I'm trying to use subprocess.Popen() to run a command in my script. The code is:
output = Popen(["hrun DAR_MeasLogDump " + log_file_name], stdout=subprocess.PIPE, stderr = subprocess.PIPE, executable="/bin/csh", cwd=cwdir, encoding='utf-8')
When I print the output, it's printing out the created shell output and not the actual command that's in the list. I tried getting rid of executable='/bin/csh', but then Popen wouldn't even run.
I also tried using subprocess.communicate(), but it didn't work either. I would also get the shell output and not the actual command run.
I want to completely avoid using shell=True because of security issues.
EDIT: In many different attempts, "hrun" is not being recoognized. "hrun" is a Pearl script that is being called, DAR_MeasLogDump is the action and log_file_name is the file that the script will call its action on. Is there any sort of set up or configuration that needs to be done in order for "hrun" to be recognized?
I think the problem is that Popen requires a list of every part of the command (command + options), the documentation for Popen inside subprocess has an example for that. So for that line in your script to work, you would need to write it like this:
output = Popen(["/bin/csh", "hrun", "DAR_MeasLogDump", log_file_name], stdout=subprocess.PIPE, stderr = subprocess.PIPE)
I've removed the executable argument, but I guess it could work that way as well.
Try:
output = Popen(["-c", "hrun DAR_MeasLogDump " +log_file_name], stdout=subprocess.PIPE, stderr = subprocess.PIPE, executable="/bin/csh", cwd=cwdir, encoding='utf-8')
csh is expecting -c "full command here". Without -c I think it just tries to open it as a file.
Specifying an odd shell and an explicit cwd seems completely out of place here (assuming cwdir is defined to the current directory).
If the first argument to subprocess is a list, no shell is involved.
result = subprocess.run(["hrun", "DAR_MeasLogDump", log_file_name],
stdout=subprocess.PIPE, stderr = subprocess.PIPE,
universal_newlines=True, check=True)
output = result.stdout
If you need this to be run under a legacy version of Python, maybe use check_output instead of run.
You generally want to avoid Popen unless you need to do something which the higher-level wrapper functions cannot do.
You are creating an instance of subprocess.Popen but not executing it.
You should try:
p = Popen(["hrun", "DAR_MeasLogDump ", log_file_name], stdout=subprocess.PIPE, stderr = subprocess.PIPE, cwd=cwdir, encoding='utf-8')
out, err = p.communicate() # This will get you output
Args should be passed as a sequence if you do not use shell=True, and then using executable should not be required.
Note that if you are not using advanced features from Popen, the doc recommends using subprocess.run:
from subprocess import run
p = run(["hrun", "DAR_MeasLogDump ", log_file_name], capture_output=True, cwd=cwdir, encoding='utf-8')
out, err = p.communicate() # This will get you output
This works with cat example:
import subprocess
log_file_name='-123.txt'
output = subprocess.Popen(['cat', 'DAR_MeasLogDump' + log_file_name],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
stdout, stderr = output.communicate()
print (stdout)
print (stderr)
I think you need only change to your 'hrun' command
It seems the same problem that I had at the beginning of a project: you have tried with windows "environment variables". It turns out that when entering the CMD or powershell it does not recognize perl, java, etc. unless you go to the folder where the .exe .py .java, etc. is located and enter the cmd, where the java.exe, python.py, etc. is.
In my ADB project, once I added in my environment variables, I no longer needed to go to the folder where the .exe .py or adb code was located.
Now you can open a CMD and it will execute any command even from your perl , so the interpreter that uses powershell will find and recognize the command.
Related
I am facing difficulties calling a command line from my script.I run the script but I don't get any result. Through this command line in my script I want to run a tool which produces a folder that has the output files for each line.The inputpath is already defined. Can you please help me?
for line in inputFile:
cmd = 'python3 CRISPRcasIdentifier.py -f %s/%s.fasta -o %s/%s.csv -st dna -co %s/'%(inputpath,line.strip(),outputfolder,line.strip(),outputfolder)
os.system(cmd)
You really want to use the Python standard library module subprocess. Using functions from that module, you can construct you command line as a list of strings, and each would be processed as one file name, option or value. This bypasses the shell's escaping, and eliminates the need to massage you script arguments before calling.
