I'm testing subprocesses pipelines with python. I'm aware that I can do what the programs below do in python directly, but that's not the point. I just want to test the pipeline so I know how to use it.
My system is Linux Ubuntu 9.04 with default python 2.6.
I started with this documentation example.
from subprocess import Popen, PIPE
p1 = Popen(["grep", "-v", "not"], stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
output = p2.communicate()[0]
print output
That works, but since p1's stdin is not being redirected, I have to type stuff in the terminal to feed the pipe. When I type ^D closing stdin, I get the output I want.
However, I want to send data to the pipe using a python string variable. First I tried writing on stdin:
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
p1.stdin.write('test\n')
output = p2.communicate()[0] # blocks forever here
Didn't work. I tried using p2.stdout.read() instead on last line, but it also blocks. I added p1.stdin.flush() and p1.stdin.close() but it didn't work either. I Then I moved to communicate:
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
p1.communicate('test\n') # blocks forever here
output = p2.communicate()[0]
So that's still not it.
I noticed that running a single process (like p1 above, removing p2) works perfectly. And passing a file handle to p1 (stdin=open(...)) also works. So the problem is:
Is it possible to pass data to a pipeline of 2 or more subprocesses in python, without blocking? Why not?
I'm aware I could run a shell and run the pipeline in the shell, but that's not what I want.
UPDATE 1: Following Aaron Digulla's hint below I'm now trying to use threads to make it work.
First I've tried running p1.communicate on a thread.
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
t = threading.Thread(target=p1.communicate, args=('some data\n',))
t.start()
output = p2.communicate()[0] # blocks forever here
Okay, didn't work. Tried other combinations like changing it to .write() and also p2.read(). Nothing. Now let's try the opposite approach:
def get_output(subp):
output = subp.communicate()[0] # blocks on thread
print 'GOT:', output
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
t = threading.Thread(target=get_output, args=(p2,))
t.start()
p1.communicate('data\n') # blocks here.
t.join()
code ends up blocking somewhere. Either in the spawned thread, or in the main thread, or both. So it didn't work. If you know how to make it work it would make easier if you can provide working code. I'm trying here.
UPDATE 2
Paul Du Bois answered below with some information, so I did more tests.
I've read entire subprocess.py module and got how it works. So I tried applying exactly that to code.
I'm on linux, but since I was testing with threads, my first approach was to replicate the exact windows threading code seen on subprocess.py's communicate() method, but for two processes instead of one. Here's the entire listing of what I tried:
import os
from subprocess import Popen, PIPE
import threading
def get_output(fobj, buffer):
while True:
chunk = fobj.read() # BLOCKS HERE
if not chunk:
break
buffer.append(chunk)
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
b = [] # create a buffer
t = threading.Thread(target=get_output, args=(p2.stdout, b))
t.start() # start reading thread
for x in xrange(100000):
p1.stdin.write('hello world\n') # write data
p1.stdin.flush()
p1.stdin.close() # close input...
t.join()
Well. It didn't work. Even after p1.stdin.close() was called, p2.stdout.read() still blocks.
Then I tried the posix code on subprocess.py:
import os
from subprocess import Popen, PIPE
import select
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
numwrites = 100000
to_read = [p2.stdout]
to_write = [p1.stdin]
b = [] # create buffer
while to_read or to_write:
read_now, write_now, xlist = select.select(to_read, to_write, [])
if read_now:
data = os.read(p2.stdout.fileno(), 1024)
if not data:
p2.stdout.close()
to_read = []
else:
b.append(data)
if write_now:
if numwrites > 0:
numwrites -= 1
p1.stdin.write('hello world!\n'); p1.stdin.flush()
else:
p1.stdin.close()
to_write = []
print b
Also blocks on select.select(). By spreading prints around, I found out this:
Reading is working. Code reads many times during execution.
Writing is also working. Data is written to p1.stdin.
At the end of numwrites, p1.stdin.close() is called.
When select() starts blocking, only to_read has something, p2.stdout. to_write is already empty.
os.read() call always returns something, so p2.stdout.close() is never called.
Conclusion from both tests: Closing the stdin of the first process on the pipeline (grep in the example) is not making it dump its buffered output to the next and die.
No way to make it work?
PS: I don't want to use a temporary file, I've already tested with files and I know it works. And I don't want to use windows.
I found out how to do it.
It is not about threads, and not about select().
When I run the first process (grep), it creates two low-level file descriptors, one for each pipe. Lets call those a and b.
When I run the second process, b gets passed to cut sdtin. But there is a brain-dead default on Popen - close_fds=False.
