# Copyright (C) 2015-2018 Regents of the University of California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from __future__ import absolute_import, print_function
from future import standard_library
standard_library.install_aliases()
from builtins import object
from abc import abstractmethod, ABCMeta
from contextlib import contextmanager
from threading import Semaphore, Event
from future.utils import with_metaclass
import dill
import logging
import os
import tempfile
from toil.lib.objects import abstractclassmethod
from toil.lib.misc import WriteWatchingStream
from toil.common import cacheDirName
from toil.fileStores import FileID
logger = logging.getLogger(__name__)
[docs]class AbstractFileStore(with_metaclass(ABCMeta, object)):
"""
Interface used to allow user code run by Toil to read and write files.
Also provides the interface to other Toil facilities used by user code,
including:
* normal (non-real-time) logging
* finding the correct temporary directory for scratch work
* importing and exporting files into and out of the workflow
Stores user files in the jobStore, but keeps them separate from actual
jobs.
May implement caching.
Passed as argument to the :meth:`toil.job.Job.run` method.
Access to files is only permitted inside the context manager provided by
:meth:`toil.fileStores.abstractFileStore.AbstractFileStore.open`.
Also responsible for committing completed jobs back to the job store with
an update operation, and allowing that commit operation to be waited for.
"""
# Variables used for syncing reads/writes
_pendingFileWritesLock = Semaphore()
_pendingFileWrites = set()
_terminateEvent = Event() # Used to signify crashes in threads
[docs] def __init__(self, jobStore, jobGraph, localTempDir, waitForPreviousCommit):
"""
Create a new file store object.
:param toil.jobStores.abstractJobStore.AbstractJobStore jobStore: the job store
in use for the current Toil run.
:param toil.jobGraph.JobGraph jobGraph: the job graph object for the currently
running job.
:param str localTempDir: the per-worker local temporary directory, under which
per-job directories will be created. Assumed to be inside the
workflow directory, which is assumed to be inside the work directory.
:param waitForPreviousCommit: the waitForCommit method of the previous job's file
store, when jobs are running in sequence on the same worker. Used to
prevent this file store's startCommit and the previous job's
startCommit methods from running at the same time and racing. If
they did race, it might be possible for the later job to be fully
marked as completed in the job store before the eralier job was.
"""
self.jobStore = jobStore
self.jobGraph = jobGraph
self.localTempDir = os.path.abspath(localTempDir)
self.workFlowDir = os.path.dirname(self.localTempDir)
self.workDir = os.path.dirname(self.localTempDir)
self.jobName = self.jobGraph.command.split()[1]
self.waitForPreviousCommit = waitForPreviousCommit
self.loggingMessages = []
# Records file IDs of files deleted during the current job. Doesn't get
# committed back until the job is completely successful, because if the
# job is re-run it will need to be able to re-delete these files.
# This is a set of str objects, not FileIDs.
self.filesToDelete = set()
# Records IDs of jobs that need to be deleted when the currently
# running job is cleaned up.
# May be modified by the worker to actually delete jobs!
self.jobsToDelete = set()
@staticmethod
def createFileStore(jobStore, jobGraph, localTempDir, waitForPreviousCommit, caching):
# Defer these imports until runtime, since these classes depend on us
from toil.fileStores.cachingFileStore import CachingFileStore
from toil.fileStores.nonCachingFileStore import NonCachingFileStore
fileStoreCls = CachingFileStore if caching else NonCachingFileStore
return fileStoreCls(jobStore, jobGraph, localTempDir, waitForPreviousCommit)
[docs] @staticmethod
def shutdownFileStore(workflowDir, workflowID):
"""
Carry out any necessary filestore-specific cleanup.
This is a destructive operation and it is important to ensure that there are no other running
processes on the system that are modifying or using the file store for this workflow.
This is the intended to be the last call to the file store in a Toil run, called by the
batch system cleanup function upon batch system shutdown.
:param str workflowDir: The path to the cache directory
:param str workflowID: The workflow ID for this invocation of the workflow
"""
# Defer these imports until runtime, since these classes depend on our file
from toil.fileStores.cachingFileStore import CachingFileStore
from toil.fileStores.nonCachingFileStore import NonCachingFileStore
cacheDir = os.path.join(workflowDir, cacheDirName(workflowID))
if os.path.exists(cacheDir):
# The presence of the cacheDir suggests this was a cached run. We don't need the cache lock
# for any of this since this is the final cleanup of a job and there should be no other
# conflicting processes using the cache.
CachingFileStore.shutdown(cacheDir)
else:
# This absence of cacheDir suggests otherwise.
NonCachingFileStore.shutdown(workflowDir)
[docs] @abstractmethod
@contextmanager
def open(self, job):
"""
The context manager used to conduct tasks prior-to, and after a job has
been run. File operations are only permitted inside the context
manager.
:param toil.job.Job job: The job instance of the toil job to run.
