I am trying to write a script where I pass file name as argument from shell script to python script and python script processes that script.It is giving me keyerror but if I run the same script hardcoding the file name it works fine.
#!/bin/sh
LOCKFILE=./test.txt
if [ -e ${LOCKFILE} ] && kill -0 `cat ${LOCKFILE}`; then
echo "already running"
exit
fi
trap "rm -f ${LOCKFILE}; exit" INT TERM EXIT
echo $$ > ${LOCKFILE}
# do stuff
FILES=/home/sugoi/script/csv/*
for file in $FILES
do
python ./csvTest.py $file
#mv $file ./archive
done
rm -f ${LOCKFILE}
exit
Python:
from pymongo import MongoClient
import csv
import json
import sys
client = MongoClient()
db = client.test
for arg in sys.argv:
try:
csvfile = open(arg, 'r')#if i hardcode file name here it works fine
except IOError as e:
#write to error log
sys.exit(100)
reader = csv.DictReader(csvfile)
header=reader.next()
for each in reader:
row={}
for field in header:
row[field]=each[field]
db.test.update({"_id": row["CustomerId"]}, {"$push": {"activities":{"action": row["Action"],"date" :row["Timestamp"],"productId":row["productId"]}}},True)
What am I doing wrong ?
Two issues.
Your shell script isn't expanding the file list correctly.
FILES=/home/sugoi/script/csv/* needs to be something like:
FILES=`ls -1 /home/sugoi/script/csv/*;`
Your argument to the python script will only be one file at a time, so why loop through sys.argv?
Just use the argument itself, sys.argv[1]. As #Brian Besmanoff pointed out, that needs to be indexed 1 because the script name itself is stored in sys.argv[0].
try:
csvfile = open(sys.argv[1], 'r')
except IOError as e:
(...)
Finally: you can just parse directories with Python instead of looping in a shell script. Look at the os module, particularly os.listdir(). A little more work and you can have the whole thing running inside one Python script instead of juggling between shell and calling a script.
The first value in sys.argv is going to be the name of the script. reference
Related
I am trying to run python subprocess.run function to execute following command:
pdftoppm -jpeg -f 1 -scale-to 200 data/andromeda.pdf and-page
pdftoppm - is part of poppler utility and it generates images from pdf files.
File data/andromeda.pdf exists. Folder data is on same level with python script and/or where I run command from.
Command basically will generate a jpeg file, from page 1 (-f 1) 200px wide (-scale-to) from given file of and-page-1.jpeg format (so called ppmtroot).
Long story short: from command line it works as expected i.e. if I call the above command either from zsh or bash shell, manually - it generates thumbnail as expected. However if I run it from python subprocess module - it fails it returns 99 error code!
Following is python code (file name is sc_02_thumbnails.py):
import subprocess
import sys
def main(filename, ppmroot):
cmd = [
'pdftoppm',
'-f 1',
'-scale-to 200',
'-jpeg',
filename,
ppmroot
]
result = subprocess.run(
cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE
)
if result.returncode:
print("Failed to generate thumbnail. Return code: {}. stderr: {}".format(
result.returncode,
result.stderr
))
print("Used cmd: {}".format(' '.join(cmd)))
sys.exit(1)
else:
print("Success!")
if __name__ == "__main__":
if len(sys.argv) > 2:
filename = sys.argv[1]
ppmroot = sys.argv[2]
else:
print("Usage: {} <pdffile> <ppmroot>".format(sys.argv[0]))
sys.exit(1)
main(filename, ppmroot)
And here is repo which includes data/andromeda.pdf file as well.
I call my script with as (from zsh):
$ chmod +x ./sc_02_thumbnauils.py
$ ./sc_02_thumbnails.py data/andromeda.pdf and-page
and ... thumbnail generating fails!
I have tried executing python script from both, from zsh and bash shells :(
What I am doing wrong?
The quoting is wrong, you should have '-f', '1', etc
Using Python's sh, I am running 3rd party shell script that requests my input (not that it matters much, but to be precise, I'm running an Ansible2 playbook with the --step option)
As an oversimplification of what is happening, I built a simple bash script that requests an input. I believe that if make this simple example work I can make the original case work too.
So please consider this bash script hello.sh:
#!/bin/bash
echo "Please input your name and press Enter:"
read name
echo "Hello $name"
I can run it from python using sh module, but it fails to receive my input...
import errno
import sh
cmd = sh.Command('./hello.sh')
for line in cmd(_iter=True, _iter_noblock=True):
if line == errno.EWOULDBLOCK:
pass
else:
print(line)
How could I make this work?
