Hi Eric,

thanks a lot for the info and help! I'm running version 16.04 and my apache 
conf is a bit different because I balance over multiple galaxy web servers:


    # API requests get routed through balancer with no authentication
    RewriteCond %{QUERY_STRING} key=
    RewriteRule ^/api/(.*) balancer://galaxy-noauth/api/$1 [P]

    # Regular requests get routed through balancer with LDAP authentication
    RewriteRule ^(.*) balancer://galaxy$1 [P]

    <Proxy balancer://galaxy/*>
        BalancerMember  http://localhost:8080
        BalancerMember  http://localhost:8081
        BalancerMember  http://localhost:8082
        BalancerMember  http://localhost:8083

RequestHeader set X-URL-SCHEME https

        AuthType Basic
        AuthBasicProvider ldap
        AuthName               "UL HPC Platform Authorized Users Only"
        AuthLDAPBindAuthoritative off
        AuthLDAPURL "ldap://…";
        Require valid-user
        RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e

        XSendFile on
        XSendFilePath /

        SetOutputFilter DEFLATE
        SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
    </Proxy>

    <Proxy balancer://galaxy-noauth/*>
        BalancerMember  http://localhost:8080
        BalancerMember  http://localhost:8081
        BalancerMember  http://localhost:8082
        BalancerMember  http://localhost:8083

RequestHeader set X-URL-SCHEME https

        Satisfy any

        XSendFile on
        XSendFilePath /

        SetOutputFilter DEFLATE
        SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
        SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
    </Proxy>

What doesn't work when configured this way is data libraries' import from user 
directory function. Can you tell if my apache configuration is equivalent to 
yours? Does the import functionality in the data libraries work for you?

This configuration worked fine with release 15.10, but doesn't anymore since I 
upgraded. Between those two version the default data libraries interface 
changed. What used to be "beta" before is now the default and only available 
option.

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.di...@uni.lu<mailto:sarah.di...@uni.lu>     
http://lcsb.uni.lu<http://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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From: Eric Rasche <e...@tamu.edu<mailto:e...@tamu.edu>>
Organization: TAMU
Date: Monday 8 August 2016 15:09
To: Sarah DIEHL <sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" 
<galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: [galaxy-dev] External user auth and API

Hi Sarah,


On 08. aug. 2016 07:44, Sarah DIEHL wrote:
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.

Our configuration looks like the following (just switching CAS for LDAP.)

    <Location "/galaxy/api/">
        Satisfy Any
        Allow from all
    </Location>

    <Location "/galaxy">
        AuthName "CAS"
        AuthType CAS
        Require valid-user
        RequestHeader set X-URL-SCHEME https
        XSendFile on
        XSendFilePath /
        RequestHeader set CAS-User 
"%{REMOTE_USER}s...@tamu.edu"<mailto:%{REMOTE_USER}s...@tamu.edu>
    </Location>
    ProxyPass /galaxy uwsgi://127.0.0.1:4001/

I.e. we disable authentication on the /api route. On 16.01+ (I think it was 
patched then, but 16.04 is a safer bet) this will work correctly and your users 
will be able to use the API. On previous versions the /api route would fail for 
web users if exposed in this manner.

If I switch to the new galaxy-internal LDAP auth features, will that solve this 
problem?
Yes, this is an alternate solution.

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
<mailto:sarah.di...@uni.lu>sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>     
<https://urldefense.proofpoint.com/v2/url?u=http-3A__lcsb.uni.lu_&d=CwMFAw&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=VV-vUll4GtQX9nsboaQbXHu4z31_SAdpkA-8nu-bzUk&s=bJ6NwuiRobXf-sPXjKoJ3KtEQaDOvG_ViZwLwKKumv8&e=>
 http://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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From: galaxy-dev 
<<mailto:galaxy-dev-boun...@lists.galaxyproject.org>galaxy-dev-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>>
 on behalf of Sarah DIEHL <sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>>
Date: Monday 1 August 2016 13:06
To: Nicola Soranzo 
<<mailto:nsora...@tiscali.it>nsora...@tiscali.it<mailto:nsora...@tiscali.it>>, 
"galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" 
<galaxy-dev@lists.galaxyproject.org<mailto: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
<mailto:sarah.di...@uni.lu>sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>     
<https://urldefense.proofpoint.com/v2/url?u=http-3A__lcsb.uni.lu_&d=CwMFAw&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=VV-vUll4GtQX9nsboaQbXHu4z31_SAdpkA-8nu-bzUk&s=bJ6NwuiRobXf-sPXjKoJ3KtEQaDOvG_ViZwLwKKumv8&e=>
 http://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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From: Nicola Soranzo 
<nicola.sora...@gmail.com<mailto:nicola.sora...@gmail.com>> on behalf of Nicola 
Soranzo 
<<mailto:nsora...@tiscali.it>nsora...@tiscali.it<mailto:nsora...@tiscali.it>>
Date: Monday 1 August 2016 12:58
To: Sarah DIEHL <sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" 
<galaxy-dev@lists.galaxyproject.org<mailto: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/<https://urldefense.proofpoint.com/v2/url?u=https-3A__letsencrypt.org_&d=CwMFAw&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=VV-vUll4GtQX9nsboaQbXHu4z31_SAdpkA-8nu-bzUk&s=NYyw6a4m49frmrTEPhp4x8j9TIotoRZOht1LReOprJ8&e=>

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.di...@uni.lu><mailto:sarah.di...@uni.lu>sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>
     
<https://urldefense.proofpoint.com/v2/url?u=http-3A__lcsb.uni.lu_&d=CwMFAw&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=VV-vUll4GtQX9nsboaQbXHu4z31_SAdpkA-8nu-bzUk&s=bJ6NwuiRobXf-sPXjKoJ3KtEQaDOvG_ViZwLwKKumv8&e=>
 http://lcsb.uni.lu
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--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, Biochemistry & Biophysics
Texas A&M University
College Station, TX 77843
e...@tamu.edu<mailto:e...@tamu.edu>
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