Dear all,
since no one replied so far to the main problem I had and it might have gotten lost in the conversation, I ask again: Does somebody know how to configure external user auth with apache such that API (from external, e.g. bioblend) and dataset import in the data libraries work? When I configure apache to require auth for everything, the API does not work. If I except the API from the apache auth, the dataset import does not work.
If I switch to the new galaxy-internal LDAP auth features, will that solve this problem?
Any hints are appreciated!
Best regards, Sarah
---- 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.diehl@uni.lumailto:sarah.diehl@uni.lu http://lcsb.uni.luhttp://lcsb.uni.lu/ ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----
From: galaxy-dev <galaxy-dev-bounces@lists.galaxyproject.orgmailto:galaxy-dev-bounces@lists.galaxyproject.org> on behalf of Sarah DIEHL <sarah.diehl@uni.lumailto:sarah.diehl@uni.lu> Date: Monday 1 August 2016 13:06 To: Nicola Soranzo <nsoranzo@tiscali.itmailto:nsoranzo@tiscali.it>, "galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Remote user auth and API
Hi Nicola,
thanks a lot for the help! Yes, it's a self-signed certificate, I didn't bother with letsencrypt yet ;-).
So now the error turned to
ConnectionError: GET: error 401: b'<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401 Authorization Required</title>\n</head><body>\n<h1>Authorization Required</h1>\n<p>This server could not verify that you\nare authorized to access the document\nrequested. Either you supplied the wrong\ncredentials (e.g., bad password), or your\nbrowser doesn't understand how to supply\nthe credentials required.</p>\n</body></html>\n', 0 attempts left: None
which is what I expected, since apache now wants the authentication through LDAP.
So anybody know what the right settings are to get both the dataset import and the API working with external user auth over apache and LDAP?
Thanks, Sarah
---- 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.diehl@uni.lumailto:sarah.diehl@uni.lu http://lcsb.uni.luhttp://lcsb.uni.lu/ ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----
From: Nicola Soranzo <nicola.soranzo@gmail.commailto:nicola.soranzo@gmail.com> on behalf of Nicola Soranzo <nsoranzo@tiscali.itmailto:nsoranzo@tiscali.it> Date: Monday 1 August 2016 12:58 To: Sarah DIEHL <sarah.diehl@uni.lumailto:sarah.diehl@uni.lu>, "galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.orgmailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] Remote user auth and API
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
---- 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 mailto:sarah.diehl@uni.lusarah.diehl@uni.lumailto:sarah.diehl@uni.lu http://lcsb.uni.luhttp://lcsb.uni.lu/ ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----
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