subject:"\[galaxy\-dev\] external authentication \- empty REMOTE

Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-22 Thread Floreline TOUCHARD

Hi, thanks for the quick reply !

I did edit the remoteuser.py file and started the daemon again, but there's
no change in the output in paster.log.
Am I missing something ?

F.T

2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD 
:

> Hi,
>
> I've got an issue with my external authentication configuration. I use
> Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
> NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under "@
> example.org" regardless of the authentication account. That's why I think
> the REMOTE_USER passed to Galaxy is not 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
> [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-22 Thread Floreline TOUCHARD

Hi,

here is some additional information :

- I have no change in my paster.log with my current galaxy.conf file.

- If I force the connexion with a user (with a RequestHeader set
REMOTE_USER "" in galaxy.conf), it works. My galaxy instance open
on my user session, and I get a "galaxy.web.framework.webapp WARNING
2015-10-22 10:37:19,762 User logged in as '@example.fr'
externally, but has a cookie as '@example.fr' invalidating session" in the
paster.log.

Is it a syntax problem in my galaxy.conf file ?

F.T

2015-10-21 12:11 GMT+02:00 Floreline TOUCHARD 
:

> Hi,
>
> I've got an issue with my external authentication configuration. I use
> Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
> NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under "@
> example.org" regardless of the authentication account. That's why I think
> the REMOTE_USER passed to Galaxy is not 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
> [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
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[galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Floreline TOUCHARD

Hi,

I've got an issue with my external authentication configuration. I use
Apache and the mod_perl

modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS
accounts.

I have the authentication form  when I try to access galaxy web page.
But after a successful authentication it seems that the REMOTE_USER
variable is not passed to my galaxy instance. I'm connected under "@
example.org" regardless of the authentication account. That's why I think
the REMOTE_USER passed to Galaxy is not 'null' but empty.

I tested the value of the variable with the following php script:

 $key_value) {
print $key_name . " = " . $key_value . "";

}

?>

I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.

I don't understand where my problem lies.



Here is my galaxy.conf file :

Listen 2208




RewriteEngine on
DocumentRoot "/path/to/static"


   

Options +Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
Allow from all


AuthType Basic
AuthName "Authentifiez vous"
PerlAuthenHandler Apache2::AuthenNIS
PerlAuthzHandler Apache2::AuthzNIS
PerlSetVar AllowAlternateAuth no
require valid-user


   


RewriteEngine on
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
RequestHeader set REMOTE_USER %{RU}e



   RewriteRule ^/galaxy$ /galaxy/ [R]
   RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
[L]
   RewriteRule ^/static/scripts/(.*)
/softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1

[L]
   RewriteRule ^/static/(.*) /path/to/static/$1 [L]
   RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
   RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
   RewriteRule ^(.*) http://localhost:2209$1 [P]





Thanks in advance !

F.T
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Ryan G

I just recently submitted a patch that will display all the environment 
variables being passed to Galaxy in pastor.log.  That should help you determine 
if the variables are set and to what. 


Please excuse any typos -- Sent from my iPhone

> On Oct 21, 2015, at 6:11 AM, Floreline TOUCHARD 
>  wrote:
> 
> Hi,
> 
> I've got an issue with my external authentication configuration. I use Apache 
> and the mod_perl
> 
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with NIS 
> accounts.
> 
> I have the authentication form  when I try to access galaxy web page. 
> But after a successful authentication it seems that the REMOTE_USER variable 
> is not passed to my galaxy instance. I'm connected under "@example.org" 
> regardless of the authentication account. That's why I think the REMOTE_USER 
> passed to Galaxy is not 'null' but empty.
> 
> I tested the value of the variable with the following php script:
> 
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
> 
> }
> 
> ?>
> 
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
> 
> I don't understand where my problem lies.
> 
>  
> 
> Here is my galaxy.conf file :
> 
> Listen 2208
> 
> 
> 
> 
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
> 
>
> 
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
> 
> 
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
> 
> 
>
> 
> 
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
> 
> 
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*) 
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
> 
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
> 
> 
> 
> 
> 
> Thanks in advance !
> 
> F.T
> 
> ___
> 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:
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> 
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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:
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Floreline TOUCHARD

Thank you ! Can you tell me which files are to update or download ?
I installed my application on a server that was not open to the outside.
Currently I do not support different versions or updates of my application
with git.
I can download the files to edit and transfer them to the server but not to
update the entire application at the moment.

F. T
Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" 
a écrit :

> Hi,
>
> I've got an issue with my external authentication configuration. I use
> Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
> NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under "@
> example.org" regardless of the authentication account. That's why I think
> the REMOTE_USER passed to Galaxy is not 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*) /path/to/static/june_2007_style/blue/$1
> [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
___
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:
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Eric Rasche

Hi Floreline,

The files from Ryan's pull request are visible here:
https://github.com/galaxyproject/galaxy/pull/823/files

It's a pretty simple change to enable some extra debugging information that 
might help you discover the cause of your issue.


