Source code for toil.jobStores.abstractJobStore

# Copyright (C) 2015-2016 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

from future import standard_library
standard_library.install_aliases()
from builtins import str
from builtins import map
from builtins import object
import shutil

import re
from abc import ABCMeta, abstractmethod
from contextlib import contextmanager, closing
from datetime import timedelta
from uuid import uuid4

# Python 3 compatibility imports
from six import itervalues
from six.moves.urllib.request import urlopen
import six.moves.urllib.parse as urlparse

from bd2k.util.retry import retry_http

from toil.fileStore import FileID
from toil.job import JobException
from bd2k.util import memoize
from bd2k.util.objects import abstractclassmethod
from future.utils import with_metaclass

try:
    import cPickle as pickle
except ImportError:
    import pickle

import logging

logger = logging.getLogger(__name__)


class InvalidImportExportUrlException(Exception):
    def __init__(self, url):
        """
        :param urlparse.ParseResult url:
        """
        super(InvalidImportExportUrlException, self).__init__(
            "The URL '%s' is invalid" % url.geturl())


[docs]class NoSuchJobException(Exception): """Indicates that the specified job does not exist."""
[docs] def __init__(self, jobStoreID): """ :param str jobStoreID: the jobStoreID that was mistakenly assumed to exist """ super(NoSuchJobException, self).__init__("The job '%s' does not exist" % jobStoreID)
[docs]class ConcurrentFileModificationException(Exception): """Indicates that the file was attempted to be modified by multiple processes at once."""
[docs] def __init__(self, jobStoreFileID): """ :param str jobStoreFileID: the ID of the file that was modified by multiple workers or processes concurrently """ super(ConcurrentFileModificationException, self).__init__( 'Concurrent update to file %s detected.' % jobStoreFileID)
[docs]class NoSuchFileException(Exception): """Indicates that the specified file does not exist."""
[docs] def __init__(self, jobStoreFileID, customName=None): """ :param str jobStoreFileID: the ID of the file that was mistakenly assumed to exist :param str customName: optionally, an alternate name for the nonexistent file """ if customName is None: message = "File '%s' does not exist" % jobStoreFileID else: message = "File '%s' (%s) does not exist" % (customName, jobStoreFileID) super(NoSuchFileException, self).__init__(message)
[docs]class NoSuchJobStoreException(Exception): """Indicates that the specified job store does not exist."""
[docs] def __init__(self, locator): super(NoSuchJobStoreException, self).__init__( "The job store '%s' does not exist, so there is nothing to restart" % locator)
[docs]class JobStoreExistsException(Exception): """Indicates that the specified job store already exists."""
[docs] def __init__(self, locator): super(JobStoreExistsException, self).__init__( "The job store '%s' already exists. Use --restart to resume the workflow, or remove " "the job store with 'toil clean' to start the workflow from scratch" % locator)
[docs]class AbstractJobStore(with_metaclass(ABCMeta, object)): """ Represents the physical storage for the jobs and files in a Toil workflow. """
[docs] def __init__(self): """ Create an instance of the job store. The instance will not be fully functional until either :meth:`.initialize` or :meth:`.resume` is invoked. Note that the :meth:`.destroy` method may be invoked on the object with or without prior invocation of either of these two methods. """ self.__config = None
[docs] def initialize(self, config): """ Create the physical storage for this job store, allocate a workflow ID and persist the given Toil configuration to the store. :param toil.common.Config 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 """ assert config.workflowID is None config.workflowID = str(uuid4()) logger.info("The workflow ID is: '%s'" % config.workflowID) self.__config = config self.writeConfig()
[docs] def writeConfig(self): """ Persists the value of the :attr:`AbstractJobStore.config` attribute to the job store, so that it can be retrieved later by other instances of this class. """ with self.writeSharedFileStream('config.pickle', isProtected=False) as fileHandle: pickle.dump(self.__config, fileHandle, pickle.HIGHEST_PROTOCOL)
