Develop Reference

Python: piping pcap file to stdout gives error

I am trying to pipe the output of xz to a custom python script:
xz -cd file.pcap.xz | myscripy.py
However, I get an error when the script attempts to run this line:
#!/usr/bin/env python2.7
from __future__ import print_function
import pcap
import io
STDIN_ALIAS = '/proc/self/fd/0'
pcap.pcap(io.open(STDIN_ALIAS, 'r'))
and received an error
pcap.pcap(io.open(STDIN_ALIAS, 'r'))
File "pcap.pyx", line 196, in pcap.pcap.__init__
TypeError: expected string or Unicode object, _io.TextIOWrapper found
I am on Ubuntu 18.04 and running under python 2.7.

You can't use Python to pass in packets from a file to pcap.pcap(). The pypcap library you are using is a thin wrapper around the pcap_open_offline() and pcap_create() C functions, and offers no facilities for passing in a Python file object. This wrapper only accepts a filename or a network interface name, nothing else.
The pcap_open_offline() function does accept - as an alias for stdin, so just pass that in directly:
import pcap
sniffer = pcap.pcap('-')

The error message already tell you what happened. You need a string to the pcap() function, not a file object. To fix this, try
pcap.pcap(io.open(STDIN_ALIAS, 'r').read())
But I am not sure this will work as your file might be binary instead of text. In such case, you may want to open with 'rb' instead of 'r' flag, and do some conversion afterwards (especially if you use Python 3 instead of Python 2.7).
I see another issue: your code is not portable as it depends on this:
STDIN_ALIAS = '/proc/self/fd/0'
A pythonic way to read the stdin is the follows (see Reading binary data from stdin)
import sys
string = sys.stdin.read()

Have you tried upgrading PyPcap to work on Python 3? This could help, since Unicode handling is a lot cleaner and less prone to surprises on Python 3. The appropriate package is available, at least on Debian (and probably derived distros as well). Look for: python3-pypcap.

Getting csv.Sniffer to work with quoted values

I'm trying to use python's CSV sniffer tool as suggested in many StackOverflow answers to guess if a given CSV file is delimited by ; or ,.
It's working fine with basic files, but when a value contains a delimiter, it is surrounded by double quotes (as the standard goes), and the sniffer throws _csv.Error: Could not determine delimiter.
Has anyone experienced that before?
Here is a minimal failing CSV file:
column1,column2
0,"a, b"
And the proof of concept:
Python 3.5.1 (default, Dec 7 2015, 12:58:09)
[GCC 5.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import csv
>>> f = open("example.csv", "r")
>>> f.seek(0);
0
>>> csv.Sniffer().sniff(f.read(), delimiters=';,')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.5/csv.py", line 186, in sniff
raise Error("Could not determine delimiter")
_csv.Error: Could not determine delimiter
I have total control over the generation of input CSV file; but sometimes it is modified by a third party using MS Office and the delimiter is replaced by semicolumns, so I have to use this guessing approach.
I know I could stop using commas in the input file, but I would like to know if I'm doing something wrong first.

You are giving the sniffer too much input. Your sample file does work if you run:
csv.Sniffer().sniff(f.readline())
which uses only the header row to determine the delimiter character. If you want to understand why the Sniffer heuristics fail for more data, there is no substitute for reading the csv.py library source code.

Unable to load .pkl file [duplicate]

When I am trying to load something I dumped using cPickle, I get the error message:
ValueError: insecure string pickle
Both the dumping and loading work are done on the same computer, thus same OS: Ubuntu 8.04.
How could I solve this problem?

"are much more likely than a never-observed bug in Python itself in a functionality that's used billions of times a day all over the world": it always amazes me how cross people get in these forums.
One easy way to get this problem is by forgetting to close the stream that you're using for dumping the data structure. I just did
>>> out = open('xxx.dmp', 'w')
>>> cPickle.dump(d, out)
>>> k = cPickle.load(open('xxx.dmp', 'r'))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: insecure string pickle
Which is why I came here in the first place, because I couldn't see what I'd done wrong.
And then I actually thought about it, rather than just coming here, and realized that I should have done:
>>> out = open('xxx.dmp', 'w')
>>> cPickle.dump(d, out)
>>> out.close() # close it to make sure it's all been written
>>> k = cPickle.load(open('xxx.dmp', 'r'))
Easy to forget. Didn't need people being told that they are idiots.

