python – 如何使用call调用子进程/ Popen继承环境变量

首先,对我所确定的显而易见的道歉是我对bash,shell和子进程的基本理解.

我正在尝试使用Python来自动调用一个名为Freesurfer的程序(实际上,我正在调用的子程序称为recon-all.)

如果我直接在命令行执行此操作,我将“源”一个名为mySetUpFreeSurfer.sh的脚本,除了设置三个环境变量之外什么都不做,然后“源”另一个脚本FreeSurferEnv.sh. FreesurferEnv.sh在我看来并没有做任何事情,只是设置了很多环境变量并向终端回应了一些东西,但它比其他bash脚本更复杂,所以我不确定.

这就是我现在所拥有的：

from subprocess import Popen, PIPE, call, check_output
import os

root = "/media/foo/"

#I got this function from another Stack Overflow question.

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

source('~/scripts/mySetUpFreeSurfer.sh')
source('/usr/local/freesurfer/FreeSurferEnv.sh')

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 " + path + " -subjid " + sub
            check_output(cmd1, shell=True)
            call(cmd1, shell=True)
            cmd2 = "recon-all -all -subjid " + sub,
            call(cmd2, shell=True)

这是失败的：

Traceback (most recent call last):
     File "/home/katie/scripts/autoReconSO.py", line 28, in <module>
        check_output(cmd1, shell=True)
      File "/usr/lib/python2.7/subprocess.py", line 544, in check_output
        raise CalledProcessError(retcode, cmd, output=output)
    CalledProcessError: Command 'recon-all -i /media/foo/bar -subjid s1001' returned non-zero exit status 127

我也许明白为什么会这样.我在脚本后面的“调用”是引发新的子进程,这些子进程不会从通过调用source()函数引发的进程继承环境变量.我做了很多事情来试图证实我的理解.一个例子 – 我把这些行：

mkdir ~/testFreeSurferEnv
export TEST_ENV_VAR=~/testFreeSurferEnv

在FreeSurferEnv.sh脚本中.目录变得很好,但在Python脚本中：

cmd = 'mkdir $TEST_ENV_VAR/test'
check_output(cmd, shell=True)

像这样失败：

File "/usr/lib/python2.7/subprocess.py", line 544, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
CalledProcessError: Command 'mkdir $TEST_ENV_VAR/test' returned non-zero exit status 1

题：

如何使运行“recon-all”的子进程继承其所需的环境变量？或者我怎么能做我需要做的一切 – 运行脚本来设置环境变量,并在同一个过程中调用recon-all？或者我应该以另一种方式解决问题？或者我可能误解了这个问题？

解决方法:

关于

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

我认为你最好使用Python来自动化编写过程
shell脚本newscript.sh,然后通过一次调用调用此脚本
subprocess.check_output(而不是对Popen的多次调用,check_output,
电话等)：

newscript.sh：

#!/bin/bash
source ~/scripts/mySetUpFreeSurfer.sh
source /usr/local/freesurfer/FreeSurferEnv.sh
recon-all -i /media/foo/bar -subjid s1001
...

然后打电话

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

import subprocess
import tempfile
import os
import stat


with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
    f.write('''\
#!/bin/bash
source ~/scripts/mySetUpFreeSurfer.sh
source /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.name
os.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,如果脚本包含类似的内容

VAR=`ls -1`
export VAR

然后

. script; env

可能会返回输出

VAR=file1
file2
file3

这将导致源(脚本)引发ValueError：

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

有一种方法可以修复源：使用零字节而不是模糊的换行来分隔环境变量：

def source(script, update=True):
    """
    http://pythonwise.blogspot.fr/2010/04/sourcing-shell-script.html (Miki Tebeka)
    https://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.decode('utf8')
    env = dict((line.split("=", 1) for line in output.split('\x00') if line))
    if update:
        os.environ.update(env)
    return env

是否可以修复,但是,你仍然可能更好地构建一个
conglomerate shell脚本(如上所示)比解析env和
将env dicts传递给子进程调用.

python – 如何使用call调用子进程/ Popen继承环境变量

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