[docs] def resume(self): """ Connect this instance to the physical storage it represents and load the Toil configuration into the :attr:`AbstractJobStore.config` attribute. :raises NoSuchJobStoreException: if the physical storage for this job store doesn't exist """ with self.readSharedFileStream('config.pickle') as fileHandle: config = pickle.load(fileHandle) assert config.workflowID is not None self.__config = config
@property def config(self): """ The Toil configuration associated with this job store. :rtype: toil.common.Config """ return self.__config rootJobStoreIDFileName = 'rootJobStoreID'
[docs] def setRootJob(self, rootJobStoreID): """ Set the root job of the workflow backed by this job store :param str rootJobStoreID: The ID of the job to set as root """ with self.writeSharedFileStream(self.rootJobStoreIDFileName) as f: f.write(rootJobStoreID)
[docs] def loadRootJob(self): """ Loads 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 :return: The root job. :rtype: toil.jobGraph.JobGraph """ try: with self.readSharedFileStream(self.rootJobStoreIDFileName) as f: rootJobStoreID = f.read() except NoSuchFileException: raise JobException('No job has been set as the root in this job store') if not self.exists(rootJobStoreID): raise JobException("The root job '%s' doesn't exist. Either the Toil workflow " "is finished or has never been started" % rootJobStoreID) return self.load(rootJobStoreID)
# FIXME: This is only used in tests, why do we have it?
[docs] def createRootJob(self, *args, **kwargs): """ Create a new job and set it as the root job in this job store :rtype: toil.jobGraph.JobGraph """ rootJob = self.create(*args, **kwargs) self.setRootJob(rootJob.jobStoreID) return rootJob
[docs] def getRootJobReturnValue(self): """ Parse the return value from the root job. Raises an exception if the root job hasn't fulfilled its promise yet. """ # Parse out the return value from the root job with self.readSharedFileStream('rootJobReturnValue') as fH: return pickle.load(fH)
@property @memoize def _jobStoreClasses(self): """ A list of concrete AbstractJobStore implementations whose dependencies are installed. :rtype: list[AbstractJobStore] """ jobStoreClassNames = ( "toil.jobStores.azureJobStore.AzureJobStore", "toil.jobStores.fileJobStore.FileJobStore", "toil.jobStores.googleJobStore.GoogleJobStore", "toil.jobStores.aws.jobStore.AWSJobStore", "toil.jobStores.abstractJobStore.JobStoreSupport") jobStoreClasses = [] for className in jobStoreClassNames: moduleName, className = className.rsplit('.', 1) from importlib import import_module try: module = import_module(moduleName) except ImportError: logger.debug("Unable to import '%s' as is expected if the corresponding extra was " "omitted at installation time.", moduleName) else: jobStoreClass = getattr(module, className) jobStoreClasses.append(jobStoreClass) return jobStoreClasses def _findJobStoreForUrl(self, url, export=False): """ Returns the AbstractJobStore subclass that supports the given URL. :param urlparse.ParseResult url: The given URL :param bool export: The URL for :rtype: toil.jobStore.AbstractJobStore """ for jobStoreCls in self._jobStoreClasses: if jobStoreCls._supportsUrl(url, export): return jobStoreCls raise RuntimeError("No job store implementation supports %sporting for URL '%s'" % ('ex' if export else 'im', url.geturl()))
[docs] def importFile(self, srcUrl, sharedFileName=None): """ 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. Currently supported schemes are: - 's3' for objects in Amazon S3 e.g. s3://bucket/key - 'wasb' for blobs in Azure Blob Storage e.g. wasb://container/blob - 'file' for local files e.g. file:///local/file/path - 'http' e.g. http://someurl.com/path :param str srcUrl: URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an Azure Blob Storage container. :param str sharedFileName: Optional name to assign to the imported file within the job store :return: The jobStoreFileId of the imported file or None if sharedFileName was given :rtype: FileID or None """ # Note that the helper method _importFile is used to read from the source and write to # destination (which is the current job store in this case). To implement any # optimizations that circumvent this, the _importFile method should be overridden by # subclasses of AbstractJobStore. srcUrl = urlparse.urlparse(srcUrl) otherCls = self._findJobStoreForUrl(srcUrl) return self._importFile(otherCls, srcUrl, sharedFileName=sharedFileName)
