def __init__(self, path, fanOut=1000):
"""
:param str path: Path to directory holding the job store
:param int fanOut: Number of items to have in a directory before making
subdirectories
"""
super(FileJobStore, self).__init__()
self.jobStoreDir = absSymPath(path)
logger.debug("Path to job store directory is '%s'.", self.jobStoreDir)
# Directory where actual job files go, and their job-associated temp files
self.jobsDir = os.path.join(self.jobStoreDir, 'jobs')
# Directory where stats files go
self.statsDir = os.path.join(self.jobStoreDir, 'stats')
# Directory where non-job-associated files for the file store go
self.filesDir = os.path.join(self.jobStoreDir, 'files/no-job')
# Directory where job-associated files for the file store go.
# Each per-job directory in here will have separate directories for
# files to clean up and files to not clean up when the job is deleted.
self.jobFilesDir = os.path.join(self.jobStoreDir, 'files/for-job')
# Directory where shared files go
self.sharedFilesDir = os.path.join(self.jobStoreDir, 'files/shared')
self.fanOut = fanOut
self.linkImports = None
self.moveExports = None
def __init__(self, path):
"""
:param str path: Path to directory holding the job store
"""
super(FileJobStore, self).__init__()
self.jobStoreDir = absSymPath(path)
logger.debug("Path to job store directory is '%s'.", self.jobStoreDir)
# Directory where temporary files go
self.tempFilesDir = os.path.join(self.jobStoreDir, 'tmp')
def __init__(self, path):
"""
:param str path: Path to directory holding the job store
"""
super(FileJobStore, self).__init__()
self.jobStoreDir = absSymPath(path)
logger.debug("Path to job store directory is '%s'.", self.jobStoreDir)
# Directory where temporary files go
self.tempFilesDir = os.path.join(self.jobStoreDir, 'tmp')
def toilPackageDirPath():
"""
Returns the absolute path of the directory that corresponds to the top-level toil package. The return value is
guaranteed to end in '/toil'.
"""
import toil.jobWrapper
result = os.path.dirname(absSymPath(toil.jobWrapper.__file__))
assert result.endswith('/toil')
return result
def toilPackageDirPath():
"""
Returns the absolute path of the directory that corresponds to the top-level toil package. The return value is
guaranteed to end in '/toil'.
"""
import toil.batchJob
result = os.path.dirname(absSymPath(toil.batchJob.__file__))
assert result.endswith('/toil')
return result
def __init__(self, jobStoreDir, config=None):
#This is root directory in which everything in the store is kept
self.jobStoreDir = absSymPath(jobStoreDir)
logger.info("Jobstore directory is: %s", self.jobStoreDir)
self.tempFilesDir = os.path.join(self.jobStoreDir, "tmp")
if not os.path.exists(self.jobStoreDir):
os.mkdir(self.jobStoreDir)
os.mkdir(self.tempFilesDir)
#Parameters for creating temporary files
self.validDirs = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"
self.levels = 2
super(FileJobStore, self).__init__(config=config)
def __init__(self, jobStoreDir, config=None):
#This is root directory in which everything in the store is kept
self.jobStoreDir = absSymPath(jobStoreDir)
logger.info("Jobstore directory is: %s", self.jobStoreDir)
self.tempFilesDir = os.path.join(self.jobStoreDir, "tmp")
if not os.path.exists(self.jobStoreDir):
os.mkdir(self.jobStoreDir)
os.mkdir(self.tempFilesDir)
#Parameters for creating temporary files
self.validDirs = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"
self.levels = 2
super( FileJobStore, self ).__init__( config=config )
def __init__(self, path):
"""
:param str path: Path to directory holding the job store
"""
super(FileJobStore, self).__init__()
self.jobStoreDir = absSymPath(path)
logger.debug("Path to job store directory is '%s'.", self.jobStoreDir)
# Directory where temporary files go
self.tempFilesDir = os.path.join(self.jobStoreDir, 'tmp')
self.linkImports = None
# This flag is used by self._recursiveDelete to limit warning count
self._warnedOnNfs = False
def __init__(self, jobStoreDir, config=None):
"""
:param jobStoreDir: Place to create jobStore
:param config: See jobStores.abstractJobStore.AbstractJobStore.__init__
:raise RuntimeError: if config != None and the jobStore already exists or
config == None and the jobStore does not already exists.
"""
#This is root directory in which everything in the store is kept
self.jobStoreDir = absSymPath(jobStoreDir)
logger.info("Jobstore directory is: %s", self.jobStoreDir)
#Safety checks for existing jobStore
self._checkJobStoreCreation(config != None, os.path.exists(self.jobStoreDir), self.jobStoreDir)
#Directory where temporary files go
self.tempFilesDir = os.path.join(self.jobStoreDir, "tmp")
#Creation of jobStore, if necessary
if config != None:
os.mkdir(self.jobStoreDir)
os.mkdir(self.tempFilesDir)
#Parameters for creating temporary files
self.validDirs = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"
self.levels = 2
super( FileJobStore, self ).__init__( config=config )
def __init__(self, jobStoreDir, config=None):
"""
:param jobStoreDir: Place to create jobStore
:param config: See jobStores.abstractJobStore.AbstractJobStore.__init__
:raise RuntimeError: if config != None and the jobStore already exists or
config == None and the jobStore does not already exists.
"""
# This is root directory in which everything in the store is kept
self.jobStoreDir = absSymPath(jobStoreDir)
logger.info("Jobstore directory is: %s", self.jobStoreDir)
# Safety checks for existing jobStore
self._checkJobStoreCreation(create=config is not None,
exists=os.path.exists(self.jobStoreDir),
jobStoreString=self.jobStoreDir)
# Directory where temporary files go
self.tempFilesDir = os.path.join(self.jobStoreDir, "tmp")
# Creation of jobStore, if necessary
if config is not None:
os.mkdir(self.jobStoreDir)
os.mkdir(self.tempFilesDir)
# Parameters for creating temporary files
self.validDirs = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789"
self.levels = 2
super(FileJobStore, self).__init__(config=config)
def __init__(self, path):
"""
:param str path: Path to directory holding the job store
"""
self.jobStoreDir = absSymPath(path)
logger.debug("Path to job store directory is '%s'.", self.jobStoreDir)