def _createJobStore(self, config=None):
from toil.jobStores.aws.jobStore import AWSJobStore
partSize = self._partSize()
for encrypted in (True, False):
self.assertTrue(AWSJobStore.FileInfo.maxInlinedSize(encrypted) < partSize)
AWSJobStore.FileInfo.defaultS3PartSize = partSize
return AWSJobStore.loadOrCreateJobStore(self.testRegion + ':' + self.namePrefix, config=config, partSize=2**20*5)
def _createJobStore(self, config=None):
from toil.jobStores.aws.jobStore import AWSJobStore
partSize = self._partSize()
for encrypted in (True, False):
self.assertTrue(AWSJobStore.FileInfo.maxInlinedSize(encrypted) < partSize)
AWSJobStore.FileInfo.defaultS3PartSize = partSize
return AWSJobStore.loadOrCreateJobStore(self.testRegion + ':' + self.namePrefix,
config=config,
partSize=5 * 2 ** 20)
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(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 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)