def _importFile(self, otherCls, url, sharedFileName=None): """ Import the file at the given URL using the given job store class to retrieve that file. See also :meth:`.importFile`. This method applies a generic approach to importing: it asks the other job store class for a stream and writes that stream as either a regular or a shared file. :param AbstractJobStore otherCls: The concrete subclass of AbstractJobStore that supports reading from the given URL and getting the file size from the URL. :param urlparse.ParseResult url: The location of the file to import. :param str sharedFileName: Optional name to assign to the imported file within the job store :return The jobStoreFileId of imported file or None if sharedFileName was given :rtype: FileID or None """ if sharedFileName is None: with self.writeFileStream() as (writable, jobStoreFileID): otherCls._readFromUrl(url, writable) return FileID(jobStoreFileID, otherCls.getSize(url)) else: self._requireValidSharedFileName(sharedFileName) with self.writeSharedFileStream(sharedFileName) as writable: otherCls._readFromUrl(url, writable) return None
[docs] def exportFile(self, jobStoreFileID, dstUrl): """ Exports file to destination pointed at by the destination URL. Refer to :meth:`.AbstractJobStore.importFile` 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. :param str jobStoreFileID: The id of the file in the job store that should be exported. :param str dstUrl: URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an Azure Blob Storage container. """ dstUrl = urlparse.urlparse(dstUrl) otherCls = self._findJobStoreForUrl(dstUrl, export=True) self._exportFile(otherCls, jobStoreFileID, dstUrl)
def _exportFile(self, otherCls, jobStoreFileID, url): """ Refer to exportFile docstring for information about this method. :param AbstractJobStore otherCls: The concrete subclass of AbstractJobStore that supports exporting to the given URL. Note that the type annotation here is not completely accurate. This is not an instance, it's a class, but there is no way to reflect that in :pep:`484` type hints. :param str jobStoreFileID: The id of the file that will be exported. :param urlparse.ParseResult url: The parsed URL of the file to export to. """ with self.readFileStream(jobStoreFileID) as readable: otherCls._writeToUrl(readable, url) @abstractclassmethod
[docs] def getSize(cls, url): """ returns the size of the file at the given URL """ raise NotImplementedError
@abstractclassmethod def _readFromUrl(cls, url, writable): """ Reads the contents of the object at the specified location and writes it to the given writable stream. Refer to AbstractJobStore.importFile documentation for currently supported URL schemes. :param urlparse.ParseResult url: URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an Azure Blob Storage container. :param writable: a writable stream """ raise NotImplementedError() @abstractclassmethod def _writeToUrl(cls, readable, url): """ Reads the contents of the given readable stream and writes it to the object at the specified location. Refer to AbstractJobStore.importFile documentation for currently supported URL schemes. :param urlparse.ParseResult url: URL that points to a file or object in the storage mechanism of a supported URL scheme e.g. a blob in an Azure Blob Storage container. :param readable: a readable stream """ raise NotImplementedError() @abstractclassmethod def _supportsUrl(cls, url, export=False): """ Returns True if the job store supports the URL's scheme. Refer to AbstractJobStore.importFile documentation for currently supported URL schemes. :param bool export: Determines if the url is supported for exported :param urlparse.ParseResult url: a parsed URL that may be supported :return bool: returns true if the cls supports the URL """ raise NotImplementedError() @abstractmethod
[docs] def destroy(self): """ The inverse of :meth:`.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. """ raise NotImplementedError()
[docs] def getEnv(self): """ Returns a dictionary of environment variables that this job store requires to be set in order to function properly on a worker. :rtype: dict[str,str] """ return {}
