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python compressed 4Gb bz2 EOFError: end of stream was already found nested subfolders

I'm trying to read a specific file from a compressed file bz2 using python.
tar = tarfile.open(filename, "r|bz2", bufsize=57860311)
for tarinfo in tar:
print tarinfo.name, "is", tarinfo.size, "bytes in size and is",
if tarinfo.isreg():
print "a regular file."
# read the file
f = tar.extractfile(tarinfo)
#print f.read()
elif tarinfo.isdir():
print "a directory."
else:
print "something else."
tar.close()
But at the end I got the error:
/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.pyc in read(self, size)
577 buf = "".join(t)
578 else:
--> 579 buf = self._read(size)
580 self.pos += len(buf)
581 return buf
/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.pyc in _read(self, size)
594 break
595 try:
--> 596 buf = self.cmp.decompress(buf)
597 except IOError:
598 raise ReadError("invalid compressed data")
EOFError: end of stream was already found
I also tried to list the files within the tar through 'tar.list()' and again ...
-rwxr-xr-x lindauer/or3uunp 0 2013-05-21 00:58:36 r3.2/
-rw-r--r-- lindauer/or3uunp 6057 2012-01-05 14:41:00 r3.2/readme.txt
-rw-r--r-- lindauer/or3uunp 44732 2012-01-04 10:08:54 r3.2/psychometric.csv
-rw-r--r-- lindauer/or3uunp 57860309 2012-01-04 09:58:20 r3.2/logon.csv
/usr/local/Cellar/python#2/2.7.15_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/tarfile.pyc in _read(self, size)
594 break
595 try:
--> 596 buf = self.cmp.decompress(buf)
597 except IOError:
598 raise ReadError("invalid compressed data")
EOFError: end of stream was already found
I listed the files inside the archive using the tar command. Here is the result:
tar -tvf r3.2.tar.bz2
drwxr-xr-x 0 lindauer or3uunp 0 May 21 2013 r3.2/
-rw-r--r-- 0 lindauer or3uunp 6057 Jan 5 2012 r3.2/readme.txt
-rw-r--r-- 0 lindauer or3uunp 44732 Jan 4 2012 r3.2/psychometric.csv
-rw-r--r-- 0 lindauer or3uunp 57860309 Jan 4 2012 r3.2/logon.csv
-rw-r--r-- 0 lindauer or3uunp 12494829865 Jan 5 2012 r3.2/http.csv
-rw-r--r-- 0 lindauer or3uunp 1066622500 Jan 5 2012 r3.2/email.csv
-rw-r--r-- 0 lindauer or3uunp 218962503 Jan 5 2012 r3.2/file.csv
-rw-r--r-- 0 lindauer or3uunp 29156988 Jan 4 2012 r3.2/device.csv
drwxr-xr-x 0 lindauer or3uunp 0 May 20 2013 r3.2/LDAP/
-rw-r--r-- 0 lindauer or3uunp 140956 Jan 4 2012 r3.2/LDAP/2011-01.csv
-rw-r--r-- 0 lindauer or3uunp 147370 Jan 4 2012 r3.2/LDAP/2010-05.csv
-rw-r--r-- 0 lindauer or3uunp 149221 Jan 4 2012 r3.2/LDAP/2010-02.csv
-rw-r--r-- 0 lindauer or3uunp 141717 Jan 4 2012 r3.2/LDAP/2010-12.csv
-rw-r--r-- 0 lindauer or3uunp 148931 Jan 4 2012 r3.2/LDAP/2010-03.csv
-rw-r--r-- 0 lindauer or3uunp 147370 Jan 4 2012 r3.2/LDAP/2010-04.csv
-rw-r--r-- 0 lindauer or3uunp 149793 Jan 4 2012 r3.2/LDAP/2009-12.csv
-rw-r--r-- 0 lindauer or3uunp 143979 Jan 4 2012 r3.2/LDAP/2010-09.csv
-rw-r--r-- 0 lindauer or3uunp 145591 Jan 4 2012 r3.2/LDAP/2010-07.csv
-rw-r--r-- 0 lindauer or3uunp 139444 Jan 4 2012 r3.2/LDAP/2011-03.csv
-rw-r--r-- 0 lindauer or3uunp 142347 Jan 4 2012 r3.2/LDAP/2010-11.csv
-rw-r--r-- 0 lindauer or3uunp 138285 Jan 4 2012 r3.2/LDAP/2011-04.csv
-rw-r--r-- 0 lindauer or3uunp 149793 Jan 4 2012 r3.2/LDAP/2010-01.csv
-rw-r--r-- 0 lindauer or3uunp 146008 Jan 4 2012 r3.2/LDAP/2010-06.csv
-rw-r--r-- 0 lindauer or3uunp 144711 Jan 4 2012 r3.2/LDAP/2010-08.csv
-rw-r--r-- 0 lindauer or3uunp 137967 Jan 4 2012 r3.2/LDAP/2011-05.csv
-rw-r--r-- 0 lindauer or3uunp 140085 Jan 4 2012 r3.2/LDAP/2011-02.csv
-rw-r--r-- 0 lindauer or3uunp 143420 Jan 4 2012 r3.2/LDAP/2010-10.csv
-r--r--r-- 0 lindauer or3uunp 3923 Jan 4 2012 r3.2/license.txt
I think this is due to the fact the archive has subfolders and for some reason python libraries have problems in dealing with subfolders extractions?
I also tried to open the tar file manually and I have no problems so I don't think the file is corrupted. Any help appreciated.

