Python script does not print output as supposed - python-3.x

I have a very simple (test) code which I'm running either from a Linux shell, or in interactive mode, and I have two different behaviours I cannot figure out the reason of.
I have a file generated by a Popen call, previously, where each line is a file path. This is the code used to generate the file:
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
(Incidentally, I was trying to build a PIPE originally, namely inputting the output of this command to a grep command, and since I wasn't successful in any way, I decided to break the problem down and just read the file paths from a file, and process them one by one. So maybe there is a common issue that is blocking me somewhere in this procedure).
Since in this second step I wasn't even able to open and process the files by opening the addresses contained in each line of the find.txt file, I just tried to print the file lines out, because for sure they're available in there:
with open('find.txt','r') as g:
for l in g.readlines():
print(l)
Now, the interesting part:
if I paste the lines above into a python shell, everything works fine and I get my outputs as expected
if, on the other hand, I try to run python test.py, where test.py is the name of the file containing the lines above, no output appears in the shell's stdout.
I've tried sys.stdout.flush() to no avail. I've also inserted some dummy print() statements along the way: everything gets printed but what's after the g.readlines() statement.
Here's the full script I'm trying to make work (a pre-precursor of what I'm actually after, tbh).
#!/usr/bin/env python3
import subprocess
import sys
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
print('hello')
with open('find.txt','r') as g:
print('hello?')
for l in g.readlines():
print('help me!')
print(l)
sys.stdout.flush()
output being:
{ancis:>106> python test.py
hello
hello?
{ancis:>106>
EDIT
I've quickly tried the very same lines (but without the call to find, which isn't available) on my python installation in Windows: it works as expected)
Based on that, I've tried to run the simpler code below:
print('hello')
with open('find.txt','r') as g:
print('hello?')
for l in g.readlines():
print('help me!')
print(l)
sys.stdout.flush()
as a script, in Linux - This also works w/o problems.
This should mean that somehow I'm messing things up with the call to Popen... But what?

This is a race condition.
Your call to
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
is opening another process and running your find command which takes a bit of time to fully execute.
Python then continues on and reaches the reading of the file portion before the command is fully executed and the file is generated.
Want to test it out?
Add a time.sleep(1) just before the opening of the file.
Full test script:
#!/usr/bin/env python3
import subprocess
import time
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
time.sleep(1)
with open('find.txt','r') as g:
for l in g:
print(l)
To block until the process is complete you can use find.communicate().
With this you can also optionally set a timeout if that's something that you want.
#!/usr/bin/env python3
import subprocess
with open('find.txt','w') as f:
find = subprocess.Popen(["find",".","-name","myfile.out"],stdout=f)
find.communicate()
with open('find.txt','r') as g:
for l in g:
print(l)
Source:
https://docs.python.org/3/library/subprocess.html#subprocess.Popen.communicate

Related

Is there a way to extract only specific lines from a text file using python

I have a big text file that has around 200K lines of records/lines.
But I need to extract only specific lines which Start with CLM. For example, if the file has 100K lines that start with CLM I should print all that 100K lines alone.
Can anyone help me to achieve this using python script?
There can be multiple ways to achieve this.
you can simply iterate through the lines and search for a pattern using the re library
Solution 1
# Note :- Regex is faster in terms of execution as compared to string match
import re
pattern = re.compile("CLM")
for line in open("sample.txt"):
for match in re.finditer(pattern, line):
print(line)
If you want you can also run the bash command inside the python script.
Solution 2
There are two popular modules to use:- os and subprocess
os is kind of deprecated, I would recommend using the subprocess module as below:-
Below is the code to print the output on the console: -
import subprocess
process = subprocess.Popen(['grep', '-i', '^hel*', 'sample.txt'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,universal_newlines=True)
stdout, stderr = process.communicate()
print(stdout)
In the above, we are passing the argument universal_newlines=True because the output (stdout) is of type bytes.
In the above grep command I have passes -i argument to ignore case sensitivity. If you want only to search for CLM and not clm, remove that and use it
I have used the grep command to depict the use case, you can also use awk or sed or any command as per your requirement.
Just an addon, if you want to save the output in some file, let's say ouput.txt you can achieve this as below:-
import subprocess
with open('output.txt', 'w') as f:
process = subprocess.Popen(['grep', '-i', '^hel*', 'file.txt'], stdout=f)
If your file is extremely large, you can also do a poll and check for the subprocess execution status. Refer to the below link for more details on that.
Python-Shell-Commands
try:
with open('file.txt') as f:
for line in f:
if line.startswith('CLM'):
print(line.rstrip())