# Cleanup functions
[docs] def clean(self, jobCache=None): """ 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. :param dict[str,toil.jobGraph.JobGraph] jobCache: if a value it must be a dict from job ID keys to JobGraph 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. """ if jobCache is None: logger.warning("Cleaning jobStore recursively. This may be slow.") # Functions to get and check the existence of jobs, using the jobCache # if present def getJob(jobId): if jobCache is not None: try: return jobCache[jobId] except KeyError: self.load(jobId) else: return self.load(jobId) def haveJob(jobId): if jobCache is not None: if jobId in jobCache: return True else: return self.exists(jobId) else: return self.exists(jobId) def getJobs(): if jobCache is not None: return itervalues(jobCache) else: return self.jobs() # Iterate from the root jobGraph and collate all jobs that are reachable from it # All other jobs returned by self.jobs() are orphaned and can be removed reachableFromRoot = set() def getConnectedJobs(jobGraph): if jobGraph.jobStoreID in reachableFromRoot: return reachableFromRoot.add(jobGraph.jobStoreID) # Traverse jobs in stack for jobs in jobGraph.stack: for successorJobStoreID in [x.jobStoreID for x in jobs]: if (successorJobStoreID not in reachableFromRoot and haveJob(successorJobStoreID)): getConnectedJobs(getJob(successorJobStoreID)) # Traverse service jobs for jobs in jobGraph.services: for serviceJobStoreID in [x.jobStoreID for x in jobs]: if haveJob(serviceJobStoreID): assert serviceJobStoreID not in reachableFromRoot reachableFromRoot.add(serviceJobStoreID) logger.info("Checking job graph connectivity...") getConnectedJobs(self.loadRootJob()) logger.info("%d jobs reachable from root." % len(reachableFromRoot)) # Cleanup jobs that are not reachable from the root, and therefore orphaned jobsToDelete = [x for x in getJobs() if x.jobStoreID not in reachableFromRoot] for jobGraph in jobsToDelete: # clean up any associated files before deletion for fileID in jobGraph.filesToDelete: # Delete any files that should already be deleted logger.warn("Deleting file '%s'. It is marked for deletion but has not yet been " "removed.", fileID) self.deleteFile(fileID) # Delete the job self.delete(jobGraph.jobStoreID) jobGraphsReachableFromRoot = {id: getJob(id) for id in reachableFromRoot} # Clean up any checkpoint jobs -- delete any successors it # may have launched, and restore the job to a pristine # state jobsDeletedByCheckpoints = set() for jobGraph in [jG for jG in jobGraphsReachableFromRoot.values() if jG.checkpoint is not None]: if jobGraph.jobStoreID in jobsDeletedByCheckpoints: # This is a checkpoint that was nested within an # earlier checkpoint, so it and all its successors are # already gone. continue logger.info("Restarting checkpointed job %s" % jobGraph) deletedThisRound = jobGraph.restartCheckpoint(self) jobsDeletedByCheckpoints |= set(deletedThisRound) for jobID in jobsDeletedByCheckpoints: del jobGraphsReachableFromRoot[jobID] # Clean up jobs that are in reachable from the root for jobGraph in jobGraphsReachableFromRoot.values(): # jobGraphs here are necessarily in reachable from root. changed = [False] # This is a flag to indicate the jobGraph state has # changed # If the job has files to delete delete them. if len(jobGraph.filesToDelete) != 0: # Delete any files that should already be deleted for fileID in jobGraph.filesToDelete: logger.critical("Removing file in job store: %s that was " "marked for deletion but not previously removed" % fileID) self.deleteFile(fileID) jobGraph.filesToDelete = [] changed[0] = True # For a job whose command is already executed, remove jobs from the stack that are # already deleted. This cleans up the case that the jobGraph had successors to run, # but had not been updated to reflect this. if jobGraph.command is None: stackSizeFn = lambda: sum(map(len, jobGraph.stack)) startStackSize = stackSizeFn() # Remove deleted jobs jobGraph.stack = [[y for y in x if self.exists(y.jobStoreID)] for x in jobGraph.stack] # Remove empty stuff from the stack jobGraph.stack = [x for x in jobGraph.stack if len(x) > 0] # Check if anything got removed if stackSizeFn() != startStackSize: changed[0] = True # Cleanup any services that have already been finished. # Filter out deleted services and update the flags for services that exist # If there are services then renew # the start and terminate flags if they have been removed def subFlagFile(jobStoreID, jobStoreFileID, flag): if self.fileExists(jobStoreFileID): return jobStoreFileID # Make a new flag newFlag = self.getEmptyFileStoreID() # Load the jobGraph for the service and initialise the link serviceJobGraph = getJob(jobStoreID) if flag == 1: logger.debug("Recreating a start service flag for job: %s, flag: %s", jobStoreID, newFlag) serviceJobGraph.startJobStoreID = newFlag elif flag == 2: logger.debug("Recreating a terminate service flag for job: %s, flag: %s", jobStoreID, newFlag) serviceJobGraph.terminateJobStoreID = newFlag else: logger.debug("Recreating a error service flag for job: %s, flag: %s", jobStoreID, newFlag) assert flag == 3 serviceJobGraph.errorJobStoreID = newFlag # Update the service job on disk self.update(serviceJobGraph) changed[0] = True return newFlag servicesSizeFn = lambda: sum(map(len, jobGraph.services)) startServicesSize = servicesSizeFn() def replaceFlagsIfNeeded(serviceJobNode): serviceJobNode.startJobStoreID = subFlagFile(serviceJobNode.jobStoreID, serviceJobNode.startJobStoreID, 1) serviceJobNode.terminateJobStoreID = subFlagFile(serviceJobNode.jobStoreID, serviceJobNode.terminateJobStoreID, 2) serviceJobNode.errorJobStoreID = subFlagFile(serviceJobNode.jobStoreID, serviceJobNode.errorJobStoreID, 3) # jobGraph.services is a list of lists containing serviceNodes # remove all services that no longer exist services = jobGraph.services jobGraph.services = [] for serviceList in services: existingServices = [service for service in serviceList if self.exists(service.jobStoreID)] if existingServices: jobGraph.services.append(existingServices) list(map(lambda serviceList: list(map(replaceFlagsIfNeeded, serviceList)), jobGraph.services)) if servicesSizeFn() != startServicesSize: changed[0] = True # Reset the retry count of the jobGraph if jobGraph.remainingRetryCount != self._defaultTryCount(): jobGraph.remainingRetryCount = self._defaultTryCount() changed[0] = True # This cleans the old log file which may # have been left if the jobGraph is being retried after a jobGraph failure. if jobGraph.logJobStoreFileID != None: self.delete(jobGraph.logJobStoreFileID) jobGraph.logJobStoreFileID = None changed[0] = True if changed[0]: # Update, but only if a change has occurred logger.critical("Repairing job: %s" % jobGraph.jobStoreID) self.update(jobGraph) # Remove any crufty stats/logging files from the previous run logger.info("Discarding old statistics and logs...") # We have to manually discard the stream to avoid getting # stuck on a blocking write from the job store. def discardStream(stream): """Read the stream 4K at a time until EOF, discarding all input.""" while len(stream.read(4096)) != 0: pass self.readStatsAndLogging(discardStream) logger.info("Job store is clean") # TODO: reloading of the rootJob may be redundant here return self.loadRootJob()
########################################## # The following methods deal with creating/loading/updating/writing/checking for the # existence of jobs ########################################## @contextmanager
[docs] def batch(self): """ All calls to create() with this context manager active will be performed in a batch after the context manager is released. :rtype: None """ yield
@abstractmethod
[docs] def create(self, jobNode): """ Creates a job graph from the given job node & writes it to the job store. :rtype: toil.jobGraph.JobGraph """ raise NotImplementedError()
@abstractmethod
[docs] def exists(self, jobStoreID): """ Indicates whether the job with the specified jobStoreID exists in the job store :rtype: bool """ raise NotImplementedError()
# One year should be sufficient to finish any pipeline ;-) publicUrlExpiration = timedelta(days=365) @abstractmethod
[docs] def getPublicUrl(self, fileName): """ 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. :param str fileName: the jobStoreFileID of the file to generate a URL for :raise NoSuchFileException: if the specified file does not exist in this job store :rtype: str """ raise NotImplementedError()
@abstractmethod
[docs] def getSharedPublicUrl(self, sharedFileName): """ Differs from :meth:`getPublicUrl` in that this method is for generating URLs for shared files written by :meth:`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. :param str sharedFileName: The name of the shared file to generate a publically accessible url for. :raise NoSuchFileException: raised if the specified file does not exist in the store :rtype: str """ raise NotImplementedError()
@abstractmethod
[docs] def load(self, jobStoreID): """ Loads the job referenced by the given ID and returns it. :param str jobStoreID: the ID of the job to load :raise NoSuchJobException: if there is no job with the given ID :rtype: toil.jobGraph.JobGraph """ raise NotImplementedError()
@abstractmethod
