def loadJobStore(jobStoreString, config=None):
"""
Loads a jobStore.
:param jobStoreString: see exception message below
:param config: see AbstractJobStore.__init__
:return: an instance of a concrete subclass of AbstractJobStore
:rtype: jobStores.abstractJobStore.AbstractJobStore
"""
if jobStoreString[0] in '/.':
jobStoreString = 'file:' + jobStoreString
try:
jobStoreName, jobStoreArgs = jobStoreString.split(':', 1)
except ValueError:
raise RuntimeError(
'Job store string must either be a path starting in . or / or a contain at least one '
'colon separating the name of the job store implementation from an initialization '
'string specific to that job store. If a path starting in . or / is passed, the file '
'job store will be used for backwards compatibility.')
if jobStoreName == 'file':
from toil.jobStores.fileJobStore import FileJobStore
return FileJobStore(jobStoreArgs, config=config)
elif jobStoreName == 'aws':
from toil.jobStores.aws.jobStore import AWSJobStore
return AWSJobStore.createJobStore(jobStoreArgs, config=config)
elif jobStoreName == 'azure':
from toil.jobStores.azureJobStore import AzureJobStore
account, namePrefix = jobStoreArgs.split(':', 1)
return AzureJobStore(account, namePrefix, config=config)
else:
raise RuntimeError("Unknown job store implementation '%s'" %
jobStoreName)
def _hashTestFile(self, url):
from toil.jobStores.azureJobStore import AzureJobStore
url = urlparse.urlparse(url)
blobService, containerName, blobName = AzureJobStore._extractBlobInfoFromUrl(
url)
content = blobService.get_blob_to_bytes(containerName, blobName)
return hashlib.md5(content).hexdigest()
def getJobStore(cls, locator):
"""
Create an instance of the concrete job store implementation that matches the given locator.
:param str locator: The location of the job store to be represent by the instance
:return: an instance of a concrete subclass of AbstractJobStore
:rtype: toil.jobStores.abstractJobStore.AbstractJobStore
"""
name, rest = cls.parseLocator(locator)
if name == 'file':
from toil.jobStores.fileJobStore import FileJobStore
return FileJobStore(rest)
elif name == 'aws':
from toil.jobStores.aws.jobStore import AWSJobStore
return AWSJobStore(rest)
elif name == 'azure':
from toil.jobStores.azureJobStore import AzureJobStore
return AzureJobStore(rest)
elif name == 'google':
from toil.jobStores.googleJobStore import GoogleJobStore
projectID, namePrefix = rest.split(':', 1)
return GoogleJobStore(namePrefix, projectID)
else:
raise RuntimeError("Unknown job store implementation '%s'" % name)
def _hashTestFile(self, url):
from toil.jobStores.azureJobStore import AzureJobStore, retry_azure
url = urlparse.urlparse(url)
blob = AzureJobStore._parseWasbUrl(url)
for attempt in retry_azure():
with attempt:
content = blob.service.get_blob_to_bytes(blob.container, blob.name)
return hashlib.md5(content).hexdigest()
def _hashTestFile(self, url):
from toil.jobStores.azureJobStore import AzureJobStore, retry_azure
url = urlparse.urlparse(url)
blob = AzureJobStore._parseWasbUrl(url)
for attempt in retry_azure():
with attempt:
content = blob.service.get_blob_to_bytes(blob.container, blob.name)
return hashlib.md5(content).hexdigest()
def loadOrCreateJobStore(jobStoreString, config=None):
"""
Loads an existing jobStore if it already exists. Otherwise a new instance of a jobStore is
created and returned.
:param str jobStoreString: see exception message below
:param toil.common.Config config: see AbstractJobStore.__init__
:return: an instance of a concrete subclass of AbstractJobStore
:rtype: toil.jobStores.abstractJobStore.AbstractJobStore
"""
if jobStoreString[0] in '/.':
jobStoreString = 'file:' + jobStoreString
try:
jobStoreName, jobStoreArgs = jobStoreString.split(':', 1)
except ValueError:
raise RuntimeError(
'A job store string must either be a path starting in . or / or a contain at '
'least one colon separating the name of the job store implementation from an '
'initialization string specific to that job store. If a path starting in . or / '
'is passed, the file job store will be used for backwards compatibility.'