After following this tutorial, this works for my use case:
#!/usr/bin/env python3
import errno
import sh
import sys
def sh_interact(char, stdin):
global aggregated
sys.stdout.write(char)
sys.stdout.flush()
aggregated += char
if aggregated.endswith(":"):
val = input()
stdin.put(val + "\n")
cmd = sh.Command('./hello.sh')
aggregated = ""
cmd(_out=sh_interact, _out_bufsize=0)
For example, the output is:
$ ./testinput.py
Please input your name and press Enter:arod
Hello arod
There are two ways to solve this:
Using _in:
using _in, we can pass a list which can be taken as input in the python script
cmd = sh.Command('./read.sh')
stdin = ['hello']
for line in cmd(_iter=True, _iter_noblock=True, _in=stdin):
if line == errno.EWOULDBLOCK:
pass
else:
print(line)
Using command line args if you are willing to modify the script.
I have a python code in which I am calling a shell command. The part of the code where I did the shell command is:
try:
def parse(text_list):
text = '\n'.join(text_list)
cwd = os.getcwd()
os.chdir("/var/www/html/alenza/hdfs/user/alenza/sree_account/sree_project/src/core/data_analysis/syntaxnet/models/syntaxnet")
synnet_output = subprocess.check_output(["echo '%s' | syntaxnet/demo.sh 2>/dev/null"%text], shell = True)
os.chdir(cwd)
return synnet_output
except Exception as e:
sys.stdout.write(str(e))
Now, when i run this code on a local file with some sample input (I did cat /home/sree/example.json | python parse.py) it works fine and I get the required output. But I am trying to run the code with an input on my HDFS (the same cat command but input file path is from HDFS) which contains exactly the same type of json entries and it fails with an error:
/bin/sh: line 62: to: command not found
list index out of range
I read similar questions on Stack Overflow and the solution was to include a Shebang line for the shell script that is being called. I do have the shebang line #!/usr/bin/bash in demo.sh script.
Also, which bash gives /usr/bin/bash.
Someone please elaborate.
You rarely, if ever, want to combine passing a list argument with shell=True. Just pass the string:
synnet_output = subprocess.check_output("echo '%s' | syntaxnet/demo.sh 2>/dev/null"%(text,), shell=True)
However, you don't really need a shell pipeline here.
from subprocess import check_output
from StringIO import StringIO # from io import StringIO in Python 3
synnet_output = check_output(["syntaxnet/demo.sh"],
stdin=StringIO(text),
stderr=os.devnull)
There was a problem with some special characters appearing in the text string that i was inputting to demo.sh. I solved this by storing text into a temporary file and sending the contents of that file to demo.sh.
That is:
try:
def parse(text_list):
text = '\n'.join(text_list)
cwd = os.getcwd()
with open('/tmp/data', 'w') as f:
f.write(text)
os.chdir("/var/www/html/alenza/hdfs/user/alenza/sree_account/sree_project/src/core/data_analysis/syntaxnet/models/syntaxnet")
synnet_output = subprocess.check_output(["cat /tmp/data | syntaxnet/demo.sh 2>/dev/null"%text], shell = True)
os.chdir(cwd)
return synnet_output
except Exception as e:
sys.stdout.write(str(e))
I write lots of small scripts to manipulate files on a Bash-based server. I would like to have a mechanism by which to log which commands created which files in a given directory. However, I don't just want to capture every input command, all the time.
Approach 1: a wrapper script that uses a Bash builtin (a la history or fc -ln -1) to grab the last command and write it to a log file. I have not been able to figure out any way to do this, as the shell builtin commands do not appear to be recognized outside of the interactive shell.
Approach 2: a wrapper script that pulls from ~/.bash_history to get the last command. This, however, requires setting up the Bash shell to flush every command to history immediately (as per this comment) and seems also to require that the history be allowed to grow inexorably. If this is the only way, so be it, but it would be great to avoid having to edit the ~/.bashrc file on every system where this might be implemented.
Approach 3: use script. My problem with this is that it requires multiple commands to start and stop the logging, and because it launches its own shell it is not callable from within another script (or at least, doing so complicates things significantly).
I am trying to figure out an implementation that's of the form log_this.script other_script other_arg1 other_arg2 > file, where everything after the first argument is logged. The emphasis here is on efficiency and minimizing syntax overhead.
