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,
# See the License for the specific language governing permissions and
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import os
import stat
from typing import Any

[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: str, *args: Any) -> 'FileID': return super().__new__(cls, fileStoreID)
[docs] def __init__(self, fileStoreID: str, size: int, executable: bool = False) -> None: # 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().__init__() self.size = size self.executable = executable
[docs] def pack(self) -> str: """Pack the FileID into a string so it can be passed through external code.""" return f'{self.size}:{int(self.executable)}:{self}'
[docs] @classmethod def forPath(cls, fileStoreID: str, filePath: str) -> 'FileID': 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: str) -> 'FileID': """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)