The effect of that is that cut also inherits a. So grep can't die even if I close a, because stdin is still open on cut's process (cut ignores it).
The following code now runs perfectly.
from subprocess import Popen, PIPE
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE, close_fds=True)
p1.stdin.write('Hello World\n')
p1.stdin.close()
result = p2.stdout.read()
assert result == "Hello Worl\n"
close_fds=True SHOULD BE THE DEFAULT on unix systems. On windows it closes all fds, so it prevents piping.
EDIT:
PS: For people with a similar problem reading this answer: As pooryorick said in a comment, that also could block if data written to p1.stdin is bigger than the buffers. In that case you should chunk the data into smaller pieces, and use select.select() to know when to read/write. The code in the question should give a hint on how to implement that.
EDIT2: Found another solution, with more help from pooryorick - instead of using close_fds=True and close ALL fds, one could close the fds that belongs to the first process, when executing the second, and it will work. The closing must be done in the child so the preexec_fn function from Popen comes very handy to do just that. On executing p2 you can do:
p2 = Popen(cmd2, stdin=p1.stdout, stdout=PIPE, stderr=devnull, preexec_fn=p1.stdin.close)
Working with large files
Two principles need to be applied uniformly when working with large files in Python.
Since any IO routine can block, we must keep each stage of the pipeline in a different thread or process. We use threads in this example, but subprocesses would let you avoid the GIL.
We must use incremental reads and writes so that we don't wait for EOF before starting to make progress.
An alternative is to use nonblocking IO, though this is cumbersome in standard Python. See gevent for a lightweight threading library that implements the synchronous IO API using nonblocking primitives.
Example code
We'll construct a silly pipeline that is roughly
{cat /usr/share/dict/words} | grep -v not \
| {upcase, filtered tee to stderr} | cut -c 1-10 \
| {translate 'E' to '3'} | grep K | grep Z | {downcase}
where each stage in braces {} is implemented in Python while the others use standard external programs. TL;DR: See this gist.
We start with the expected imports.
#!/usr/bin/env python
from subprocess import Popen, PIPE
import sys, threading
Python stages of the pipeline
All but the last Python-implemented stage of the pipeline needs to go in a thread so that it's IO does not block the others. These could instead run in Python subprocesses if you wanted them to actually run in parallel (avoid the GIL).
def writer(output):
for line in open('/usr/share/dict/words'):
output.write(line)
output.close()
def filter(input, output):
for line in input:
if 'k' in line and 'z' in line: # Selective 'tee'
sys.stderr.write('### ' + line)
output.write(line.upper())
output.close()
def leeter(input, output):
for line in input:
output.write(line.replace('E', '3'))
output.close()
Each of these needs to be put in its own thread, which we'll do using this convenience function.
def spawn(func, **kwargs):
t = threading.Thread(target=func, kwargs=kwargs)
t.start()
return t
Create the pipeline
Create the external stages using Popen and the Python stages using spawn. The argument bufsize=-1 says to use the system default buffering (usually 4 kiB). This is generally faster than the default (unbuffered) or line buffering, but you'll want line buffering if you want to visually monitor the output without lags.
grepv = Popen(['grep','-v','not'], stdin=PIPE, stdout=PIPE, bufsize=-1)
cut = Popen(['cut','-c','1-10'], stdin=PIPE, stdout=PIPE, bufsize=-1)
grepk = Popen(['grep', 'K'], stdin=PIPE, stdout=PIPE, bufsize=-1)
grepz = Popen(['grep', 'Z'], stdin=grepk.stdout, stdout=PIPE, bufsize=-1)
twriter = spawn(writer, output=grepv.stdin)
tfilter = spawn(filter, input=grepv.stdout, output=cut.stdin)
tleeter = spawn(leeter, input=cut.stdout, output=grepk.stdin)
Drive the pipeline
Assembled as above, all the buffers in the pipeline will fill up, but since nobody is reading from the end (grepz.stdout), they will all block. We could read the entire thing in one call to grepz.stdout.read(), but that would use a lot of memory for large files. Instead, we read incrementally.
for line in grepz.stdout:
sys.stdout.write(line.lower())
The threads and processes clean up once they reach EOF. We can explicitly clean up using
for t in [twriter, tfilter, tleeter]: t.join()
for p in [grepv, cut, grepk, grepz]: p.wait()
Python-2.6 and earlier
Internally, subprocess.Popen calls fork, configures the pipe file descriptors, and calls exec. The child process from fork has copies of all file descriptors in the parent process, and both copies will need to be closed before the corresponding reader will get EOF. This can be fixed by manually closing the pipes (either by close_fds=True or a suitable preexec_fn argument to subprocess.Popen) or by setting the FD_CLOEXEC flag to have exec automatically close the file descriptor. This flag is set automatically in Python-2.7 and later, see issue12786. We can get the Python-2.7 behavior in earlier versions of Python by calling
p._set_cloexec_flags(p.stdin)
before passing p.stdin as an argument to a subsequent subprocess.Popen.