I've get this error in Python 2.7 because of open mode 'rb':
with open(path_to_file, 'rb') as pickle_file:
obj = pickle.load(pickle_file)
So, for Python 2 'mode' should be 'r'
Also, I've wondered that Python 3 doesn't support pickle format of Python 2, and in case when you'll try to load pickle file created in Python 2 you'll get:
pickle.unpicklingerror: the string opcode argument must be quoted

Check this thread. Peter Otten says:
A corrupted pickle. The error is
raised if a string in the dump does
not both start and end with " or '.
and shows a simple way to reproduce such "corruption". Steve Holden, in the follow-up post, suggests another way to cause the problem would be to mismatch 'rb' and 'wb' (but in Python 2 and on Linux that particular mistake should pass unnoticed).

What are you doing with data between dump() and load()? It's quite common error to store pickled data in file opened in text mode (on Windows) or in database storage in the way that doesn't work properly for binary data (VARCHAR, TEXT columns in some databases, some key-value storages). Try to compare pickled data that you pass to storage and immediately retrieved from it.

If anyone has this error using youtube-dl, this issue has the fix: https://github.com/rg3/youtube-dl/issues/7172#issuecomment-242961695
richiecannizzo commented on Aug 28
brew install libav
Should fix it instantly on mac or
sudo apt-get install libav
#on linux

This error may also occur with python 2 (and early versions of python 3) if your pickle is large (Python Issue #11564):
Python 2.7.11 |Anaconda custom (64-bit)| (default, Dec 6 2015, 18:08:32)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import cPickle as pickle
>>> string = "X"*(2**31)
>>> pp = pickle.dumps(string)
>>> len(pp)
2147483656
>>> ss = pickle.loads(pp)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: insecure string pickle
This limitation was addressed with the introduction of pickle protocol 4 in python 3.4 (PEP 3154). Unfortunately, this feature has not been back-ported to python 2, and probably won't ever be. If this is your problem and you need to use python 2 pickle, the best you can do is reduce the size of your pickle, e.g., instead of pickling a list, pickle the elements individually into a list of pickles.

Same problem with a file that was made with python on windows, and reloaded with python on linux.
Solution : dos2unix on the file before reading in linux : works as a charm !

I got the Python ValueError: insecure string pickle message in a different way.
For me it happened after a base64 encoding a binary file and passing through urllib2 sockets.
Initially I was wrapping up a file like this
with open(path_to_binary_file) as data_file:
contents = data_file.read()
filename = os.path.split(path)[1]
url = 'http://0.0.0.0:8080/upload'
message = {"filename" : filename, "contents": contents}
pickled_message = cPickle.dumps(message)
base64_message = base64.b64encode(pickled_message)
the_hash = hashlib.md5(base64_message).hexdigest()
server_response = urllib2.urlopen(url, base64_message)
But on the server the hash kept coming out differently for some binary files
decoded_message = base64.b64decode(incoming_base64_message)
the_hash = hashlib.md5(decoded_message).hexdigest()
And unpickling gave insecure string pickle message
cPickle.loads(decoded_message)
BUT SUCCESS
What worked for me was to use urlsafe_b64encode()
base64_message = base64.urlsafe_b64encode(cPickle.dumps(message))
And decode with
base64_decoded_message = base64.urlsafe_b64decode(base64_message)
References
http://docs.python.org/2/library/base64.html
https://www.rfc-editor.org/rfc/rfc3548.html#section-3

This is what happened to me, might be a small section of population, but I want to put this out here nevertheless, for them:
Interpreter (Python3) would have given you an error saying it required the input file stream to be in bytes, and not as a string, and you may have changed the open mode argument from 'r' to 'rb', and now it is telling you the string is corrupt, and thats why you have come here.
The simplest option for such cases is to install Python2 (You can install 2.7) and then run your program with Python 2.7 environment, so it unpickles your file without issue. Basically I wasted a lot of time scanning my string seeing if it was indeed corrupt when all I had to do was change the mode of opening the file from rb to r, and then use Python2 to unpickle the file. So I'm just putting this information out there.

I ran into this earlier, found this thread, and assumed that I was immune to the file closing issue mentioned in a couple of these answers since I was using a with statement:
with tempfile.NamedTemporaryFile(mode='wb') as temp_file:
pickle.dump(foo, temp_file)
# Push file to another machine
_send_file(temp_file.name)
However, since I was pushing the temp file from inside the with, the file still wasn't closed, so the file I was pushing was truncated. This resulted in the same insecure string pickle error in the script that read the file on the remote machine.
Two potential fixes to this: Keep the file open and force a flush:
with tempfile.NamedTemporaryFile(mode='wb') as temp_file:
pickle.dump(foo, temp_file)
temp_file.flush()
# Push file to another machine
_send_file(temp_file.name)
Or make sure the file is closed before doing anything with it:
file_name = ''
with tempfile.NamedTemporaryFile(mode='wb', delete=False) as temp_file:
file_name = temp_file.name
pickle.dump(foo, temp_file)
# Push file to another machine
_send_file(file_name)