"""
raise NotImplementedError()
# Functions related to temp files and directories
[docs] def getLocalTempDir(self):
"""
Get a new local temporary directory in which to write files that persist for the duration of
the job.
:return: The absolute path to a new local temporary directory. This directory will exist
for the duration of the job only, and is guaranteed to be deleted once the job
terminates, removing all files it contains recursively.
:rtype: str
"""
return os.path.abspath(tempfile.mkdtemp(prefix="t", dir=self.localTempDir))
[docs] def getLocalTempFile(self):
"""
Get a new local temporary file that will persist for the duration of the job.
:return: The absolute path to a local temporary file. This file will exist for the
duration of the job only, and is guaranteed to be deleted once the job terminates.
:rtype: str
"""
handle, tmpFile = tempfile.mkstemp(prefix="tmp", suffix=".tmp", dir=self.localTempDir)
os.close(handle)
return os.path.abspath(tmpFile)
[docs] def getLocalTempFileName(self):
"""
Get a valid name for a new local file. Don't actually create a file at the path.
:return: Path to valid file
:rtype: str
"""
# Create, and then delete a temp file. Creating will guarantee you a unique, unused
# file name. There is a very, very, very low chance that another job will create the
# same file name in the span of this one being deleted and then being used by the user.
tempFile = self.getLocalTempFile()
os.remove(tempFile)
return tempFile
# Functions related to reading, writing and removing files to/from the job store
[docs] @abstractmethod
def writeGlobalFile(self, localFileName, cleanup=False):
"""
Takes a file (as a path) and uploads it to the job store.
:param string localFileName: The path to the local file to upload.
:param bool cleanup: if True then the copy of the global file will be deleted once the
job and all its successors have completed running. If not the global file must be
deleted manually.
:return: an ID that can be used to retrieve the file.
:rtype: toil.fileStores.FileID
"""
raise NotImplementedError()
[docs] @contextmanager
def writeGlobalFileStream(self, cleanup=False):
"""
Similar to writeGlobalFile, but allows the writing of a stream to the job store.
The yielded file handle does not need to and should not be closed explicitly.
:param bool cleanup: is as in :func:`toil.fileStores.abstractFileStore.AbstractFileStore.writeGlobalFile`.
:return: A context manager yielding a tuple of
1) a file handle which can be written to and
2) the toil.fileStores.FileID of the resulting file in the job store.
"""
# TODO: Make this work with FileID
with self.jobStore.writeFileStream(None if not cleanup else self.jobGraph.jobStoreID) as (backingStream, fileStoreID):
# We have a string version of the file ID, and the backing stream.
# We need to yield a stream the caller can write to, and a FileID
# that accurately reflects the size of the data written to the
# stream. We assume the stream is not seekable.
# Make and keep a reference to the file ID, which is currently empty
fileID = FileID(fileStoreID, 0)
# Wrap the stream to increment the file ID's size for each byte written
wrappedStream = WriteWatchingStream(backingStream)
# When the stream is written to, count the bytes
def handle(numBytes):
# No scope problem here, because we don't assign to a fileID local
fileID.size += numBytes
wrappedStream.onWrite(handle)
yield wrappedStream, fileID
[docs] @abstractmethod
def readGlobalFile(self, fileStoreID, userPath=None, cache=True, mutable=False, symlink=False):
"""
Makes the file associated with fileStoreID available locally. If mutable is True,
then a copy of the file will be created locally so that the original is not modified
and does not change the file for other jobs. If mutable is False, then a link can
be created to the file, saving disk resources.
If a user path is specified, it is used as the destination. If a user path isn't
specified, the file is stored in the local temp directory with an encoded name.
The destination file must not be deleted by the user; it can only be
deleted through deleteLocalFile.
:param toil.fileStores.FileID or str fileStoreID: job store id for the file
:param string userPath: a path to the name of file to which the global file will be copied
or hard-linked (see below).
:param bool cache: Described in :func:`toil.fileStores.CachingFileStore.readGlobalFile`
:param bool mutable: Described in :func:`toil.fileStores.CachingFileStore.readGlobalFile`
:return: An absolute path to a local, temporary copy of the file keyed by fileStoreID.
:rtype: str
"""
raise NotImplementedError()
[docs] @abstractmethod
def readGlobalFileStream(self, fileStoreID):
"""
Similar to readGlobalFile, but allows a stream to be read from the job store. The yielded
file handle does not need to and should not be closed explicitly.
:return: a context manager yielding a file handle which can be read from.
"""
raise NotImplementedError()
[docs] def getGlobalFileSize(self, fileStoreID):
"""
Get the size of the file pointed to by the given ID, in bytes.
If a FileID or something else with a non-None 'size' field, gets that.
Otherwise, asks the job store to poll the file's size.
Note that the job store may overestimate the file's size, for example
if it is encrypted and had to be augmented with an IV or other
encryption framing.
