def _hashTestFile(self, url): import boto from toil.jobStores.googleJobStore import GoogleJobStore projectID, uri = GoogleJobStore._getResources(urlparse.urlparse(url)) uri = boto.storage_uri(uri) contents = uri.get_contents_as_string(headers=self.headers) return hashlib.md5(contents).hexdigest()
def _createExternalStore(): import boto from toil.jobStores.googleJobStore import GoogleJobStore uriString = "gs://import-export-test-%s" % str(uuid.uuid4()) uri = boto.storage_uri(uriString) return GoogleJobStore._retryCreateBucket( uri=uri, headers=GoogleJobStoreTest.headers)
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 _hashUrl(url): import boto from toil.jobStores.googleJobStore import GoogleJobStore projectID, uri = GoogleJobStore._getResources(urlparse.urlparse(url)) return hashlib.md5( boto.storage_uri(uri).get_contents_as_string( headers=GoogleJobStoreTest.headers)).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 _cleanUpExternalStore(url): import boto from toil.jobStores.googleJobStore import GoogleJobStore projectID, uri = GoogleJobStore._getResources(urlparse.urlparse(url)) uri = boto.storage_uri(uri) headers = {"x-goog-project-id": projectID} bucket = uri.get_bucket(headers=headers, validate=True) if bucket is not None: while True: for key in bucket.list(): try: key.delete() except boto.exception.GSResponseError as e: if e.status == 404: pass else: raise e try: uri.delete_bucket() except boto.exception.GSResponseError as e: if e.status == 404: break else: continue
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.googleJobStore import GoogleJobStore return GoogleJobStore.createJobStore(self.namePrefix + ":" + GoogleJobStoreTest.projectID, config=config)
def _createJobStore(self): from toil.jobStores.googleJobStore import GoogleJobStore return GoogleJobStore.initialize(GoogleJobStoreTest.projectID + ":" + self.namePrefix)
def _createExternalStore(self): import boto from toil.jobStores.googleJobStore import GoogleJobStore uriString = "gs://import-export-test-%s" % str(uuid.uuid4()) uri = boto.storage_uri(uriString) return GoogleJobStore._retryCreateBucket(uri=uri, headers=self.headers)
def _hashUrl(url): import boto from toil.jobStores.googleJobStore import GoogleJobStore projectID, uri = GoogleJobStore._getResources(urlparse.urlparse(url)) return hashlib.md5(boto.storage_uri(uri).get_contents_as_string(headers=GoogleJobStoreTest.headers)).hexdigest()