There are three main tricks to making pipes work as expected
Make sure each end of the pipe is used in a different thread/process
(some of the examples near the top suffer from this problem).
explicitly close the unused end of the pipe in each process
deal with buffering by either disabling it (Python -u option), using
pty's, or simply filling up the buffer with something that won't affect the
data, ( maybe '\n', but whatever fits).
The examples in the Python "pipeline" module (I'm the author) fit your scenario
exactly, and make the low-level steps fairly clear.
http://pypi.python.org/pypi/pipeline/
More recently, I used the subprocess module as part of a
producer-processor-consumer-controller pattern:
http://www.darkarchive.org/w/Pub/PythonInteract
This example deals with buffered stdin without resorting to using a pty, and
also illustrates which pipe ends should be closed where. I prefer processes to
threading, but the principle is the same. Additionally, it illustrates
synchronizing Queues to which feed the producer and collect output from the consumer,
and how to shut them down cleanly (look out for the sentinels inserted into the
queues). This pattern allows new input to be generated based on recent output,
allowing for recursive discovery and processing.
Nosklo's offered solution will quickly break if too much data is written to the receiving end of the pipe:
from subprocess import Popen, PIPE
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE, close_fds=True)
p1.stdin.write('Hello World\n' * 20000)
p1.stdin.close()
result = p2.stdout.read()
assert result == "Hello Worl\n"
If this script doesn't hang on your machine, just increase "20000" to something that exceeds the size of your operating system's pipe buffers.
This is because the operating system is buffering the input to "grep", but once that buffer is full, the p1.stdin.write call will block until something reads from p2.stdout. In toy scenarios, you can get way with writing to/reading from a pipe in the same process, but in normal usage, it is necessary to write from one thread/process and read from a separate thread/process. This is true for subprocess.popen, os.pipe, os.popen*, etc.
Another twist is that sometimes you want to keep feeding the pipe with items generated from earlier output of the same pipe. The solution is to make both the pipe feeder and the pipe reader asynchronous to the man program, and implement two queues: one between the main program and the pipe feeder and one between the main program and the pipe reader. PythonInteract is an example of that.
Subprocess is a nice convenience model, but because it hides the details of the os.popen and os.fork calls it does under the hood, it can sometimes be more difficult to deal with than the lower-level calls it utilizes. For this reason, subprocess is not a good way to learn about how inter-process pipes really work.
You must do this in several threads. Otherwise, you'll end up in a situation where you can't send data: child p1 won't read your input since p2 doesn't read p1's output because you don't read p2's output.
So you need a background thread that reads what p2 writes out. That will allow p2 to continue after writing some data to the pipe, so it can read the next line of input from p1 which again allows p1 to process the data which you send to it.
Alternatively, you can send the data to p1 with a background thread and read the output from p2 in the main thread. But either side must be a thread.
Responding to nosklo's assertion (see other comments to this question) that it can't be done without close_fds=True:
close_fds=True is only necessary if you've left other file
descriptors open. When opening multiple child processes, it's always good to
keep track of open files that might get inherited, and to explicitly close any
that aren't needed:
from subprocess import Popen, PIPE
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p1.stdin.write('Hello World\n')
p1.stdin.close()
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
result = p2.stdout.read()
assert result == "Hello Worl\n"
close_fds defaults to False because subprocess
prefers to trust the calling program to know what it's doing with open file
descriptors, and just provide the caller with an easy option to close them all
if that's what it wants to do.
But the real issue is that pipe buffers will bite you for all but toy examples.
As I have said in my other answers to this question, the rule of thumb is to
not have your reader and your writer open in the same process/thread. Anyone
who wants to use the subprocess module for two-way communication would be
well-served to study os.pipe and os.fork, first. They're actually not that
hard to use if you have a good example to look at.
I think you may be examining the wrong problem. Certainly as Aaron says if you try to be both a producer to the beginning of a pipeline, and a consumer of the end of the pipeline, it is easy to get into a deadlock situation. This is the problem that communicate() solves.
communicate() isn't exactly correct for you since stdin and stdout are on different subprocess objects; but if you take a look at the implementation in subprocess.py you'll see that it does exactly what Aaron suggested.
