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)