I don't know what the particular issue is - I do know that after a lot of trial and error we were able to get Postgres + SSL working at MSI before I left my previous job there - so there is hope.
I will say however, upgrading even to one newer Galaxy - namely 16.01 might solve this issue. We re-did Galaxy's dependency handling to use virtualenvs, pip, and wheels in 16.01. It is much closer to a standard Python dependency management stack. I think our wheel came bundled with SSL support and even if I'm wrong about that support any random online tutorial about debugging this problem in Python should be applicable after the upgrade.
-John
On Mon, Jan 2, 2017 at 12:22 PM, Floreline TOUCHARD floreline.touchard@gmail.com wrote:
Hi Galaxy Community,
I have the same problem than Nikolay few years ago (http://dev.list.galaxyproject.org/connecting-to-a-DB-on-a-different-host-td4...) : I would like to connect my Galaxy instance to my postgresql database using SSL encryption and Auth method md5. I have no problems connecting to the DB via the command line with SSL encryption.
When setting the galaxy.ini file with postgresql database connection to "postgresql://<USERNAME>:<PWD>@<HOST>:5432/<DB_NAME>?sslmode=require", I get the following message : "OperationalError: (psycopg2.OperationalError) sslmode value "require" invalid when SSL support is not compiled in"
Regarding the former post I thought that it might come from the module psycopg2's compilation.
I followed the steps of the post but encounter a different error.
What I did:
- Downloaded a tar.gz of psycopg2 2.5.1 (I saw the needed version in the
file eggs.ini) to <install dir>/galaxy/ and unpacked it there 2. cd into psycopg2, modified the setup.py according to the instructions (added the line containing scramble_lib) 3. export the path to pg_config (export PATH=<path/to/postgresql>/bin:$PATH) 4. added the file ez_setup.py (downloaded from https://bootstrap.pypa.io/ez_setup.py) to <install dir>/galaxy/scripts/scramble/lib/, the same dir where scramble_lib.py is located 5. ran PYTHONPATH=<install dir>/galaxy/scripts/scramble/lib python setup.py egg_info --tag-build=_9.4.4_static bdist_egg And get the following error :
" Traceback (most recent call last): File "setup.py", line 57, in <module> from scramble_lib import * File "<install dir>/galaxy/scripts/scramble/lib/scramble_lib.py", line 150, in <module> use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) File "<install dir>/galaxy/scripts/scramble/lib/ez_setup.py", line 160, in use_setuptools version = _resolve_version(version) File "<install dir>/galaxy/scripts/scramble/lib/ez_setup.py", line 368, in _resolve_version resp = urlopen(meta_url) File "/usr/lib64/python2.6/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib64/python2.6/urllib2.py", line 391, in open response = self._open(req, data) File "/usr/lib64/python2.6/urllib2.py", line 409, in _open '_open', req) File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib64/python2.6/urllib2.py", line 1198, in https_open return self.do_open(httplib.HTTPSConnection, req) File "/usr/lib64/python2.6/urllib2.py", line 1165, in do_open raise URLError(err) urllib2.URLError: <urlopen error [Errno -2] Name or service not known> "
Could it be because I have no internet access ? What module should I install to enable SSL encryption ?
Additional information :
- Postgresql version 9.4.4
- Galaxy version 15.10
- I use virtualenv for python environment
Thanks in advance, Floreline
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