Comment: I tried the debug=3 and I get : ReadError: bad checksum
Found the following related Infos:
tar: directory checksum error
Cause
This error message from tar(1) indicates that the checksum of the directory and the files it has read from tape does not match the checksum advertised in the header block. Usually this message indicates the wrong blocking factor, although it could indicate corrupt data on tape.
Action
To resolve this problem, make certain that the blocking factor you specify on the command line (after -b) matches the blocking factor originally specified. If in doubt, leave out the block size and let tar(1) determine it automatically. If that remedy does not help, the tape data could be corrupted.
SE:tar-ignore-or-fix-checksum
I'd try the -i switch to see if you can just ignore and messages regarding EOF.
-i, --ignore-zeros ignore zeroed blocks in archive (means EOF)
Example
$ tar xivf backup.tar
bugs.python.org:tarfile-headererror
The comment in tarfile.py reads (Don't know the date of the file!):
- # We shouldn't rely on this checksum, because some tar programs
- # calculate it differently and it is merely validating the
- # header block.
ReadError: unexpected end of data
From the tarfile Documentation
The tarfile module defines the following exceptions:
exception tarfile.ReadError
Is raised when a tar archive is opened, that either cannot be handled by the tarfile module or is somehow invalid.
First, try with another tar archiv file to verify your python environent.
Second, check if your tar archiv file match the following format:
tarfile.DEFAULT_FORMAT
The default format for creating archives. This is currently GNU_FORMAT.
Third, instead of using tarfile.open(...), to create a tarfile instance, try to use the following, to set debug=3.
tar = tarfile.TarFile(name=filename, debug=3)
tar.open()
...
class tarfile.TarFile(name=None, mode='r', fileobj=None, format=DEFAULT_FORMAT, tarinfo=TarInfo, dereference=False, ignore_zeros=False, encoding=ENCODING, errors='surrogateescape', pax_headers=None, debug=0, errorlevel=0)

