Hi Nate,
Great to read from you :).
In the time between my request and your answer I tried out some things starting from the codes and googled a lot. As I left the desk soon after I could add it up to now. I'll try to keep it short and as comprehensible as possible:
* The issue is related to Python itself, not necessarely Unix. 'wget' on the URL you also used works fine, so proxying is ok. * There are bugreports on the 'urllib' libraries (there are three of them), for the two older ones there is no indication for a fix. Here https://github.com/kennethreitz/requests/issues/1204 a bug report on the 'requests' module appears, the guys where waiting for a fix in 'urllib3' (which was finally introduced). But: the tool shed package comes around with libraries 'urllib' ad 'urllib2', only. * Generally, it looks like the issue is due to a default behaviour of Python 2.x's 'ssl' module that may have been no problem in the past: the handshake is by default performed with SSLv2.3. As on a rising number of servers SSLv2 gets deactivated for security reasons, connections fail (SSLv3 is expected and maybe sent - client and server don't unterstand each other anymore). Check out the second and third highest ranked answer on this issue: http://stackoverflow.com/questions/14102416/python-requests-requests-excepti.... The second also includes a link to relevant line of code. For me it sounds reasonable, but I am a relative noob on web protocols...
Consequently, the answer to your question is the following:
---
import urllib urllib.urlretrieve("https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requ...")
Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib64/python2.6/urllib.py", line 93, in urlretrieve return _urlopener.retrieve(url, filename, reporthook, data) File "/usr/lib64/python2.6/urllib.py", line 239, in retrieve fp = self.open(url, data) File "/usr/lib64/python2.6/urllib.py", line 207, in open return getattr(self, name)(url) File "/usr/lib64/python2.6/urllib.py", line 441, in open_https h.endheaders() File "/usr/lib64/python2.6/httplib.py", line 914, in endheaders self._send_output() File "/usr/lib64/python2.6/httplib.py", line 786, in _send_output self.send(msg) File "/usr/lib64/python2.6/httplib.py", line 745, in send self.connect() File "/usr/lib64/python2.6/httplib.py", line 1122, in connect self.sock = ssl.wrap_socket(sock, self.key_file, self.cert_file) File "/usr/lib64/python2.6/ssl.py", line 338, in wrap_socket suppress_ragged_eofs=suppress_ragged_eofs) File "/usr/lib64/python2.6/ssl.py", line 120, in __init__ self.do_handshake() File "/usr/lib64/python2.6/ssl.py", line 279, in do_handshake self._sslobj.do_handshake() IOError: [Errno socket error] [Errno 1] _ssl.c:497: error:140770FC:SSL routines:SSL23_GET_SERVER_HELLO:unknown protocol ---
I also encountered the same error message when I try to install or update Python packages via 'easy_install' or 'pip' - both cannot connect to repositories. Also I don't know if the failed handshake is at the target server or our proxy - any idea for a command to check this?
Finally, I am running out of ideas what to do, for me it looks like it is too deep in the code for establishing a general workaround. On top, if I interpreted correctly the findings from the above bullet point list, this may have an impact on many pieces of software. For every case, where Python 2.x-driven instances try to access repositories on servers not offering SSLv2 anymore (maybe via proxy server).
Ideas? :)
Cheers, Sebastian
On Thu, Feb 11, 2016 at 12:43 PM, Sebastian Schaaf < schaaf@ibe.med.uni-muenchen.de> wrote:
Hey all,
I am currently trying to install Gemini (v0.18.1) via the test toolshed. It finally fails in dependencies as 'package_gemini_0_18_1' finds dependency 'gemini' to end in error state. There the message looks like the following:
2016-02-11 16:34:47 (72.4 MB/s) - `Miniconda-latest-Linux-x86_64.sh' saved [25416725/25416725]
Python 2.7.11 :: Continuum Analytics, Inc. Traceback (most recent call last): File "gemini_install.py", line 190, in <module> main(parser.parse_args()) File "gemini_install.py", line 80, in main gemini = install_conda_pkgs(anaconda, remotes, args) File "gemini_install.py", line 97, in install_conda_pkgs urllib.urlretrieve(remotes["requirements_conda"], filename=req_file) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 98, in urlretrieve return opener.retrieve(url, filename, reporthook, data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 245, in retrieve fp = self.open(url, data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 213, in open return getattr(self, name)(url) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 443, in open_https h.endheaders(data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 1049, in endheaders self._send_output(message_body) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 893, in _send_output self.send(msg) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 855, in send self.connect() File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 1274, in connect server_hostname=server_hostname) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 352, in wrap_socket _context=self) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 579, in __init__ self.do_handshake() File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 808, in do_handshake self._sslobj.do_handshake() IOError: [Errno socket error] [SSL: UNKNOWN_PROTOCOL] unknown protocol (_ssl.c:590)
Hi Sebastian,
I believe the URL that it's attempting to fetch is:
https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requ...
Using the Python interpreter that your Galaxy instance is using, what happens if you do:
import urllib urllib.urlretrieve("
https://raw.githubusercontent.com/arq5x/gemini/master/versioning/0.18.0/requ... ")
--nate
Some browsing at Google brought hints on three common cases where this could appear *plus* a fourth one which looks by error code pretty much what I got:
http://blog.techstacks.com/2010/03/3-common-causes-of-unknown-ssl-protocol-e...
So, may I be right that there is a typo in an URL needed for downloading during the setup process? Or is it, according to
http://stackoverflow.com/questions/10667960/python-requests-throwing-up-ssle... due to some failed SSL certificate check?
Some help (or ideas for targeted checking) would be great :).
Cheers, Sebastian
-- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499
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