Linux - Redirection of a shell script into a text file

I'm new to Linux, and have been trying to solve an assignment but to no avail.
I have a shell script which prints out lines of a text file in a certain manner (a line within every few seconds):
python << END
import time,random
a= open ('/home/ch/pshety/course/fielding_history.txt','r')
flag =False
for i in range(1000):
b=a.readline()
if i==402 or flag:
print(a.readline())
flag=True
time.sleep(2)
END
sh th.sh
If I run it without trying to redirect it anywhere, I get the output on the terminal. However, when I tried to redirect it into a new text file, it doesn't do anything - the text remains empty:
sh th.sh > debug.txt
I've tried looking for answers, I've stumbled upon a lot of suggestions including tee but nothing helps - the file remains empty.
What am I doing wrong?
Try this:
import time,random
a = open('/home/ch/pshety/course/fielding_history.txt', 'r')
for i in range(1000):
b = a.readline()
if i >= 402:
print(b, flush=True)
time.sleep(2)
Your Python script likely needs to flush the contents of the output buffer before you can see it.
Note: aside from the sleep() call, Unix provides other ways of accomplishing this. I would take a look at man tail and read about the -f and -n switches.
Edit: didn't realize that tail has a switch (-s) to sleep as well!

Can i access the variables of the python script after run that python script with console?

I run the python script using terminal command
python3 myScript.py
It's simply run my program but if i want to open python console after complete run of my script so that i can access my script's variables.
So, What should i do ? and How can i get my script's variables after run the code using terminal ?
Open a python terminal (type 'python' in cmd);
Paste this (replace 'myScript.py' with your script filename):
def run():
t = ""
with open('myScript.py') as f:
t = f.read()
return t
Type exec(run()). Now you will have access to the variables defined in myScript.py.
I needed to do this so I could explore the result of a request from the requests library, without having to paste the code to make the requests every time.
Make the program run the other program you want with the variables as arguments. For example:
#program1
var1=7
var2="hi"
import os
os.system("python %s %d %s" % (filename, var1, var2))
#program2
import sys
#do something such as:
print(sys.argv[1]) #for var1
print(sys.argv[2]) #for var2
Basically, you are running program2 with arguments that can be referenced later.
Hope this helps :)

subprocess.call() problems using the '>'

I'm having trouble with the call function
I'm trying to redirect the output of a program to a text file by using the '>'
This is what I've tried:
import subprocess
subprocess.call(["python3", "test.py", ">", "file.txt"])
but it still displaying the output on the command prompt and not in the txt file
There are two approaches to solving this.
Have python handle the redirection:
with open('file.txt', 'w') as f:
subprocess.call(["python3", "test.py"], stdout=f)
Have the shell handle redirection:
subprocess.call(["python3 test.py >file.txt"], shell=True)
Generally, the first is to be preferred because it avoids the vagaries of the shell.
Lastly, you should look into the possibility that test.py can be run as an imported module rather than calling it via subprocess. Python is designed so that it is easy to write scripts so that the same functionality is available either at the command line (python3 test.py) or as a module (import test).

Testing python programs without using python shell

I would like to easily test my python programs without constantly using the python shell since each time the program is modified you have to quit, re-enter the python shell and import the program again. I am using a 2012 Macbook pro with OSX. I have the following code:
import sys
def read_strings(filename):
with open(filename) as file:
return file.read().split('>')[1:0]
file1 = sys.argv[1]
filename = read_strings(file1)
Essentially I would like to read into and split a txt file containing:
id1>id2>id3>id4
I am entering this into my command line:
pal-nat184-102-127:python_stuff ceb$ python3 program.py string.txt
However when I try the sys.argv approach on the command line my program returns nothing. Is this a good approach to testing code, could anyone point me in the correct direction?
This is what I would like to happen:
pal-nat184-102-127:python_stuff ceb$ python3 program.py string.txt
['id1', 'id2', 'id3', 'id4']
Let's take this a piece at a time:
However when I try the sys.argv approach on the command line my
program returns nothing
The final result of your program is that it writes a string into the variable filename. It's a little strange to have a program "return" a value. Generally, you want a program to print it's something out or save something to a file. I'm guessing it would ease your debugging if you modified your program by adding,
print (filename)
at the end: you'd be able to see the result of your program.
could anyone point me in the correct direction?
One other debugging note: It can be useful to write your .py files so that they can be run both independently at the command line or in a python shell. How you've currently structured your code, this will work semi-poorly. (Starting a shell and then importing your file will cause an error because sys.argv[1] isn't defined.)
A solution to this is to change your the bottom section of your code as follows:
if __name__ == '__main__':
file1 = sys.argv[1]
filename = read_strings(file1)
The if guard at the top says, "If running as a standalone script, then run what's below me. If you imported me from some place else, then do not execute what's below me."
Feel free to follow up below if I misinterpreted your question.
You never do anything with the result of read_strings. Try:
print(read_strings(file1))

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