Once you see that communicate both reads and writes, you'll see that in your second try communicate() competes with p2 for the output of p1:
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
# ...
p1.communicate('data\n') # reads from p1.stdout, as does p2
I am running on win32, which definitely has different i/o and buffering characteristics, but this works for me:
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
t = threading.Thread(target=get_output, args=(p2,))
t.start()
p1.stdin.write('hello world\n' * 100000)
p1.stdin.close()
t.join()
I tuned the input size to produce a deadlock when using a naive unthreaded p2.read()
You might also try buffering into a file, eg
fd, _ = tempfile.mkstemp()
os.write(fd, 'hello world\r\n' * 100000)
os.lseek(fd, 0, os.SEEK_SET)
p1 = Popen(["grep", "-v", "not"], stdin=fd, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE)
print p2.stdout.read()
That also works for me without deadlocks.
In one of the comments above, I challenged nosklo to either post some code to back up his assertions about select.select or to upvote my responses he had previously down-voted. He responded with the following code:
from subprocess import Popen, PIPE
import select
p1 = Popen(["grep", "-v", "not"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cut", "-c", "1-10"], stdin=p1.stdout, stdout=PIPE, close_fds=True)
data_to_write = 100000 * 'hello world\n'
to_read = [p2.stdout]
to_write = [p1.stdin]
b = [] # create buffer
written = 0
while to_read or to_write:
read_now, write_now, xlist = select.select(to_read, to_write, [])
if read_now:
data = p2.stdout.read(1024)
if not data:
p2.stdout.close()
to_read = []
else:
b.append(data)
if write_now:
if written < len(data_to_write):
part = data_to_write[written:written+1024]
written += len(part)
p1.stdin.write(part); p1.stdin.flush()
else:
p1.stdin.close()
to_write = []
print b
One problem with this script is that it second-guesses the size/nature of the
system pipe buffers. The script would experience fewer failures if it could remove
magic numbers like 1024.
The big problem is that this script code only works consistently with the right
combination of data input and external programs. grep and cut both work with
lines, and so their internal buffers behave a bit differently. If we use a
more generic command like "cat", and write smaller bits of data into the pipe,
the fatal race condition will pop up more often:
from subprocess import Popen, PIPE
import select
import time
p1 = Popen(["cat"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["cat"], stdin=p1.stdout, stdout=PIPE, close_fds=True)
data_to_write = 'hello world\n'
to_read = [p2.stdout]
to_write = [p1.stdin]
b = [] # create buffer
written = 0
while to_read or to_write:
time.sleep(1)
read_now, write_now, xlist = select.select(to_read, to_write, [])
if read_now:
print 'I am reading now!'
data = p2.stdout.read(1024)
if not data:
p1.stdout.close()
to_read = []
else:
b.append(data)
if write_now:
print 'I am writing now!'
if written < len(data_to_write):
part = data_to_write[written:written+1024]
written += len(part)
p1.stdin.write(part); p1.stdin.flush()
else:
print 'closing file'
p1.stdin.close()
to_write = []
print b
In this case, two different results will manifest:
write, write, close file, read -> success
write, read -> hang
So again, I challenge nosklo to either post code showing the use of
select.select to handle arbitrary input and pipe buffering from a
single thread, or to upvote my responses.
Bottom line: don't try to manipulate both ends of a pipe from a single thread.
It's just not worth it. See
pipeline for a nice low-level
example of how to do this correctly.
What about using a SpooledTemporaryFile ? This bypasses (but perhaps doesn't solve) the issue:
http://docs.python.org/library/tempfile.html#tempfile.SpooledTemporaryFile
You can write to it like a file, but it's actually a memory block.
Or am I totally misunderstanding...
Here's an example of using Popen together with os.fork to accomplish the same
thing. Instead of using close_fds it just closes the pipes at the
right places. Much simpler than trying to use select.select, and
takes full advantage of system pipe buffers.
from subprocess import Popen, PIPE
import os
import sys
p1 = Popen(["cat"], stdin=PIPE, stdout=PIPE)
pid = os.fork()
if pid: #parent
p1.stdin.close()
p2 = Popen(["cat"], stdin=p1.stdout, stdout=PIPE)
data = p2.stdout.read()
sys.stdout.write(data)
p2.stdout.close()
else: #child
data_to_write = 'hello world\n' * 100000
p1.stdin.write(data_to_write)
p1.stdin.close()
It's much simpler than you think!
import sys
from subprocess import Popen, PIPE
# Pipe the command here. It will read from stdin.
# So cat a file, to stdin, like (cat myfile | ./this.py),
# or type on terminal and hit control+d when done, etc
# No need to handle this yourself, that's why we have shell's!
p = Popen("grep -v not | cut -c 1-10", shell=True, stdout=PIPE)
nextData = None
while True:
nextData = p.stdout.read()
if nextData in (b'', ''):
break
sys.stdout.write ( nextData.decode('utf-8') )
p.wait()
This code is written for python 3.6, and works with python 2.7.
