Python CSV error: line contains NULL byte

Question

I'm working with some CSV files, with the following code:

reader = csv.reader(open(filepath, "rU"))
try:
    for row in reader:
        print 'Row read successfully!', row
except csv.Error, e:
    sys.exit('file %s, line %d: %s' % (filename, reader.line_num, e))

And one file is throwing this error:

file my.csv, line 1: line contains NULL byte

What can I do? Google seems to suggest that it may be an Excel file that's been saved as a .csv improperly. Is there any way I can get round this problem in Python?

== UPDATE ==

Following @JohnMachin's comment below, I tried adding these lines to my script:

print repr(open(filepath, 'rb').read(200)) # dump 1st 200 bytes of file
data = open(filepath, 'rb').read()
print data.find('\x00')
print data.count('\x00')

And this is the output I got:

'\xd0\xcf\x11\xe0\xa1\xb1\x1a\xe1\x00\x00\x00\x00\x00\x00\x00\x00\ .... <snip>
8
13834

So the file does indeed contain NUL bytes.

Answer 1

As @S.Lott says, you should be opening your files in 'rb' mode, not 'rU' mode. However that may NOT be causing your current problem. As far as I know, using 'rU' mode would mess you up if there are embedded \r in the data, but not cause any other dramas. I also note that you have several files (all opened with 'rU' ??) but only one causing a problem.

If the csv module says that you have a "NULL" (silly message, should be "NUL") byte in your file, then you need to check out what is in your file. I would suggest that you do this even if using 'rb' makes the problem go away.

repr() is (or wants to be) your debugging friend. It will show unambiguously what you've got, in a platform independant fashion (which is helpful to helpers who are unaware what od is or does). Do this:

print repr(open('my.csv', 'rb').read(200)) # dump 1st 200 bytes of file

and carefully copy/paste (don't retype) the result into an edit of your question (not into a comment).

Also note that if the file is really dodgy e.g. no \r or \n within reasonable distance from the start of the file, the line number reported by reader.line_num will be (unhelpfully) 1. Find where the first \x00 is (if any) by doing

data = open('my.csv', 'rb').read()
print data.find('\x00')

and make sure that you dump at least that many bytes with repr or od.

What does data.count('\x00') tell you? If there are many, you may want to do something like

for i, c in enumerate(data):
    if c == '\x00':
        print i, repr(data[i-30:i]) + ' *NUL* ' + repr(data[i+1:i+31])

so that you can see the NUL bytes in context.

If you can see \x00 in the output (or \0 in your od -c output), then you definitely have NUL byte(s) in the file, and you will need to do something like this:

fi = open('my.csv', 'rb')
data = fi.read()
fi.close()
fo = open('mynew.csv', 'wb')
fo.write(data.replace('\x00', ''))
fo.close()

By the way, have you looked at the file (including the last few lines) with a text editor? Does it actually look like a reasonable CSV file like the other (no "NULL byte" exception) files?

Answer 2

data_initial = open("staff.csv", "rb")
data = csv.reader((line.replace('\0','') for line in data_initial), delimiter=",")

This works for me.

Answer 3

Reading it as UTF-16 was also my problem.

Here's my code that ended up working:

f=codecs.open(location,"rb","utf-16")
csvread=csv.reader(f,delimiter='\t')
csvread.next()
for row in csvread:
    print row

Where location is the directory of your csv file.

Answer 4

You could just inline a generator to filter out the null values if you want to pretend they don't exist. Of course this is assuming the null bytes are not really part of the encoding and really are some kind of erroneous artifact or bug.

with open(filepath, "rb") as f:
    reader = csv.reader( (line.replace('\0','') for line in f) )

    try:
        for row in reader:
            print 'Row read successfully!', row
    except csv.Error, e:
        sys.exit('file %s, line %d: %s' % (filename, reader.line_num, e))

Answer 5

I bumped into this problem as well. Using the Python csv module, I was trying to read an XLS file created in MS Excel and running into the NULL byte error you were getting. I looked around and found the xlrd Python module for reading and formatting data from MS Excel spreadsheet files. With the xlrd module, I am not only able to read the file properly, but I can also access many different parts of the file in a way I couldn't before.

I thought it might help you.

Answer 6

Converting the encoding of the source file from UTF-16 to UTF-8 solve my problem.