:param toil.fileStores.FileID or str fileStoreID: File ID for the file
:return: File's size in bytes, as stored in the job store
:rtype: int
"""
# First try and see if the size is still attached
size = getattr(fileStoreID, 'size', None)
if size is None:
# It fell off
# Someone is mixing FileStore and JobStore file APIs, or serializing FileIDs as strings.
size = self.jobStore.getFileSize(fileStoreID)
return size
[docs] @abstractmethod
def deleteLocalFile(self, fileStoreID):
"""
Deletes local copies of files associated with the provided job store ID.
The files deleted are all those previously read from this file ID via
readGlobalFile by the current job into the job's file-store-provided
temp directory, plus the file that was written to create the given file
ID, if it was written by the current job from the job's
file-store-provided temp directory.
:param toil.fileStores.FileID or str fileStoreID: File Store ID of the file to be deleted.
"""
raise NotImplementedError()
[docs] @abstractmethod
def deleteGlobalFile(self, fileStoreID):
"""
Deletes local files with the provided job store ID and then permanently deletes them from
the job store. To ensure that the job can be restarted if necessary, the delete will not
happen until after the job's run method has completed.
:param toil.fileStores.FileID or str fileStoreID: the File Store ID of the file to be deleted.
"""
raise NotImplementedError()
# Functions used to read and write files directly between a source url and the job store.
def importFile(self, srcUrl, sharedFileName=None):
return self.jobStore.importFile(srcUrl, sharedFileName=sharedFileName)
def exportFile(self, jobStoreFileID, dstUrl):
raise NotImplementedError()
# A utility method for accessing filenames
def _resolveAbsoluteLocalPath(self, filePath):
"""
Return the absolute path to filePath. This is a wrapper for os.path.abspath because mac OS
symlinks /tmp and /var (the most common places for a default tempdir) to /private/tmp and
/private/var respectively.
:param str filePath: The absolute or relative path to the file. If relative, it must be
relative to the local temp working dir
:return: Absolute path to key
:rtype: str
"""
if os.path.isabs(filePath):
return os.path.abspath(filePath)
else:
return os.path.join(self.localTempDir, filePath)
class _StateFile(object):
"""
Utility class to read and write dill-ed state dictionaries from/to a file into a namespace.
"""
def __init__(self, stateDict):
assert isinstance(stateDict, dict)
self.__dict__.update(stateDict)
@abstractclassmethod
@contextmanager
def open(cls, outer=None):
"""
This is a context manager that state file and reads it into an object that is returned
to the user in the yield.
:param outer: Instance of the calling class (to use outer methods).
"""
raise NotImplementedError()
@classmethod
def _load(cls, fileName):
"""
Load the state of the cache from the state file
:param str fileName: Path to the cache state file.
:return: An instance of the state as a namespace.
:rtype: _StateFile
"""
# Read the value from the cache state file then initialize and instance of
# _CacheState with it.
with open(fileName, 'rb') as fH:
infoDict = dill.load(fH)
return cls(infoDict)
def write(self, fileName):
"""
Write the current state into a temporary file then atomically rename it to the main
state file.
:param str fileName: Path to the state file.
"""
with open(fileName + '.tmp', 'wb') as fH:
# Based on answer by user "Mark" at:
# http://stackoverflow.com/questions/2709800/how-to-pickle-yourself
# We can't pickle nested classes. So we have to pickle the variables of the class
# If we ever change this, we need to ensure it doesn't break FileID
dill.dump(self.__dict__, fH)
os.rename(fileName + '.tmp', fileName)
# Functions related to logging
[docs] def logToMaster(self, text, level=logging.INFO):
"""
Send a logging message to the leader. The message will also be \
logged by the worker at the same level.
:param text: The string to log.
:param int level: The logging level.
"""
logger.log(level=level, msg=("LOG-TO-MASTER: " + text))
self.loggingMessages.append(dict(text=text, level=level))
# Functions run after the completion of the job.
[docs] @abstractmethod
def startCommit(self, jobState=False):
"""
Update the status of the job on the disk.
May start an asynchronous process. Call waitForCommit() to wait on that process.
:param bool jobState: If True, commit the state of the FileStore's job,
and file deletes. Otherwise, commit only file creates/updates.
"""
raise NotImplementedError()
[docs] @abstractmethod
def waitForCommit(self):
"""
Blocks while startCommit is running. This function is called by this job's
successor to ensure that it does not begin modifying the job store until after this job has
finished doing so.
Might be called when startCommit is never called on a particular
instance, in which case it does not block.
:return: Always returns True
:rtype: bool
"""
raise NotImplementedError()
[docs] @abstractclassmethod
def shutdown(cls, dir_):
"""
Shutdown the filestore on this node.
This is intended to be called on batch system shutdown.
:param dir_: The implementation-specific directory containing the required information for
shutting down the file store and removing all its state and all job local temp
directories from the node.
"""
raise NotImplementedError()