Use it like:
cat README.md | python ./example.py
or
python example.py < README.md
To pipe the contents of "README.md" to this program.
But.. at this point, why not just use "cat" directly, and pipe the output like you want? like:
cat filename | grep -v not | cut -c 1-10
typed into the console will do the job as well. I personally would only use the code option if I was further processing the output, otherwise a shell script would be easier to maintain and be retained.
You just, use the shell to do the piping for you. In one, out the other. That's what she'll are GREAT at doing, managing processes, and managing single-width chains of input and output. Some would call it a shell's best non-interactive feature..
Related
I know how to do several "nested" pipes using subprocesses however I have another doubt. I want to do the following:
p1=Popen(cmd1,stdout=PIPE)
p2=Popen(cmd2,stdin=p1.stdout)
p3=Popen(cmd3,stdin=p1.stdout)
Take into account that p3 uses p1.stdout instead of p2.stdout. The problem is that after doing p2, p1.stdout is blank. Please help me!
You can't send the same pipe to two different processes. Or, rather, if you do, they end up accessing the same pipe, meaning if one process reads something, it's no longer available to the other one.
What you need to do is "tee" the data in some way.
If you don't need to stream the data as they come in, you can read all the output from p1, then send it as input to both p2 and p3. This is easy:
output = check_output(cmd1)
p2 = Popen(cmd2, stdin=PIPE)
p2.communicate(output)
p3 = Popen(cmd3, stdin=PIPE)
p3.communicate(output)
If you just need p2 and p3 to run in parallel, you can just run them each in a thread.
But if you actually need real-time streaming, you have to connect things up more carefully. If you can be sure that p2 and p3 will always consume their input, without blocking, faster than p1 can supply it, you can do this without threads (just loop on p1.stdout.read()), but otherwise, you'll need an output thread for each consumer process, and a Queue or some other way to pass the data around. See the source code to communicate for more ideas on how to synchronize the separate threads.
If you want to copy the output from a subprocess to other processes without reading all output at once then here's an implementation of #abarnert's suggestion to loop over p1.stdout that achieves it:
from subprocess import Popen, PIPE
# start subprocesses
p1 = Popen(cmd1, stdout=PIPE, bufsize=1)
p2 = Popen(cmd2, stdin=PIPE, bufsize=1)
p3 = Popen(cmd3, stdin=PIPE, bufsize=1)
# "tee" the data
for line in iter(p1.stdout.readline, b''): # assume line-oriented data
p2.stdin.write(line)
p3.stdin.write(line)
# clean up
for pipe in [p1.stdout, p2.stdin, p3.stdin]:
pipe.close()
for proc in [p1, p2, p3]:
proc.wait()
I know parts of this question have been asked before, but I have some related questions.
I'm trying to execute
mysqldump -u uname -ppassword --add-drop-database --databases databaseName | gzip > fileName
I'm potentially dumping a very large (200GB?) db. Is that in itself a dumb thing to do? I then want to send the zipped file over the network for storage, delete the local dump, and purge a couple of tables.
Anyway, I was using subprocess like this, because there doesn't seem to be a way to execute the entire original call without subprocess considering | to be a table name.:
from subprocess import Popen, PIPE
f = open(FILENAME, 'wb')
args = ['mysqldump', '-u', 'UNAME', '-pPASSWORD', '--add-drop-database', '--databases', 'DB']
p1 = Popen(args, stdout=PIPE)
P2 = Popen('gzip', stdin=p1.stdout, stdout=f)
p2.communicate()
but then I read that communicate caches the data in memory, which wouldn't work for me. Is this true?
What I ended up doing for now is:
import gzip
subprocess.call(args, stdout=f)
f.close()
f = open(filename, 'rb')
zipFilename = filename + '.gz'
f2 = gzip.open(zipFilename, 'wb')
f2.writelines(f)
f2.close()
f.close()
of course this takes a million years, and I hate it.
My Questions:
1. Can I use my first approach on a very large db?
2. Could I possibly pipe the output of mysqldump to a socket and fire it across the network and save it when it arrives, rather than sending a zipped file?
Thanks!
