Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

2016-07-22 Thread Hans-Rudolf Hotz 

Hi Dannon

Thank you very much for the quick reply:

Our sysadmin installed:

openldap-devel
cyrus-sasl-devel

on our (Red Hat 7.2) box.

And, I can now run

> . .venv/bin/activate
> pip install python-ldap


looks like it is working nowexcept, that I now have to figure out 
the correct settings in auth_conf.xml




Regards, Hans-Rudolf



On 07/22/2016 01:24 PM, Dannon Baker wrote:

There's an open PR with a few build issues to build a Galaxy-side wheel
for python-ldap here:
https://github.com/galaxyproject/starforge/pull/97, and once that's
resolved it should be automatically installed as a conditional
dependency the usual Galaxy way.

Until then, yeah, a workaround is to activate the virtualenv and pip
install it.  As you found out, to do that you'll need a few system
packages -- I had to install both libldap2-dev and libsasl2-dev on an
ubuntu box here to get it to build.  Good luck!

-Dannon

On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz mailto:h...@fmi.ch>> wrote:

Dear all

I am looking into authentication through LDAP using the auth_conf file
(we are currently using Apache to handle this). And it looks like, I am
stuck at a very early step:


I have started with a fresh checkout of release 16.04
(git clone -b master https://github.com/galaxyproject/galaxy.git)

some modifications in galaxy.ini (host, port) and:

auth_config_file = config/auth_conf.xml


I start galaxy, and I try to login. In the log file I get:

galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
authenticate: email is hansrudolf.h...@fmi.ch

galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
authenticate: 

This is what I expect...so far so good

but further down, I get:

galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP
authenticate: could not load ldap module


According to our sysadmin, "python-ldap" is installed on the machine
(running Red Hat 7.2). But I assume, it has to be within the galaxy
created virtual env, hasn't-it?


Hence I have tried the following


cd 
. .venv/bin/activate
pip install python-ldap


Is this the right way to do it?


Doing this, I have been running into the following error:

Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
#include "lber.h"


So I guess I have to tell my sysadmin to install "openldap-devel in
order to have 'lber.h' on the system?


Or do I have to do something else?




Thank you very much for your help
Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: [galaxy-dev] activate authentication through LDAP using the auth_conf file

2016-07-22 Thread Dannon Baker 
There's an open PR with a few build issues to build a Galaxy-side wheel for
python-ldap here: https://github.com/galaxyproject/starforge/pull/97, and
once that's resolved it should be automatically installed as a conditional
dependency the usual Galaxy way.

Until then, yeah, a workaround is to activate the virtualenv and pip
install it.  As you found out, to do that you'll need a few system packages
-- I had to install both libldap2-dev and libsasl2-dev on an ubuntu box
here to get it to build.  Good luck!

-Dannon

On Fri, Jul 22, 2016 at 7:07 AM Hans-Rudolf Hotz  wrote:

> Dear all
>
> I am looking into authentication through LDAP using the auth_conf file
> (we are currently using Apache to handle this). And it looks like, I am
> stuck at a very early step:
>
>
> I have started with a fresh checkout of release 16.04
> (git clone -b master https://github.com/galaxyproject/galaxy.git)
>
> some modifications in galaxy.ini (host, port) and:
>
> auth_config_file = config/auth_conf.xml
>
>
> I start galaxy, and I try to login. In the log file I get:
>
> galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741
> trans.app.config.auth_config_file: ./config/auth_conf.xml
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
> authenticate: email is hansrudolf.h...@fmi.ch
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP
> authenticate: 
>
> This is what I expect...so far so good
>
> but further down, I get:
>
> galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP
> authenticate: could not load ldap module
>
>
> According to our sysadmin, "python-ldap" is installed on the machine
> (running Red Hat 7.2). But I assume, it has to be within the galaxy
> created virtual env, hasn't-it?
>
>
> Hence I have tried the following
>
>
> cd 
> . .venv/bin/activate
> pip install python-ldap
>
>
> Is this the right way to do it?
>
>
> Doing this, I have been running into the following error:
>
> Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
> #include "lber.h"
>
>
> So I guess I have to tell my sysadmin to install "openldap-devel in
> order to have 'lber.h' on the system?
>
>
> Or do I have to do something else?
>
>
>
>
> Thank you very much for your help
> Hans-Rudolf
>
>
>
>
>
> --
>
>
>
> Hans-Rudolf Hotz, PhD
> Bioinformatics Support
>
> Friedrich Miescher Institute for Biomedical Research
> Maulbeerstrasse 66
> 4058 Basel/Switzerland
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] activate authentication through LDAP using the auth_conf file

2016-07-22 Thread Hans-Rudolf Hotz 

Dear all

I am looking into authentication through LDAP using the auth_conf file 
(we are currently using Apache to handle this). And it looks like, I am 
stuck at a very early step:



I have started with a fresh checkout of release 16.04
(git clone -b master https://github.com/galaxyproject/galaxy.git)

some modifications in galaxy.ini (host, port) and:

auth_config_file = config/auth_conf.xml


I start galaxy, and I try to login. In the log file I get:

galaxy.webapps.galaxy.controllers.user DEBUG 2016-07-22 12:41:50,741 
trans.app.config.auth_config_file: ./config/auth_conf.xml
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP 
authenticate: email is hansrudolf.h...@fmi.ch
galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,741 LDAP 
authenticate: 


This is what I expect...so far so good

but further down, I get:

galaxy.auth.providers.ldap_ad DEBUG 2016-07-22 12:41:50,742 LDAP 
authenticate: could not load ldap module



According to our sysadmin, "python-ldap" is installed on the machine 
(running Red Hat 7.2). But I assume, it has to be within the galaxy 
created virtual env, hasn't-it?



Hence I have tried the following


cd 
. .venv/bin/activate
pip install python-ldap


Is this the right way to do it?


Doing this, I have been running into the following error:

Modules/errors.h:8:18: fatal error: lber.h: No such file or directory
#include "lber.h"


So I guess I have to tell my sysadmin to install "openldap-devel in 
order to have 'lber.h' on the system?



Or do I have to do something else?




Thank you very much for your help
Hans-Rudolf





--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/