locally attached file system. To be compatible with

Module Contents

toil.jobStores.fileJobStore.logger

class toil.jobStores.fileJobStore.FileJobStore(path, fanOut=1000)

Bases: toil.jobStores.abstractJobStore.AbstractJobStore

A job store that uses a directory on a locally attached file system. To be compatible with distributed batch systems, that file system must be shared by all worker nodes.

Parameters:

• path (str)

• fanOut (int)

validDirs = 'abcdefghijklmnopqrstuvwxyz0123456789'

validDirsSet

JOB_DIR_PREFIX = 'instance-'

JOB_NAME_DIR_PREFIX = 'kind-'

BUFFER_SIZE = 10485760

default_caching()

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

jobStoreDir

jobsDir

statsDir

filesDir

jobFilesDir

sharedFilesDir

fanOut

linkImports = None

moveExports = None

symlink_job_store_reads = None

__repr__()

initialize(config)

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 – 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

resume()

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

destroy()

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.

assign_job_id(job_description)

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

create_job(job_description)

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

batch()

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.

job_exists(job_id)

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

Return type:

bool

get_public_url(jobStoreFileID)

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

get_shared_public_url(sharedFileName)

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_job(job_id)

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 – the ID of the job to load

Raises:

NoSuchJobException – if there is no job with the given ID

update_job(job)

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

Must call jobDescription.pre_update_hook()

Parameters:

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

delete_job(job_id)

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

jobs()

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]

optional_hard_copy(hardlink)

write_file(local_path, job_id=None, cleanup=False)

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

Parameters:

• local_path (str) – the path to the local file that will be uploaded to the job store. The last path component (basename of the file) will remain associated with the file in the file store, if supported, so that the file can be searched for by name or name glob.

• job_id (str) – the id of a job, or None. If specified, the may be associated with that job in a job-store-specific way. This may influence the returned ID.

• cleanup (bool) – Whether to attempt to delete the file when the job whose jobStoreID was given as jobStoreID is deleted with jobStore.delete(job). If jobStoreID was not given, does nothing.

Raises:

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

• NoSuchJobException – if the job specified via jobStoreID does not exist

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

write_file_stream(job_id=None, cleanup=False, basename=None, encoding=None, errors=None)

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

Parameters:

• job_id (str) – the id of a job, or None. If specified, the may be associated with that job in a job-store-specific way. This may influence the returned ID.

• cleanup (bool) – Whether to attempt to delete the file when the job whose jobStoreID was given as jobStoreID is deleted with jobStore.delete(job). If jobStoreID was not given, does nothing.

• basename (str) – If supported by the implementation, use the given file basename so that when searching the job store with a query matching that basename, the file will be detected.

• encoding (str) – the name of the encoding used to encode the file. Encodings are the same as for encode(). Defaults to None which represents binary mode.

• errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Raises:

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

• NoSuchJobException – if the job specified via jobStoreID does not exist

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]]

get_empty_file_store_id(jobStoreID=None, cleanup=False, basename=None)

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

update_file(file_id, local_path)

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

Throws an exception if the file does not exist.

Parameters:

• file_id – the ID of the file in the job store to be updated

• local_path – the local path to a file that will overwrite the current version in the job store

Raises:

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

• NoSuchFileException – if the specified file does not exist

read_file(file_id, local_path, symlink=False)

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

delete_file(file_id)

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

file_exists(file_id)

Determine whether a file exists in this job store.

Parameters:

file_id – an ID referencing the file to be checked

get_file_size(file_id)

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

update_file_stream(file_id, encoding=None, errors=None)

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

Parameters:

• file_id (str) – the ID of the file in the job store to be updated

• encoding (str) – the name of the encoding used to encode the file. Encodings are the same as for encode(). Defaults to None which represents binary mode.

• errors (str) – an optional string that specifies how encoding errors are to be handled. Errors are the same as for open(). Defaults to ‘strict’ when an encoding is specified.

Raises:

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

• NoSuchFileException – if the specified file does not exist

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

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

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

write_shared_file_stream(shared_file_name, encrypted=None, encoding=None, errors=None)

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]]

read_shared_file_stream(shared_file_name, encoding=None, errors=None)

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]]

list_all_file_names(for_job=None)

Get all the file names (not file IDs) of files stored in the job store.

Used for debugging.

Parameters:

for_job (Optional[str]) – If set, restrict the list to files for a particular job.

Return type:

Iterable[str]

write_logs(msg)

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

read_logs(callback, read_all=False)

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