On 10/21/2015 07:40 AM, Floreline TOUCHARD wrote:
> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my
> application with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
>
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD"
> > a
> écrit :
>
> Hi,
>
> I've got an issue with my external authentication configuration. I
> use Apache and the mod_perl
>
> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy
> with NIS accounts.
>
> I have the authentication form  when I try to access galaxy web page.
> But after a successful authentication it seems that the REMOTE_USER
> variable is not passed to my galaxy instance. I'm connected under
> "@example.org " regardless of the authentication
> account. That's why I think the REMOTE_USER passed to Galaxy is not
> 'null' but empty.
>
> I tested the value of the variable with the following php script:
>
>  foreach($_SERVER as $key_name => $key_value) {
> print $key_name . " = " . $key_value . "";
>
> }
>
> ?>
>
> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>
> I don't understand where my problem lies.
>
>  
>
> Here is my galaxy.conf file :
>
> Listen 2208
>
> 
>
>
> RewriteEngine on
> DocumentRoot "/path/to/static"
>
>
>
>
> Options +Indexes FollowSymLinks MultiViews
> AllowOverride None
> Order allow,deny
> Allow from all
>
>
> AuthType Basic
> AuthName "Authentifiez vous"
> PerlAuthenHandler Apache2::AuthenNIS
> PerlAuthzHandler Apache2::AuthzNIS
> PerlSetVar AllowAlternateAuth no
> require valid-user
>
>
>
>
>
> RewriteEngine on
> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
> RequestHeader set REMOTE_USER %{RU}e
>
>
>
>RewriteRule ^/galaxy$ /galaxy/ [R]
>RewriteRule ^/static/style/(.*)
> /path/to/static/june_2007_style/blue/$1 [L]
>RewriteRule ^/static/scripts/(.*)
> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>
> [L]
>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>RewriteRule ^(.*) http://localhost:2209$1 [P]
>
>
> 
>
>
> Thanks in advance !
>
> F.T
>
>
>
> ___
> 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:
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>
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>
Ciao,
Eric
-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A University
College Station, TX 77843
404-692-2048
e...@tamu.edu

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Re: [galaxy-dev] external authentication - empty REMOTE_USER

2015-10-21 Thread Ryan G

Here is the pull request:  https://github.com/galaxyproject/galaxy/pull/823

You can see what file was edited

On Wed, Oct 21, 2015 at 8:40 AM, Floreline TOUCHARD <
floreline.touch...@gmail.com> wrote:

> Thank you ! Can you tell me which files are to update or download ?
> I installed my application on a server that was not open to the outside.
> Currently I do not support different versions or updates of my application
> with git.
> I can download the files to edit and transfer them to the server but not
> to update the entire application at the moment.
>
> F. T
> Le 21 oct. 2015 12:11 PM, "Floreline TOUCHARD" <
> floreline.touch...@gmail.com> a écrit :
>
>> Hi,
>>
>> I've got an issue with my external authentication configuration. I use
>> Apache and the mod_perl
>>
>> modules (AuthenNIS + AuthzNIS + Net-NIS) to authenticate to galaxy with
>> NIS accounts.
>>
>> I have the authentication form  when I try to access galaxy web page.
>> But after a successful authentication it seems that the REMOTE_USER
>> variable is not passed to my galaxy instance. I'm connected under "@
>> example.org" regardless of the authentication account. That's why I
>> think the REMOTE_USER passed to Galaxy is not 'null' but empty.
>>
>> I tested the value of the variable with the following php script:
>>
>> > foreach($_SERVER as $key_name => $key_value) {
>> print $key_name . " = " . $key_value . "";
>>
>> }
>>
>> ?>
>>
>> I've got a REMOTE_USER et HTTP_REMOTE_USER with a username value.
>>
>> I don't understand where my problem lies.
>>
>>
>>
>> Here is my galaxy.conf file :
>>
>> Listen 2208
>>
>> 
>>
>>
>> RewriteEngine on
>> DocumentRoot "/path/to/static"
>>
>>
>>
>>
>> Options +Indexes FollowSymLinks MultiViews
>> AllowOverride None
>> Order allow,deny
>> Allow from all
>>
>>
>> AuthType Basic
>> AuthName "Authentifiez vous"
>> PerlAuthenHandler Apache2::AuthenNIS
>> PerlAuthzHandler Apache2::AuthzNIS
>> PerlSetVar AllowAlternateAuth no
>> require valid-user
>>
>>
>>
>>
>>
>> RewriteEngine on
>> RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
>> RequestHeader set REMOTE_USER %{RU}e
>>
>>
>>
>>RewriteRule ^/galaxy$ /galaxy/ [R]
>>RewriteRule ^/static/style/(.*)
>> /path/to/static/june_2007_style/blue/$1 [L]
>>RewriteRule ^/static/scripts/(.*)
>> /softhpc/galaxy/test/galaxy-master/static/scripts/packed/$1
>>
>> [L]
>>RewriteRule ^/static/(.*) /path/to/static/$1 [L]
>>RewriteRule ^/favicon.ico /path/to/static/favicon.ico [L]
>>RewriteRule ^/robots.txt /path/to/static/robots.txt [L]
>>RewriteRule ^(.*) http://localhost:2209$1 [P]
>>
>>
>> 
>>
>>
>> Thanks in advance !
>>
>> F.T
>>
>
> ___
> 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/
>
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Re: [galaxy-dev] external authentication - empty REMOTE_USER

Re: [galaxy-dev] external authentication - empty REMOTE_USER

[galaxy-dev] external authentication - empty REMOTE_USER

Re: [galaxy-dev] external authentication - empty REMOTE_USER

Re: [galaxy-dev] external authentication - empty REMOTE_USER

Re: [galaxy-dev] external authentication - empty REMOTE_USER

Re: [galaxy-dev] external authentication - empty REMOTE_USER

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