You don't need communicate(). Its only there as a convenience method if you want to read stdout/stderr to completion. But since you are chaining the commands, they are doing that for you. Just wait for them to complete.
from subprocess import Popen, PIPE
args = ['mysqldump', '-u', 'UNAME', '-pPASSWORD', '--add-drop-database', '--databases', 'DB']
with open(FILENAME, 'wb', 0) as f:
p1 = Popen(args, stdout=PIPE)
p2 = Popen('gzip', stdin=p1.stdout, stdout=f)
p1.stdout.close() # force write error (/SIGPIPE) if p2 dies
p2.wait()
p1.wait()
You are quite close to where you want:
from subprocess import Popen, PIPE
f = open(FILENAME, 'wb')
args = ['mysqldump', '-u', 'UNAME', '-pPASSWORD', '--add-drop-database', '--databases', 'DB']
p1 = Popen(args, stdout=PIPE)
Till here it is right.
p2 = Popen('gzip', stdin=p1.stdout, stdout=PIPE)
This one takes p1's output and processes it. Afterwards we can (and should) immediately p1.stdout.close().
Now we have a p2.stdout which can be read from and, without using a temporary file, send it via the network:
s = socket.create_connection(('remote_pc', port))
while True:
r = p2.stdout.read(65536)
if not r: break
s.send(r)
Yup the data is buffered in memory:
"Note The data read is buffered in memory, so do not use this method
if the data size is large or unlimited." - subprocess docs
Unfortunately at the moment there is no way to asynchronously use Popen: PEP3145
Rather than doing this all in python you can manually do
os.system("mysqldump -u uname -ppassword --add-drop-database --databases databaseName | gzip > fileName
")
with the appropriate string replacements using string.format of course; otherwise you're putting an unnecessary amount of stress on your computer, especially trying to communicate 200gb via a pipe ...
Can you elaborate on what you are trying to do? Right now it sounds like you're both dumping and zipping on the same computer.
Yes you can stream a file across the network .. I don't know if you want to directly stream the output of mysql directly though - you might want to look at your network capabilities before considering that
bash:
#!/bin/bash
mysqldump -u uname -ppassword --add-drop-database --databases databaseName | gzip > fileName
#transfer fileName to other computer
^ you can also put this in a crontab and have it run at intervals :)
Your example code using two subprocess.Popen calls is correct (albeit slightly-improve-able), and this:
... I read that communicate caches the data in memory
is also correct—it reads into memory all of the standard-output and standard-error-output that the "communicating command" produces on a subprocess.PIPE—but not a problem here, because you have this:
p1 = Popen(args, stdout=PIPE)
P2 = Popen('gzip', stdin=p1.stdout, stdout=f)
p2.communicate()
You're calling communicate() on p2, whose stdout output is sent to f (an opened file), and whose stderr output—which is probably empty anyway (no errors occur)—is not being sent to a PIPE. Thus, p2.communicate() would at worst have to read and buffer-up a grand total of zero bytes of stdout plus zero bytes of stderr. It's actually a bit more clever, noticing that there is no PIPE, so it returns the tuple (None, None).
If you were to call p1.communicate(), that would be more of an issue (although in this case you'd then be fighting with p2, the gzip process, for the output from p1, which would be even worse). But you are not; p1's output flows to p2, and p2's output flows to a file.
Since none of p2's output is sent to a PIPE, there is no need to call p2.communicate() here: you can simply call p2.wait(). That makes it clearer that there's no data flowing back from p2 (which I would say is a minor improvement to the code, although if you decide you want to capture p2's stderr after all, you'd have to change that back).
Edit to add: as in glglgl's answer, it's important to close p1's pipe to p2 after creating p2, otherwise p2 will wait for your Python process to send data to p2, too.
I have been fighting against Popen in python for couple of days now, so I decided to put all my doubts here, hopefully all of them can be clarified by python experts.
Initially I use Popen to execute a command and grep the result(as one command using pipe, something like xxx | grep yyy), with shell=False, as you can imagine, that doesn't work quite well. Following the guide in this post, I changed my code to the following:
checkCmd = ["sudo", "pyrit", "-r", self.capFile, "analyze"]
checkExec = Popen(checkCmd, shell=False, stdout=PIPE, stderr=STDOUT)
grepExec = Popen(["grep", "good"], stdin=checkExec.stdout, stdout=PIPE)
output = grepExec.stdout.readline()
output = grepExec.communicate()[0]
But I realized that the checkExec runs slowly and since Popen is non-blocking, grepExec always get executed before checkExec shows any result, thus the grep output would always be blank. How can I postpone the execution of grepExec till checkExec is finished?
