toil.jobStores.aws.jobStore

Module Contents

Classes

AWSJobStore

A job store that uses Amazon's S3 for file storage and SimpleDB for storing job info and

Attributes

boto3_session

s3_boto3_resource

s3_boto3_client

logger

CONSISTENCY_TICKS

CONSISTENCY_TIME

aRepr

custom_repr

toil.jobStores.aws.jobStore.boto3_session
toil.jobStores.aws.jobStore.s3_boto3_resource
toil.jobStores.aws.jobStore.s3_boto3_client
toil.jobStores.aws.jobStore.logger
toil.jobStores.aws.jobStore.CONSISTENCY_TICKS = 5
toil.jobStores.aws.jobStore.CONSISTENCY_TIME = 1
exception toil.jobStores.aws.jobStore.ChecksumError

Bases: Exception

Raised when a download from AWS does not contain the correct data.

class toil.jobStores.aws.jobStore.AWSJobStore(locator, partSize=50 << 20)

Bases: toil.jobStores.abstractJobStore.AbstractJobStore

A job store that uses Amazon’s S3 for file storage and SimpleDB for storing job info and enforcing strong consistency on the S3 file storage. There will be SDB domains for jobs and files and a versioned S3 bucket for file contents. Job objects are pickled, compressed, partitioned into chunks of 1024 bytes and each chunk is stored as a an attribute of the SDB item representing the job. UUIDs are used to identify jobs and files.

Parameters:

  • locator (str)

  • partSize (int)

class FileInfo(fileID, ownerID, encrypted, version=None, content=None, numContentChunks=0, checksum=None)

Bases: toil.jobStores.aws.utils.SDBHelper

Represents a file in this job store.

property fileID
property ownerID
property version
property previousVersion
property content
property checksum
outer
Type:

AWSJobStore

classmethod create(ownerID)
classmethod presenceIndicator()

The key that is guaranteed to be present in the return value of binaryToAttributes(). Assuming that binaryToAttributes() is used with SDB’s PutAttributes, the return value of this method could be used to detect the presence/absence of an item in SDB.

classmethod exists(jobStoreFileID)
classmethod load(jobStoreFileID)
classmethod loadOrCreate(jobStoreFileID, ownerID, encrypted)
classmethod loadOrFail(jobStoreFileID, customName=None)
Return type:

AWSJobStore.FileInfo

Returns:

an instance of this class representing the file with the given ID

Raises:

NoSuchFileException – if given file does not exist

classmethod fromItem(item)

Convert an SDB item to an instance of this class.

toItem()

Convert this instance to an attribute dictionary suitable for SDB put_attributes().

Return type:

(dict,int)

Returns:

the attributes dict and an integer specifying the the number of chunk attributes in the dictionary that are used for storing inlined content.

static maxInlinedSize()
save()
upload(localFilePath, calculateChecksum=True)
uploadStream(multipart=True, allowInlining=True, encoding=None, errors=None)

Context manager that gives out a binary or text mode upload stream to upload data.

copyFrom(srcObj)

Copies contents of source key into this file.

Parameters:

srcObj (S3.Object) – The key (object) that will be copied from

copyTo(dstObj)

Copies contents of this file to the given key.

Parameters:

dstObj (S3.Object) – The key (object) to copy this file’s content to

download(localFilePath, verifyChecksum=True)
downloadStream(verifyChecksum=True, encoding=None, errors=None)

Context manager that gives out a download stream to download data.

delete()
getSize()

Return the size of the referenced item in bytes.

__repr__()

Return repr(self).

property sseKeyPath
bucketNameRe
minBucketNameLen = 3
maxBucketNameLen = 63
maxNameLen = 10
nameSeparator = '--'
jobsPerBatchInsert = 25
itemsPerBatchDelete = 25
sharedFileOwnerID
statsFileOwnerID
readStatsFileOwnerID
versionings
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

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.

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

job_exists(job_id)

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

Return type:

bool

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]

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_description)

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

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

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:

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:

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]]

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]]

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:
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:
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

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.

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

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]]]

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]]

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

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

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(shared_file_name)

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

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.

toil.jobStores.aws.jobStore.aRepr
toil.jobStores.aws.jobStore.custom_repr
exception toil.jobStores.aws.jobStore.BucketLocationConflictException(bucketRegion)

Bases: toil.jobStores.abstractJobStore.LocatorException

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