TypeError: 'str' does not support the buffer interface & configparser

I'm newbie here and I wouldn't want to ask such a easy question as my first post but I don't know anything about Python even I'm a PHP/C programmer.
I have a python script in Figway tools which is called RegisterDevice.py to register my own sensor hardware to FIWARE Lab. But some code lines of that script doesn't work as I expected because of Python3.4. This may not be my problem but I don't have too much time to wait an official solution that's why I thought that I could resolve it as a person who is familiar to the programming.
I've searched on the web for solution but I couldn't find any exact solution for it yet. As far as I read bytes and unicode strings are two different types in Python3.x but I couldn't realize where I have to encode or maybe decode string to other type on the code. Maybe I have to do something else...
Here is the part of script which gave me error like above.
# Load the configuration file
with open(CONFIG_FILE,'r+') as f:
sample_config = f.read()
#config = ConfigParser.RawConfigParser(allow_no_value=True)
config = configparser.RawConfigParser(allow_no_value=True)
config.readfp(io.BytesIO(sample_config))
Error:
Traceback (most recent call last):
File "RegisterDevice.py", line 47, in <module>
config.readfp(io.BytesIO(sample_config))
TypeError: 'str' does not support the buffer interface

Firstly readfp() is deprecated in Python3 and you should use read_file().
The best way is probably using the read() function directly when you want to work with a file. You should set encoding as the second parameter if you expect non-ASCII characters inside the file.
The alternative is to read_string() and give it a string directly.

I have been doing work very similar to this, and I believe this script runs, but you will have to verify if it gives you the desired results:
import configparser
with open('.coveragerc','r+') as f:
#config = ConfigParser.RawConfigParser(allow_no_value=True)
config = configparser.RawConfigParser(allow_no_value=True)
config.readfp(f)

How to use Pyvisa1.4 in Python3.2, a lot of unexpected errors generated

Previously I've used PyVisa1.4 in Python2.7, and everything works fine.
Now I need to use Pyvisa1.4 in Python3.2.
I knew that some syntax are changed in Python3.2. Therefore I use the 2to3 to convert the originalPysiva .py files into the new format which are supposed to fit the Python3.2.
But now, unexpected error is generated which is related to ctypes. And I read through the Pyvisa package .py files and try to fix this but still don't know how to do deal with this.
I'm just trying to use the simple get_instruments_list() command like below:
>>> import visa
>>> get_instruments_list()
Traceback (most recent call last):
File "<pyshell#3>", line 1, in <module>
get_instruments_list()
File "C:\Python32\Lib\site-packages\pyvisa\visa.py", line 254, in get_instruments_list
vpp43.find_resources(resource_manager.session, "?*::INSTR")
File "C:\Python32\Lib\site-packages\pyvisa\vpp43.py", line 581, in find_resources
instrument_description)
ctypes.ArgumentError: argument 2: <class 'TypeError'>: wrong type
The MAIN problem I'm facing now is how to correctly use PyVisa in Python3.2.

PyVISA 1.5 (which is in beta now) provides, among other things, full Python 3 support. Take a look at the (new) documentation for instructions about how to download the latest development version at http://pyvisa.readthedocs.org/

The problem is the str that is passed as second argument.
In Python 3 the str was radically changed in order to support unicode.
To correct this problem all strings before being passed to the DLL library must be encoded in ASCII.
Conversely, the return strings are returned as bytes should be converted back into str.
I have corrected this on the visa.py, on the
CR = "\r" replaces CR = b"\r"
LF = "\n" replaces LF = b"\n"
ResourceTemplate init
self.vi = vpp43.open(resource_manager.session, resource_name.encode("ASCII"),
keyw.get("lock", VI_NO_LOCK))
instead of
self.vi = vpp43.open(resource_manager.session, resource_name,
keyw.get("lock", VI_NO_LOCK))
Instrument.write
vpp43.write(self.vi, message.encode("ASCII"))
instead of
vpp43.write(self.vi, message)
conversely on the read_raw the final return is replaced by
return str(buffer)
and on get_instruments_list()
vpp43.find_resources(resource_manager.session, "?*::INSTR".encode("ASCII"))

The newest version of Pyvisa doesn't support Python3.2
Even thouhg you convert the syntax of Pyvisa1.4 for Python2.X to Python3.X by using 2to3 tool, it still won't work