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.
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?
data_initial = open("staff.csv", "rb")
data = csv.reader((line.replace('\0','') for line in data_initial), delimiter=",")
This works for me.
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.
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))
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.
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)
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.
appparently it's a XLS file and not a CSV file as http://www.garykessler.net/library/file_sigs.html confirm
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(";")
I got the same error. Saved the file in UTF-8 and it worked.
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.
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!
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.
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.
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.
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
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.
I want to create a CSV string which is being sent by mail. I'd like to avoid temporary files because it's just not necessary for me to deal with the file system. As I said, the data is passed to a mail class.
I found this neat solution
output = io.StringIO()
writer = csv.writer(output, delimiter=';', dialect='excel-tab')
writer.writerows(data)
It works perfectly except that it creates a UTF-8 file which will have messed up special characters if you open it in Excel.
I tried to pass a BOM to the StringIO constructor, but nothing worked:
output = io.StringIO('\ufeff')
I tried to somehow set the encoding to utf-8-sig but I couldn't find a way except using a file...
Any ideas how to solve this problem?
Thanks!
StringIO is strings which means unicode. To do what you want, I think you need to use BytesIO instead.
After reading this and this I think the problem is that StringIO is strings only and therefore no encoding.
You could try this [extrapolated from the first link above]:
bio = io.BytesIO()
StreamWriter = codecs.getwriter('utf-8-sig')
wrapper_file = StreamWriter(bio)
csv.writer(wrapper_file,...
writer.writerows(data)
Python character encoding makes my head hurt...
I have the task of converting utf-8 csv file to excel file, but it is not read properly in excel. Because there was no byte order mark (BOM) at the beginning of the file
I see how:
https://stackoverflow.com/a/38025106/6102332
with open('test.csv', 'w', newline='', encoding='utf-8-sig') as f:
w = csv.writer(f)
# Write Unicode strings.
w.writerow([u'English', u'Chinese'])
w.writerow([u'American', u'美国人'])
w.writerow([u'Chinese', u'中国人'])
But it seems like that only works with brand new files.
But not work for my file already has data.
Are there any easy ways to share?
Is there any other way than this? : https://stackoverflow.com/a/6488070/6102332
Save the exported file as a csv
Open Excel
Import the data using Data-->Import External Data --> Import Data
Select the file type of "csv" and browse to your file
In the import wizard change the File_Origin to "65001 UTF" (or choose correct language character identifier)
Change the Delimiter to comma
Select where to import to and Finish
Read the file in and write it back out with the encoding desired:
with open('input.csv','r',encoding='utf-8-sig') as fin:
with open('output.csv','w',encoding='utf-8-sig') as fout:
fout.write(fin.read())
utf-8-sig codec will remove BOM if present on read, and will add BOM on write, so the above can safely run on files with or without BOM originally.
You can convert in place by doing:
file = 'test.csv'
with open(file,'r',encoding='utf-8-sig') as f:
data = f.read()
with open(file,'w',encoding='utf-8-sig') as f:
f.write(data)
Note also that utf16 works as well. Some older Excels don't handle UTF-8 correctly.
Thank You!
I have found a way to automatically handle the missing BOM utf-8 signature.
In addition to the lack of BOM signature, there is another problem is that duplicate BOM signature is mixed in the file data. Excel does not show clearly and transparently. and make a mistake other data when compared, calculated. eg :
data -> Excel
Chinese -> Chinese
12 -> 12
If you compare it, obviously ChineseBOM will not be equal to Chinese.
Code python to solve the problem:
import codecs
bom_utf8 = codecs.BOM_UTF8
def fix_duplicate_bom_utf8(file, bom=bom_utf8):
with open(file, 'rb') as f:
data_f = f.read()
data_finish = bom + data_f.replace(bom, b'')
with open(file, 'wb') as f:
f.write(data_finish)
return
# Use:
file_csv = r"D:\data\d20200114.csv" # American, 美国人
fix_duplicate_bom_utf8(file_csv)
# file_csv -> American, 美国人
I'm using pycharm and Python 3.7.
I would like to write data in a csv, but my code writes in the File just the first line of my data... someone knows why?
This is my code:
from pytrends.request import TrendReq
import csv
pytrend = TrendReq()
pytrend.build_payload(kw_list=['auto model A',
'auto model C'])
# Interest Over Time
interest_over_time_df = pytrend.interest_over_time()
print(interest_over_time_df.head(100))
writer=csv.writer(open("C:\\Users\\
Desktop\\Data\\c.csv", 'w', encoding='utf-8'))
writer.writerow(interest_over_time_df)
try using pandas,
import pandas as pd
interest_over_time_df.to_csv("file.csv")
Once i encountered the same problem and solve it like below:
with open("file.csv", "rb", encoding="utf-8) as fh:
precise details:
r = read mode
b = mode specifier in the open() states that the file shall be treated as binary,
so contents will remain a bytes. No decoding attempt will happen this way.
As we know python tries to convert a byte-array (a bytes which it assumes to be a utf-8-encoded string) to a unicode string (str). This process of course is a decoding according to utf-8 rules. When it tries this, it encounters a byte sequence which is not allowed in utf-8-encoded strings (namely this 0xff at position 0).
You could try something like:
import csv
with open(<path to output_csv>, "wb") as csv_file:
writer = csv.writer(csv_file, delimiter=',')
for line in interest_over_time_df:
writer.writerow(line)
Read more here: https://www.pythonforbeginners.com/files/with-statement-in-python
You need to loop over the data and write in line by line
I have an csv sheet that i read it like this:
with open(csvFilePath, 'rU') as csvFile:
reader = csv.reader(csvFile, delimiter= '|')
numberOfMovies = 0
for row in reader:
title = row[1:2][0]
as you see, i am taking the value of title
Then i surf the internet for some info about that value and then i write to a file, the writing is like this:
def writeRDFToFile(rdf, fileName):
f = open("movies/" + fileName + '.ttl','a')
try:
#rdf = rdf.encode('UTF-8')
f.write(rdf) # python will convert \n to os.linesep
except:
print "exception happened for movie " + movieTitle
f.close()
In that function, i am writing the rdf variable to a file.
As you see there is a commetted line
If the value of rdf variable contains unicode char and that line was not commeted, that code doesn't write anything to the file.
However, if I just commet that line, that code writes to a file.
Okay you can say that: commit that line and everything will be fine, but that is not correct, because i have another java process (which is Fuseki server) that reads the file and if the file contains unicode chars, it throws an error.
so i need to solve the file myself, i need to encode that data to ut8,
help please
The normal csv library can have difficulty writing unicode to files. I suggest you use the unicodecsv library instead of the csv library. It supports writing unicode to CSVs.
Practically speaking, just write:
import unicodecsv as csv