[docs] def update(self, job): """ Persists the job in this store atomically. :param toil.jobGraph.JobGraph job: the job to write to this job store """ raise NotImplementedError()
@abstractmethod
[docs] def delete(self, jobStoreID): """ Removes from store atomically, can not then subsequently call load(), write(), update(), etc. with the job. This operation is idempotent, i.e. deleting a job twice or deleting a non-existent job will succeed silently. :param str jobStoreID: the ID of the job to delete from this job store """ raise NotImplementedError()
[docs] def jobs(self): """ Best effort attempt to return iterator on all jobs in the store. The iterator may not return all jobs and may also contain orphaned jobs that have already finished succesfully and should not be rerun. To guarantee you get any and all jobs that can be run instead construct a more expensive ToilState object :return: Returns iterator on jobs in the store. The iterator may or may not contain all jobs and may contain invalid jobs :rtype: Iterator[toil.jobGraph.JobGraph] """ raise NotImplementedError()
########################################## # The following provide an way of creating/reading/writing/updating files # associated with a given job. ########################################## @abstractmethod
[docs] def writeFile(self, localFilePath, jobStoreID=None): """ 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. :param str localFilePath: the path to the local file that will be uploaded to the job store. :param jobStoreID: If specified the file will be associated with that job and when jobStore.delete(job) is called all files written with the given job.jobStoreID will be removed from the job store. :type jobStoreID: str or None :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method :raise NoSuchJobException: if the job specified via jobStoreID does not exist FIXME: some implementations may not raise this :return: an ID referencing the newly created file and can be used to read the file in the future. :rtype: str """ raise NotImplementedError()
@abstractmethod @contextmanager
[docs] def writeFileStream(self, jobStoreID=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. :param str jobStoreID: the id of a job, or None. If specified, the file will be associated with that job and when when jobStore.delete(job) is called all files written with the given job.jobStoreID will be removed from the job store. :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method :raise NoSuchJobException: if the job specified via jobStoreID does not exist FIXME: some implementations may not raise this :return: an ID that references the newly created file and can be used to read the file in the future. :rtype: str """ raise NotImplementedError()
@abstractmethod
[docs] def getEmptyFileStoreID(self, jobStoreID=None): """ Creates an empty file in the job store and returns its ID. Call to fileExists(getEmptyFileStoreID(jobStoreID)) will return True. :param str jobStoreID: the id of a job, or None. If specified, the file will be associated with that job and when jobStore.delete(job) is called a best effort attempt is made to delete all files written with the given job.jobStoreID :return: a jobStoreFileID that references the newly created file and can be used to reference the file in the future. :rtype: str """ raise NotImplementedError()
@abstractmethod
[docs] def readFile(self, jobStoreFileID, localFilePath): """ Copies 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. The file at the given local path may not be modified after this method returns! :param str jobStoreFileID: ID of the file to be copied :param str localFilePath: the local path indicating where to place the contents of the given file in the job store """ raise NotImplementedError()
@abstractmethod @contextmanager
[docs] def readFileStream(self, jobStoreFileID): """ 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. :param str jobStoreFileID: ID of the file to get a readable file handle for """ raise NotImplementedError()
@abstractmethod
[docs] def deleteFile(self, jobStoreFileID): """ 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. :param str jobStoreFileID: ID of the file to delete """ raise NotImplementedError()
@abstractmethod
[docs] def fileExists(self, jobStoreFileID): """ Determine whether a file exists in this job store. :param str jobStoreFileID: an ID referencing the file to be checked :rtype: bool """ raise NotImplementedError()
@abstractmethod
