Subprocess.run() inside loop

Question

I would like to loop over files using subprocess.run(), something like:

import os
import subprocess

path = os.chdir("/test")
files = []
for file in os.listdir(path):
     if file.endswith(".bam"):
        files.append(file)

for file in files:
     process = subprocess.run("java -jar picard.jar CollectHsMetrics I=file", shell=True)

How do I correctly call the files?

Answer 1

shell=True is insecure if you are including user input in it. @eatmeimadanish's answer allows anybody who can write a file in /test to execute arbitrary code on your machine. This is a huge security vulnerability !

Instead, supply a list of command-line arguments to the subprocess.run call. You likely also want to pass in check=True – otherwise, your program would finish without an exception if the java commands fails!

import os
import subprocess

os.chdir("/test")
for file in os.listdir("."):
    if file.endswith(".bam"):
        subprocess.run(
            ["java", "-jar", "picard.jar", "CollectHsMetrics", "I=" + file], check=True)

Answer 2

Seems like you might be over complicating it.

import os
import subprocess

path = os.chdir("/test")
for file in os.listdir(path):
     if file.endswith(".bam"):
        subprocess.run("java -jar picard.jar CollectHsMetrics I={}".format(file), shell=True)