In another Popen in my program, I tried to keep a service open at the back, so I use a separate thread to execute it. When all the tasks are done, I notify this thread to quit, and I explicitly call Popen.kill() to stop the service. However, my system ends up with a zombie process that is not reaped. I don't know if there's a nice way to clean up everything in this background thread after it finishes?
What are the differences between Popen.communicate()[0] and Popen.stdout.readline()? Can I use a loop to keep reading output from both of them?
Your example would work if you do it like this:
checkCmd = ["sudo", "pyrit", "-r", self.capFile, "analyze"]
checkExec = Popen(checkCmd, shell=False, stdout=PIPE, stderr=STDOUT)
grepExec = Popen(["grep", "good"], stdin=checkExec.stdout, stdout=PIPE)
for line in grepExec.stdout:
# do something with line
You use communicate when you want to give some input to a process and read all output on stdout, stderr of the process at the same time. This is probably not what you want for your case. communicate is more for the cases where you want to start an application, feed all the input it needs to it and read its output.
As other answers have pointed out you can use shell=True to create the pipeline in your call to subprocess, but an alternative which I would prefer is to leverage python and instead of setting up a pipeline doing:
checkCmd = ["sudo", "pyrit", "-r", self.capFile, "analyze"]
checkExec = Popen(checkCmd, shell=False, stdout=PIPE, stderr=STDOUT)
for line in checkExec.stdout:
if line.find('good') != -1:
do something with the matched line here
Use subprocess instead of popen, then you can simplify things drastically with the complete commandline.
http://docs.python.org/library/subprocess.html
eg.
import subprocess as sub
f = open('/dev/null', 'w')
proc = sub.call("cat file | grep string", executable="/bin/bash", shell=True)
Hi I had a question about linking input and output with sub-processes in python. I am trying to simplify the program by skipping the output of one step by passing it to another subprocess rather than output it to a file. Then open another process to run on that file.
E.g. First process uses SAMTOOLS to output a specific chromosome from a large bam file.
So...
bigfile.bam is read in and outputs chromosome22.bam
The next subprocess uses BEDTOOLS to convert that chromosome22.bam to chromosome22.bed
So...
chromosome22.bam is read in and outputs chromosome22.bed
What I want to do is pass the stdout of the first process into the second so there is no need for the intermediate file.
So far I have this...
for x in 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,'X','Y':
subprocess.call("%s view -bh %s %s > %s/%s/%s.bam" % (samtools,bam,x,bampath,out,x), shell=True)
This makes the chromosome[1-22,X,Y].bam files. But can I avoid this and put another subprocess command in the same loop to convert them to bed files?
The command for bed conversion is:
bedpath/bedtools bamtobed -i [bamfile] > [bedfile]
Please have a look at the replacing shell pipeline example in the documentation.
output=$(dmesg | grep hda)
becomes:
p1 = Popen(["dmesg"], stdout=PIPE)
p2 = Popen(["grep", "hda"], stdin=p1.stdout, stdout=PIPE)
p1.stdout.close() # Allow p1 to receive a SIGPIPE if p2 exits.
output = p2.communicate()[0]
The explanation is:
The p1.stdout.close() call after starting the p2 is important in order for p1 to receive a SIGPIPE if p2 exits before p1.
No need to use python here. Much easier in shell. But essentially, it works the same as in python.
If bedtools can read from stdin, you can e.g. do
#!/bin/sh
for x in `seq 1 22` X Y; do
$samtools view -bh $bam $x | $bedtools bamtobed > $bampath/$out/$x.bam
done
Depending on how bedtools was desinged, you might also need to use -i - to have it read from stdin.
If you stick with python, I strongly recommend about learning how to do this
without doing it in all shell,
without producing shell commands, that you need to escape properly to avoid errors
subprocess is more safe to use when you use the array-based syntax and no shell.
Make that two subprocess invocations, one for each command. See http://docs.python.org/library/subprocess.html#replacing-shell-pipeline for more details.
cmd1 = [samtools, "view", "-bh", bam, x]
cmd2 = [bedtools, "bamtobed"]
c1 = subprocess.Popen(cmd1, stdout=subprocess.PIPE)
c2 = subprocess.Popen(cmd2, stdin=c1.stdout, stdout=open(outputfilename, "w"))
c1.stdout.close()
c2.communicate()
Yes, you can use the pipe functionality. See if you can read from stdin for the bamtobed process ... if you can, try the following. This way you save on the disk IO time assuming the processing load is light.
