carveme_init fails with "Connection reset by peer" error

[mmundy42]

Problem description

I'm following the instructions to install carveme and the carveme_init script fails with a "Connection reset by peer" error.

I worked around the problem by manually downloading the files listed in the downloads dictionary in the carveme_init script using the wget command.

Actual output

$ carveme_init
Downloading data/input/genbank_assembly_all.tsv.gz
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/bin/carveme_init", line 28, in <module>
    urllib.urlretrieve(file_url, outputfile)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py", line 98, in urlretrieve
    return opener.retrieve(url, filename, reporthook, data)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py", line 245, in retrieve
    fp = self.open(url, data)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py", line 213, in open
    return getattr(self, name)(url)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib.py", line 443, in open_https
    h.endheaders(data)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 1038, in endheaders
    self._send_output(message_body)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 882, in _send_output
    self.send(msg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 844, in send
    self.connect()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/httplib.py", line 1263, in connect
    server_hostname=server_hostname)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py", line 363, in wrap_socket
    _context=self)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py", line 611, in __init__
    self.do_handshake()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ssl.py", line 840, in do_handshake
    self._sslobj.do_handshake()
IOError: [Errno socket error] [Errno 54] Connection reset by peer

Versions

System info: OS Darwin OS-release 16.7.0 Python 2.7.13 Package

$ pip show carveme pandas framed
Name: carveme
Version: 0.1.4
Summary: CarveMe: automated metabolic model reconstruction
Home-page: https://github.com/cdanielmachado/carveme
Author: Daniel Machado, Sergej Andrejev
Author-email: cdanielmachado@gmail.com
License: Apache Software License 2.0
Location: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requires: pandas, framed
---
Name: pandas
Version: 0.20.3
Summary: Powerful data structures for data analysis, time series,and statistics
Home-page: http://pandas.pydata.org
Author: The PyData Development Team
Author-email: pydata@googlegroups.com
License: BSD
Location: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requires: numpy, python-dateutil, pytz
---
Name: framed
Version: 0.3.5
Summary: framed - metabolic modeling for python
Home-page: https://github.com/cdanielmachado/framed
Author: Daniel Machado
Author-email: cdanielmachado@gmail.com
License: Apache License Version 2.0
Location: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requires: matplotlib, sympy, python-libsbml, scipy, numpy

[cdanielmachado]

Thanks for reporting. That's rather strange. If you can get them with wget then the connection works just fine.

Let's see if more people report this problem. Then I might need to replace urllib with something more reliable.

[cdanielmachado]

These files are now included within the pip installer, so this download step is no longer necessary.