)
if jobStoreName == 'file':
from toil.jobStores.fileJobStore import FileJobStore
return FileJobStore(jobStoreArgs, config=config)
elif jobStoreName == 'aws':
from toil.jobStores.aws.jobStore import AWSJobStore
return AWSJobStore.loadOrCreateJobStore(jobStoreArgs,
config=config)
elif jobStoreName == 'azure':
from toil.jobStores.azureJobStore import AzureJobStore
account, namePrefix = jobStoreArgs.split(':', 1)
return AzureJobStore(account, namePrefix, config=config)
elif jobStoreName == 'google':
from toil.jobStores.googleJobStore import GoogleJobStore
projectID, namePrefix = jobStoreArgs.split(':', 1)
return GoogleJobStore(namePrefix, projectID, config=config)
else:
raise RuntimeError("Unknown job store implementation '%s'" %
jobStoreName)
def loadOrCreateJobStore(locator, config=None):
"""
Loads an existing jobStore if it already exists. Otherwise a new instance of a jobStore is
created and returned.
:param str locator: The location of the job store.
:param toil.common.Config config: see AbstractJobStore.__init__
:return: an instance of a concrete subclass of AbstractJobStore
:rtype: toil.jobStores.abstractJobStore.AbstractJobStore
"""
if locator[0] in '/.':
locator = 'file:' + locator
try:
jobStoreName, jobStoreArgs = locator.split(':', 1)
except ValueError:
raise RuntimeError('Invalid job store locator for proper formatting check locator '
'documentation for each job store.')
if jobStoreName == 'file':
from toil.jobStores.fileJobStore import FileJobStore
return FileJobStore(jobStoreArgs, config=config)
elif jobStoreName == 'aws':
from toil.jobStores.aws.jobStore import AWSJobStore
return AWSJobStore.loadOrCreateJobStore(jobStoreArgs, config=config)
elif jobStoreName == 'azure':
from toil.jobStores.azureJobStore import AzureJobStore
account, namePrefix = jobStoreArgs.split(':', 1)
return AzureJobStore(account, namePrefix, config=config)
elif jobStoreName == 'google':
from toil.jobStores.googleJobStore import GoogleJobStore
projectID, namePrefix = jobStoreArgs.split(':', 1)
return GoogleJobStore(namePrefix, projectID, config=config)
else:
raise RuntimeError("Unknown job store implementation '%s'" % jobStoreName)
def getJobStore(locator):
"""
Create an instance of the concrete job store implementation that matches the given locator.
:param str locator: The location of the job store to be represent by the instance
:return: an instance of a concrete subclass of AbstractJobStore
:rtype: toil.jobStores.abstractJobStore.AbstractJobStore
"""
if locator[0] in '/.':
locator = 'file:' + locator
try:
name, rest = locator.split(':', 1)
except ValueError:
raise RuntimeError('Invalid job store locator syntax.')
if name == 'file':
from toil.jobStores.fileJobStore import FileJobStore
return FileJobStore(rest)
elif name == 'aws':
from toil.jobStores.aws.jobStore import AWSJobStore
return AWSJobStore(rest)
elif name == 'azure':
from toil.jobStores.azureJobStore import AzureJobStore
account, namePrefix = rest.split(':', 1)
return AzureJobStore(rest)
elif name == 'google':
from toil.jobStores.googleJobStore import GoogleJobStore
projectID, namePrefix = rest.split(':', 1)
return GoogleJobStore(namePrefix, projectID, config=config)
else:
raise RuntimeError("Unknown job store implementation '%s'" % name)
def _createJobStore(self, config=None):
from toil.jobStores.azureJobStore import AzureJobStore
return AzureJobStore(self.accountName, self.namePrefix, config=config)
def _createJobStore(self):
from toil.jobStores.azureJobStore import AzureJobStore
return AzureJobStore(self.accountName + ':' + self.namePrefix)
def _cleanUpExternalStore(url):
from toil.jobStores.azureJobStore import AzureJobStore
blobService, containerName, _ = AzureJobStore._extractBlobInfoFromUrl(urlparse.urlparse(url))
blobService.delete_container(containerName)
def _hashUrl(url):
from toil.jobStores.azureJobStore import AzureJobStore
blobService, containerName, blobName = AzureJobStore._extractBlobInfoFromUrl(urlparse.urlparse(url))
content = blobService.get_blob_to_bytes(containerName, blobName)
return hashlib.md5(content).hexdigest()
def _cleanUpExternalStore(url):
from toil.jobStores.azureJobStore import AzureJobStore
blobService, containerName, _ = AzureJobStore._extractBlobInfoFromUrl(
urlparse.urlparse(url))
blobService.delete_container(containerName)
def _createJobStore(self, config=None):
from toil.jobStores.azureJobStore import AzureJobStore
return AzureJobStore('toiltest',
self.namePrefix,
config=config,
jobChunkSize=128)