EDIT: iLoveTux and I both came up with similar solutions. For those interested, my own implementation follows. It is somewhat more constrained in its functionality than the accepted answer, but it also auto-updates any existing logfile entries with changes (though not deletions).
Sample usage:
$ cmdlog.py "python3 test_script.py > test_file.txt"
creates a log file in the parent directory of the output file with the following:
2015-10-12#10:47:09 test_file.txt "python3 test_script.py > test_file.txt"
Additional file changes are added to the log;
$ cmdlog.py "python3 test_script.py > test_file_2.txt"
the log now contains
2015-10-12#10:47:09 test_file.txt "python3 test_script.py > test_file.txt"
2015-10-12#10:47:44 test_file_2.txt "python3 test_script.py > test_file_2.txt"
Running on the original file name again changes the file order in the log, based on modification time of the files:
$ cmdlog.py "python3 test_script.py > test_file.txt"
produces
2015-10-12#10:47:44 test_file_2.txt "python3 test_script.py > test_file_2.txt"
2015-10-12#10:48:01 test_file.txt "python3 test_script.py > test_file.txt"
Full script:
#!/usr/bin/env python3
'''
A wrapper script that will write the command-line
args associated with any files generated to a log
file in the directory where the files were made.
'''
import sys
import os
from os import listdir
from os.path import isfile, join
import subprocess
import time
from datetime import datetime
def listFiles(mypath):
"""
Return relative paths of all files in mypath
"""
return [join(mypath, f) for f in listdir(mypath) if
isfile(join(mypath, f))]
def read_log(log_file):
"""
Reads a file history log and returns a dictionary
of {filename: command} entries.
Expects tab-separated lines of [time, filename, command]
"""
entries = {}
with open(log_file) as log:
for l in log:
l = l.strip()
mod, name, cmd = l.split("\t")
# cmd = cmd.lstrip("\"").rstrip("\"")
entries[name] = [cmd, mod]
return entries
def time_sort(t, fmt):
"""
Turn a strftime-formatted string into a tuple
of time info
"""
parsed = datetime.strptime(t, fmt)
return parsed
ARGS = sys.argv[1]
ARG_LIST = ARGS.split()
# Guess where logfile should be put
if (">" or ">>") in ARG_LIST:
# Get position after redirect in arg list
redirect_index = max(ARG_LIST.index(e) for e in ARG_LIST if e in ">>")
output = ARG_LIST[redirect_index + 1]
output = os.path.abspath(output)
out_dir = os.path.dirname(output)
elif ("cp" or "mv") in ARG_LIST:
output = ARG_LIST[-1]
out_dir = os.path.dirname(output)
else:
out_dir = os.getcwd()
# Set logfile location within the inferred output directory
LOGFILE = out_dir + "/cmdlog_history.log"
# Get file list state prior to running
all_files = listFiles(out_dir)
pre_stats = [os.path.getmtime(f) for f in all_files]
# Run the desired external commands
subprocess.call(ARGS, shell=True)
# Get done time of external commands
TIME_FMT = "%Y-%m-%d#%H:%M:%S"
log_time = time.strftime(TIME_FMT)
# Get existing entries from logfile, if present
if LOGFILE in all_files:
logged = read_log(LOGFILE)
else:
logged = {}
# Get file list state after run is complete
post_stats = [os.path.getmtime(f) for f in all_files]
post_files = listFiles(out_dir)
# Find files whose states have changed since the external command
changed = [e[0] for e in zip(all_files, pre_stats, post_stats) if e[1] != e[2]]
new = [e for e in post_files if e not in all_files]
all_modded = list(set(changed + new))
if not all_modded: # exit early, no need to log
sys.exit(0)
# Replace files that have changed, add those that are new
for f in all_modded:
name = os.path.basename(f)
logged[name] = [ARGS, log_time]
# Write changed files to logfile
with open(LOGFILE, 'w') as log:
for name, info in sorted(logged.items(), key=lambda x: time_sort(x[1][1], TIME_FMT)):
cmd, mod_time = info
if not cmd.startswith("\""):
cmd = "\"{}\"".format(cmd)
log.write("\t".join([mod_time, name, cmd]) + "\n")
sys.exit(0)
You can use the tee command, which stores its standard input to a file and outputs it on standard output. Pipe the command line into tee, and pipe tee's output into a new invocation of your shell:
echo '<command line to be logged and executed>' | \
tee --append /path/to/your/logfile | \
$SHELL
i.e., for your example of other_script other_arg1 other_arg2 > file,
echo 'other_script other_arg1 other_arg2 > file' | \
tee --append /tmp/mylog.log | \
$SHELL
If your command line needs single quotes, they need to be escaped properly.