How to error check list index out of range

I have a read.log file that will have lines such as...
10.2.177.170 Tue Jun 19 03:30:55 CDT 2018
10.2.177.170 Tue Jun 19 03:31:03 CDT 2018
10.2.177.170 Tue Jun 19 03:31:04 CDT 2018
10.2.177.170 Tue Jun 19 03:32:04 CDT 2018
10.2.177.170 Tue Jun 19 03:33:04 CDT 2018
My code will read the 3rd to last line and combine strings. So the normal output would be:
2018:19:03:32:04
My problem is, if there are only 4 or less lines of data such as
10.1.177.170 Tue Jun 19 03:30:55 CDT 2018
10.1.177.170 Tue Jun 19 03:31:03 CDT 2018
10.1.177.170 Tue Jun 19 03:31:04 CDT 2018
10.1.177.170 Tue Jun 19 03:32:04 CDT 2018
I get an error
x1 = line.split()[0]
IndexError: list index out of range
How can I error check this or keep it from happening? I have been trying to check how many lines there are in the log and if less than 5, print a notice. Are there better options?
def run():
f = open('read.log', 'r')
lnumber = dict()
for num,line in enumerate(f,1):
x1 = line.split()[0]
log_day = line.split()[3]
log_time = line.split()[4]
log_year = line.split()[6]
if x1 in lnumber:
lnumber[x1].append((log_year + ":" + log_day + ":" + log_time))
else:
lnumber[x1] = [(num,log_time)]
if x1 in lnumber and len(lnumber.get(x1,None)) > 2:
# if there are less than 3 lines in document, this will fail
line_time = (lnumber[x1][-3].__str__())
print(line_time)
else:
print('nothing')
f.close
run()

f.readlines() gives you a list of lines in a file. So, you could try reading in all the lines in a file:
f = open('firewall.log', 'r')
lines = f.readlines()
And exiting if there are 4 or less lines:
if len(lines) <= 4:
f.close()
print("4 or less lines in file")
exit()
That IndexError you're getting is because you're calling split() on a line with nothing on it. I would suggest doing something like if not line: continue to avoid that case.

Python - Parsing a text file into a csv file

I have a text file that is output from a command that I ran with Netmiko to retrieve data from a Cisco WLC of things that are causing interference on our WiFi network. I stripped out just what I needed from the original 600k lines of code down to a couple thousand lines like this:
AP Name.......................................... 010-HIGH-FL4-AP04
Microwave Oven 11 10 -59 Mon Dec 18 08:21:23 2017
WiMax Mobile 11 0 -84 Fri Dec 15 17:09:45 2017
WiMax Fixed 11 0 -68 Tue Dec 12 09:29:30 2017
AP Name.......................................... 010-2nd-AP04
Microwave Oven 11 10 -61 Sat Dec 16 11:20:36 2017
WiMax Fixed 11 0 -78 Mon Dec 11 12:33:10 2017
AP Name.......................................... 139-FL1-AP03
Microwave Oven 6 18 -51 Fri Dec 15 12:26:56 2017
AP Name.......................................... 010-HIGH-FL3-AP04
Microwave Oven 11 10 -55 Mon Dec 18 07:51:23 2017
WiMax Mobile 11 0 -83 Wed Dec 13 16:16:26 2017
The goal is to end up with a csv file that strips out the 'AP Name ...' and puts what left on the same line as the rest of the information in the next line. The problem is some have two lines below the AP name and some have 1 or none. I have been at it for 8 hours and cannot find the best way to make this happen.
This is the latest version of code that I was trying to use, any suggestions for making this work? I just want something I can load up in excel and create a report with:
with open(outfile_name, 'w') as out_file:
with open('wlc-interference_raw.txt', 'r')as in_file:
#Variables
_ap_name = ''
_temp = ''
_flag = False
for i in in_file:
if 'AP Name' in i:
#write whatever was put in the temp file to disk because new ap now
#add another temp variable in case an ap has more than 1 interferer and check if new AP name
out_file.write(_temp)
out_file.write('\n')
#print(_temp)
_ap_name = i.lstrip('AP Name.......................................... ')
_ap_name = _ap_name.rstrip('\n')
_temp = _ap_name
#print(_temp)
elif '----' in i:
pass
elif 'Class Type' in i:
pass
else:
line_split = i.split()
for x in line_split:
_temp += ','
_temp += x
_temp += '\n'

