如何使用call / Popen调用的子流程继承环境变量

关于

If I were doing this directly at the command line, I'd "source" a scriptcalled mySetUpFreeSurfer.sh that does nothing but set three environmentvariables, and then "source" another script, FreeSurferEnv.sh.

我想你会过得更好用Python编写自动化shell脚本的过程

newscript.sh

subprocess.check_output

Popen

check_output

call

newscript.sh：

#!/bin/bashsource ~/scripts/mySetUpFreeSurfer.shsource /usr/local/freesurfer/FreeSurferEnv.shrecon-all -i /media/foo/bar -subjid s1001...

然后打电话

subprocess.check_output(['newscript.sh'])

import subprocessimport tempfileimport osimport statwith tempfile.NamedTemporaryFile(mode='w', delete=False) as f:    f.write('''#!/bin/bashsource ~/scripts/mySetUpFreeSurfer.shsource /usr/local/freesurfer/FreeSurferEnv.sh''')    root = "/media/foo/"    for sub_dir in os.listdir(root):        sub = "s" + sub_dir[0:4]        anat_dir = os.path.join(root, sub_dir, "anatomical")        for directory in os.listdir(anat_dir): time_dir = os.path.join(anat_dir, directory) for d in os.listdir(time_dir):     dicoms_dir = os.path.join(time_dir, d, 'dicoms')     dicom_list = os.listdir(dicoms_dir)     dicom = dicom_list[0]     path = os.path.join(dicoms_dir, dicom)     cmd1 = "recon-all -i {}  -subjid {}n".format(path, sub)     f.write(cmd1)     cmd2 = "recon-all -all -subjid {}n".format(sub)     f.write(cmd2)filename = f.nameos.chmod(filename, stat.S_IRUSR | stat.S_IXUSR)subprocess.call([filename])os.unlink(filename)

顺便说说，

def source(script, update=1):    pipe = Popen(". %s; env" % script, stdout=PIPE, shell=True)    data = pipe.communicate()[0]    env = dict((line.split("=", 1) for line in data.splitlines()))    if update:        os.environ.update(env)    return env

被打破。例如，如果

script

VAR=`ls -1`export VAR

然后

. script; env

可能会像

VAR=file1file2file3

这将导致

source(script)

ValueError

env = dict((line.split("=", 1) for line in data.splitlines()))ValueError: dictionary update sequence element #21 has length 1; 2 is required

有一种解决方法

source

env

def source(script, update=True):    """    http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html (Miki Tebeka)    http://stackoverflow.com/questions/3503719/#comment28061110_3505826 (ahal)    """    import subprocess    import os    proc = subprocess.Popen(        ['bash', '-c', 'set -a && source {} && env -0'.format(script)],         stdout=subprocess.PIPE, shell=False)    output, err = proc.communicate()    output = output.depre('utf8')    env = dict((line.split("=", 1) for line in output.split('x00') if line))    if update:        os.environ.update(env)    return env

但是，无论是否可修复，构造一个综合性的shell脚本（如上所示）仍然比解析

env

env

subprocess