[docs] def updateFile(self, jobStoreFileID, localFilePath): """ Replaces the existing version of a file in the job store. Throws an exception if the file does not exist. :param str jobStoreFileID: the ID of the file in the job store to be updated :param str localFilePath: the local path to a file that will overwrite the current version in the job store :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method :raise NoSuchFileException: if the specified file does not exist """ raise NotImplementedError()
@abstractmethod
[docs] def updateFileStream(self, jobStoreFileID): """ 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. :param str jobStoreFileID: the ID of the file in the job store to be updated :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method :raise NoSuchFileException: if the specified file does not exist """ raise NotImplementedError()
########################################## # The following methods deal with shared files, i.e. files not associated # with specific jobs. ########################################## sharedFileNameRegex = re.compile(r'^[a-zA-Z0-9._-]+$') # FIXME: Rename to updateSharedFileStream @abstractmethod @contextmanager
[docs] def writeSharedFileStream(self, sharedFileName, isProtected=None): """ Returns a context manager yielding a writable file handle to the global file referenced by the given name. :param str sharedFileName: A file name matching AbstractJobStore.fileNameRegex, unique within this job store :param bool isProtected: True if the file must be encrypted, None if it may be encrypted or False if it must be stored in the clear. :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method """ raise NotImplementedError()
@abstractmethod @contextmanager
[docs] def readSharedFileStream(self, sharedFileName): """ Returns a context manager yielding a readable file handle to the global file referenced by the given name. :param str sharedFileName: A file name matching AbstractJobStore.fileNameRegex, unique within this job store """ raise NotImplementedError()
@abstractmethod
[docs] def writeStatsAndLogging(self, statsAndLoggingString): """ Adds the given statistics/logging string to the store of statistics info. :param str statsAndLoggingString: the string to be written to the stats file :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method """ raise NotImplementedError()
@abstractmethod
[docs] def readStatsAndLogging(self, callback, readAll=False): """ Reads stats/logging strings accumulated by the writeStatsAndLogging() method. For each stats/logging string this method calls the given callback function with an open, readable file handle from which the stats string can be read. Returns the number of stats/logging strings processed. Each stats/logging string is only processed once unless the readAll parameter is set, in which case the given callback will be invoked for all existing stats/logging strings, including the ones from a previous invocation of this method. :param Callable callback: a function to be applied to each of the stats file handles found :param bool readAll: a boolean indicating whether to read the already processed stats files in addition to the unread stats files :raise ConcurrentFileModificationException: if the file was modified concurrently during an invocation of this method :return: the number of stats files processed :rtype: int """ raise NotImplementedError()
## Helper methods for subclasses def _defaultTryCount(self): return int(self.config.retryCount + 1) @classmethod def _validateSharedFileName(cls, sharedFileName): return bool(cls.sharedFileNameRegex.match(sharedFileName)) @classmethod def _requireValidSharedFileName(cls, sharedFileName): if not cls._validateSharedFileName(sharedFileName): raise ValueError("Not a valid shared file name: '%s'." % sharedFileName)
class JobStoreSupport(with_metaclass(ABCMeta, AbstractJobStore)): @classmethod def _supportsUrl(cls, url, export=False): return url.scheme.lower() in ('http', 'https', 'ftp') and not export @classmethod def getSize(cls, url): if url.scheme.lower() == 'ftp': return None for attempt in retry_http(): with attempt: with closing(urlopen(url.geturl())) as readable: # just read the header for content length return int(readable.info().get('content-length')) @classmethod def _readFromUrl(cls, url, writable): for attempt in retry_http(): with attempt: with closing(urlopen(url.geturl())) as readable: shutil.copyfileobj(readable, writable)