I think your best option is to read all lines of the file, then split into sections starting with AP Name. Then you can work on parsing each section.
Example
s = """AP Name.......................................... 010-HIGH-FL4-AP04
Microwave Oven 11 10 -59 Mon Dec 18 08:21:23 2017
WiMax Mobile 11 0 -84 Fri Dec 15 17:09:45 2017
WiMax Fixed 11 0 -68 Tue Dec 12 09:29:30 2017
AP Name.......................................... 010-2nd-AP04
Microwave Oven 11 10 -61 Sat Dec 16 11:20:36 2017
WiMax Fixed 11 0 -78 Mon Dec 11 12:33:10 2017
AP Name.......................................... 139-FL1-AP03
Microwave Oven 6 18 -51 Fri Dec 15 12:26:56 2017
AP Name.......................................... 010-HIGH-FL3-AP04
Microwave Oven 11 10 -55 Mon Dec 18 07:51:23 2017
WiMax Mobile 11 0 -83 Wed Dec 13 16:16:26 2017"""
import re
class AP:
"""
A class holding each section of the parsed file
"""
def __init__(self):
self.header = ""
self.content = []
sections = []
section = None
for line in s.split('\n'): # Or 'for line in file:'
# Starting new section
if line.startswith('AP Name'):
# If previously had a section, add to list
if section is not None:
sections.append(section)
section = AP()
section.header = line
else:
if section is not None:
section.content.append(line)
sections.append(section) # Add last section outside of loop
for section in sections:
ap_name = section.header.lstrip("AP Name.") # lstrip takes all the characters given, not a literal string
for line in section.content:
print(ap_name + ",", end="")
# You can extract the date separately, if needed
# Splitting on more than one space using a regex
line = ",".join(re.split(r'\s\s+', line))
print(line.rstrip(',')) # Remove trailing comma from imperfect split
Output
010-HIGH-FL4-AP04,Microwave Oven,11,10,-59,Mon Dec 18 08:21:23 2017
010-HIGH-FL4-AP04,WiMax Mobile,11,0,-84,Fri Dec 15 17:09:45 2017
010-HIGH-FL4-AP04,WiMax Fixed,11,0,-68,Tue Dec 12 09:29:30 2017
010-2nd-AP04,Microwave Oven,11,10,-61,Sat Dec 16 11:20:36 2017
010-2nd-AP04,WiMax Fixed,11,0,-78,Mon Dec 11 12:33:10 2017
139-FL1-AP03,Microwave Oven,6,18,-51,Fri Dec 15 12:26:56 2017
010-HIGH-FL3-AP04,Microwave Oven,11,10,-55,Mon Dec 18 07:51:23 2017
010-HIGH-FL3-AP04,WiMax Mobile,11,0,-83,Wed Dec 13 16:16:26 2017
Tip:
You don't need Python to write the CSV, you can output to a file using the command line
python script.py > output.csv

Python regex is not extracting a substring from my log file

I'm using
date = re.findall(r"^(?:\w{3} ){2}\d{2} (?:[\d]{2}:){2}\d{2} \d{4}$", message)
in Python 2.7 to extract the substrings:
Wed Feb 04 13:29:49 2015
Thu Feb 05 13:45:08 2015
from a log file like this:
1424,Wed Feb 04 13:29:49 2015,51
1424,Thu Feb 05 13:45:08 2015,29
It is not working, and I'm required to use regex for this task, otherwise I would have split() it. What am I doing wrong?

