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
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import os
import stat
from typing import Any




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)



    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




    def pack(self) -> str:
        """Pack the FileID into a string so it can be passed through external code."""
        return f'{self.size}:{"1" if self.executable else "0"}:{self}'




    @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)




    @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 = (vals[1] == "1")
        value = vals[2]
        # Create the FileID
        return cls(value, size, executable)