Besides, your code would not work, because the body block of the for statement is not indented. Python would simply not accept this code (could be you pasted into the questiong without the proper indentations).
as mentioned before, executing command vias: os.system(command) is not recomended. please use subprocess (read in python docs about this modulesubprocess_module_docs). see the code here:
for command in input_file:
p = subprocess.Popen(command, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
# use this if you want to communicate with child process
# p = subprocess.Popen(command, stdout=subprocess.PIPE, stdin=subprocess.PIPE, stderr=subprocess.PIPE)
p.communicate()
# --- do the rest
I usually do like this for static command
from subprocess import check_output
def sh(command):
return check_output(command, shell=True, universal_newlines=True)
output = sh('echo hello world | sed s/h/H/')
BUT THIS IS NOT SAFE!!! It's vunerable to shell injection you should do
from subprocess import check_output
from shlex import split
def sh(command):
return check_output(split(command), universal_newlines=True)
output = sh('echo hello world')
The difference is subtle but important. shell=True will create a new shell, so pipes, etc will work. I use this when I have a big command line with pipes and that is static, I mean, it do not depend on user input. This is because this variant is vunerable to shell injection, a user can input something; rm -rf / and it will run.
The second variant only accepts one command, it will not spawn a shell, instead it will run the command directly. So no pipes and such shell things will work, and is safer.
universal_newlines=True is for getting output as string instead of bytes. Use it for text output, if you need binary output just ommit it. The default is false.
So here is the full example
from subprocess import check_output
from shlex import split
def sh(command):
return check_output(split(command), universal_newlines=True)
for line in inputFile:
cmd = 'python3 CRISPRcasIdentifier.py -f %s/%s.fasta -o %s/%s.csv -st dna -co %s/'%(inputpath,line.strip(),outputfolder,line.strip(),outputfolder)
sh(cmd)
Ps: I didn't test this
I have a python process running, having a logger object configured to print logs in a log file.
Now, I am trying to call a scala script through this python process, by using subprocess module of Python.
subprocess.Popen(scala_run_command, stdout=subprocess.PIPE, shell=True)
The issue is, whenever the python process exits, it hangs the shell, which comes to life only after explicitly running stty sane command. My guess is that it is caused because the scala script outputs to shell and hence the shell hangs, because of its stdout [something in its stdout causes the shell to lose its sanity].
For the same reason, I wanted to try to put the output of scala run script to be captured in my default log file, which does not seem to be happening using multiple ways.
So, the query boils down to, how to the get the stdout output of shell command ran through subprocess module in a log file. Even if there is a better way to achieve this instead of subprocess, run, I would love to know the ideas.
The current state of code looks like this.
__echo_command = 'echo ":load %s"'
__spark_console_command = 'spark;'
def run_scala_script(self, script):
echo_command = self.__echo_command % script
spark_console_command = self.__spark_console_command
echo_result = subprocess.run(echo_command, stdout=subprocess.PIPE, shell=True)
result = subprocess.run(spark_console_command, stdout=subprocess.PIPE, shell=True, input=echo_result.stdout)
logger.info('Scala script %s completed successfully' % script)
logger.info(result.stdout)
Use
p = subprocess.Popen(...)
followed by
stdout, stderr = p.communicate()
and then stdout and stderr will contain the output bytes from the subprocess' output streams. You can then log the stdout value.
I'm new to Python, and haven't used Linux in years, so I'm not sure where I'm getting tangled up. I'm trying to use Popen to run sql files in MySQL on Ubuntu.
Here is the relevant code:
command = ['mysql', '-uUSER', '-pPWD','-h192.168.1.132', '--database=dbName', '<', './1477597236_foo.sql' ]
print("command is: "+subprocess.list2cmdline(command))
proc = subprocess.Popen(
command, stderr=subprocess.PIPE, stdout=subprocess.PIPE, cwd='.'