As your sub-strings doesn't began from the first part of your string you dont need to assert position at start and end of the string so you can remove ^ and $
:
>>> s ="""
1424,Wed Feb 04 13:29:49 2015,51
1424,Thu Feb 05 13:45:08 2015,29"""
>>> date = re.findall(r"(?:\w{3} ){2}\d{2} (?:[\d]{2}:){2}\d{2} \d{4}", s)
>>> date
['Wed Feb 04 13:29:49 2015', 'Thu Feb 05 13:45:08 2015']
Also as an alternative proposition you can just use a positive look-behind :
>>> date = re.findall(r"(?<=\d{4},).*", s)
>>> date
['Wed Feb 04 13:29:49 2015,51', 'Thu Feb 05 13:45:08 2015,29']
or without using regex you can use str.split() and str.partition() for such tasks :
>>> s ="""
1424,Wed Feb 04 13:29:49 2015,51
1424,Thu Feb 05 13:45:08 2015,29"""
>>> [i.partition(',')[-1] for i in s.split('\n')]
['Wed Feb 04 13:29:49 2015,51', 'Thu Feb 05 13:45:08 2015,29']

a simple way to do this is just match by the commas
message = '1424,Wed Feb 04 13:29:49 2015,51 1424,Thu Feb 05 13:45:08 2015,29'
date = re.findall(r",(.*?),", message)
print date
>>> ['Wed Feb 04 13:29:49 2015', 'Thu Feb 05 13:45:08 2015']
DEMO

You dont need regex, use split.
line = "1424,Wed Feb 04 13:29:49 2015,51"
date = line.split(",")[1]
print date
>>>Wed Feb 04 13:29:49 2015

Order a sequence of dates as they occur in calendar year

I've got a series of pipes to convert dates in a text file into unique, human readable output and pull out MM DD. Now I would like to resort the output so that the dates display in the order in which they occur during the year. Anybody know a good technique using the standard shell or with a readily installable package on *nix?
Feb 4
Feb 5
Feb 6
Feb 7
Feb 8
Jan 1
Jan 10
Jan 11
Jan 12
Jan 13
Jan 2
Jan 25
Jan 26
Jan 27
Jan 28
Jan 29
Jan 3
Jan 30
Jan 31
Jan 4
Jan 5
Jan 6
Jan 7
Jan 8
Jan 9

There is a utility called sort with an option -M for sorting by month. If you have it installed, you could use that. For instance:
sort -k1 -M test.txt
-k1: First column
-M: Sort by month
Edited per twalberg's suggestion below:
sort -k1,1M -k2,2n test.txt

In two steps:
$ while read line; do date -d "$line" "+%Y%m%d"; done < file | sort -n > temp
$ while read line; do date -d "$line" "+%b %d"; done < temp > file
Firstly we convert dates to YYYYMMDD and order them:
$ while read line; do date -d "$line" "+%Y%m%d"; done < file | sort -n > temp
$ cat temp
20130101
20130102
20130103
20130104
20130105
20130106
20130107
20130108
20130109
20130110
20130111
20130112
20130113
20130125
20130126
20130127
20130128
20130129
20130130
20130131
20130204
20130205
20130206
20130207
20130208
Then we print them back to previous format %b %d:
$ while read line; do date -d "$line" "+%b %d"; done < temp > file
$ cat file
Jan 01
Jan 02
Jan 03
Jan 04
Jan 05
Jan 06
Jan 07
Jan 08
Jan 09
Jan 10
Jan 11
Jan 12
Jan 13
Jan 25
Jan 26
Jan 27
Jan 28
Jan 29
Jan 30
Jan 31
Feb 04
Feb 05
Feb 06
Feb 07
Feb 08

and sed -n "1 {
H
x
s/.(\n)./01 Jan\102 Feb\103 Mar\104 Apr\105 May\106 Jun\107 Jul\105 Aug\109 Sep\110 Oct\111 Nov\112 Dec/
x
}
s/^\(.\{3\}\) \([0-9]\) *$/\1 0\2/
H
$ {
x
t subs
: subs
s/^\([0-9]\{2\}\) \([[:alpha:]]\{3\}\)\(\n\)\(.*\)\n\2/\1 \2\3\4\3\1 \2/
t subs
s/^[0-9]\{2\} [[:alpha:]]\{3\}\n//
t subs
p
}
" | sort | sed "s/^[0-9][0-9] //"
still need a sort (or a lot more complex sed for sorting) and when sort -M doesn't work