Hi Sarah!
I guess that your problem is with an untrusted certificate, you can get one for free at https://letsencrypt.org/


You can disable certificate verification in bioblend as in the example below:

import bioblend.galaxy
gi = bioblend.galaxy.GalaxyInstance(url=my_server, key=my_key)
gi.verify = False

Cheers,
Nicola

On 01/08/16 09:08, Sarah DIEHL wrote:
Dear all,

since the recent update to 16.04 I get the following error when trying to import a file from a user directory to a data library:

AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not provided

I use apache as a proxy and use an LDAP server for authentication. In order to get the API to work previously the apache had to be set to not check authentication for the requests to /api. In the logs I can see that the dataset import is an request to the API, so since the auth is not checked then, there is also no REMOTE_USER header set.

What is the recommended way to solve this issue with the current Galaxy version? I disabled the special settings for /api and the dataset import works now.

I tried to check the API with an old test script based on bioblend, but I now get the following error:

ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:645), 0 attempts left: None

Previously I could disable it with

import requests
requests.packages.urllib3.disable_warnings()

but that doesn't seem to work anymore (switched to Python 3 now). Since bioblend wraps all the requests methods, I cannot apply any of the common solutions I found online (e.g. set verify=False).

Any help to solve these issues is highly appreciated :-).

Best regards,
Sarah



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Sarah Diehl
HPC System Administrator
UNIVERSITÉ DU LUXEMBOURG
LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu <mailto:sarah.di...@uni.lu>http://lcsb.uni.lu <http://lcsb.uni.lu/>
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