How to convert a file to utf-8 in Python?

import codecs
BLOCKSIZE = 1048576 # or some other, desired size in bytes
with codecs.open(sourceFileName, "r", "utf-16") as sourceFile:
    with codecs.open(targetFileName, "w", "utf-8") as targetFile:
        while True:
            contents = sourceFile.read(BLOCKSIZE)
            if not contents:
                break
            targetFile.write(contents)

Answer 7

Why are you doing this?

 reader = csv.reader(open(filepath, "rU"))

The docs are pretty clear that you must do this:

with open(filepath, "rb") as src:
    reader= csv.reader( src )

The mode must be "rb" to read.

http://docs.python.org/library/csv.html#csv.reader

If csvfile is a file object, it must be opened with the ‘b’ flag on platforms where that makes a difference.

Answer 8

appparently it's a XLS file and not a CSV file as http://www.garykessler.net/library/file_sigs.html confirm

Answer 9

Instead of csv reader I use read file and split function for string:

lines = open(input_file,'rb') 

for line_all in lines:

    line=line_all.replace('\x00', '').split(";")

Answer 10

I got the same error. Saved the file in UTF-8 and it worked.

Answer 11

This happened to me when I created a CSV file with OpenOffice Calc. It didn't happen when I created the CSV file in my text editor, even if I later edited it with Calc.

I solved my problem by copy-pasting in my text editor the data from my Calc-created file to a new editor-created file.

Answer 12

I had the same problem opening a CSV produced from a webservice which inserted NULL bytes in empty headers. I did the following to clean the file:

with codecs.open ('my.csv', 'rb', 'utf-8') as myfile:
    data = myfile.read()
    # clean file first if dirty
    if data.count( '\x00' ):
        print 'Cleaning...'
        with codecs.open('my.csv.tmp', 'w', 'utf-8') as of:
            for line in data:
                of.write(line.replace('\x00', ''))

        shutil.move( 'my.csv.tmp', 'my.csv' )

with codecs.open ('my.csv', 'rb', 'utf-8') as myfile:
    myreader = csv.reader(myfile, delimiter=',')
    # Continue with your business logic here...

Disclaimer: Be aware that this overwrites your original data. Make sure you have a backup copy of it. You have been warned!

Answer 13

I opened and saved the original csv file as a .csv file through Excel's "Save As" and the NULL byte disappeared.

I think the original encoding for the file I received was double byte unicode (it had a null character every other character) so saving it through excel fixed the encoding.

Answer 14

Remove or replace null bytes:

with open('your_file.csv', 'rb') as file:
    data = file.read().replace(b'\x00', b'')
with open('your_file.csv', 'wb') as file:
    file.write(data)

Answer 15

For all those 'rU' filemode haters: I just tried opening a CSV file from a Windows machine on a Mac with the 'rb' filemode and I got this error from the csv module:

Error: new-line character seen in unquoted field - do you need to 
open the file in universal-newline mode?

Opening the file in 'rU' mode works fine. I love universal-newline mode -- it saves me so much hassle.

Answer 16

I encountered this when using scrapy and fetching a zipped csvfile without having a correct middleware to unzip the response body before handing it to the csvreader. Hence the file was not really a csv file and threw the line contains NULL byte error accordingly.

Answer 17

Have you tried using gzip.open?

with gzip.open('my.csv', 'rb') as data_file:

I was trying to open a file that had been compressed but had the extension '.csv' instead of 'csv.gz'. This error kept showing up until I used gzip.open

Answer 18

What worked for me is taking a more manual approach of blacklisting certain characters. In the data I was working with, an ASCII control character indicated that the row was corrupted. This script looks for any "bad" characters, and if found, skips the row entirely. It assumes that the CSV header in the first row isn't corrupted though. With this approach, the corrupted data is intercepted before it reaches csv.DictReader which then throws a null byte error.

import io, csv

# Problematic ASCII control characters.
ascii_control_characters = list(range(0, 31))
ascii_control_characters.append(127) # Delete.
ascii_control_characters.remove(10) # Line feed.
ascii_control_characters.remove(13) # Carriage return.

with open('/foo/bar/baz.csv', 'r') as data_file:
    header = ''

    for index, line in enumerate(data_file):
        # Search line for problematic ASCII characters.
        bad_character_found = False

        for character in line:
            if ord(character) in ascii_control_characters:
                bad_character_found = True
                break

        # If a bad character is found, skip the line altogether.
        if bad_character_found:
            print(
                'Corrupted data found on line: ' + \
                 str(index + 1) + \
                 '. Skipping...'
            )

            continue

        if index == 0:
            header += line
            continue

        csv_data = header + line

        reader = csv.DictReader(io.StringIO(csv_data))

        for row in reader:
            # Process each CSV row here.
            pass

Answer 19

One case is that - If the CSV file contains empty rows this error may show up. Check for row is necessary before we proceed to write or read.

for row in csvreader:
        if (row):       
            do something

I solved my issue by adding this check in the code.