)
the output from this is the same as if had run 'mysql --help'. The puzzling thing to me is that if i take the command output by subprocess.list2cmdline and run it directly, it runs perfectly. Also, if i replace '< file.sql' with '-e select * from foo', it runs. So, the '<' and file are causing my problem. I know WHAT is causing the problem, but nothing I've tried so far has fixed it.
tia, Craig
When a redirection or pipe or built-in command is present in the command line, shell=True is required. However, in simple cases like this, shell=True is overkill. There's a much cleaner way in order to avoid shell=True which gives better control on the input file.
if the input file doesn't exist, you get an exception before reaching the subprocess, which is easier to handle
the process runs without the shell: better portability & performance
the code:
command = ['mysql', '-uUSER', '-pPWD','-h192.168.1.132', '--database=dbName' ]
with open('./1477597236_foo.sql') as input_file:
proc = subprocess.Popen(
command, stdin = input_file, stderr=subprocess.PIPE, stdout=subprocess.PIPE )
output,error = proc.communicate()
(I added the next line which should be a communicate call: since both stdout & stderr are redirected, it's the only simple way to avoid deadlocks between both output streams)
So you need to add shell=True to your Popen call. < is a part of the shell and you can't use shell features without that parameter.
proc = subprocess.Popen( command, stderr=subprocess.PIPE, stdout=subprocess.PIPE, cwd='.',shell=True )
I tried to write a code that can execute python codes easily.
but when I used subprocess library such:
import subprocess
print(subprocess.Popen("py setup.py install", shell = True, stdout = subprocess.PIPE).stdout.read())
print(subprocess.Popen("py setup.py py2exe", shell = True, stdout = subprocess.PIPE).stdout.read())
I saw just this result
b''
please help me please
Most likely the commands you are trying to run are producing a stderr, which your code does not display. It is possible to send the stderr messages to stdout if you don't want to handle it separately.
I'll use a different command in the subprocess that is relatively safe. And I will break it up a little instead of having one long line.
import subprocess
p = subprocess.Popen("python filedoesntexist",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
print(p.stdout.read())
See that I added the parameter stderr=subprocess.STDOUT, this sends all the error messages to stdout. The subprocess tries to run "python filedoesntexist" and since filedoesntexist is a file that doesn't exists, it will print this message:
b"python: can't open file 'filedoesntexist': [Errno 2] No such file or directory\n"
But you might just want to get the string instead of bytes, and you can add the parameter universal_newlines=True like this:
p = subprocess.Popen("python filedoesntexist",
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
universal_newlines=True)
print(p.stdout.read())
Now it prints just the string like this:
python: can't open file 'filedoesntexist': [Errno 2] No such file or directory
For additional information, visit the python documentation
Edit
The documentation recommends using run(), which can be done like this (updated after comments from J.F. Sebastian) :
subprocess.run(["python", "filedoesntexist"])
If you need to handle stdout in some way, add parameters described earlier in the Popen examples.
I'm trying to run a .mpkg installer on UNIX and when I run this code:
p = subprocess.Popen(['/Path/to/File.mpkg'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)
return p
The output is this:
<subprocess.Popen object at 0x11384xxx>
My first question is - Is there an easier way to run a mpkg installer on UNIX?
Secondly - I can't seem to figure out how to use the subprocess.Popen object to my benefit.
Sadly I’m not sure what mpkg is, but there are two options.
Either it is a self-running package, perhaps a shell script, akin to the .run format sometimes used for Unix software. In this case, your invocation of Popen is correct, as long as you have the execute permission on File.mpkg (check with ls -l /Path/to/File.mpkg). The installer should be running fine.
Or, it is intended to be processed by a system tool, like .deb packages are handled with the dpkg program. In this case, you need something like this:
p = subprocess.Popen(['/usr/bin/dpkg', '-i', '/Path/to/File.deb'], ...)
or, alternatively:
p = subprocess.Popen('dpkg -i /Path/to/File.deb', ..., shell=True)
Now, what you do with this Popen object depends on what you want to achieve. If you wish to get the output of the process, you need to call Popen.communicate, like this:
p = subprocess.Popen(
['/Path/to/File.mpkg'],
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
stdin=subprocess.PIPE)
(out, err) = p.communicate()
Now out contains the standard output and err the standard error.
If you just want to invoke the command and wait until it completes, you can also use the subprocess.call shortcut.