OK, so you don't mention Python in your question, but it is tagged Python, so I figured I would see what I could do. I came up with this script:
import sys
from os.path import expanduser, join
from subprocess import Popen, PIPE
def issue_command(command):
process = Popen(command, stdout=PIPE, stderr=PIPE, shell=True)
return process.communicate()
home = expanduser("~")
log_file = join(home, "command_log")
command = sys.argv[1:]
with open(log_file, "a") as fout:
fout.write("{}\n".format(" ".join(command)))
out, err = issue_command(command)
which you can call like (if you name it log_this and make it executable):
$ log_this echo hello world
and it will put "echo hello world" in a file ~/command_log, note though that if you want to use pipes or redirection you have to quote your command (this may be a real downfall for your use case or it may not be, but I haven't figured out how to do this just yet without the quotes) like this:
$ log_this "echo hello world | grep h >> /tmp/hello_world"
but since it's not perfect, I thought I would add a little something extra.
The following script allows you to specify a different file to log your commands to as well as record the execution time of the command:
#!/usr/bin/env python
from subprocess import Popen, PIPE
import argparse
from os.path import expanduser, join
from time import time
def issue_command(command):
process = Popen(command, stdout=PIPE, stderr=PIPE, shell=True)
return process.communicate()
home = expanduser("~")
default_file = join(home, "command_log")
parser = argparse.ArgumentParser()
parser.add_argument("-f", "--file", type=argparse.FileType("a"), default=default_file)
parser.add_argument("-p", "--profile", action="store_true")
parser.add_argument("command", nargs=argparse.REMAINDER)
args = parser.parse_args()
if args.profile:
start = time()
out, err = issue_command(args.command)
runtime = time() - start
entry = "{}\t{}\n".format(" ".join(args.command), runtime)
args.file.write(entry)
else:
out, err = issue_command(args.command)
entry = "{}\n".format(" ".join(args.command))
args.file.write(entry)
args.file.close()
You would use this the same way as the other script, but if you wanted to specify a different file to log to just pass -f <FILENAME> before your actual command and your log will go there, and if you wanted to record the execution time just provide the -p (for profile) before your actual command like so:
$ log_this -p -f ~/new_log "echo hello world | grep h >> /tmp/hello_world"
I will try to make this better, but if you can think of anything else this could do for you, I am making a github project for this where you can submit bug reports and feature requests.
What I'd like to achieve is the launch of the following shell command:
mysql -h hostAddress -u userName -p userPassword
databaseName < fileName
From within a python 2.4 script with something not unlike:
cmd = ["mysql", "-h", ip, "-u", mysqlUser, dbName, "<", file]
subprocess.call(cmd)
This pukes due to the use of the redirect symbol (I believe) - mysql doesn't receive the input file.
I've also tried:
subprocess.call(cmd, stdin=subprocess.PIPE)
no go there ether
Can someone specify the syntax to make a shell call such that I can feed in a file redirection ?
Thanks in advance.
You have to feed the file into mysql stdin by yourself. This should do it.
import subprocess
...
filename = ...
cmd = ["mysql", "-h", ip, "-u", mysqlUser, dbName]
f = open(filename)
subprocess.call(cmd, stdin=f)
The symbol < has this meaning (i. e. reading a file to stdin) only in shell. In Python you should use either of the following:
1) Read file contents in your process and push it to stdin of the child process:
fd = open(filename, 'rb')
try:
subprocess.call(cmd, stdin=fd)
finally:
fd.close()
2) Read file contents via shell (as you mentioned), but redirect stdin of your process accordingly:
# In file myprocess.py
subprocess.call(cmd, stdin=subprocess.PIPE)
# In shell command line
$ python myprocess.py < filename
As Andrey correctly noticed, the < redirection operator is interpreted by shell. Hence another possible solution:
import os
os.system("mysql -h " + ip + " -u " + mysqlUser + " " + dbName)
It works because os.system passes its argument to the shell.
Note that I assumed that all used variables come from a trusted source, otherwise you need to validate them in order to prevent arbitrary code execution. Also those variables should not contain whitespace (default IFS value) or shell special characters.