Source code for toil.fileStores

# Copyright (C) 2015-2021 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
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import os
import stat

[docs]class FileID(str): """ A small wrapper around Python's builtin string class. It is used to represent a file's ID in the file store, and has a size attribute that is the file's size in bytes. This object is returned by importFile and writeGlobalFile. Calls into the file store can use bare strings; size will be queried from the job store if unavailable in the ID. """ def __new__(cls, fileStoreID, *args): return super(FileID, cls).__new__(cls, fileStoreID)
[docs] def __init__(self, fileStoreID, size, executable=False): # Don't pass an argument to parent class's __init__. # In Python 3 we can have super(FileID, self) hand us object's __init__ which chokes on any arguments. super(FileID, self).__init__() self.size = size self.executable = executable
[docs] def pack(self): """ Pack the FileID into a string so it can be passed through external code. """ return '{}:{}:{}'.format(self.size, int(self.executable), self)
@classmethod def forPath(cls, fileStoreID, filePath): executable = os.stat(filePath).st_mode & stat.S_IXUSR != 0 return cls(fileStoreID, os.stat(filePath).st_size, executable)
[docs] @classmethod def unpack(cls, packedFileStoreID): """ Unpack the result of pack() into a FileID object. """ # Only separate twice in case the FileID itself has colons in it vals = packedFileStoreID.split(':', 2) # Break up the packed value size = int(vals[0]) executable = bool(vals[1]) value = vals[2] # Create the FileID return cls(value, size, executable)