SLIGHT modification:
proc1.stdout is now the stdin for the 2nd process.
proc1 = subprocess.call("%s view -bh %s %s" % (samtools,bam,x,bampath,out,x), shell=True, stdout=subprocess.PIPE)
proc2 = subprocess.call("bedpath/bedtools bamtobed > %s" % (outFileName, ), shell=True, stdin=proc1.stdout)
I am trying to use Python's subprocess module. What I require is to send input to the first process whose output becomes the input of the second process.
The situation is basically almost the same as the example given in the documentation here:
http://docs.python.org/library/subprocess.html#replacing-shell-pipeline
except that I need to provide input the first command.
Here is that example copied:
p1 = Popen(["dmesg"], stdout=PIPE)
p2 = Popen(["grep", "hda"], stdin=p1.stdout, stdout=PIPE)
p1.stdout.close() # Allow p1 to receive a SIGPIPE if p2 exits.
output = p2.communicate()[0]
If we change the first line to:
p1 = Popen(["cat"], stdout=PIPE, stdin=PIPE)
How do I provide the input string to the process?
If I attempt it by changing the final line to:
output = p2.communicate(input=inputstring)[0]
This doesn't work.
I do have a working version, which just stores the output of the first command in a string and then passes that to the second command. This isn't terrible as there is essentially no concurrency that can be exploited (in my actual use case the first command will exit rather quickly and produce all of its output at the end).
Here is the working version in full:
import subprocess
simple = """Writing some text
with some lines in which the
word line occurs but others
where it does
not
"""
def run ():
catcommand = [ "cat" ]
catprocess = subprocess.Popen(catcommand,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
(catout, caterr) = catprocess.communicate(input=simple)
grepcommand = [ "grep", "line" ]
grepprocess = subprocess.Popen(grepcommand,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
(grepout, greperr) = grepprocess.communicate(input=catout)
print "--- output ----"
print grepout
print "--- error ----"
print greperr
if __name__ == "__main__":
run()
I hope I've been clear enough, thanks for any help.
If you do
from subprocess import Popen, PIPE
p1 = Popen(["cat"], stdout=PIPE, stdin=PIPE)
You should do p1.communicate("Your Input to the p1") and that will flow through the PIPE.
The stdin is the process's input and you should communicate to that only.
The program which have given is absolutely fine, there seems no problem with that.
I assume that cat, grep are just example commands otherwise you could use a pure Python solution without subprocesses e.g.:
for line in simple.splitlines():
if "line" in line:
print(line)
Or if you want to use grep:
from subprocess import Popen, PIPE
output = Popen(['grep', 'line'], stdin=PIPE, stdout=PIPE).communicate(simple)[0]
print output,
You can pass the output of the first command to the second one without storing it in a string first:
from subprocess import Popen, PIPE
from threading import Thread
# start commands in parallel
first = Popen(first_command, stdin=PIPE, stdout=PIPE)
second = Popen(second_command, stdin=first.stdout, stdout=PIPE)
first.stdout.close() # notify `first` if `second` exits
first.stdout = None # avoid I/O on it in `.communicate()`
# feed input to the first command
Thread(target=first.communicate, args=[simple]).start() # avoid blocking
# get output from the second command at the same time
output = second.communicate()[0]
print output,
If you don't want to store all input/output in memory; you might need threads (to read/write in chunks without blocking) or a select loop (works on POSIX).
If there are multiple commands, it might be more readable just to use the shell directly as suggested by #Troels Folke or use a library such as plumbum that hides all the gory details of emulating the shell by hand.
Hmm, why not mix in a bit of (ba)sh? :-)
from subprocess import Popen, PIPE
cproc = Popen('cat | grep line', stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True)
out, err = cproc.communicate("this line has the word line in it")
BEWARE though:
This only works on systems that use a Bourne Shell compatible shell (like most *nix'es)
Usign shell=True and putting user input in the command string is a bad idea, unless you escape the user input first. Read the subprocess docs -> "Frequently Used Arguments" for details.
This is ugly, non portable, non pythonic and so on...
EDIT:
There is no need to use cat though, if all you want to do is grep. Just feed the input directly to grep, or even better, use python regular expressions.
I faced a similar problem where I wanted to have several piped Popen.
This worked for me:
from subprocess import Popen, PIPE
p1 = Popen(["cat"], stdin=PIPE, stdout=PIPE)
p2 = Popen(["grep", "hda"], stdin=p1.stdout, stdout=PIPE)
p1.stdin.write(inputstring)
p1.stdin.close()
output = p2.communicate()[0]
However, the #jfs solution with threads seems more robust.