I have a zip-file that can be opened/extracted with 7zip but gives an error when I try work with it in python:
Py2 (2.7.3 / Linux/Debian7):
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/zipfile.py", line 714, in __init__
    self._GetContents()
  File "/usr/lib/python2.7/zipfile.py", line 748, in _GetContents
    self._RealGetContents()
  File "/usr/lib/python2.7/zipfile.py", line 763, in _RealGetContents
    raise BadZipfile, "File is not a zip file"
zipfile.BadZipfile: File is not a zip file


Py3 (3.4.3 / Windows 7 /64bit):
Traceback (most recent call last):
  File "<pyshell#20>", line 1, in <module>
    badzip = ZipFile(bad)
  File "C:\Python34\lib\zipfile.py", line 937, in __init__
    self._RealGetContents()
  File "C:\Python34\lib\zipfile.py", line 978, in _RealGetContents
    raise BadZipFile("File is not a zip file")
zipfile.BadZipFile: File is not a zip file

The zip-file is attached.

unzip can't proceed this file too.

$ unzip -v not_working.zip 
Archive:  not_working.zip
  End-of-central-directory signature not found.  Either this file is not
  a zipfile, or it constitutes one disk of a multi-part archive.  In the
  latter case the central directory and zipfile comment will be found on
  the last disk(s) of this archive.
unzip:  cannot find zipfile directory in one of not_working.zip or
        not_working.zip.zip, and cannot find not_working.zip.ZIP, period.

not_working.zip has 85972 extra null bytes at the end. This doesn't look as common ZIP file, and adding support such files can be considered as new feature (if it is worth to do at all). How did you get this file Yasar?

7z archiver could extract this ZIP archive without any problems:
~/tmp $ 7z x not_working.zip 

7-Zip [64] 9.20  Copyright (c) 1999-2010 Igor Pavlov  2010-11-18
p7zip Version 9.20 (locale=en_US.utf8,Utf16=on,HugeFiles=on,4 CPUs)

Processing archive: not_working.zip

Extracting  CoordinateData.AmplitudesDataType
Extracting  CoordinateData.Amplitudes
Extracting  CoordinateData.VolumesDataType
Extracting  CoordinateData.Volumes

Everything is Ok

Files: 4
Size:       103746
Compressed: 176384

@Serhiy These files are inside another Zip-bundle exported from a commercial control software for chromatography (UNICORN 6+ by GE Healthcare). Some of the other Zip-Files in the bundle work fine but some (like this one) don't.

I'm writing a script to extract/decode the deta so I'd be happy to get them extracted via python in some way (without requiring external dependencies).

Would it help to remove the offending bytes and then feed the bytes-object to ZipFile?

> Would it help to remove the offending bytes and then feed the bytes-object to ZipFile?

Yes, it will.

import zipfile, struct, io
with open('not_working.zip', 'rb') as f:
    data = f.read()

i = data.rindex(b'PK\5\6') + 22
i += struct.unpack('<H', data[i-2: i])[0]
if data[i:].strip(b'\0') == b'':
    data = data[:i]

zf = zipfile.ZipFile(io.BytesIO(data))

It is common to prepend some data (e.g. self-extractor exacutable) to ZIP file, but it is not common to append data to ZIP file. In this case all appended data is zero bytes, and it looks as particularity of particular software rather than common case. Thus I am closing this issue.